Starting phenix.real_space_refine
on Sun May 18 06:25:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tmo_41396/05_2025/8tmo_41396.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tmo_41396/05_2025/8tmo_41396.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tmo_41396/05_2025/8tmo_41396.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tmo_41396/05_2025/8tmo_41396.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tmo_41396/05_2025/8tmo_41396.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tmo_41396/05_2025/8tmo_41396.cif"
  }
  resolution = 3.1
  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=   0.014 sd=   0.040
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 793 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Mg      3      5.21       5
     S      58      5.16       5
     C   10437      2.51       5
     N    2613      2.21       5
     O    2948      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 16059
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "L"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 803
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 969
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 2, 'TRANS': 123}
    Chain: "A"
      Number of atoms: 2805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2805
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 13, 'TRANS': 321}
    Chain: "B"
      Number of atoms: 2917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2917
          Classifications: {'peptide': 350}
          Link IDs: {'PTRANS': 15, 'TRANS': 334}
    Chain: "C"
      Number of atoms: 2812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2812
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 13, 'TRANS': 322}
    Chain: "D"
      Number of atoms: 2860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2860
          Classifications: {'peptide': 343}
          Link IDs: {'PTRANS': 15, 'TRANS': 327}
    Chain: "E"
      Number of atoms: 2890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 347, 2890
          Classifications: {'peptide': 347}
          Link IDs: {'PTRANS': 15, 'TRANS': 331}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 9.42, per 1000 atoms: 0.59
  Number of scatterers: 16059
  At special positions: 0
  Unit cell: (124.371, 142.442, 139.253, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      58     16.00
     Mg      3     11.99
     O    2948      8.00
     N    2613      7.00
     C   10437      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.11
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3726

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 11 sheets defined
      52.0% alpha, 17.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 4.067A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 55
      removed outlier: 3.772A  pdb=" N   ARG A  54 " --> pdb=" O   LEU A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 81
      removed outlier: 3.525A  pdb=" N   VAL A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 92
      removed outlier: 3.641A  pdb=" N   LEU A  87 " --> pdb=" O   HIS A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 157
    Processing helix  chain 'A' and resid 165 through 202
      removed outlier: 3.604A  pdb=" N   LEU A 169 " --> pdb=" O   ARG A 165 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLU A 197 " --> pdb=" O   ASP A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 238
      Proline residue:  A 227  - end of helix
    Processing helix  chain 'A' and resid 244 through 246
      No H-bonds generated for 'chain 'A' and resid 244 through 246'
    Processing helix  chain 'A' and resid 247 through 280
      removed outlier: 3.602A  pdb=" N   PHE A 251 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 311
      removed outlier: 3.850A  pdb=" N   LYS A 286 " --> pdb=" O   SER A 282 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   THR A 287 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ASN A 288 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
      Proline residue:  A 303  - end of helix
    Processing helix  chain 'A' and resid 325 through 348
    Processing helix  chain 'B' and resid 47 through 54
      Proline residue:  B  52  - end of helix
    Processing helix  chain 'B' and resid 69 through 81
    Processing helix  chain 'B' and resid 83 through 92
    Processing helix  chain 'B' and resid 147 through 157
    Processing helix  chain 'B' and resid 160 through 164
    Processing helix  chain 'B' and resid 165 through 202
      removed outlier: 3.531A  pdb=" N   LEU B 169 " --> pdb=" O   ARG B 165 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   PHE B 182 " --> pdb=" O   VAL B 178 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   VAL B 183 " --> pdb=" O   ASP B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 238
      removed outlier: 3.577A  pdb=" N   VAL B 208 " --> pdb=" O   GLU B 204 " (cutoff:3.500A)
      Proline residue:  B 227  - end of helix
    Processing helix  chain 'B' and resid 247 through 311
      removed outlier: 3.529A  pdb=" N   PHE B 251 " --> pdb=" O   THR B 247 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ASP B 270 " --> pdb=" O   GLU B 266 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU B 280 " --> pdb=" O   LEU B 276 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   ILE B 300 " --> pdb=" O   ILE B 296 " (cutoff:3.500A)
      Proline residue:  B 303  - end of helix
      removed outlier: 3.552A  pdb=" N   ILE B 307 " --> pdb=" O   PRO B 303 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ALA B 308 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 348
    Processing helix  chain 'C' and resid 70 through 80
    Processing helix  chain 'C' and resid 83 through 86
    Processing helix  chain 'C' and resid 87 through 92
      removed outlier: 4.033A  pdb=" N   ASN C  92 " --> pdb=" O   GLU C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 157
    Processing helix  chain 'C' and resid 167 through 202
    Processing helix  chain 'C' and resid 205 through 238
      removed outlier: 4.300A  pdb=" N   GLN C 209 " --> pdb=" O   LYS C 205 " (cutoff:3.500A)
      Proline residue:  C 227  - end of helix
      removed outlier: 3.754A  pdb=" N   ASP C 238 " --> pdb=" O   SER C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 311
      Proline residue:  C 303  - end of helix
    Processing helix  chain 'C' and resid 325 through 348
    Processing helix  chain 'D' and resid 46 through 51
      removed outlier: 3.566A  pdb=" N   SER D  49 " --> pdb=" O   ASP D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 69 through 81
      removed outlier: 4.198A  pdb=" N   VAL D  73 " --> pdb=" O   ARG D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 90
    Processing helix  chain 'D' and resid 147 through 157
    Processing helix  chain 'D' and resid 165 through 202
      removed outlier: 3.936A  pdb=" N   ASP D 180 " --> pdb=" O   ALA D 176 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   TYR D 181 " --> pdb=" O   LEU D 177 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   PHE D 182 " --> pdb=" O   VAL D 178 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   VAL D 183 " --> pdb=" O   ASP D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 206 through 238
      Proline residue:  D 227  - end of helix
      removed outlier: 3.644A  pdb=" N   LEU D 232 " --> pdb=" O   LEU D 228 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ASP D 238 " --> pdb=" O   SER D 234 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 247 through 312
      removed outlier: 3.914A  pdb=" N   LEU D 276 " --> pdb=" O   VAL D 272 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   ASP D 277 " --> pdb=" O   SER D 273 " (cutoff:3.500A)
      Proline residue:  D 303  - end of helix
    Processing helix  chain 'D' and resid 325 through 348
      removed outlier: 3.704A  pdb=" N   VAL D 329 " --> pdb=" O   TRP D 325 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 56
      removed outlier: 3.589A  pdb=" N   SER E  56 " --> pdb=" O   PHE E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 69 through 81
      removed outlier: 4.092A  pdb=" N   VAL E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 83 through 92
    Processing helix  chain 'E' and resid 147 through 156
    Processing helix  chain 'E' and resid 165 through 202
    Processing helix  chain 'E' and resid 204 through 238
      Proline residue:  E 227  - end of helix
      removed outlier: 3.730A  pdb=" N   GLU E 230 " --> pdb=" O   TRP E 226 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASP E 238 " --> pdb=" O   SER E 234 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 247 through 312
      removed outlier: 4.161A  pdb=" N   LEU E 276 " --> pdb=" O   VAL E 272 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   ASP E 277 " --> pdb=" O   SER E 273 " (cutoff:3.500A)
      Proline residue:  E 303  - end of helix
    Processing helix  chain 'E' and resid 325 through 348
    Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AA2, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.358A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.358A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.692A  pdb=" N   ILE H  34 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   SER H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER H  52 " --> pdb=" O   SER H  57 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   SER H  57 " --> pdb=" O   SER H  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.855A  pdb=" N   TYR H 115 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   TYR H 100 " --> pdb=" O   MET H 113 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   MET H 113 " --> pdb=" O   TYR H 100 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   TYR H 102 " --> pdb=" O   ASN H 111 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   ASN H 111 " --> pdb=" O   TYR H 102 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 39 through 44
      removed outlier: 3.542A  pdb=" N   CYS A 135 " --> pdb=" O   THR A 132 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 44
      removed outlier: 4.283A  pdb=" N   GLU B 121 " --> pdb=" O   ASP B 116 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASP B 116 " --> pdb=" O   GLU B 121 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 39 through 44
      removed outlier: 3.524A  pdb=" N   VAL C 136 " --> pdb=" O   THR C  60 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   MET C 138 " --> pdb=" O   ILE C  62 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLU C 123 " --> pdb=" O   THR C 114 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   THR C 114 " --> pdb=" O   GLU C 123 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 39 through 44
      removed outlier: 3.732A  pdb=" N   GLU D 123 " --> pdb=" O   THR D 114 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 39 through 44

    1019 hydrogen bonds defined for protein.
    2925 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: 4.70

  Time building geometry restraints manager: 4.80 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 5055
        1.34 -     1.46: 3005
        1.46 -     1.57: 8256
        1.57 -     1.69: 0
        1.69 -     1.81: 107
  Bond restraints: 16423
  Sorted by residual:
  bond pdb=" CG  LEU B 304 "
       pdb=" CD2 LEU B 304 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.13e+00
  bond pdb=" CG1 ILE C 192 "
       pdb=" CD1 ILE C 192 "
    ideal  model  delta    sigma   weight residual
    1.513  1.463  0.050 3.90e-02 6.57e+02 1.66e+00
  bond pdb=" N   ASN C 134 "
       pdb=" CA  ASN C 134 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.014 1.29e-02 6.01e+03 1.23e+00
  bond pdb=" C   PRO D 240 "
       pdb=" N   PRO D 241 "
    ideal  model  delta    sigma   weight residual
    1.334  1.360 -0.026 2.34e-02 1.83e+03 1.21e+00
  bond pdb=" CG  LEU B 173 "
       pdb=" CD1 LEU B 173 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.20e+00
  ... (remaining 16418 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 21989
        2.36 -     4.72: 247
        4.72 -     7.08: 30
        7.08 -     9.44: 5
        9.44 -    11.80: 1
  Bond angle restraints: 22272
  Sorted by residual:
  angle pdb=" CA  MET A 291 "
        pdb=" CB  MET A 291 "
        pdb=" CG  MET A 291 "
      ideal   model   delta    sigma   weight residual
     114.10  122.19   -8.09 2.00e+00 2.50e-01 1.63e+01
  angle pdb=" C   LEU A 235 "
        pdb=" N   TYR A 236 "
        pdb=" CA  TYR A 236 "
      ideal   model   delta    sigma   weight residual
     122.53  115.31    7.22 1.92e+00 2.71e-01 1.41e+01
  angle pdb=" N   THR D  45 "
        pdb=" CA  THR D  45 "
        pdb=" C   THR D  45 "
      ideal   model   delta    sigma   weight residual
     114.56  109.88    4.68 1.27e+00 6.20e-01 1.36e+01
  angle pdb=" C   LEU B 235 "
        pdb=" N   TYR B 236 "
        pdb=" CA  TYR B 236 "
      ideal   model   delta    sigma   weight residual
     122.54  116.50    6.04 1.65e+00 3.67e-01 1.34e+01
  angle pdb=" CA  LEU B 304 "
        pdb=" CB  LEU B 304 "
        pdb=" CG  LEU B 304 "
      ideal   model   delta    sigma   weight residual
     116.30  128.10  -11.80 3.50e+00 8.16e-02 1.14e+01
  ... (remaining 22267 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 8743
       18.00 -    35.99: 908
       35.99 -    53.99: 169
       53.99 -    71.99: 30
       71.99 -    89.99: 17
  Dihedral angle restraints: 9867
    sinusoidal: 4102
      harmonic: 5765
  Sorted by residual:
  dihedral pdb=" CB  CYS L  24 "
           pdb=" SG  CYS L  24 "
           pdb=" SG  CYS L  89 "
           pdb=" CB  CYS L  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.36  -53.36     1      1.00e+01 1.00e-02 3.87e+01
  dihedral pdb=" CA  PRO D 240 "
           pdb=" C   PRO D 240 "
           pdb=" N   PRO D 241 "
           pdb=" CA  PRO D 241 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.92  -20.08     0      5.00e+00 4.00e-02 1.61e+01
  dihedral pdb=" CA  ILE E 300 "
           pdb=" C   ILE E 300 "
           pdb=" N   PHE E 301 "
           pdb=" CA  PHE E 301 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.10  -18.90     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 9864 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1884
       0.045 -    0.091: 503
       0.091 -    0.136: 136
       0.136 -    0.181: 9
       0.181 -    0.226: 1
  Chirality restraints: 2533
  Sorted by residual:
  chirality pdb=" CG  LEU B 304 "
            pdb=" CB  LEU B 304 "
            pdb=" CD1 LEU B 304 "
            pdb=" CD2 LEU B 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.82    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CB  VAL D 239 "
            pdb=" CA  VAL D 239 "
            pdb=" CG1 VAL D 239 "
            pdb=" CG2 VAL D 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.16e-01
  chirality pdb=" CA  HIS C 212 "
            pdb=" N   HIS C 212 "
            pdb=" C   HIS C 212 "
            pdb=" CB  HIS C 212 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.70e-01
  ... (remaining 2530 not shown)

  Planarity restraints: 2785
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 240 "   -0.040 5.00e-02 4.00e+02   6.01e-02 5.77e+00
        pdb=" N   PRO C 241 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO C 241 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 241 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D 240 "   -0.033 5.00e-02 4.00e+02   4.99e-02 3.99e+00
        pdb=" N   PRO D 241 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO D 241 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D 241 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS C 212 "   -0.017 2.00e-02 2.50e+03   1.51e-02 3.44e+00
        pdb=" CG  HIS C 212 "    0.030 2.00e-02 2.50e+03
        pdb=" ND1 HIS C 212 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 HIS C 212 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 HIS C 212 "   -0.012 2.00e-02 2.50e+03
        pdb=" NE2 HIS C 212 "    0.001 2.00e-02 2.50e+03
  ... (remaining 2782 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 263
        2.69 -     3.24: 16170
        3.24 -     3.79: 25567
        3.79 -     4.35: 32810
        4.35 -     4.90: 54151
  Nonbonded interactions: 128961
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN D 260 "
            pdb=" O   HIS E  94 "
     model   vdw
     2.133 3.120
  nonbonded pdb=" O   TYR B  34 "
            pdb=" OG1 THR B  58 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OH  TYR B  23 "
            pdb=" OE2 GLU B 123 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   LYS A 111 "
            pdb=" OH  TYR A 181 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   GLU A 204 "
            pdb=" OG1 THR A 207 "
     model   vdw
     2.215 3.040
  ... (remaining 128956 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 17 through 350)
  selection = (chain 'B' and resid 17 through 350)
  selection = (chain 'C' and resid 17 through 350)
  selection = (chain 'D' and resid 17 through 350)
  selection = (chain 'E' and resid 17 through 350)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.49 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:             3.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.630
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     35.750
  Find NCS groups from input model:        0.720
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
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      :  0.003   0.050  16425  Z= 0.153
  Angle     :  0.627  11.797  22276  Z= 0.332
  Chirality :  0.043   0.226   2533
  Planarity :  0.005   0.060   2785
  Dihedral  : 15.055  89.987   6135
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.82 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.55 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.20), residues: 1930
  helix:  1.72 (0.17), residues: 963
  sheet:  0.60 (0.27), residues: 359
  loop : -1.72 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.013   0.001   HIS C 212 
 PHE   0.019   0.001   PHE E  27 
 TYR   0.021   0.001   TYR B 279 
 ARG   0.003   0.000   ARG D 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12282 ( 1003)
  hydrogen bonds       : angle       6.02423 ( 2925)
  SS BOND              : bond        0.00261 (    2)
  SS BOND              : angle       1.46112 (    4)
  covalent geometry    : bond        0.00335 (16423)
  covalent geometry    : angle       0.62630 (22272)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 363
  time to evaluate  : 1.883 
Fit side-chains
   revert: symmetry clash
REVERT: H   13 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7984 (mm110)
REVERT: H  123 THR cc_start: 0.8072 (p) cc_final: 0.7816 (p)
REVERT: H  124 VAL cc_start: 0.8382 (t) cc_final: 0.8019 (m)
REVERT: A   89 ASP cc_start: 0.6842 (m-30) cc_final: 0.6625 (m-30)
REVERT: A  125 GLU cc_start: 0.8007 (tt0) cc_final: 0.7209 (tt0)
REVERT: A  193 ASP cc_start: 0.6942 (t70) cc_final: 0.6701 (t70)
REVERT: A  197 GLU cc_start: 0.6303 (mm-30) cc_final: 0.5816 (mp0)
REVERT: A  272 VAL cc_start: 0.8491 (t) cc_final: 0.8148 (m)
REVERT: A  331 LEU cc_start: 0.6093 (tt) cc_final: 0.5877 (tt)
REVERT: C  260 GLN cc_start: 0.6720 (mm110) cc_final: 0.6505 (mm-40)
REVERT: D   29 ILE cc_start: 0.8360 (mt) cc_final: 0.8134 (mt)
REVERT: D   45 THR cc_start: 0.7013 (p) cc_final: 0.6057 (p)
REVERT: D  112 MET cc_start: 0.7131 (ttp) cc_final: 0.6894 (mtp)
REVERT: E  291 MET cc_start: 0.7510 (ttm) cc_final: 0.7154 (ttp)
REVERT: E  314 ASN cc_start: 0.5372 (m-40) cc_final: 0.5160 (m110)
  outliers start: 1
  outliers final: 0
  residues processed: 363
  average time/residue: 0.2530
  time to fit residues: 137.8857
Evaluate side-chains
  307 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 307
  time to evaluate  : 2.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 161 optimal weight:    2.9990
   chunk 144 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    8.9990
   chunk 77 optimal weight:    0.6980
   chunk 149 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   chunk 91 optimal weight:    8.9990
   chunk 111 optimal weight:   10.0000
   chunk 173 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
A 217 ASN
B 104 ASN
C  33 ASN
C  63 ASN
** C  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  74 GLN
** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  94 HIS
D 260 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.166074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.135508 restraints weight = 28862.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 2.53
r_work: 0.3622 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3626
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3626 r_free = 0.3626    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3624 r_free = 0.3624    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3624
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.1071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  16425  Z= 0.195
  Angle     :  0.629   8.811  22276  Z= 0.336
  Chirality :  0.044   0.186   2533
  Planarity :  0.005   0.058   2785
  Dihedral  :  4.405  20.113   2155
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.40 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.51 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.19), residues: 1930
  helix:  1.91 (0.16), residues: 973
  sheet:  0.72 (0.28), residues: 344
  loop : -1.77 (0.25), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.007   0.001   HIS C 212 
 PHE   0.034   0.002   PHE C  53 
 TYR   0.026   0.002   TYR B 279 
 ARG   0.005   0.000   ARG C  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05814 ( 1003)
  hydrogen bonds       : angle       4.91236 ( 2925)
  SS BOND              : bond        0.00233 (    2)
  SS BOND              : angle       1.71573 (    4)
  covalent geometry    : bond        0.00447 (16423)
  covalent geometry    : angle       0.62871 (22272)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  365 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 328
  time to evaluate  : 1.779 
Fit side-chains
   revert: symmetry clash
REVERT: H   76 LYS cc_start: 0.8096 (ptmm) cc_final: 0.7847 (ptmm)
REVERT: H  123 THR cc_start: 0.8114 (p) cc_final: 0.7873 (p)
REVERT: H  124 VAL cc_start: 0.8625 (t) cc_final: 0.8260 (m)
REVERT: A   89 ASP cc_start: 0.7122 (m-30) cc_final: 0.6873 (m-30)
REVERT: A  197 GLU cc_start: 0.6456 (mm-30) cc_final: 0.5945 (mp0)
REVERT: A  270 ASP cc_start: 0.7685 (m-30) cc_final: 0.7405 (m-30)
REVERT: A  289 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6586 (mt-10)
REVERT: A  291 MET cc_start: 0.6941 (mmp) cc_final: 0.6586 (mmt)
REVERT: A  318 MET cc_start: 0.6902 (ppp) cc_final: 0.6698 (ppp)
REVERT: B   74 GLN cc_start: 0.8487 (tt0) cc_final: 0.8194 (tt0)
REVERT: C  260 GLN cc_start: 0.7094 (mm110) cc_final: 0.6751 (mm-40)
REVERT: D  260 GLN cc_start: 0.8280 (tt0) cc_final: 0.8054 (tt0)
REVERT: E  263 ASP cc_start: 0.7178 (m-30) cc_final: 0.6950 (m-30)
REVERT: E  314 ASN cc_start: 0.5562 (m-40) cc_final: 0.5303 (m110)
  outliers start: 37
  outliers final: 25
  residues processed: 342
  average time/residue: 0.2663
  time to fit residues: 136.3561
Evaluate side-chains
  326 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 301
  time to evaluate  : 1.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  270 ASP
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  112 MET
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  330 VAL
Chi-restraints excluded: chain D residue  134 ASN
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  120 HIS
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  293 VAL
Chi-restraints excluded: chain E residue  313 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 180 optimal weight:    0.8980
   chunk 157 optimal weight:    0.0270
   chunk 185 optimal weight:    1.9990
   chunk 155 optimal weight:    0.8980
   chunk 119 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0570
   overall best weight:    0.5156

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

Flipped N/Q/H residues before XYZ refinement:
H  13 GLN
A  95 GLN
A 217 ASN
B 104 ASN
C  68 HIS
D  94 HIS
D 209 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.164859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.133034 restraints weight = 28955.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 2.41
r_work: 0.3630 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3632
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3632 r_free = 0.3632    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3632 r_free = 0.3632    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3632
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16425  Z= 0.152
  Angle     :  0.592   8.316  22276  Z= 0.315
  Chirality :  0.043   0.177   2533
  Planarity :  0.004   0.056   2785
  Dihedral  :  4.310  19.353   2155
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.25 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.33 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.20), residues: 1930
  helix:  2.03 (0.16), residues: 977
  sheet:  0.62 (0.28), residues: 353
  loop : -1.72 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 226 
 HIS   0.006   0.001   HIS C 212 
 PHE   0.032   0.001   PHE C  53 
 TYR   0.021   0.001   TYR B 279 
 ARG   0.002   0.000   ARG D 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05300 ( 1003)
  hydrogen bonds       : angle       4.64015 ( 2925)
  SS BOND              : bond        0.00348 (    2)
  SS BOND              : angle       1.09156 (    4)
  covalent geometry    : bond        0.00333 (16423)
  covalent geometry    : angle       0.59165 (22272)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  363 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 314
  time to evaluate  : 1.925 
Fit side-chains
   revert: symmetry clash
REVERT: H   76 LYS cc_start: 0.8019 (ptmm) cc_final: 0.7810 (ptmm)
REVERT: H  123 THR cc_start: 0.8075 (p) cc_final: 0.7809 (p)
REVERT: H  124 VAL cc_start: 0.8622 (t) cc_final: 0.8279 (m)
REVERT: A   89 ASP cc_start: 0.7169 (m-30) cc_final: 0.6922 (m-30)
REVERT: A  113 PHE cc_start: 0.8689 (m-80) cc_final: 0.8447 (m-80)
REVERT: A  134 ASN cc_start: 0.6752 (t0) cc_final: 0.6496 (t0)
REVERT: A  197 GLU cc_start: 0.6392 (mm-30) cc_final: 0.5862 (mp0)
REVERT: A  270 ASP cc_start: 0.7622 (m-30) cc_final: 0.7394 (m-30)
REVERT: A  289 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6684 (mt-10)
REVERT: A  291 MET cc_start: 0.6983 (mmp) cc_final: 0.6760 (mmt)
REVERT: B   74 GLN cc_start: 0.8414 (tt0) cc_final: 0.8124 (tt0)
REVERT: B  288 ASN cc_start: 0.7691 (t0) cc_final: 0.7488 (t0)
REVERT: C  116 ASP cc_start: 0.8055 (t0) cc_final: 0.7840 (t0)
REVERT: C  260 GLN cc_start: 0.6953 (mm110) cc_final: 0.6590 (mm-40)
REVERT: C  318 MET cc_start: 0.4798 (mtm) cc_final: 0.4064 (ptp)
REVERT: D   79 PHE cc_start: 0.7396 (t80) cc_final: 0.6987 (t80)
REVERT: D   95 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7713 (tm-30)
REVERT: D  112 MET cc_start: 0.7761 (mtp) cc_final: 0.7491 (mtp)
REVERT: D  126 GLN cc_start: 0.7596 (tp-100) cc_final: 0.7341 (tp-100)
REVERT: E  256 ASP cc_start: 0.7245 (m-30) cc_final: 0.7004 (m-30)
REVERT: E  263 ASP cc_start: 0.7108 (m-30) cc_final: 0.6887 (m-30)
  outliers start: 49
  outliers final: 39
  residues processed: 341
  average time/residue: 0.2526
  time to fit residues: 130.4620
Evaluate side-chains
  334 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 295
  time to evaluate  : 1.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  112 MET
Chi-restraints excluded: chain C residue  118 ASN
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  330 VAL
Chi-restraints excluded: chain D residue  127 VAL
Chi-restraints excluded: chain D residue  134 ASN
Chi-restraints excluded: chain D residue  138 MET
Chi-restraints excluded: chain D residue  167 ASP
Chi-restraints excluded: chain D residue  209 GLN
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain E residue   32 MET
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue   94 HIS
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  120 HIS
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain E residue  293 VAL
Chi-restraints excluded: chain E residue  313 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 174 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 167 optimal weight:    0.3980
   chunk 89 optimal weight:    1.9990
   chunk 168 optimal weight:    2.9990
   chunk 162 optimal weight:    3.9990
   chunk 92 optimal weight:    5.9990
   chunk 148 optimal weight:    0.9990
   chunk 104 optimal weight:    0.8980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
H  13 GLN
A 217 ASN
B 104 ASN
D  94 HIS
D 209 GLN
** E  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.165790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.135340 restraints weight = 29063.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 2.57
r_work: 0.3602 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  16425  Z= 0.179
  Angle     :  0.606   8.569  22276  Z= 0.321
  Chirality :  0.044   0.167   2533
  Planarity :  0.004   0.057   2785
  Dihedral  :  4.328  19.417   2155
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.51 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 15.60 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.19), residues: 1930
  helix:  2.00 (0.16), residues: 970
  sheet:  0.70 (0.28), residues: 337
  loop : -1.75 (0.24), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.006   0.001   HIS C 212 
 PHE   0.030   0.002   PHE C  53 
 TYR   0.019   0.001   TYR H 103 
 ARG   0.004   0.000   ARG E  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05335 ( 1003)
  hydrogen bonds       : angle       4.63491 ( 2925)
  SS BOND              : bond        0.00930 (    2)
  SS BOND              : angle       1.08701 (    4)
  covalent geometry    : bond        0.00409 (16423)
  covalent geometry    : angle       0.60591 (22272)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  386 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 318
  time to evaluate  : 1.790 
Fit side-chains
   revert: symmetry clash
REVERT: L   79 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8182 (mp)
REVERT: H  123 THR cc_start: 0.8098 (p) cc_final: 0.7847 (p)
REVERT: H  124 VAL cc_start: 0.8626 (t) cc_final: 0.8286 (m)
REVERT: A   89 ASP cc_start: 0.7125 (m-30) cc_final: 0.6875 (m-30)
REVERT: A  113 PHE cc_start: 0.8765 (m-80) cc_final: 0.8415 (m-80)
REVERT: A  134 ASN cc_start: 0.6833 (t0) cc_final: 0.6554 (t0)
REVERT: A  163 LYS cc_start: 0.8505 (mtmt) cc_final: 0.8157 (mtmt)
REVERT: A  197 GLU cc_start: 0.6449 (mm-30) cc_final: 0.5944 (mp0)
REVERT: A  289 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6695 (mt-10)
REVERT: B   74 GLN cc_start: 0.8441 (tt0) cc_final: 0.8136 (tt0)
REVERT: B  261 ILE cc_start: 0.8253 (mm) cc_final: 0.8052 (mt)
REVERT: C  116 ASP cc_start: 0.8091 (t0) cc_final: 0.7814 (t0)
REVERT: C  260 GLN cc_start: 0.6987 (mm110) cc_final: 0.6597 (mm-40)
REVERT: D   95 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7744 (tm-30)
REVERT: D  126 GLN cc_start: 0.7587 (tp-100) cc_final: 0.7347 (tp-100)
REVERT: D  207 THR cc_start: 0.7883 (OUTLIER) cc_final: 0.7613 (t)
REVERT: E  263 ASP cc_start: 0.7181 (m-30) cc_final: 0.6967 (m-30)
REVERT: E  291 MET cc_start: 0.8086 (ttp) cc_final: 0.7884 (ttt)
  outliers start: 68
  outliers final: 48
  residues processed: 359
  average time/residue: 0.2558
  time to fit residues: 139.8722
Evaluate side-chains
  349 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 299
  time to evaluate  : 1.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain L residue   86 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   83 HIS
Chi-restraints excluded: chain C residue  112 MET
Chi-restraints excluded: chain C residue  118 ASN
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  330 VAL
Chi-restraints excluded: chain D residue  134 ASN
Chi-restraints excluded: chain D residue  138 MET
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  207 THR
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain E residue   32 MET
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  120 HIS
Chi-restraints excluded: chain E residue  156 TYR
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain E residue  293 VAL
Chi-restraints excluded: chain E residue  313 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 141 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 133 optimal weight:    0.0770
   chunk 25 optimal weight:    0.3980
   chunk 158 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 110 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 217 ASN
B 104 ASN
D  94 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.164880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.133119 restraints weight = 29624.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 2.83
r_work: 0.3595 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  16425  Z= 0.157
  Angle     :  0.594   8.389  22276  Z= 0.314
  Chirality :  0.043   0.169   2533
  Planarity :  0.004   0.057   2785
  Dihedral  :  4.295  18.991   2155
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.35 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 17.37 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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:  1.02 (0.19), residues: 1930
  helix:  2.08 (0.16), residues: 970
  sheet:  0.79 (0.28), residues: 336
  loop : -1.75 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.006   0.001   HIS C 212 
 PHE   0.029   0.001   PHE C  53 
 TYR   0.017   0.001   TYR B 279 
 ARG   0.004   0.000   ARG C  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05166 ( 1003)
  hydrogen bonds       : angle       4.54359 ( 2925)
  SS BOND              : bond        0.00250 (    2)
  SS BOND              : angle       1.01466 (    4)
  covalent geometry    : bond        0.00350 (16423)
  covalent geometry    : angle       0.59410 (22272)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  388 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 318
  time to evaluate  : 1.908 
Fit side-chains
   revert: symmetry clash
REVERT: L   79 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8151 (mp)
REVERT: H  123 THR cc_start: 0.8080 (p) cc_final: 0.7831 (p)
REVERT: H  124 VAL cc_start: 0.8644 (t) cc_final: 0.8298 (m)
REVERT: A   89 ASP cc_start: 0.7147 (m-30) cc_final: 0.6857 (m-30)
REVERT: A  113 PHE cc_start: 0.8762 (m-80) cc_final: 0.8380 (m-80)
REVERT: A  134 ASN cc_start: 0.6825 (t0) cc_final: 0.6524 (t0)
REVERT: A  163 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8223 (mtmt)
REVERT: A  197 GLU cc_start: 0.6416 (mm-30) cc_final: 0.5874 (mp0)
REVERT: A  246 GLU cc_start: 0.7623 (pp20) cc_final: 0.7343 (pp20)
REVERT: A  289 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6798 (mt-10)
REVERT: A  291 MET cc_start: 0.7311 (mmt) cc_final: 0.7108 (mmt)
REVERT: B   74 GLN cc_start: 0.8418 (tt0) cc_final: 0.8111 (tt0)
REVERT: B  121 GLU cc_start: 0.6394 (mm-30) cc_final: 0.6112 (mm-30)
REVERT: B  261 ILE cc_start: 0.8260 (mm) cc_final: 0.8042 (mt)
REVERT: C  116 ASP cc_start: 0.8154 (t0) cc_final: 0.7816 (t0)
REVERT: C  260 GLN cc_start: 0.6941 (mm110) cc_final: 0.6511 (mm-40)
REVERT: C  318 MET cc_start: 0.5058 (mtm) cc_final: 0.3980 (ptp)
REVERT: D   95 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7757 (tm-30)
REVERT: D  126 GLN cc_start: 0.7633 (tp-100) cc_final: 0.7423 (tp-100)
REVERT: D  311 TYR cc_start: 0.7278 (m-80) cc_final: 0.6885 (m-80)
REVERT: E   23 TYR cc_start: 0.6854 (m-10) cc_final: 0.6614 (m-80)
REVERT: E  142 LYS cc_start: 0.8043 (mmtm) cc_final: 0.7839 (mtmm)
REVERT: E  263 ASP cc_start: 0.7201 (m-30) cc_final: 0.6965 (m-30)
REVERT: E  291 MET cc_start: 0.8136 (ttp) cc_final: 0.7856 (ttt)
  outliers start: 70
  outliers final: 54
  residues processed: 362
  average time/residue: 0.2552
  time to fit residues: 139.9110
Evaluate side-chains
  358 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 303
  time to evaluate  : 1.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain L residue   86 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   83 HIS
Chi-restraints excluded: chain C residue  112 MET
Chi-restraints excluded: chain C residue  118 ASN
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  330 VAL
Chi-restraints excluded: chain D residue  134 ASN
Chi-restraints excluded: chain D residue  138 MET
Chi-restraints excluded: chain D residue  167 ASP
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  207 THR
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain E residue   32 MET
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  120 HIS
Chi-restraints excluded: chain E residue  156 TYR
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain E residue  293 VAL
Chi-restraints excluded: chain E residue  313 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 115 optimal weight:    0.5980
   chunk 129 optimal weight:    5.9990
   chunk 128 optimal weight:    0.7980
   chunk 101 optimal weight:    2.9990
   chunk 174 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 145 optimal weight:    1.9990
   chunk 112 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   chunk 166 optimal weight:    0.7980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 217 ASN
B 104 ASN
D  94 HIS
D 209 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.160638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.129861 restraints weight = 29543.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 2.49
r_work: 0.3590 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  16425  Z= 0.207
  Angle     :  0.630   9.022  22276  Z= 0.334
  Chirality :  0.045   0.175   2533
  Planarity :  0.005   0.058   2785
  Dihedral  :  4.381  19.122   2155
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.82 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 18.92 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.19), residues: 1930
  helix:  2.00 (0.16), residues: 968
  sheet:  0.52 (0.27), residues: 350
  loop : -1.81 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.005   0.001   HIS D  94 
 PHE   0.030   0.002   PHE C  53 
 TYR   0.021   0.002   TYR H 103 
 ARG   0.004   0.000   ARG C  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05395 ( 1003)
  hydrogen bonds       : angle       4.64356 ( 2925)
  SS BOND              : bond        0.00204 (    2)
  SS BOND              : angle       1.26979 (    4)
  covalent geometry    : bond        0.00482 (16423)
  covalent geometry    : angle       0.62939 (22272)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  378 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 309
  time to evaluate  : 1.795 
Fit side-chains
REVERT: L   79 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8237 (mp)
REVERT: H  123 THR cc_start: 0.8121 (p) cc_final: 0.7871 (p)
REVERT: H  124 VAL cc_start: 0.8660 (t) cc_final: 0.8327 (m)
REVERT: A   89 ASP cc_start: 0.7115 (m-30) cc_final: 0.6834 (m-30)
REVERT: A  134 ASN cc_start: 0.6864 (t0) cc_final: 0.6543 (t0)
REVERT: A  163 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8248 (mtmt)
REVERT: A  246 GLU cc_start: 0.7486 (pp20) cc_final: 0.7195 (pp20)
REVERT: A  270 ASP cc_start: 0.7614 (m-30) cc_final: 0.7295 (m-30)
REVERT: A  289 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6733 (mt-10)
REVERT: A  291 MET cc_start: 0.7255 (mmt) cc_final: 0.7027 (mmt)
REVERT: A  315 PHE cc_start: 0.7017 (m-80) cc_final: 0.6722 (m-80)
REVERT: B   74 GLN cc_start: 0.8440 (tt0) cc_final: 0.8134 (tt0)
REVERT: B  261 ILE cc_start: 0.8235 (mm) cc_final: 0.8025 (mt)
REVERT: C  111 LYS cc_start: 0.7686 (tptt) cc_final: 0.7459 (tptp)
REVERT: C  116 ASP cc_start: 0.8172 (t0) cc_final: 0.7887 (t0)
REVERT: C  260 GLN cc_start: 0.6970 (mm110) cc_final: 0.6575 (mm-40)
REVERT: C  318 MET cc_start: 0.5049 (mtm) cc_final: 0.3913 (ptp)
REVERT: D  311 TYR cc_start: 0.7382 (m-80) cc_final: 0.6969 (m-80)
REVERT: E  263 ASP cc_start: 0.7246 (m-30) cc_final: 0.7035 (m-30)
  outliers start: 69
  outliers final: 58
  residues processed: 349
  average time/residue: 0.2595
  time to fit residues: 137.5218
Evaluate side-chains
  361 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 302
  time to evaluate  : 1.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain L residue   86 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   83 HIS
Chi-restraints excluded: chain C residue  112 MET
Chi-restraints excluded: chain C residue  118 ASN
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  307 ILE
Chi-restraints excluded: chain C residue  330 VAL
Chi-restraints excluded: chain D residue  134 ASN
Chi-restraints excluded: chain D residue  138 MET
Chi-restraints excluded: chain D residue  167 ASP
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  207 THR
Chi-restraints excluded: chain D residue  209 GLN
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain E residue   32 MET
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  120 HIS
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  156 TYR
Chi-restraints excluded: chain E residue  180 ASP
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain E residue  293 VAL
Chi-restraints excluded: chain E residue  313 MET
Chi-restraints excluded: chain E residue  314 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 93 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 115 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0170
   chunk 53 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.7022

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

Flipped N/Q/H residues before XYZ refinement:
A 217 ASN
B 104 ASN
C  74 GLN
D  94 HIS
D 126 GLN
D 209 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.162317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.129595 restraints weight = 29359.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 2.49
r_work: 0.3599 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  16425  Z= 0.175
  Angle     :  0.620   8.587  22276  Z= 0.327
  Chirality :  0.044   0.183   2533
  Planarity :  0.004   0.059   2785
  Dihedral  :  4.354  18.841   2155
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.56 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 19.86 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.19), residues: 1930
  helix:  2.05 (0.16), residues: 969
  sheet:  0.69 (0.28), residues: 339
  loop : -1.80 (0.24), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.006   0.001   HIS D  94 
 PHE   0.032   0.002   PHE C  53 
 TYR   0.019   0.001   TYR H 103 
 ARG   0.004   0.000   ARG C  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05264 ( 1003)
  hydrogen bonds       : angle       4.59407 ( 2925)
  SS BOND              : bond        0.00202 (    2)
  SS BOND              : angle       1.06871 (    4)
  covalent geometry    : bond        0.00399 (16423)
  covalent geometry    : angle       0.61971 (22272)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 305
  time to evaluate  : 2.121 
Fit side-chains
REVERT: L   79 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8195 (mp)
REVERT: H  123 THR cc_start: 0.8083 (p) cc_final: 0.7828 (p)
REVERT: H  124 VAL cc_start: 0.8655 (t) cc_final: 0.8321 (m)
REVERT: A   89 ASP cc_start: 0.7126 (m-30) cc_final: 0.6841 (m-30)
REVERT: A  134 ASN cc_start: 0.6841 (t0) cc_final: 0.6524 (t0)
REVERT: A  163 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8265 (mtmt)
REVERT: A  246 GLU cc_start: 0.7491 (pp20) cc_final: 0.7164 (pp20)
REVERT: A  270 ASP cc_start: 0.7544 (m-30) cc_final: 0.7175 (m-30)
REVERT: A  289 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6742 (mt-10)
REVERT: A  315 PHE cc_start: 0.7108 (m-80) cc_final: 0.6849 (m-80)
REVERT: B   74 GLN cc_start: 0.8408 (tt0) cc_final: 0.8084 (tt0)
REVERT: B  261 ILE cc_start: 0.8247 (mm) cc_final: 0.8031 (mt)
REVERT: C  116 ASP cc_start: 0.8166 (t0) cc_final: 0.7859 (t0)
REVERT: C  260 GLN cc_start: 0.6960 (mm110) cc_final: 0.6490 (mm-40)
REVERT: C  318 MET cc_start: 0.5033 (mtm) cc_final: 0.3859 (ptp)
REVERT: D   95 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7649 (tm-30)
REVERT: D  130 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7709 (mm)
REVERT: D  311 TYR cc_start: 0.7447 (m-80) cc_final: 0.6987 (m-80)
REVERT: E  263 ASP cc_start: 0.7181 (m-30) cc_final: 0.6948 (m-30)
  outliers start: 71
  outliers final: 59
  residues processed: 345
  average time/residue: 0.2830
  time to fit residues: 149.8128
Evaluate side-chains
  361 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 300
  time to evaluate  : 1.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain L residue   86 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   83 HIS
Chi-restraints excluded: chain C residue  112 MET
Chi-restraints excluded: chain C residue  118 ASN
Chi-restraints excluded: chain C residue  156 TYR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  251 PHE
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  307 ILE
Chi-restraints excluded: chain C residue  330 VAL
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue  130 ILE
Chi-restraints excluded: chain D residue  134 ASN
Chi-restraints excluded: chain D residue  138 MET
Chi-restraints excluded: chain D residue  167 ASP
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  207 THR
Chi-restraints excluded: chain D residue  209 GLN
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain E residue   32 MET
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  120 HIS
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  156 TYR
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain E residue  293 VAL
Chi-restraints excluded: chain E residue  313 MET
Chi-restraints excluded: chain E residue  314 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 155 optimal weight:    0.9990
   chunk 124 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 134 optimal weight:    1.9990
   chunk 139 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 73 optimal weight:    0.6980
   chunk 142 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 217 ASN
B 104 ASN
** C  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  74 GLN
D  94 HIS
D 209 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.162629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.130604 restraints weight = 29320.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3720 rms_B_bonded: 2.88
r_work: 0.3570 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  16425  Z= 0.190
  Angle     :  0.640  10.063  22276  Z= 0.336
  Chirality :  0.044   0.177   2533
  Planarity :  0.004   0.059   2785
  Dihedral  :  4.387  18.830   2155
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.72 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 20.19 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.19), residues: 1930
  helix:  2.03 (0.16), residues: 969
  sheet:  0.64 (0.28), residues: 339
  loop : -1.84 (0.24), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  47 
 HIS   0.006   0.001   HIS D  94 
 PHE   0.032   0.002   PHE C  53 
 TYR   0.020   0.001   TYR H 103 
 ARG   0.005   0.000   ARG D 162 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05319 ( 1003)
  hydrogen bonds       : angle       4.61155 ( 2925)
  SS BOND              : bond        0.00173 (    2)
  SS BOND              : angle       1.11892 (    4)
  covalent geometry    : bond        0.00439 (16423)
  covalent geometry    : angle       0.63943 (22272)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  370 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 298
  time to evaluate  : 1.994 
Fit side-chains
REVERT: L   79 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8299 (mp)
REVERT: H  123 THR cc_start: 0.8115 (p) cc_final: 0.7862 (p)
REVERT: H  124 VAL cc_start: 0.8679 (t) cc_final: 0.8342 (m)
REVERT: A   65 THR cc_start: 0.5795 (OUTLIER) cc_final: 0.5556 (p)
REVERT: A   89 ASP cc_start: 0.7156 (m-30) cc_final: 0.6879 (m-30)
REVERT: A  134 ASN cc_start: 0.6832 (t0) cc_final: 0.6515 (t0)
REVERT: A  163 LYS cc_start: 0.8532 (mtmt) cc_final: 0.8296 (mtmt)
REVERT: A  246 GLU cc_start: 0.7516 (pp20) cc_final: 0.7181 (pp20)
REVERT: A  270 ASP cc_start: 0.7623 (m-30) cc_final: 0.7259 (m-30)
REVERT: A  289 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6764 (mt-10)
REVERT: B   74 GLN cc_start: 0.8455 (tt0) cc_final: 0.8151 (tt0)
REVERT: B  261 ILE cc_start: 0.8243 (mm) cc_final: 0.8035 (mt)
REVERT: C  116 ASP cc_start: 0.8198 (t0) cc_final: 0.7876 (t0)
REVERT: C  260 GLN cc_start: 0.7009 (mm110) cc_final: 0.6558 (mm-40)
REVERT: C  318 MET cc_start: 0.5119 (mtm) cc_final: 0.3925 (ptp)
REVERT: D  130 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7684 (mm)
REVERT: D  311 TYR cc_start: 0.7444 (m-80) cc_final: 0.6947 (m-80)
REVERT: E   85 LEU cc_start: 0.8071 (mm) cc_final: 0.7852 (mt)
REVERT: E  263 ASP cc_start: 0.7225 (m-30) cc_final: 0.6997 (m-30)
REVERT: E  299 THR cc_start: 0.6725 (m) cc_final: 0.6474 (p)
REVERT: E  344 TYR cc_start: 0.5171 (OUTLIER) cc_final: 0.4102 (p90)
  outliers start: 72
  outliers final: 59
  residues processed: 340
  average time/residue: 0.2653
  time to fit residues: 137.9202
Evaluate side-chains
  360 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 297
  time to evaluate  : 1.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain L residue   86 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   83 HIS
Chi-restraints excluded: chain C residue  112 MET
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  118 ASN
Chi-restraints excluded: chain C residue  156 TYR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  251 PHE
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  307 ILE
Chi-restraints excluded: chain C residue  330 VAL
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue  130 ILE
Chi-restraints excluded: chain D residue  134 ASN
Chi-restraints excluded: chain D residue  138 MET
Chi-restraints excluded: chain D residue  167 ASP
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  207 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain E residue   32 MET
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  120 HIS
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  156 TYR
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain E residue  293 VAL
Chi-restraints excluded: chain E residue  313 MET
Chi-restraints excluded: chain E residue  314 ASN
Chi-restraints excluded: chain E residue  344 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 110 optimal weight:    3.9990
   chunk 120 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 163 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 126 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 81 optimal weight:    0.8980
   chunk 138 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 217 ASN
B 104 ASN
** C  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  74 GLN
D  94 HIS
** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.161178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.129234 restraints weight = 29440.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 2.83
r_work: 0.3568 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  16425  Z= 0.196
  Angle     :  0.651   9.842  22276  Z= 0.342
  Chirality :  0.045   0.180   2533
  Planarity :  0.005   0.060   2785
  Dihedral  :  4.431  18.711   2155
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.77 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 20.13 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.19), residues: 1930
  helix:  1.97 (0.16), residues: 977
  sheet:  0.44 (0.27), residues: 352
  loop : -1.84 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  47 
 HIS   0.006   0.001   HIS D  94 
 PHE   0.031   0.002   PHE C  53 
 TYR   0.021   0.001   TYR H 103 
 ARG   0.009   0.000   ARG D 162 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05383 ( 1003)
  hydrogen bonds       : angle       4.63238 ( 2925)
  SS BOND              : bond        0.00142 (    2)
  SS BOND              : angle       1.13027 (    4)
  covalent geometry    : bond        0.00453 (16423)
  covalent geometry    : angle       0.65123 (22272)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  375 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 303
  time to evaluate  : 1.818 
Fit side-chains
REVERT: L   79 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8271 (mp)
REVERT: H   76 LYS cc_start: 0.8067 (ptmm) cc_final: 0.7447 (ptmm)
REVERT: H  123 THR cc_start: 0.8100 (p) cc_final: 0.7843 (p)
REVERT: H  124 VAL cc_start: 0.8682 (t) cc_final: 0.8341 (m)
REVERT: A   89 ASP cc_start: 0.7182 (m-30) cc_final: 0.6912 (m-30)
REVERT: A  134 ASN cc_start: 0.6819 (t0) cc_final: 0.6498 (t0)
REVERT: A  163 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8293 (mtmt)
REVERT: A  246 GLU cc_start: 0.7514 (pp20) cc_final: 0.7172 (pp20)
REVERT: A  270 ASP cc_start: 0.7623 (m-30) cc_final: 0.7244 (m-30)
REVERT: A  289 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6761 (mt-10)
REVERT: B   74 GLN cc_start: 0.8439 (tt0) cc_final: 0.8126 (tt0)
REVERT: C  111 LYS cc_start: 0.7588 (tptt) cc_final: 0.7318 (tptp)
REVERT: C  116 ASP cc_start: 0.8166 (t0) cc_final: 0.7869 (t0)
REVERT: C  260 GLN cc_start: 0.7010 (mm110) cc_final: 0.6524 (mm-40)
REVERT: C  318 MET cc_start: 0.5146 (mtm) cc_final: 0.4923 (ttm)
REVERT: D   95 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7634 (tm-30)
REVERT: D  130 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7702 (mm)
REVERT: D  311 TYR cc_start: 0.7464 (m-80) cc_final: 0.6957 (m-80)
REVERT: E   85 LEU cc_start: 0.8077 (mm) cc_final: 0.7859 (mt)
REVERT: E  263 ASP cc_start: 0.7237 (m-30) cc_final: 0.7001 (m-30)
REVERT: E  299 THR cc_start: 0.6689 (m) cc_final: 0.6419 (p)
REVERT: E  344 TYR cc_start: 0.5147 (OUTLIER) cc_final: 0.4102 (p90)
  outliers start: 72
  outliers final: 61
  residues processed: 345
  average time/residue: 0.2456
  time to fit residues: 129.0577
Evaluate side-chains
  358 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 294
  time to evaluate  : 1.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain L residue   86 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   83 HIS
Chi-restraints excluded: chain C residue  112 MET
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  118 ASN
Chi-restraints excluded: chain C residue  156 TYR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  251 PHE
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  307 ILE
Chi-restraints excluded: chain C residue  330 VAL
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue  130 ILE
Chi-restraints excluded: chain D residue  134 ASN
Chi-restraints excluded: chain D residue  138 MET
Chi-restraints excluded: chain D residue  167 ASP
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  207 THR
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain E residue   32 MET
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  120 HIS
Chi-restraints excluded: chain E residue  140 GLN
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  156 TYR
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain E residue  293 VAL
Chi-restraints excluded: chain E residue  313 MET
Chi-restraints excluded: chain E residue  314 ASN
Chi-restraints excluded: chain E residue  344 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 85 optimal weight:    0.0040
   chunk 33 optimal weight:    1.9990
   chunk 147 optimal weight:    0.9980
   chunk 73 optimal weight:    0.5980
   chunk 16 optimal weight:    0.2980
   chunk 109 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 67 optimal weight:    0.8980
   chunk 182 optimal weight:    0.7980
   chunk 49 optimal weight:    0.5980
   chunk 115 optimal weight:    0.8980
   overall best weight:    0.4192

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

Flipped N/Q/H residues before XYZ refinement:
A 217 ASN
B 104 ASN
D  94 HIS
** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.164384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.132854 restraints weight = 29595.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 2.67
r_work: 0.3610 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16425  Z= 0.148
  Angle     :  0.636  13.300  22276  Z= 0.331
  Chirality :  0.044   0.176   2533
  Planarity :  0.004   0.059   2785
  Dihedral  :  4.347  18.439   2155
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.30 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 20.52 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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 (0.20), residues: 1930
  helix:  2.16 (0.16), residues: 977
  sheet:  0.69 (0.28), residues: 338
  loop : -1.78 (0.24), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 226 
 HIS   0.007   0.001   HIS D  94 
 PHE   0.032   0.001   PHE C  53 
 TYR   0.016   0.001   TYR H 103 
 ARG   0.010   0.000   ARG D 162 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05087 ( 1003)
  hydrogen bonds       : angle       4.50485 ( 2925)
  SS BOND              : bond        0.00178 (    2)
  SS BOND              : angle       0.78654 (    4)
  covalent geometry    : bond        0.00323 (16423)
  covalent geometry    : angle       0.63639 (22272)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 315
  time to evaluate  : 1.981 
Fit side-chains
REVERT: L   79 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8218 (mp)
REVERT: H  123 THR cc_start: 0.8070 (p) cc_final: 0.7813 (p)
REVERT: H  124 VAL cc_start: 0.8650 (t) cc_final: 0.8318 (m)
REVERT: A   65 THR cc_start: 0.5782 (OUTLIER) cc_final: 0.5540 (p)
REVERT: A   89 ASP cc_start: 0.7158 (m-30) cc_final: 0.6892 (m-30)
REVERT: A  113 PHE cc_start: 0.8787 (m-80) cc_final: 0.8415 (m-80)
REVERT: A  134 ASN cc_start: 0.6772 (t0) cc_final: 0.6474 (t0)
REVERT: A  163 LYS cc_start: 0.8520 (mtmt) cc_final: 0.8292 (mtmt)
REVERT: A  246 GLU cc_start: 0.7445 (pp20) cc_final: 0.7092 (pp20)
REVERT: A  270 ASP cc_start: 0.7587 (m-30) cc_final: 0.7217 (m-30)
REVERT: A  289 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6673 (mt-10)
REVERT: B   74 GLN cc_start: 0.8418 (tt0) cc_final: 0.8125 (tt0)
REVERT: B  134 ASN cc_start: 0.7916 (m-40) cc_final: 0.7676 (m-40)
REVERT: C   74 GLN cc_start: 0.7040 (mm-40) cc_final: 0.6553 (mm-40)
REVERT: C  111 LYS cc_start: 0.7624 (tptt) cc_final: 0.7355 (tptp)
REVERT: C  116 ASP cc_start: 0.8205 (t0) cc_final: 0.7885 (t0)
REVERT: C  260 GLN cc_start: 0.6948 (mm110) cc_final: 0.6511 (mm-40)
REVERT: C  318 MET cc_start: 0.5092 (mtm) cc_final: 0.4850 (ttm)
REVERT: D   95 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7604 (tm-30)
REVERT: D  130 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7688 (mm)
REVERT: D  311 TYR cc_start: 0.7413 (m-80) cc_final: 0.6742 (m-80)
REVERT: E   85 LEU cc_start: 0.8016 (mm) cc_final: 0.7811 (mt)
REVERT: E  263 ASP cc_start: 0.7149 (m-30) cc_final: 0.6930 (m-30)
REVERT: E  344 TYR cc_start: 0.5144 (OUTLIER) cc_final: 0.4148 (p90)
  outliers start: 65
  outliers final: 52
  residues processed: 352
  average time/residue: 0.2510
  time to fit residues: 134.8715
Evaluate side-chains
  358 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 302
  time to evaluate  : 1.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   83 HIS
Chi-restraints excluded: chain C residue  112 MET
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  118 ASN
Chi-restraints excluded: chain C residue  156 TYR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  251 PHE
Chi-restraints excluded: chain C residue  307 ILE
Chi-restraints excluded: chain C residue  330 VAL
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue  130 ILE
Chi-restraints excluded: chain D residue  134 ASN
Chi-restraints excluded: chain D residue  138 MET
Chi-restraints excluded: chain D residue  167 ASP
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  207 THR
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain E residue   32 MET
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  120 HIS
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  156 TYR
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain E residue  293 VAL
Chi-restraints excluded: chain E residue  344 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 127 optimal weight:    5.9990
   chunk 141 optimal weight:    2.9990
   chunk 181 optimal weight:    0.3980
   chunk 156 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 177 optimal weight:    0.9990
   chunk 93 optimal weight:    4.9990
   chunk 165 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 142 optimal weight:    0.7980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
H  13 GLN
A 217 ASN
B 104 ASN
** D  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 209 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.162789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.130424 restraints weight = 29374.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 2.43
r_work: 0.3614 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  16425  Z= 0.181
  Angle     :  0.665  13.732  22276  Z= 0.346
  Chirality :  0.045   0.254   2533
  Planarity :  0.005   0.059   2785
  Dihedral  :  4.374  18.544   2155
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.72 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 20.58 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.19), residues: 1930
  helix:  2.08 (0.16), residues: 977
  sheet:  0.70 (0.28), residues: 336
  loop : -1.81 (0.24), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.009   0.001   HIS D  94 
 PHE   0.032   0.002   PHE C  53 
 TYR   0.029   0.001   TYR A 279 
 ARG   0.010   0.000   ARG D 162 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05230 ( 1003)
  hydrogen bonds       : angle       4.55373 ( 2925)
  SS BOND              : bond        0.00104 (    2)
  SS BOND              : angle       0.99110 (    4)
  covalent geometry    : bond        0.00418 (16423)
  covalent geometry    : angle       0.66475 (22272)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8729.92 seconds
wall clock time: 152 minutes 39.07 seconds (9159.07 seconds total)