Starting phenix.real_space_refine
on Mon May 12 09:58:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ezm_31389/05_2025/7ezm_31389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ezm_31389/05_2025/7ezm_31389.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ezm_31389/05_2025/7ezm_31389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ezm_31389/05_2025/7ezm_31389.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ezm_31389/05_2025/7ezm_31389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ezm_31389/05_2025/7ezm_31389.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      69      5.16       5
     C    5748      2.51       5
     N    1524      2.21       5
     O    1667      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9008
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1850
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 2561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2561
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 41
    Chain: "D"
      Number of atoms: 2362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 304, 2362
          Classifications: {'peptide': 304}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 12, 'TRANS': 291}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 58
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 44
    Chain: "G"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 421
          Classifications: {'peptide': 59}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 4, 'TRANS': 54}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "H"
      Number of atoms: 1736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1736
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 32
    Chain: "P"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'TYS:plan-2': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 5.07, per 1000 atoms: 0.56
  Number of scatterers: 9008
  At special positions: 0
  Unit cell: (104.5, 120.175, 121.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      69     16.00
     O    1667      8.00
     N    1524      7.00
     C    5748      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 114 " - pdb=" SG  CYS D 196 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.24
  Conformation dependent library (CDL) restraints added in 999.1 milliseconds
  

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2202

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 13 sheets defined
      40.1% alpha, 21.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 38
    Processing helix  chain 'A' and resid 51 through 63
    Processing helix  chain 'A' and resid 212 through 221
      removed outlier: 4.595A  pdb=" N   ILE A 217 " --> pdb=" O   ARG A 214 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   HIS A 218 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 236
    Processing helix  chain 'A' and resid 246 through 261
    Processing helix  chain 'A' and resid 262 through 266
      removed outlier: 3.550A  pdb=" N   GLN A 265 " --> pdb=" O   PRO A 262 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   ASN A 266 " --> pdb=" O   TRP A 263 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 262 through 266'
    Processing helix  chain 'A' and resid 275 through 283
    Processing helix  chain 'A' and resid 287 through 291
    Processing helix  chain 'A' and resid 301 through 315
    Processing helix  chain 'A' and resid 335 through 356
    Processing helix  chain 'B' and resid 6 through 26
      removed outlier: 4.209A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'D' and resid 39 through 69
    Processing helix  chain 'D' and resid 70 through 73
    Processing helix  chain 'D' and resid 74 through 105
      Proline residue:  D  96  - end of helix
      Proline residue:  D 101  - end of helix
    Processing helix  chain 'D' and resid 110 through 145
    Processing helix  chain 'D' and resid 147 through 152
    Processing helix  chain 'D' and resid 154 through 173
    Processing helix  chain 'D' and resid 174 through 180
      removed outlier: 3.595A  pdb=" N   ILE D 178 " --> pdb=" O   THR D 174 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 217
    Processing helix  chain 'D' and resid 218 through 248
    Processing helix  chain 'D' and resid 301 through 339
      Proline residue:  D 328  - end of helix
    Processing helix  chain 'D' and resid 339 through 348
    Processing helix  chain 'D' and resid 349 through 371
      removed outlier: 4.019A  pdb=" N   SER D 363 " --> pdb=" O   SER D 359 " (cutoff:3.500A)
      Proline residue:  D 367  - end of helix
    Processing helix  chain 'D' and resid 374 through 383
    Processing helix  chain 'G' and resid 9 through 25
      removed outlier: 3.849A  pdb=" N   LEU G  15 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE G  25 " --> pdb=" O   MET G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 52 through 56
      removed outlier: 4.106A  pdb=" N   GLY H  56 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'H' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 196
      removed outlier: 6.662A  pdb=" N   LEU A  40 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   VAL A 204 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU A  42 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   SER A 225 " --> pdb=" O   LYS A  41 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   ILE A 226 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   PHE A 272 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   PHE A 228 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   ASN A 274 " --> pdb=" O   PHE A 228 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   VAL A 230 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.882A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.675A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.354A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.749A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.814A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.649A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.827A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 184 through 186
    Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.063A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148
      removed outlier: 3.507A  pdb=" N   GLU H 246 " --> pdb=" O   VAL H 147 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)

    482 hydrogen bonds defined for protein.
    1335 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.85

  Time building geometry restraints manager: 2.58 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2088
        1.33 -     1.46: 2829
        1.46 -     1.60: 4172
        1.60 -     1.73: 1
        1.73 -     1.86: 106
  Bond restraints: 9196
  Sorted by residual:
  bond pdb=" O1  TYS P   2 "
       pdb=" S   TYS P   2 "
    ideal  model  delta    sigma   weight residual
    1.462  1.636 -0.174 2.00e-02 2.50e+03 7.56e+01
  bond pdb=" OH  TYS P   2 "
       pdb=" S   TYS P   2 "
    ideal  model  delta    sigma   weight residual
    1.679  1.526  0.153 2.00e-02 2.50e+03 5.81e+01
  bond pdb=" CA  SER B 281 "
       pdb=" CB  SER B 281 "
    ideal  model  delta    sigma   weight residual
    1.532  1.465  0.066 1.78e-02 3.16e+03 1.39e+01
  bond pdb=" N   VAL A 240 "
       pdb=" CA  VAL A 240 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.033 1.19e-02 7.06e+03 7.60e+00
  bond pdb=" N   GLY B  41 "
       pdb=" CA  GLY B  41 "
    ideal  model  delta    sigma   weight residual
    1.448  1.492 -0.044 1.88e-02 2.83e+03 5.56e+00
  ... (remaining 9191 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 11457
        1.81 -     3.62: 914
        3.62 -     5.43: 91
        5.43 -     7.24: 18
        7.24 -     9.05: 4
  Bond angle restraints: 12484
  Sorted by residual:
  angle pdb=" C   ARG D 139 "
        pdb=" CA  ARG D 139 "
        pdb=" CB  ARG D 139 "
      ideal   model   delta    sigma   weight residual
     110.68  118.72   -8.04 1.70e+00 3.46e-01 2.23e+01
  angle pdb=" C   ARG D 345 "
        pdb=" CA  ARG D 345 "
        pdb=" CB  ARG D 345 "
      ideal   model   delta    sigma   weight residual
     110.88  103.83    7.05 1.57e+00 4.06e-01 2.02e+01
  angle pdb=" N   VAL A 238 "
        pdb=" CA  VAL A 238 "
        pdb=" C   VAL A 238 "
      ideal   model   delta    sigma   weight residual
     109.20  102.41    6.79 1.55e+00 4.16e-01 1.92e+01
  angle pdb=" N   ALA H 136 "
        pdb=" CA  ALA H 136 "
        pdb=" C   ALA H 136 "
      ideal   model   delta    sigma   weight residual
     113.02  107.99    5.03 1.20e+00 6.94e-01 1.75e+01
  angle pdb=" CA  VAL A 238 "
        pdb=" C   VAL A 238 "
        pdb=" O   VAL A 238 "
      ideal   model   delta    sigma   weight residual
     121.92  117.04    4.88 1.17e+00 7.31e-01 1.74e+01
  ... (remaining 12479 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.36: 4939
       16.36 -    32.71: 413
       32.71 -    49.06: 76
       49.06 -    65.42: 22
       65.42 -    81.77: 5
  Dihedral angle restraints: 5455
    sinusoidal: 2051
      harmonic: 3404
  Sorted by residual:
  dihedral pdb=" CB  CYS B 121 "
           pdb=" SG  CYS B 121 "
           pdb=" SG  CYS B 149 "
           pdb=" CB  CYS B 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.95  -63.95     1      1.00e+01 1.00e-02 5.38e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.59   28.41     0      5.00e+00 4.00e-02 3.23e+01
  dihedral pdb=" CA  THR B 165 "
           pdb=" C   THR B 165 "
           pdb=" N   CYS B 166 "
           pdb=" CA  CYS B 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.84   27.16     0      5.00e+00 4.00e-02 2.95e+01
  ... (remaining 5452 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 1137
       0.081 -    0.163: 272
       0.163 -    0.244: 23
       0.244 -    0.325: 3
       0.325 -    0.407: 2
  Chirality restraints: 1437
  Sorted by residual:
  chirality pdb=" CA  ARG A 210 "
            pdb=" N   ARG A 210 "
            pdb=" C   ARG A 210 "
            pdb=" CB  ARG A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.92   -0.41 2.00e-01 2.50e+01 4.14e+00
  chirality pdb=" CA  ARG D 345 "
            pdb=" N   ARG D 345 "
            pdb=" C   ARG D 345 "
            pdb=" CB  ARG D 345 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.87   -0.36 2.00e-01 2.50e+01 3.23e+00
  chirality pdb=" CG  LEU A 316 "
            pdb=" CB  LEU A 316 "
            pdb=" CD1 LEU A 316 "
            pdb=" CD2 LEU A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.86    0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 1434 not shown)

  Planarity restraints: 1576
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 313 "    0.048 9.50e-02 1.11e+02   4.23e-02 1.69e+01
        pdb=" NE  ARG D 313 "   -0.026 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 313 "    0.070 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 313 "   -0.024 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 313 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO D 367 "   -0.020 2.00e-02 2.50e+03   4.08e-02 1.67e+01
        pdb=" C   PRO D 367 "    0.071 2.00e-02 2.50e+03
        pdb=" O   PRO D 367 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   ILE D 368 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 202 "   -0.006 9.50e-02 1.11e+02   3.17e-02 1.25e+01
        pdb=" NE  ARG A 202 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 202 "   -0.061 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 202 "    0.021 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 202 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1573 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1292
        2.76 -     3.30: 9206
        3.30 -     3.83: 15416
        3.83 -     4.37: 19126
        4.37 -     4.90: 32178
  Nonbonded interactions: 77218
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 356 "
            pdb=" OE1 GLN D 153 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   TYR D 360 "
            pdb=" OG  SER D 363 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   MET D  72 "
            pdb=" ND2 ASN D  77 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OD1 ASN D  98 "
            pdb=" OH  TYR D 360 "
     model   vdw
     2.260 3.040
  ... (remaining 77213 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.470
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7171
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      :  0.011   0.174   9200  Z= 0.561
  Angle     :  1.074   9.054  12492  Z= 0.645
  Chirality :  0.068   0.407   1437
  Planarity :  0.009   0.102   1576
  Dihedral  : 13.160  81.772   3241
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  3.34 %
    Favored  : 95.72 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.87 (0.23), residues: 1150
  helix: -0.43 (0.23), residues: 404
  sheet: -0.10 (0.30), residues: 278
  loop : -0.83 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.008   TRP B  82 
 HIS   0.019   0.006   HIS D 157 
 PHE   0.025   0.006   PHE B 241 
 TYR   0.046   0.009   TYR H 175 
 ARG   0.071   0.009   ARG D 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16802 (  482)
  hydrogen bonds       : angle       7.01862 ( 1335)
  SS BOND              : bond        0.01126 (    4)
  SS BOND              : angle       1.86097 (    8)
  covalent geometry    : bond        0.01068 ( 9196)
  covalent geometry    : angle       1.07377 (12484)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 308
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.7426 (p) cc_final: 0.6994 (p)
REVERT: A    9 ASP cc_start: 0.6886 (m-30) cc_final: 0.6420 (m-30)
REVERT: A   39 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6529 (mt-10)
REVERT: A  237 GLN cc_start: 0.7324 (mt0) cc_final: 0.7086 (mt0)
REVERT: A  275 LYS cc_start: 0.7832 (mttt) cc_final: 0.7625 (mttt)
REVERT: B   67 SER cc_start: 0.7986 (m) cc_final: 0.7689 (t)
REVERT: B   74 SER cc_start: 0.7782 (t) cc_final: 0.7454 (t)
REVERT: B   98 SER cc_start: 0.7826 (p) cc_final: 0.7445 (t)
REVERT: B  118 ASP cc_start: 0.6246 (p0) cc_final: 0.5987 (p0)
REVERT: B  184 THR cc_start: 0.8506 (p) cc_final: 0.8296 (t)
REVERT: B  220 GLN cc_start: 0.8247 (mt0) cc_final: 0.7890 (mt0)
REVERT: B  221 THR cc_start: 0.7915 (m) cc_final: 0.7714 (t)
REVERT: B  277 SER cc_start: 0.8359 (t) cc_final: 0.8149 (t)
REVERT: B  334 SER cc_start: 0.7768 (m) cc_final: 0.7554 (p)
REVERT: D   76 THR cc_start: 0.7375 (m) cc_final: 0.7143 (m)
REVERT: D  111 SER cc_start: 0.8252 (t) cc_final: 0.8007 (p)
REVERT: H  141 THR cc_start: 0.7753 (m) cc_final: 0.7420 (p)
REVERT: H  180 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7688 (mtt180)
  outliers start: 9
  outliers final: 4
  residues processed: 315
  average time/residue: 1.0312
  time to fit residues: 348.8216
Evaluate side-chains
  277 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 273
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 ASN
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  250 GLU
Chi-restraints excluded: chain H residue  135 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 85 optimal weight:    7.9990
   chunk 47 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0170
   chunk 88 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 102 optimal weight:    5.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
B 132 ASN
D 131 ASN
D 374 ASN
H 142 GLN
H 179 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.136454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.122441 restraints weight = 12166.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.91
r_work: 0.3370 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9200  Z= 0.156
  Angle     :  0.623   6.811  12492  Z= 0.330
  Chirality :  0.045   0.164   1437
  Planarity :  0.004   0.042   1576
  Dihedral  :  6.901  72.494   1271
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 13.36 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.55 (0.25), residues: 1150
  helix:  1.35 (0.26), residues: 409
  sheet: -0.23 (0.29), residues: 282
  loop :  0.02 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 339 
 HIS   0.005   0.001   HIS B  62 
 PHE   0.033   0.002   PHE A  55 
 TYR   0.014   0.002   TYR H 190 
 ARG   0.008   0.001   ARG D 345 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04202 (  482)
  hydrogen bonds       : angle       5.16140 ( 1335)
  SS BOND              : bond        0.00162 (    4)
  SS BOND              : angle       2.29726 (    8)
  covalent geometry    : bond        0.00348 ( 9196)
  covalent geometry    : angle       0.62025 (12484)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 272
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8202 (p) cc_final: 0.7885 (p)
REVERT: A   39 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7399 (mt-10)
REVERT: A  201 PHE cc_start: 0.8320 (m-80) cc_final: 0.7826 (m-80)
REVERT: A  212 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7674 (mt-10)
REVERT: A  276 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7389 (ptpp)
REVERT: A  290 ASP cc_start: 0.7586 (m-30) cc_final: 0.7372 (m-30)
REVERT: B   52 ARG cc_start: 0.7721 (ttm110) cc_final: 0.7519 (ptp90)
REVERT: B   68 ARG cc_start: 0.8147 (ttt180) cc_final: 0.7786 (ttt180)
REVERT: B   98 SER cc_start: 0.7718 (p) cc_final: 0.7334 (t)
REVERT: B  161 SER cc_start: 0.7550 (m) cc_final: 0.7345 (p)
REVERT: B  170 ASP cc_start: 0.7733 (t70) cc_final: 0.7349 (OUTLIER)
REVERT: B  186 ASP cc_start: 0.6992 (t0) cc_final: 0.6746 (t0)
REVERT: B  214 ARG cc_start: 0.7735 (mtm180) cc_final: 0.7492 (mtm-85)
REVERT: B  268 ASN cc_start: 0.7631 (p0) cc_final: 0.7405 (p0)
REVERT: B  271 CYS cc_start: 0.7854 (m) cc_final: 0.7557 (p)
REVERT: D   77 ASN cc_start: 0.8173 (m-40) cc_final: 0.7948 (m-40)
REVERT: D   85 VAL cc_start: 0.8387 (t) cc_final: 0.8135 (p)
REVERT: D  126 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8387 (m)
REVERT: D  202 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7507 (p0)
REVERT: D  308 LYS cc_start: 0.8220 (mmtp) cc_final: 0.7964 (mttm)
REVERT: D  344 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7606 (mt-10)
REVERT: H   34 MET cc_start: 0.8542 (mmt) cc_final: 0.8308 (mmm)
REVERT: H   68 PHE cc_start: 0.7239 (m-10) cc_final: 0.6680 (m-80)
REVERT: H   78 THR cc_start: 0.8416 (t) cc_final: 0.7820 (m)
REVERT: H  141 THR cc_start: 0.7988 (m) cc_final: 0.7616 (p)
REVERT: H  180 ARG cc_start: 0.8351 (mtt180) cc_final: 0.7979 (mtt180)
REVERT: P    8 PHE cc_start: 0.8395 (m-10) cc_final: 0.8149 (m-10)
  outliers start: 45
  outliers final: 23
  residues processed: 290
  average time/residue: 1.0556
  time to fit residues: 328.5006
Evaluate side-chains
  264 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 239
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  126 SER
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  202 ASN
Chi-restraints excluded: chain D residue  304 ASN
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  155 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 102 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 86 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 64 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
D 374 ASN
G  18 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.133416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.118963 restraints weight = 12275.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.95
r_work: 0.3318 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9200  Z= 0.191
  Angle     :  0.606   6.969  12492  Z= 0.318
  Chirality :  0.045   0.153   1437
  Planarity :  0.004   0.043   1576
  Dihedral  :  5.599  69.130   1263
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 16.39 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.64 (0.25), residues: 1150
  helix:  1.48 (0.25), residues: 417
  sheet: -0.24 (0.29), residues: 276
  loop :  0.02 (0.31), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 339 
 HIS   0.005   0.001   HIS B  62 
 PHE   0.031   0.002   PHE A  55 
 TYR   0.016   0.002   TYR D 179 
 ARG   0.008   0.001   ARG B 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04172 (  482)
  hydrogen bonds       : angle       4.93470 ( 1335)
  SS BOND              : bond        0.00744 (    4)
  SS BOND              : angle       2.44371 (    8)
  covalent geometry    : bond        0.00436 ( 9196)
  covalent geometry    : angle       0.60279 (12484)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 248
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8408 (p) cc_final: 0.8048 (p)
REVERT: A    9 ASP cc_start: 0.7994 (m-30) cc_final: 0.7618 (m-30)
REVERT: A   17 LYS cc_start: 0.8115 (mttm) cc_final: 0.7913 (mmtp)
REVERT: A   39 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7394 (mt-10)
REVERT: A  201 PHE cc_start: 0.8445 (m-80) cc_final: 0.7874 (m-80)
REVERT: A  276 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7513 (ptpp)
REVERT: A  290 ASP cc_start: 0.7704 (m-30) cc_final: 0.7418 (m-30)
REVERT: A  307 GLU cc_start: 0.8043 (tp30) cc_final: 0.7740 (tp30)
REVERT: B   52 ARG cc_start: 0.7816 (ttm110) cc_final: 0.7477 (mtp85)
REVERT: B   87 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7807 (t)
REVERT: B   98 SER cc_start: 0.8001 (p) cc_final: 0.7664 (t)
REVERT: B  212 ASP cc_start: 0.7692 (t70) cc_final: 0.7454 (t0)
REVERT: B  214 ARG cc_start: 0.7741 (mtm180) cc_final: 0.7495 (mtm180)
REVERT: B  271 CYS cc_start: 0.8037 (m) cc_final: 0.7694 (p)
REVERT: B  274 THR cc_start: 0.8063 (m) cc_final: 0.7752 (p)
REVERT: B  289 TYR cc_start: 0.7661 (m-10) cc_final: 0.7124 (m-80)
REVERT: D  202 ASN cc_start: 0.8069 (p0) cc_final: 0.7822 (p0)
REVERT: D  308 LYS cc_start: 0.8282 (mmtp) cc_final: 0.8028 (mttp)
REVERT: D  336 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7922 (ttt180)
REVERT: D  344 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7682 (mt-10)
REVERT: H   68 PHE cc_start: 0.7371 (m-10) cc_final: 0.6927 (m-10)
REVERT: H  180 ARG cc_start: 0.8558 (mtt180) cc_final: 0.8284 (mtt180)
  outliers start: 45
  outliers final: 23
  residues processed: 269
  average time/residue: 1.0568
  time to fit residues: 305.0384
Evaluate side-chains
  258 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 232
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain H residue   23 SER
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 105 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 110 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
H 194 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.130202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.115675 restraints weight = 12081.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.93
r_work: 0.3308 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9200  Z= 0.181
  Angle     :  0.582   7.159  12492  Z= 0.305
  Chirality :  0.044   0.145   1437
  Planarity :  0.004   0.044   1576
  Dihedral  :  5.451  70.009   1262
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 17.54 %
    Favored  : 77.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.69 (0.25), residues: 1150
  helix:  1.68 (0.25), residues: 409
  sheet: -0.28 (0.29), residues: 285
  loop : -0.04 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 339 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.028   0.002   PHE A  55 
 TYR   0.017   0.002   TYR D 179 
 ARG   0.007   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03972 (  482)
  hydrogen bonds       : angle       4.86292 ( 1335)
  SS BOND              : bond        0.00887 (    4)
  SS BOND              : angle       2.21037 (    8)
  covalent geometry    : bond        0.00416 ( 9196)
  covalent geometry    : angle       0.57928 (12484)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 237
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8463 (p) cc_final: 0.8102 (p)
REVERT: A    9 ASP cc_start: 0.8012 (m-30) cc_final: 0.7636 (m-30)
REVERT: A   17 LYS cc_start: 0.8138 (mttm) cc_final: 0.7928 (mmtp)
REVERT: A   39 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7233 (mt-10)
REVERT: A  201 PHE cc_start: 0.8459 (m-80) cc_final: 0.7849 (m-80)
REVERT: A  202 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.8027 (ttm-80)
REVERT: A  276 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7528 (ptpp)
REVERT: A  290 ASP cc_start: 0.7712 (m-30) cc_final: 0.7384 (m-30)
REVERT: A  307 GLU cc_start: 0.8079 (tp30) cc_final: 0.7723 (tp30)
REVERT: A  322 LYS cc_start: 0.8124 (ttmt) cc_final: 0.7851 (ttmm)
REVERT: B   52 ARG cc_start: 0.7817 (ttm110) cc_final: 0.7224 (mtt90)
REVERT: B   98 SER cc_start: 0.8033 (p) cc_final: 0.7682 (t)
REVERT: B  212 ASP cc_start: 0.7741 (t70) cc_final: 0.7491 (t0)
REVERT: B  268 ASN cc_start: 0.7936 (p0) cc_final: 0.7645 (p0)
REVERT: B  271 CYS cc_start: 0.8070 (m) cc_final: 0.7746 (p)
REVERT: B  274 THR cc_start: 0.7987 (m) cc_final: 0.7708 (p)
REVERT: B  289 TYR cc_start: 0.7747 (m-10) cc_final: 0.7006 (m-80)
REVERT: B  312 ASP cc_start: 0.7614 (t0) cc_final: 0.7354 (t70)
REVERT: D   67 ILE cc_start: 0.7556 (pt) cc_final: 0.7289 (mm)
REVERT: D   74 THR cc_start: 0.8055 (t) cc_final: 0.7647 (p)
REVERT: D   75 VAL cc_start: 0.8148 (p) cc_final: 0.7696 (t)
REVERT: D  202 ASN cc_start: 0.8120 (p0) cc_final: 0.7899 (p0)
REVERT: D  308 LYS cc_start: 0.8342 (mmtp) cc_final: 0.8129 (mttm)
REVERT: D  323 PHE cc_start: 0.8616 (m-80) cc_final: 0.8154 (m-80)
REVERT: D  336 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.8022 (ttt180)
REVERT: D  344 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7720 (mt-10)
REVERT: H   20 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7718 (pp)
REVERT: H   30 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8187 (t)
REVERT: H   63 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8210 (t)
  outliers start: 45
  outliers final: 23
  residues processed: 261
  average time/residue: 1.1116
  time to fit residues: 310.2108
Evaluate side-chains
  262 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 234
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   52 LYS
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  210 ARG
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   23 SER
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  238 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0010
   chunk 67 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 112 optimal weight:    0.0970
   chunk 86 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 26 optimal weight:    0.2980
   overall best weight:    0.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 350 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.129787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.115326 restraints weight = 12142.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 1.93
r_work: 0.3338 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9200  Z= 0.120
  Angle     :  0.546   9.568  12492  Z= 0.285
  Chirality :  0.042   0.166   1437
  Planarity :  0.004   0.042   1576
  Dihedral  :  5.220  70.840   1262
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 19.94 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.81 (0.25), residues: 1150
  helix:  1.92 (0.25), residues: 409
  sheet: -0.25 (0.29), residues: 288
  loop : -0.10 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.025   0.001   PHE A  55 
 TYR   0.016   0.001   TYR D 179 
 ARG   0.006   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03597 (  482)
  hydrogen bonds       : angle       4.70134 ( 1335)
  SS BOND              : bond        0.00559 (    4)
  SS BOND              : angle       1.68066 (    8)
  covalent geometry    : bond        0.00266 ( 9196)
  covalent geometry    : angle       0.54437 (12484)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 246
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8423 (p) cc_final: 0.8158 (p)
REVERT: A    9 ASP cc_start: 0.7957 (m-30) cc_final: 0.7645 (m-30)
REVERT: A   39 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7343 (mt-10)
REVERT: A  201 PHE cc_start: 0.8479 (m-80) cc_final: 0.7652 (m-80)
REVERT: A  276 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7538 (ttpp)
REVERT: A  290 ASP cc_start: 0.7695 (m-30) cc_final: 0.7349 (m-30)
REVERT: A  307 GLU cc_start: 0.8062 (tp30) cc_final: 0.7736 (tp30)
REVERT: A  322 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7762 (ttmm)
REVERT: B   33 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7665 (mt)
REVERT: B   52 ARG cc_start: 0.7778 (ttm110) cc_final: 0.7204 (mtt90)
REVERT: B   61 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7848 (ppp)
REVERT: B   98 SER cc_start: 0.7860 (p) cc_final: 0.7518 (t)
REVERT: B  170 ASP cc_start: 0.7957 (t70) cc_final: 0.7547 (t0)
REVERT: B  212 ASP cc_start: 0.7700 (t70) cc_final: 0.7447 (t0)
REVERT: B  227 SER cc_start: 0.8592 (m) cc_final: 0.8060 (t)
REVERT: B  271 CYS cc_start: 0.8051 (m) cc_final: 0.7744 (p)
REVERT: B  289 TYR cc_start: 0.7605 (m-10) cc_final: 0.7372 (m-80)
REVERT: B  312 ASP cc_start: 0.7613 (t0) cc_final: 0.7350 (t70)
REVERT: D   67 ILE cc_start: 0.7499 (pt) cc_final: 0.7254 (mm)
REVERT: D   74 THR cc_start: 0.8036 (t) cc_final: 0.7687 (p)
REVERT: D   75 VAL cc_start: 0.8178 (p) cc_final: 0.7699 (t)
REVERT: D  202 ASN cc_start: 0.8145 (p0) cc_final: 0.7927 (p0)
REVERT: D  323 PHE cc_start: 0.8593 (m-80) cc_final: 0.8177 (m-80)
REVERT: D  329 ILE cc_start: 0.8454 (tp) cc_final: 0.8219 (tt)
REVERT: D  336 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7936 (ttt180)
REVERT: H   63 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8101 (t)
REVERT: H  214 LEU cc_start: 0.8032 (tp) cc_final: 0.7822 (tt)
  outliers start: 34
  outliers final: 18
  residues processed: 261
  average time/residue: 1.0819
  time to fit residues: 301.8441
Evaluate side-chains
  257 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 234
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  346 ARG
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 111 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   chunk 96 optimal weight:    0.0470
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.9482

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.128553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.114345 restraints weight = 11983.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.91
r_work: 0.3327 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.3633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9200  Z= 0.185
  Angle     :  0.579   9.288  12492  Z= 0.302
  Chirality :  0.043   0.149   1437
  Planarity :  0.004   0.042   1576
  Dihedral  :  5.280  70.027   1262
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 19.21 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.77 (0.25), residues: 1150
  helix:  1.82 (0.25), residues: 412
  sheet: -0.22 (0.29), residues: 285
  loop : -0.09 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 339 
 HIS   0.005   0.001   HIS D 210 
 PHE   0.026   0.002   PHE A  55 
 TYR   0.016   0.002   TYR D 179 
 ARG   0.006   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  482)
  hydrogen bonds       : angle       4.75188 ( 1335)
  SS BOND              : bond        0.00794 (    4)
  SS BOND              : angle       2.00228 (    8)
  covalent geometry    : bond        0.00425 ( 9196)
  covalent geometry    : angle       0.57719 (12484)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 245
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8490 (p) cc_final: 0.8223 (p)
REVERT: A    9 ASP cc_start: 0.7972 (m-30) cc_final: 0.7659 (m-30)
REVERT: A   39 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7169 (mt-10)
REVERT: A  201 PHE cc_start: 0.8510 (m-80) cc_final: 0.7687 (m-80)
REVERT: A  202 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.8015 (ttm-80)
REVERT: A  290 ASP cc_start: 0.7746 (m-30) cc_final: 0.7413 (m-30)
REVERT: A  307 GLU cc_start: 0.8080 (tp30) cc_final: 0.7757 (tp30)
REVERT: A  322 LYS cc_start: 0.8071 (ttmt) cc_final: 0.7825 (ttmm)
REVERT: B   52 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7447 (mtp85)
REVERT: B   61 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7825 (tmm)
REVERT: B   98 SER cc_start: 0.8121 (p) cc_final: 0.7788 (t)
REVERT: B  212 ASP cc_start: 0.7699 (t70) cc_final: 0.7468 (t0)
REVERT: B  220 GLN cc_start: 0.8286 (mt0) cc_final: 0.7892 (mt0)
REVERT: B  227 SER cc_start: 0.8610 (m) cc_final: 0.8108 (t)
REVERT: B  271 CYS cc_start: 0.8058 (m) cc_final: 0.7762 (p)
REVERT: B  312 ASP cc_start: 0.7667 (t0) cc_final: 0.7412 (t70)
REVERT: D   74 THR cc_start: 0.8030 (t) cc_final: 0.7729 (p)
REVERT: D   75 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7809 (t)
REVERT: D  202 ASN cc_start: 0.8157 (p0) cc_final: 0.7951 (p0)
REVERT: D  213 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8066 (mp)
REVERT: D  323 PHE cc_start: 0.8621 (m-80) cc_final: 0.8122 (m-80)
REVERT: D  329 ILE cc_start: 0.8445 (tp) cc_final: 0.8232 (tt)
REVERT: D  336 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.8002 (ttt180)
REVERT: H   63 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8230 (t)
REVERT: H  199 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8139 (m)
REVERT: H  215 THR cc_start: 0.8243 (p) cc_final: 0.8040 (p)
  outliers start: 46
  outliers final: 25
  residues processed: 267
  average time/residue: 1.0844
  time to fit residues: 310.8759
Evaluate side-chains
  266 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 235
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   52 LYS
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  213 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  346 ARG
Chi-restraints excluded: chain D residue  350 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  199 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 76 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
D 304 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.126683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.112112 restraints weight = 12248.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 1.94
r_work: 0.3285 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.3847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   9200  Z= 0.264
  Angle     :  0.635   9.123  12492  Z= 0.329
  Chirality :  0.046   0.205   1437
  Planarity :  0.004   0.043   1576
  Dihedral  :  5.472  69.241   1262
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 20.15 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.62 (0.25), residues: 1150
  helix:  1.68 (0.25), residues: 411
  sheet: -0.30 (0.29), residues: 281
  loop : -0.16 (0.31), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 216 
 HIS   0.006   0.001   HIS H  35 
 PHE   0.027   0.002   PHE A  55 
 TYR   0.018   0.002   TYR H 173 
 ARG   0.007   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04230 (  482)
  hydrogen bonds       : angle       4.90045 ( 1335)
  SS BOND              : bond        0.01041 (    4)
  SS BOND              : angle       2.17613 (    8)
  covalent geometry    : bond        0.00609 ( 9196)
  covalent geometry    : angle       0.63302 (12484)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 250
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8497 (p) cc_final: 0.8190 (p)
REVERT: A    9 ASP cc_start: 0.8029 (m-30) cc_final: 0.7694 (m-30)
REVERT: A   39 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7315 (mt-10)
REVERT: A  201 PHE cc_start: 0.8579 (m-80) cc_final: 0.7724 (m-80)
REVERT: A  290 ASP cc_start: 0.7773 (m-30) cc_final: 0.7464 (m-30)
REVERT: A  294 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7556 (mm-30)
REVERT: A  307 GLU cc_start: 0.8069 (tp30) cc_final: 0.7760 (tp30)
REVERT: A  322 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7883 (ttmp)
REVERT: B   87 THR cc_start: 0.8310 (m) cc_final: 0.7986 (t)
REVERT: B   98 SER cc_start: 0.8218 (p) cc_final: 0.7880 (t)
REVERT: B  212 ASP cc_start: 0.7730 (t70) cc_final: 0.7484 (t0)
REVERT: B  247 ASP cc_start: 0.7569 (p0) cc_final: 0.7360 (p0)
REVERT: B  271 CYS cc_start: 0.8080 (m) cc_final: 0.7714 (p)
REVERT: B  312 ASP cc_start: 0.7686 (t0) cc_final: 0.7412 (t70)
REVERT: D   74 THR cc_start: 0.8043 (t) cc_final: 0.7733 (p)
REVERT: D   75 VAL cc_start: 0.8310 (p) cc_final: 0.7937 (t)
REVERT: D  200 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6309 (tp)
REVERT: D  202 ASN cc_start: 0.8193 (p0) cc_final: 0.7990 (p0)
REVERT: D  323 PHE cc_start: 0.8599 (m-80) cc_final: 0.8065 (m-80)
REVERT: D  329 ILE cc_start: 0.8458 (tp) cc_final: 0.8251 (tt)
REVERT: D  336 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.8023 (ttt180)
REVERT: H   30 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.8153 (t)
REVERT: H   63 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8230 (t)
REVERT: H  145 SER cc_start: 0.7971 (t) cc_final: 0.7756 (t)
REVERT: H  199 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8225 (m)
  outliers start: 44
  outliers final: 26
  residues processed: 270
  average time/residue: 1.0484
  time to fit residues: 303.8563
Evaluate side-chains
  279 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 248
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   52 LYS
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  241 LYS
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  346 ARG
Chi-restraints excluded: chain D residue  350 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  199 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 102 optimal weight:    0.0060
   chunk 71 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 77 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0050
   chunk 43 optimal weight:    0.0370
   chunk 97 optimal weight:    0.6980
   chunk 105 optimal weight:    0.2980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.1888

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

Flipped N/Q/H residues before XYZ refinement:
D 304 ASN
H 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.131031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.116968 restraints weight = 12205.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 1.92
r_work: 0.3359 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   9200  Z= 0.115
  Angle     :  0.557   8.130  12492  Z= 0.287
  Chirality :  0.042   0.174   1437
  Planarity :  0.004   0.042   1576
  Dihedral  :  5.212  71.037   1262
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 22.03 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.78 (0.25), residues: 1150
  helix:  1.87 (0.26), residues: 410
  sheet: -0.26 (0.29), residues: 290
  loop : -0.10 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.032   0.002   PHE A  55 
 TYR   0.016   0.001   TYR D 179 
 ARG   0.008   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03555 (  482)
  hydrogen bonds       : angle       4.75022 ( 1335)
  SS BOND              : bond        0.00506 (    4)
  SS BOND              : angle       1.62350 (    8)
  covalent geometry    : bond        0.00256 ( 9196)
  covalent geometry    : angle       0.55578 (12484)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 246
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8478 (p) cc_final: 0.8252 (p)
REVERT: A    9 ASP cc_start: 0.7883 (m-30) cc_final: 0.7658 (m-30)
REVERT: A   39 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7228 (mt-10)
REVERT: A  201 PHE cc_start: 0.8530 (m-80) cc_final: 0.7753 (m-80)
REVERT: A  290 ASP cc_start: 0.7761 (m-30) cc_final: 0.7426 (m-30)
REVERT: A  307 GLU cc_start: 0.8067 (tp30) cc_final: 0.7754 (tp30)
REVERT: A  322 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7832 (ttmm)
REVERT: B   52 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7377 (mtt90)
REVERT: B   61 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7905 (ppp)
REVERT: B   76 ASP cc_start: 0.7645 (p0) cc_final: 0.7408 (p0)
REVERT: B   98 SER cc_start: 0.8104 (p) cc_final: 0.7825 (t)
REVERT: B  170 ASP cc_start: 0.7958 (t70) cc_final: 0.7516 (t0)
REVERT: B  212 ASP cc_start: 0.7723 (t70) cc_final: 0.7492 (t0)
REVERT: B  220 GLN cc_start: 0.8172 (mt0) cc_final: 0.7817 (mt0)
REVERT: B  230 ASN cc_start: 0.8394 (m-40) cc_final: 0.8059 (m110)
REVERT: B  271 CYS cc_start: 0.8008 (m) cc_final: 0.7702 (p)
REVERT: B  312 ASP cc_start: 0.7559 (t0) cc_final: 0.7284 (t70)
REVERT: D   74 THR cc_start: 0.7977 (t) cc_final: 0.7670 (p)
REVERT: D   75 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7735 (t)
REVERT: D  126 SER cc_start: 0.8595 (t) cc_final: 0.8382 (m)
REVERT: D  170 PHE cc_start: 0.7107 (m-10) cc_final: 0.6838 (m-10)
REVERT: D  323 PHE cc_start: 0.8623 (m-80) cc_final: 0.8148 (m-80)
REVERT: D  329 ILE cc_start: 0.8429 (tp) cc_final: 0.8219 (tt)
REVERT: D  344 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7609 (mt-10)
REVERT: G   38 MET cc_start: 0.7962 (mtp) cc_final: 0.7736 (mtm)
REVERT: H   63 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8177 (t)
REVERT: H   67 ARG cc_start: 0.8194 (ttp80) cc_final: 0.7905 (ttp80)
REVERT: H  145 SER cc_start: 0.7850 (t) cc_final: 0.7646 (t)
REVERT: H  199 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8044 (m)
  outliers start: 36
  outliers final: 23
  residues processed: 261
  average time/residue: 1.1266
  time to fit residues: 314.6104
Evaluate side-chains
  265 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 238
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  241 LYS
Chi-restraints excluded: chain D residue  296 ILE
Chi-restraints excluded: chain D residue  350 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  199 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 91 optimal weight:    0.0570
   chunk 111 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0570
   chunk 27 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.4816

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.130482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.116373 restraints weight = 12120.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 1.92
r_work: 0.3360 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.3987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9200  Z= 0.134
  Angle     :  0.578   9.504  12492  Z= 0.296
  Chirality :  0.042   0.198   1437
  Planarity :  0.004   0.041   1576
  Dihedral  :  5.116  70.082   1262
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 22.23 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.75 (0.25), residues: 1150
  helix:  1.90 (0.25), residues: 411
  sheet: -0.33 (0.29), residues: 297
  loop : -0.13 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 339 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.036   0.002   PHE A  55 
 TYR   0.016   0.002   TYR D 179 
 ARG   0.010   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03667 (  482)
  hydrogen bonds       : angle       4.70626 ( 1335)
  SS BOND              : bond        0.00667 (    4)
  SS BOND              : angle       1.94274 (    8)
  covalent geometry    : bond        0.00308 ( 9196)
  covalent geometry    : angle       0.57597 (12484)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 239
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8515 (p) cc_final: 0.8233 (p)
REVERT: A    9 ASP cc_start: 0.7859 (m-30) cc_final: 0.7628 (m-30)
REVERT: A   10 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8164 (mtmm)
REVERT: A  201 PHE cc_start: 0.8556 (m-80) cc_final: 0.7796 (m-80)
REVERT: A  290 ASP cc_start: 0.7743 (m-30) cc_final: 0.7418 (m-30)
REVERT: A  307 GLU cc_start: 0.8022 (tp30) cc_final: 0.7704 (tp30)
REVERT: A  322 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7786 (ttmm)
REVERT: B   52 ARG cc_start: 0.7750 (ttm-80) cc_final: 0.7412 (mtt90)
REVERT: B   61 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7897 (ppp)
REVERT: B   98 SER cc_start: 0.8113 (p) cc_final: 0.7797 (t)
REVERT: B  170 ASP cc_start: 0.7946 (t70) cc_final: 0.7510 (t0)
REVERT: B  212 ASP cc_start: 0.7706 (t70) cc_final: 0.7464 (t0)
REVERT: B  220 GLN cc_start: 0.8091 (mt0) cc_final: 0.7731 (mt0)
REVERT: B  221 THR cc_start: 0.8160 (m) cc_final: 0.7957 (t)
REVERT: B  246 ASP cc_start: 0.7754 (m-30) cc_final: 0.7514 (m-30)
REVERT: B  271 CYS cc_start: 0.7997 (m) cc_final: 0.7666 (p)
REVERT: B  312 ASP cc_start: 0.7589 (t0) cc_final: 0.7310 (t70)
REVERT: D   43 VAL cc_start: 0.8373 (p) cc_final: 0.8123 (p)
REVERT: D   74 THR cc_start: 0.7975 (t) cc_final: 0.7614 (p)
REVERT: D   75 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7615 (t)
REVERT: D  323 PHE cc_start: 0.8609 (m-80) cc_final: 0.8155 (m-80)
REVERT: D  344 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7613 (mt-10)
REVERT: H  145 SER cc_start: 0.7778 (t) cc_final: 0.7572 (t)
  outliers start: 33
  outliers final: 26
  residues processed: 254
  average time/residue: 1.0457
  time to fit residues: 284.7913
Evaluate side-chains
  263 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 235
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   52 LYS
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  296 ILE
Chi-restraints excluded: chain D residue  350 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  199 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 60.2187 > 50:
  distance: 20 - 22:  26.410
  distance: 22 - 23:  43.730
  distance: 23 - 24:  28.680
  distance: 23 - 26:  28.044
  distance: 24 - 25:  19.410
  distance: 24 - 27:  14.708
  distance: 27 - 28:  18.554
  distance: 28 - 29:  11.457
  distance: 28 - 31:   7.311
  distance: 31 - 32:  12.522
  distance: 33 - 34:  16.341
  distance: 34 - 35:  15.411
  distance: 35 - 36:  10.333
  distance: 35 - 37:  10.581
  distance: 36 - 59:  22.919
  distance: 37 - 38:  10.022
  distance: 38 - 39:   8.170
  distance: 39 - 40:   8.274
  distance: 39 - 46:   4.050
  distance: 40 - 70:   7.542
  distance: 41 - 42:   5.128
  distance: 42 - 43:  17.953
  distance: 43 - 44:   5.849
  distance: 44 - 45:  19.442
  distance: 46 - 47:  10.934
  distance: 47 - 48:  22.269
  distance: 47 - 50:   5.416
  distance: 48 - 49:  12.732
  distance: 48 - 52:   7.678
  distance: 49 - 78:  12.553
  distance: 50 - 51:   4.857
  distance: 52 - 53:   9.885
  distance: 53 - 54:  12.047
  distance: 54 - 55:  14.653
  distance: 54 - 59:  13.868
  distance: 55 - 87:  15.634
  distance: 56 - 57:   4.305
  distance: 56 - 58:  18.290
  distance: 59 - 60:   6.275
  distance: 60 - 61:   8.534
  distance: 60 - 63:   6.139
  distance: 61 - 62:   6.039
  distance: 61 - 70:   6.833
  distance: 62 - 96:  14.162
  distance: 63 - 64:   4.451
  distance: 64 - 65:   6.229
  distance: 64 - 66:   3.108
  distance: 65 - 67:   8.884
  distance: 66 - 68:   5.281
  distance: 67 - 69:   6.452
  distance: 68 - 69:   8.222
  distance: 70 - 71:   7.642
  distance: 71 - 72:   3.716
  distance: 71 - 74:  12.810
  distance: 72 - 73:  13.110
  distance: 72 - 78:   8.476
  distance: 73 - 104:  17.453
  distance: 74 - 75:  15.027
  distance: 74 - 76:  14.466
  distance: 75 - 77:   9.438
  distance: 78 - 79:   5.076
  distance: 79 - 80:   6.783
  distance: 79 - 82:   6.634
  distance: 80 - 81:   6.330
  distance: 80 - 87:   9.201
  distance: 81 - 109:  12.305
  distance: 82 - 83:  17.826
  distance: 83 - 84:  18.893
  distance: 84 - 85:  19.436
  distance: 85 - 86:   6.259
  distance: 87 - 88:   4.892
  distance: 88 - 89:   4.772
  distance: 88 - 91:   4.626
  distance: 89 - 90:   3.589
  distance: 89 - 96:   3.056
  distance: 90 - 114:   6.350
  distance: 91 - 92:   6.026
  distance: 92 - 93:   5.978
  distance: 93 - 94:   6.153
  distance: 93 - 95:   7.209