Starting phenix.real_space_refine
on Thu May 15 12:02:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vsz_43512/05_2025/8vsz_43512.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vsz_43512/05_2025/8vsz_43512.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vsz_43512/05_2025/8vsz_43512.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vsz_43512/05_2025/8vsz_43512.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vsz_43512/05_2025/8vsz_43512.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vsz_43512/05_2025/8vsz_43512.cif"
  }
  resolution = 3.07
  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=   0.004 sd=   0.039
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      65      5.16       5
     C    8590      2.51       5
     N    2100      2.21       5
     O    2465      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13220
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2580
          Classifications: {'peptide': 316}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 307}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    C, B, E, D, F, I, H, J
  Time building chain proxies: 5.74, per 1000 atoms: 0.43
  Number of scatterers: 13220
  At special positions: 0
  Unit cell: (93.225, 91.575, 120.45, 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      65     16.00
     O    2465      8.00
     N    2100      7.00
     C    8590      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 160 " - pdb=" SG  CYS A 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 160 " - pdb=" SG  CYS C 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 160 " - pdb=" SG  CYS B 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 160 " - pdb=" SG  CYS E 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 160 " - pdb=" SG  CYS D 174 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=5, symmetry=0
  Links applied
    ALPHA1-4
      " BMA F   3 " - " MAN F   4 "
      " BMA G   3 " - " MAN G   4 "
      " BMA H   3 " - " MAN H   4 "
      " BMA I   3 " - " MAN I   4 "
      " BMA J   3 " - " MAN J   4 "
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
      " NAG I   1 " - " NAG I   2 "
      " NAG I   2 " - " BMA I   3 "
      " NAG J   1 " - " NAG J   2 "
      " NAG J   2 " - " BMA J   3 "
    NAG-ASN
      " NAG A 501 " - " ASN A 196 "
      " NAG B 501 " - " ASN B 196 "
      " NAG C 501 " - " ASN C 196 "
      " NAG D 501 " - " ASN D 196 "
      " NAG E 501 " - " ASN E 196 "
      " NAG F   1 " - " ASN A 145 "
      " NAG G   1 " - " ASN B 145 "
      " NAG H   1 " - " ASN C 145 "
      " NAG I   1 " - " ASN D 145 "
      " NAG J   1 " - " ASN E 145 "
  Number of additional bonds: simple=5, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.22
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3010

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 20 sheets defined
      36.4% alpha, 43.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 194 through 197
    Processing helix  chain 'A' and resid 201 through 205
    Processing helix  chain 'A' and resid 241 through 249
      removed outlier: 4.050A  pdb=" N   PHE A 245 " --> pdb=" O   ASN A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 263
    Processing helix  chain 'A' and resid 264 through 266
      No H-bonds generated for 'chain 'A' and resid 264 through 266'
    Processing helix  chain 'A' and resid 270 through 296
      removed outlier: 3.684A  pdb=" N   LEU A 296 " --> pdb=" O   SER A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 332
      removed outlier: 3.609A  pdb=" N   VAL A 308 " --> pdb=" O   LYS A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 420
      removed outlier: 4.334A  pdb=" N   LEU A 420 " --> pdb=" O   HIS A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 437
    Processing helix  chain 'B' and resid 194 through 197
    Processing helix  chain 'B' and resid 201 through 205
    Processing helix  chain 'B' and resid 241 through 249
      removed outlier: 4.050A  pdb=" N   PHE B 245 " --> pdb=" O   ASN B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 263
    Processing helix  chain 'B' and resid 264 through 266
      No H-bonds generated for 'chain 'B' and resid 264 through 266'
    Processing helix  chain 'B' and resid 270 through 296
      removed outlier: 3.684A  pdb=" N   LEU B 296 " --> pdb=" O   SER B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 332
      removed outlier: 3.608A  pdb=" N   VAL B 308 " --> pdb=" O   LYS B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 420
      removed outlier: 4.334A  pdb=" N   LEU B 420 " --> pdb=" O   HIS B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 437
    Processing helix  chain 'C' and resid 194 through 197
    Processing helix  chain 'C' and resid 201 through 205
    Processing helix  chain 'C' and resid 241 through 249
      removed outlier: 4.049A  pdb=" N   PHE C 245 " --> pdb=" O   ASN C 241 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 249 through 263
    Processing helix  chain 'C' and resid 264 through 266
      No H-bonds generated for 'chain 'C' and resid 264 through 266'
    Processing helix  chain 'C' and resid 270 through 296
      removed outlier: 3.684A  pdb=" N   LEU C 296 " --> pdb=" O   SER C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 304 through 332
      removed outlier: 3.608A  pdb=" N   VAL C 308 " --> pdb=" O   LYS C 304 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 415 through 420
      removed outlier: 4.334A  pdb=" N   LEU C 420 " --> pdb=" O   HIS C 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 421 through 437
    Processing helix  chain 'D' and resid 194 through 197
    Processing helix  chain 'D' and resid 201 through 205
    Processing helix  chain 'D' and resid 241 through 249
      removed outlier: 4.050A  pdb=" N   PHE D 245 " --> pdb=" O   ASN D 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 249 through 263
    Processing helix  chain 'D' and resid 264 through 266
      No H-bonds generated for 'chain 'D' and resid 264 through 266'
    Processing helix  chain 'D' and resid 270 through 296
      removed outlier: 3.684A  pdb=" N   LEU D 296 " --> pdb=" O   SER D 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 304 through 332
      removed outlier: 3.608A  pdb=" N   VAL D 308 " --> pdb=" O   LYS D 304 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 415 through 420
      removed outlier: 4.334A  pdb=" N   LEU D 420 " --> pdb=" O   HIS D 416 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 421 through 437
    Processing helix  chain 'E' and resid 194 through 197
    Processing helix  chain 'E' and resid 201 through 205
    Processing helix  chain 'E' and resid 241 through 249
      removed outlier: 4.050A  pdb=" N   PHE E 245 " --> pdb=" O   ASN E 241 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 249 through 263
    Processing helix  chain 'E' and resid 264 through 266
      No H-bonds generated for 'chain 'E' and resid 264 through 266'
    Processing helix  chain 'E' and resid 270 through 296
      removed outlier: 3.684A  pdb=" N   LEU E 296 " --> pdb=" O   SER E 292 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 304 through 332
      removed outlier: 3.608A  pdb=" N   VAL E 308 " --> pdb=" O   LYS E 304 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 415 through 420
      removed outlier: 4.333A  pdb=" N   LEU E 420 " --> pdb=" O   HIS E 416 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 421 through 437
    Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 107
      removed outlier: 3.790A  pdb=" N   ILE A 140 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ASP A  81 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER A  74 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR A  83 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE A  72 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   THR A  85 " --> pdb=" O   ALA A  70 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   MET A  93 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   GLN A  62 " --> pdb=" O   MET A  93 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 130
      removed outlier: 6.939A  pdb=" N   THR A 157 " --> pdb=" O   LYS A 126 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   SER A 128 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   THR A 155 " --> pdb=" O   SER A 128 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   LEU A 130 " --> pdb=" O   ARG A 153 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   ARG A 153 " --> pdb=" O   LEU A 130 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ASP A  81 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER A  74 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR A  83 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE A  72 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   THR A  85 " --> pdb=" O   ALA A  70 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   MET A  93 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   GLN A  62 " --> pdb=" O   MET A  93 " (cutoff:3.500A)
      removed outlier: 8.665A  pdb=" N   ARG A 200 " --> pdb=" O   LEU A  65 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   LEU A  67 " --> pdb=" O   ARG A 200 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122
    Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 122
    Processing sheet with id=AA5, first strand: chain 'B' and resid 105 through 107
      removed outlier: 3.790A  pdb=" N   ILE B 140 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ASP B  81 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   SER B  74 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR B  83 " --> pdb=" O   ILE B  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE B  72 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   THR B  85 " --> pdb=" O   ALA B  70 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   MET B  93 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   GLN B  62 " --> pdb=" O   MET B  93 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 130
      removed outlier: 6.939A  pdb=" N   THR B 157 " --> pdb=" O   LYS B 126 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   SER B 128 " --> pdb=" O   THR B 155 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   THR B 155 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   LEU B 130 " --> pdb=" O   ARG B 153 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   ARG B 153 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ASP B  81 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   SER B  74 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR B  83 " --> pdb=" O   ILE B  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE B  72 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   THR B  85 " --> pdb=" O   ALA B  70 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   MET B  93 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   GLN B  62 " --> pdb=" O   MET B  93 " (cutoff:3.500A)
      removed outlier: 8.665A  pdb=" N   ARG B 200 " --> pdb=" O   LEU B  65 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   LEU B  67 " --> pdb=" O   ARG B 200 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 122
    Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 122
    Processing sheet with id=AA9, first strand: chain 'C' and resid 105 through 107
      removed outlier: 3.790A  pdb=" N   ILE C 140 " --> pdb=" O   LEU C 107 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   ASP C  81 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER C  74 " --> pdb=" O   ASP C  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR C  83 " --> pdb=" O   ILE C  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE C  72 " --> pdb=" O   THR C  83 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   THR C  85 " --> pdb=" O   ALA C  70 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   MET C  93 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   GLN C  62 " --> pdb=" O   MET C  93 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 130
      removed outlier: 6.939A  pdb=" N   THR C 157 " --> pdb=" O   LYS C 126 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   SER C 128 " --> pdb=" O   THR C 155 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   THR C 155 " --> pdb=" O   SER C 128 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   LEU C 130 " --> pdb=" O   ARG C 153 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   ARG C 153 " --> pdb=" O   LEU C 130 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   ASP C  81 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER C  74 " --> pdb=" O   ASP C  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR C  83 " --> pdb=" O   ILE C  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE C  72 " --> pdb=" O   THR C  83 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   THR C  85 " --> pdb=" O   ALA C  70 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   MET C  93 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   GLN C  62 " --> pdb=" O   MET C  93 " (cutoff:3.500A)
      removed outlier: 8.665A  pdb=" N   ARG C 200 " --> pdb=" O   LEU C  65 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   LEU C  67 " --> pdb=" O   ARG C 200 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 120 through 122
    Processing sheet with id=AB3, first strand: chain 'C' and resid 120 through 122
    Processing sheet with id=AB4, first strand: chain 'D' and resid 105 through 107
      removed outlier: 3.790A  pdb=" N   ILE D 140 " --> pdb=" O   LEU D 107 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   ASP D  81 " --> pdb=" O   SER D  74 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER D  74 " --> pdb=" O   ASP D  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR D  83 " --> pdb=" O   ILE D  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE D  72 " --> pdb=" O   THR D  83 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   THR D  85 " --> pdb=" O   ALA D  70 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   MET D  93 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   GLN D  62 " --> pdb=" O   MET D  93 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 125 through 130
      removed outlier: 6.939A  pdb=" N   THR D 157 " --> pdb=" O   LYS D 126 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   SER D 128 " --> pdb=" O   THR D 155 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   THR D 155 " --> pdb=" O   SER D 128 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   LEU D 130 " --> pdb=" O   ARG D 153 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   ARG D 153 " --> pdb=" O   LEU D 130 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   ASP D  81 " --> pdb=" O   SER D  74 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER D  74 " --> pdb=" O   ASP D  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR D  83 " --> pdb=" O   ILE D  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE D  72 " --> pdb=" O   THR D  83 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   THR D  85 " --> pdb=" O   ALA D  70 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   MET D  93 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   GLN D  62 " --> pdb=" O   MET D  93 " (cutoff:3.500A)
      removed outlier: 8.665A  pdb=" N   ARG D 200 " --> pdb=" O   LEU D  65 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   LEU D  67 " --> pdb=" O   ARG D 200 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 120 through 122
    Processing sheet with id=AB7, first strand: chain 'D' and resid 120 through 122
    Processing sheet with id=AB8, first strand: chain 'E' and resid 105 through 107
      removed outlier: 3.791A  pdb=" N   ILE E 140 " --> pdb=" O   LEU E 107 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   ASP E  81 " --> pdb=" O   SER E  74 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER E  74 " --> pdb=" O   ASP E  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR E  83 " --> pdb=" O   ILE E  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE E  72 " --> pdb=" O   THR E  83 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   THR E  85 " --> pdb=" O   ALA E  70 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   MET E  93 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   GLN E  62 " --> pdb=" O   MET E  93 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 125 through 130
      removed outlier: 6.938A  pdb=" N   THR E 157 " --> pdb=" O   LYS E 126 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   SER E 128 " --> pdb=" O   THR E 155 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   THR E 155 " --> pdb=" O   SER E 128 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   LEU E 130 " --> pdb=" O   ARG E 153 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   ARG E 153 " --> pdb=" O   LEU E 130 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   ASP E  81 " --> pdb=" O   SER E  74 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER E  74 " --> pdb=" O   ASP E  81 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   THR E  83 " --> pdb=" O   ILE E  72 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE E  72 " --> pdb=" O   THR E  83 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   THR E  85 " --> pdb=" O   ALA E  70 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   MET E  93 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   GLN E  62 " --> pdb=" O   MET E  93 " (cutoff:3.500A)
      removed outlier: 8.665A  pdb=" N   ARG E 200 " --> pdb=" O   LEU E  65 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   LEU E  67 " --> pdb=" O   ARG E 200 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 120 through 122
    Processing sheet with id=AC2, first strand: chain 'E' and resid 120 through 122

    770 hydrogen bonds defined for protein.
    2220 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.35

  Time building geometry restraints manager: 3.77 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3999
        1.34 -     1.46: 3293
        1.46 -     1.58: 6148
        1.58 -     1.69: 0
        1.69 -     1.81: 105
  Bond restraints: 13545
  Sorted by residual:
  bond pdb=" C1  MAN J   4 "
       pdb=" C2  MAN J   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.558 -0.032 2.00e-02 2.50e+03 2.54e+00
  bond pdb=" C1  MAN I   4 "
       pdb=" C2  MAN I   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.557 -0.031 2.00e-02 2.50e+03 2.45e+00
  bond pdb=" C1  MAN F   4 "
       pdb=" C2  MAN F   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.557 -0.031 2.00e-02 2.50e+03 2.43e+00
  bond pdb=" C1  MAN G   4 "
       pdb=" C2  MAN G   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.557 -0.031 2.00e-02 2.50e+03 2.41e+00
  bond pdb=" C1  MAN H   4 "
       pdb=" C2  MAN H   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.557 -0.031 2.00e-02 2.50e+03 2.41e+00
  ... (remaining 13540 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 17932
        1.58 -     3.15: 366
        3.15 -     4.73: 87
        4.73 -     6.30: 40
        6.30 -     7.88: 10
  Bond angle restraints: 18435
  Sorted by residual:
  angle pdb=" C   LEU E 420 "
        pdb=" N   LEU E 421 "
        pdb=" CA  LEU E 421 "
      ideal   model   delta    sigma   weight residual
     122.17  115.67    6.50 1.54e+00 4.22e-01 1.78e+01
  angle pdb=" C   LEU B 420 "
        pdb=" N   LEU B 421 "
        pdb=" CA  LEU B 421 "
      ideal   model   delta    sigma   weight residual
     122.17  115.70    6.47 1.54e+00 4.22e-01 1.76e+01
  angle pdb=" C   LEU A 420 "
        pdb=" N   LEU A 421 "
        pdb=" CA  LEU A 421 "
      ideal   model   delta    sigma   weight residual
     122.17  115.71    6.46 1.54e+00 4.22e-01 1.76e+01
  angle pdb=" C   LEU D 420 "
        pdb=" N   LEU D 421 "
        pdb=" CA  LEU D 421 "
      ideal   model   delta    sigma   weight residual
     122.17  115.71    6.46 1.54e+00 4.22e-01 1.76e+01
  angle pdb=" C   LEU C 420 "
        pdb=" N   LEU C 421 "
        pdb=" CA  LEU C 421 "
      ideal   model   delta    sigma   weight residual
     122.17  115.72    6.45 1.54e+00 4.22e-01 1.75e+01
  ... (remaining 18430 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.90: 7084
       21.90 -    43.80: 919
       43.80 -    65.69: 117
       65.69 -    87.59: 45
       87.59 -   109.49: 25
  Dihedral angle restraints: 8190
    sinusoidal: 3510
      harmonic: 4680
  Sorted by residual:
  dihedral pdb=" CB  CYS C 160 "
           pdb=" SG  CYS C 160 "
           pdb=" SG  CYS C 174 "
           pdb=" CB  CYS C 174 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.47   43.53     1      1.00e+01 1.00e-02 2.64e+01
  dihedral pdb=" CB  CYS B 160 "
           pdb=" SG  CYS B 160 "
           pdb=" SG  CYS B 174 "
           pdb=" CB  CYS B 174 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.47   43.53     1      1.00e+01 1.00e-02 2.64e+01
  dihedral pdb=" CB  CYS E 160 "
           pdb=" SG  CYS E 160 "
           pdb=" SG  CYS E 174 "
           pdb=" CB  CYS E 174 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.47   43.53     1      1.00e+01 1.00e-02 2.64e+01
  ... (remaining 8187 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1871
       0.059 -    0.118: 274
       0.118 -    0.178: 25
       0.178 -    0.237: 5
       0.237 -    0.296: 10
  Chirality restraints: 2185
  Sorted by residual:
  chirality pdb=" C1  NAG C 501 "
            pdb=" ND2 ASN C 196 "
            pdb=" C2  NAG C 501 "
            pdb=" O5  NAG C 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.19e+00
  chirality pdb=" C1  NAG D 501 "
            pdb=" ND2 ASN D 196 "
            pdb=" C2  NAG D 501 "
            pdb=" O5  NAG D 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.17e+00
  chirality pdb=" C1  NAG A 501 "
            pdb=" ND2 ASN A 196 "
            pdb=" C2  NAG A 501 "
            pdb=" O5  NAG A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.17e+00
  ... (remaining 2182 not shown)

  Planarity restraints: 2245
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 261 "    0.007 2.00e-02 2.50e+03   6.16e-03 9.49e-01
        pdb=" CG  TRP B 261 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 261 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 261 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 261 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 261 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 261 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 261 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 261 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 261 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 261 "    0.007 2.00e-02 2.50e+03   6.12e-03 9.36e-01
        pdb=" CG  TRP A 261 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 261 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 261 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 261 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 261 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 261 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 261 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 261 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 261 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 261 "   -0.007 2.00e-02 2.50e+03   6.06e-03 9.18e-01
        pdb=" CG  TRP D 261 "    0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 261 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 261 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 261 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 261 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 261 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 261 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 261 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 261 "    0.000 2.00e-02 2.50e+03
  ... (remaining 2242 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 2285
        2.77 -     3.30: 12369
        3.30 -     3.83: 22277
        3.83 -     4.37: 25923
        4.37 -     4.90: 44665
  Nonbonded interactions: 107519
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 180 "
            pdb=" O   TYR B 183 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG  SER D 180 "
            pdb=" O   TYR D 183 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG  SER C 180 "
            pdb=" O   TYR C 183 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG  SER E 180 "
            pdb=" O   TYR E 183 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG  SER A 180 "
            pdb=" O   TYR A 183 "
     model   vdw
     2.234 3.040
  ... (remaining 107514 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: 0.11
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}

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:             1.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     30.800
  Find NCS groups from input model:        0.280
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13580  Z= 0.157
  Angle     :  0.664   7.879  18520  Z= 0.324
  Chirality :  0.047   0.296   2185
  Planarity :  0.002   0.023   2235
  Dihedral  : 19.650 109.487   5165
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  2.88 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 34.97 %
    Favored  : 65.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.22), residues: 1560
  helix:  2.25 (0.24), residues: 490
  sheet: -1.25 (0.28), residues: 320
  loop : -1.69 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 261 
 HIS   0.004   0.001   HIS C 204 
 PHE   0.014   0.001   PHE E 318 
 TYR   0.011   0.001   TYR D 433 
 ARG   0.002   0.000   ARG C  53 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00689 (   10)
  link_NAG-ASN         : angle       3.23518 (   30)
  link_ALPHA1-4        : bond        0.00675 (    5)
  link_ALPHA1-4        : angle       1.46442 (   15)
  link_BETA1-4         : bond        0.00472 (   10)
  link_BETA1-4         : angle       1.30839 (   30)
  hydrogen bonds       : bond        0.18703 (  625)
  hydrogen bonds       : angle       7.70836 ( 2220)
  SS BOND              : bond        0.00162 (    5)
  SS BOND              : angle       0.33597 (   10)
  covalent geometry    : bond        0.00311 (13545)
  covalent geometry    : angle       0.64952 (18435)
  Misc. bond           : bond        0.00025 (    5)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.286 
Fit side-chains
REVERT: B  285 MET cc_start: 0.7070 (tpt) cc_final: 0.6792 (tpt)
REVERT: D  304 LYS cc_start: 0.7626 (mtmm) cc_final: 0.7370 (mtmm)
REVERT: E  304 LYS cc_start: 0.7541 (mtmm) cc_final: 0.7315 (mtmm)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.2270
  time to fit residues: 43.5377
Evaluate side-chains
  118 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 1.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    9.9990
   chunk 117 optimal weight:   20.0000
   chunk 65 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 79 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 121 optimal weight:   40.0000
   chunk 47 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 90 optimal weight:    5.9990
   chunk 140 optimal weight:    6.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 204 HIS
B 204 HIS
C 204 HIS
D 204 HIS
E 204 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.237751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.204085 restraints weight = 13201.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.4186 rms_B_bonded: 1.18
r_work: 0.3818 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3539 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  13580  Z= 0.225
  Angle     :  0.720   6.968  18520  Z= 0.353
  Chirality :  0.049   0.331   2185
  Planarity :  0.004   0.028   2235
  Dihedral  : 11.534  79.943   2270
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.27 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 32.17 %
    Favored  : 64.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.22), residues: 1560
  helix:  2.50 (0.24), residues: 495
  sheet: -1.00 (0.26), residues: 315
  loop : -1.83 (0.23), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 261 
 HIS   0.005   0.001   HIS B 131 
 PHE   0.021   0.002   PHE D 316 
 TYR   0.016   0.002   TYR E 121 
 ARG   0.003   0.000   ARG B 153 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00373 (   10)
  link_NAG-ASN         : angle       2.82557 (   30)
  link_ALPHA1-4        : bond        0.00887 (    5)
  link_ALPHA1-4        : angle       3.12734 (   15)
  link_BETA1-4         : bond        0.00563 (   10)
  link_BETA1-4         : angle       2.47789 (   30)
  hydrogen bonds       : bond        0.04781 (  625)
  hydrogen bonds       : angle       4.98249 ( 2220)
  SS BOND              : bond        0.00563 (    5)
  SS BOND              : angle       1.42535 (   10)
  covalent geometry    : bond        0.00521 (13545)
  covalent geometry    : angle       0.69921 (18435)
  Misc. bond           : bond        0.00079 (    5)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 151
  time to evaluate  : 1.286 
Fit side-chains
REVERT: A  234 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8075 (tp)
REVERT: A  318 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.6885 (p90)
REVERT: C  295 SER cc_start: 0.5958 (OUTLIER) cc_final: 0.4953 (t)
REVERT: C  304 LYS cc_start: 0.7745 (mtmm) cc_final: 0.7241 (mtmt)
REVERT: D  318 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.7111 (p90)
REVERT: E  295 SER cc_start: 0.6103 (OUTLIER) cc_final: 0.5206 (t)
REVERT: E  304 LYS cc_start: 0.7812 (mtmm) cc_final: 0.7324 (mtmt)
  outliers start: 53
  outliers final: 26
  residues processed: 193
  average time/residue: 0.2064
  time to fit residues: 61.4794
Evaluate side-chains
  158 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 127
  time to evaluate  : 1.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  211 THR
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  295 SER
Chi-restraints excluded: chain C residue  432 PHE
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  211 THR
Chi-restraints excluded: chain D residue  218 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain E residue  140 ILE
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  211 THR
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  295 SER
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 63 optimal weight:    0.0470
   chunk 55 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   chunk 96 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0870
   chunk 6 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 149 optimal weight:   10.0000
   chunk 121 optimal weight:   40.0000
   overall best weight:    0.8258

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

Flipped N/Q/H residues before XYZ refinement:
A 204 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.239095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.204635 restraints weight = 13360.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.4213 rms_B_bonded: 1.26
r_work: 0.3851 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3590 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13580  Z= 0.138
  Angle     :  0.637  11.439  18520  Z= 0.305
  Chirality :  0.044   0.277   2185
  Planarity :  0.003   0.025   2235
  Dihedral  : 10.503  69.110   2270
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  2.50 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 31.54 %
    Favored  : 63.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.22), residues: 1560
  helix:  2.54 (0.24), residues: 495
  sheet: -0.96 (0.25), residues: 340
  loop : -1.44 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 261 
 HIS   0.004   0.001   HIS A 204 
 PHE   0.020   0.001   PHE B 316 
 TYR   0.011   0.001   TYR C 433 
 ARG   0.002   0.000   ARG A  89 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00466 (   10)
  link_NAG-ASN         : angle       2.37181 (   30)
  link_ALPHA1-4        : bond        0.01113 (    5)
  link_ALPHA1-4        : angle       2.11873 (   15)
  link_BETA1-4         : bond        0.00650 (   10)
  link_BETA1-4         : angle       2.67102 (   30)
  hydrogen bonds       : bond        0.04175 (  625)
  hydrogen bonds       : angle       4.31148 ( 2220)
  SS BOND              : bond        0.00572 (    5)
  SS BOND              : angle       1.35387 (   10)
  covalent geometry    : bond        0.00296 (13545)
  covalent geometry    : angle       0.61796 (18435)
  Misc. bond           : bond        0.00062 (    5)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 140
  time to evaluate  : 1.444 
Fit side-chains
REVERT: A  234 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8091 (tp)
REVERT: A  247 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7059 (tt)
REVERT: A  295 SER cc_start: 0.5559 (OUTLIER) cc_final: 0.4888 (t)
REVERT: A  318 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.6986 (p90)
REVERT: B   48 TYR cc_start: -0.0481 (OUTLIER) cc_final: -0.1560 (m-10)
REVERT: B  110 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7030 (mtm180)
REVERT: B  285 MET cc_start: 0.7064 (tpt) cc_final: 0.6800 (tpt)
REVERT: B  295 SER cc_start: 0.6113 (OUTLIER) cc_final: 0.5217 (t)
REVERT: B  304 LYS cc_start: 0.7030 (mtmt) cc_final: 0.6704 (mtmm)
REVERT: C   48 TYR cc_start: -0.0001 (OUTLIER) cc_final: -0.2451 (m-80)
REVERT: C  110 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7049 (mtm180)
REVERT: C  304 LYS cc_start: 0.7512 (mtmm) cc_final: 0.7010 (mtmt)
REVERT: D  110 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7075 (mtm180)
REVERT: D  295 SER cc_start: 0.6012 (OUTLIER) cc_final: 0.5160 (t)
REVERT: D  318 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7149 (p90)
REVERT: E   48 TYR cc_start: 0.0100 (OUTLIER) cc_final: -0.2735 (m-80)
REVERT: E  110 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7088 (mtt180)
REVERT: E  304 LYS cc_start: 0.7729 (mtmm) cc_final: 0.7173 (mtmt)
  outliers start: 68
  outliers final: 31
  residues processed: 197
  average time/residue: 0.2953
  time to fit residues: 80.9822
Evaluate side-chains
  178 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 133
  time to evaluate  : 1.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   48 TYR
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  295 SER
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain C residue   48 TYR
Chi-restraints excluded: chain C residue  110 ARG
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain C residue  432 PHE
Chi-restraints excluded: chain D residue  110 ARG
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  295 SER
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue  104 SER
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  215 TYR
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  316 PHE
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 146 optimal weight:   30.0000
   chunk 134 optimal weight:    0.2980
   chunk 65 optimal weight:    0.8980
   chunk 71 optimal weight:    5.9990
   chunk 63 optimal weight:    0.0770
   chunk 95 optimal weight:    3.9990
   chunk 154 optimal weight:    7.9990
   chunk 101 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.4802 r_free = 0.4802 target = 0.261432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.233489 restraints weight = 13394.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.4683 rms_B_bonded: 1.63
r_work: 0.4218 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.4218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13580  Z= 0.124
  Angle     :  0.628  11.006  18520  Z= 0.299
  Chirality :  0.044   0.237   2185
  Planarity :  0.003   0.024   2235
  Dihedral  :  9.538  61.869   2270
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.08 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 30.21 %
    Favored  : 63.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.22), residues: 1560
  helix:  2.65 (0.23), residues: 495
  sheet: -0.83 (0.25), residues: 345
  loop : -1.30 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 261 
 HIS   0.002   0.001   HIS A 131 
 PHE   0.019   0.001   PHE B 316 
 TYR   0.012   0.001   TYR C 433 
 ARG   0.007   0.000   ARG C  91 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00374 (   10)
  link_NAG-ASN         : angle       1.67575 (   30)
  link_ALPHA1-4        : bond        0.01221 (    5)
  link_ALPHA1-4        : angle       2.47152 (   15)
  link_BETA1-4         : bond        0.00638 (   10)
  link_BETA1-4         : angle       2.90182 (   30)
  hydrogen bonds       : bond        0.03791 (  625)
  hydrogen bonds       : angle       3.99497 ( 2220)
  SS BOND              : bond        0.00444 (    5)
  SS BOND              : angle       1.06866 (   10)
  covalent geometry    : bond        0.00262 (13545)
  covalent geometry    : angle       0.60991 (18435)
  Misc. bond           : bond        0.00054 (    5)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 145
  time to evaluate  : 1.365 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.0404 (OUTLIER) cc_final: -0.1908 (m-80)
REVERT: A  234 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7950 (tp)
REVERT: A  247 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7366 (tt)
REVERT: A  295 SER cc_start: 0.3773 (OUTLIER) cc_final: 0.3115 (t)
REVERT: A  318 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6511 (p90)
REVERT: B   48 TYR cc_start: 0.0467 (OUTLIER) cc_final: -0.1014 (m-10)
REVERT: B  110 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6971 (mtm180)
REVERT: B  255 PHE cc_start: 0.5656 (OUTLIER) cc_final: 0.4918 (m-80)
REVERT: C   48 TYR cc_start: 0.0901 (OUTLIER) cc_final: -0.1946 (m-80)
REVERT: C  108 ASP cc_start: 0.7776 (m-30) cc_final: 0.7575 (m-30)
REVERT: C  110 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6990 (mtm180)
REVERT: C  304 LYS cc_start: 0.7739 (mtmm) cc_final: 0.7369 (mtmt)
REVERT: D   48 TYR cc_start: 0.0618 (OUTLIER) cc_final: -0.0630 (m-10)
REVERT: D  110 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6963 (mtm180)
REVERT: D  318 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6471 (p90)
REVERT: E   48 TYR cc_start: 0.0634 (OUTLIER) cc_final: -0.2330 (m-80)
REVERT: E  110 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7057 (mtt180)
REVERT: E  285 MET cc_start: 0.8023 (tpt) cc_final: 0.7723 (tpt)
REVERT: E  304 LYS cc_start: 0.7757 (mtmm) cc_final: 0.7437 (mtmt)
  outliers start: 87
  outliers final: 38
  residues processed: 216
  average time/residue: 0.2523
  time to fit residues: 78.9825
Evaluate side-chains
  185 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 132
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   48 TYR
Chi-restraints excluded: chain B residue  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain C residue   48 TYR
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  110 ARG
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  211 THR
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain C residue  432 PHE
Chi-restraints excluded: chain D residue   48 TYR
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  110 ARG
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  104 SER
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  211 THR
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  316 PHE
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 134 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 141 optimal weight:    4.9990
   chunk 79 optimal weight:    0.6980
   chunk 91 optimal weight:   20.0000
   chunk 66 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 131 optimal weight:    3.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.4789 r_free = 0.4789 target = 0.259473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.214223 restraints weight = 13441.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.4440 rms_B_bonded: 3.61
r_work: 0.3904 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13580  Z= 0.150
  Angle     :  0.664  10.993  18520  Z= 0.314
  Chirality :  0.045   0.234   2185
  Planarity :  0.003   0.025   2235
  Dihedral  :  9.124  57.102   2270
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  2.82 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 30.28 %
    Favored  : 63.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.22), residues: 1560
  helix:  2.61 (0.24), residues: 500
  sheet: -0.68 (0.25), residues: 340
  loop : -1.31 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D 261 
 HIS   0.004   0.001   HIS B 131 
 PHE   0.027   0.002   PHE A 426 
 TYR   0.010   0.001   TYR C 433 
 ARG   0.006   0.000   ARG A  91 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00142 (   10)
  link_NAG-ASN         : angle       1.63380 (   30)
  link_ALPHA1-4        : bond        0.01062 (    5)
  link_ALPHA1-4        : angle       2.79570 (   15)
  link_BETA1-4         : bond        0.00612 (   10)
  link_BETA1-4         : angle       2.79026 (   30)
  hydrogen bonds       : bond        0.03799 (  625)
  hydrogen bonds       : angle       3.93091 ( 2220)
  SS BOND              : bond        0.00554 (    5)
  SS BOND              : angle       1.74801 (   10)
  covalent geometry    : bond        0.00333 (13545)
  covalent geometry    : angle       0.64648 (18435)
  Misc. bond           : bond        0.00068 (    5)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 135
  time to evaluate  : 1.289 
Fit side-chains
REVERT: A   48 TYR cc_start: -0.0978 (OUTLIER) cc_final: -0.2679 (m-80)
REVERT: A  234 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8135 (tp)
REVERT: A  318 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7118 (p90)
REVERT: B   48 TYR cc_start: -0.0961 (OUTLIER) cc_final: -0.1972 (m-10)
REVERT: B  110 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7045 (mtm180)
REVERT: B  255 PHE cc_start: 0.5193 (OUTLIER) cc_final: 0.4494 (m-80)
REVERT: B  304 LYS cc_start: 0.6996 (mtmm) cc_final: 0.6604 (mtmt)
REVERT: C   48 TYR cc_start: -0.0597 (OUTLIER) cc_final: -0.2683 (m-80)
REVERT: C  110 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7112 (mtm180)
REVERT: C  255 PHE cc_start: 0.5140 (OUTLIER) cc_final: 0.4550 (m-80)
REVERT: C  304 LYS cc_start: 0.7262 (mtmm) cc_final: 0.6762 (mtmt)
REVERT: D   48 TYR cc_start: -0.0665 (OUTLIER) cc_final: -0.1663 (m-10)
REVERT: D  110 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7035 (mtm180)
REVERT: D  318 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7273 (p90)
REVERT: E   48 TYR cc_start: -0.0601 (OUTLIER) cc_final: -0.3049 (m-80)
REVERT: E  110 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7168 (mtt180)
REVERT: E  304 LYS cc_start: 0.7416 (mtmm) cc_final: 0.6955 (mtmt)
  outliers start: 82
  outliers final: 49
  residues processed: 202
  average time/residue: 0.2337
  time to fit residues: 69.2826
Evaluate side-chains
  194 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 131
  time to evaluate  : 1.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   48 TYR
Chi-restraints excluded: chain B residue  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain C residue   48 TYR
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  110 ARG
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  255 PHE
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain C residue  432 PHE
Chi-restraints excluded: chain D residue   48 TYR
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  110 ARG
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  211 THR
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  316 PHE
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  104 SER
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  205 LEU
Chi-restraints excluded: chain E residue  211 THR
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  248 GLU
Chi-restraints excluded: chain E residue  316 PHE
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 18 optimal weight:    0.2980
   chunk 80 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:   50.0000
   chunk 103 optimal weight:    2.9990
   chunk 112 optimal weight:    0.8980
   chunk 141 optimal weight:    4.9990
   chunk 140 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0980
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 = 0.4526 r_free = 0.4526 target = 0.240160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.196722 restraints weight = 13412.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.4148 rms_B_bonded: 1.60
r_work: 0.3724 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  13580  Z= 0.123
  Angle     :  0.627  10.965  18520  Z= 0.296
  Chirality :  0.044   0.217   2185
  Planarity :  0.003   0.026   2235
  Dihedral  :  8.619  53.422   2270
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.01 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 30.70 %
    Favored  : 63.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.22), residues: 1560
  helix:  2.70 (0.24), residues: 500
  sheet: -0.65 (0.25), residues: 345
  loop : -1.22 (0.24), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP E 261 
 HIS   0.003   0.001   HIS A 131 
 PHE   0.029   0.001   PHE B  99 
 TYR   0.013   0.001   TYR C 433 
 ARG   0.005   0.000   ARG A  91 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00270 (   10)
  link_NAG-ASN         : angle       1.46139 (   30)
  link_ALPHA1-4        : bond        0.01249 (    5)
  link_ALPHA1-4        : angle       2.45538 (   15)
  link_BETA1-4         : bond        0.00658 (   10)
  link_BETA1-4         : angle       2.89720 (   30)
  hydrogen bonds       : bond        0.03605 (  625)
  hydrogen bonds       : angle       3.72610 ( 2220)
  SS BOND              : bond        0.00466 (    5)
  SS BOND              : angle       1.43819 (   10)
  covalent geometry    : bond        0.00265 (13545)
  covalent geometry    : angle       0.60942 (18435)
  Misc. bond           : bond        0.00054 (    5)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 136
  time to evaluate  : 1.416 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.0148 (OUTLIER) cc_final: -0.2053 (m-80)
REVERT: A  204 HIS cc_start: 0.5601 (m90) cc_final: 0.5387 (m-70)
REVERT: A  234 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7986 (tp)
REVERT: A  318 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.6670 (p90)
REVERT: B   48 TYR cc_start: 0.0291 (OUTLIER) cc_final: -0.1145 (m-10)
REVERT: B  110 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6925 (mtm180)
REVERT: B  255 PHE cc_start: 0.5789 (OUTLIER) cc_final: 0.4738 (m-80)
REVERT: B  304 LYS cc_start: 0.7482 (mtmm) cc_final: 0.7017 (mtmt)
REVERT: C   48 TYR cc_start: 0.0473 (OUTLIER) cc_final: -0.2148 (m-80)
REVERT: C  110 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7009 (mtm180)
REVERT: C  172 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7166 (mm-40)
REVERT: C  255 PHE cc_start: 0.5619 (OUTLIER) cc_final: 0.4633 (m-80)
REVERT: C  304 LYS cc_start: 0.7704 (mtmm) cc_final: 0.7242 (mtmt)
REVERT: D   48 TYR cc_start: 0.0322 (OUTLIER) cc_final: -0.0986 (m-10)
REVERT: D  110 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6988 (mtm180)
REVERT: D  172 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7239 (mt0)
REVERT: D  318 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6832 (p90)
REVERT: E   48 TYR cc_start: 0.0537 (OUTLIER) cc_final: -0.2481 (m-80)
REVERT: E  110 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7067 (mtt180)
REVERT: E  255 PHE cc_start: 0.5677 (OUTLIER) cc_final: 0.4652 (m-80)
REVERT: E  304 LYS cc_start: 0.7795 (mtmm) cc_final: 0.7538 (mtmm)
  outliers start: 77
  outliers final: 44
  residues processed: 199
  average time/residue: 0.2460
  time to fit residues: 72.5639
Evaluate side-chains
  194 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 133
  time to evaluate  : 1.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   48 TYR
Chi-restraints excluded: chain B residue  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain C residue   48 TYR
Chi-restraints excluded: chain C residue   68 ASP
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  110 ARG
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  172 GLN
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  255 PHE
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain C residue  432 PHE
Chi-restraints excluded: chain D residue   48 TYR
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  110 ARG
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  172 GLN
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  248 GLU
Chi-restraints excluded: chain D residue  316 PHE
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  104 SER
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  205 LEU
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  255 PHE
Chi-restraints excluded: chain E residue  316 PHE
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 130 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   chunk 78 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 113 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 125 optimal weight:    0.7980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
E 204 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.238490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.216340 restraints weight = 13218.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.4324 rms_B_bonded: 1.13
r_work: 0.3941 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13580  Z= 0.168
  Angle     :  0.681  10.860  18520  Z= 0.324
  Chirality :  0.046   0.225   2185
  Planarity :  0.003   0.024   2235
  Dihedral  :  8.388  50.789   2270
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.53 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 31.61 %
    Favored  : 63.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.22), residues: 1560
  helix:  2.68 (0.24), residues: 500
  sheet: -0.65 (0.25), residues: 340
  loop : -1.36 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 261 
 HIS   0.005   0.001   HIS E 204 
 PHE   0.027   0.002   PHE B  99 
 TYR   0.010   0.001   TYR E 121 
 ARG   0.003   0.000   ARG E  91 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00080 (   10)
  link_NAG-ASN         : angle       1.46910 (   30)
  link_ALPHA1-4        : bond        0.01015 (    5)
  link_ALPHA1-4        : angle       3.02580 (   15)
  link_BETA1-4         : bond        0.00587 (   10)
  link_BETA1-4         : angle       2.72994 (   30)
  hydrogen bonds       : bond        0.03666 (  625)
  hydrogen bonds       : angle       3.87278 ( 2220)
  SS BOND              : bond        0.00590 (    5)
  SS BOND              : angle       2.36169 (   10)
  covalent geometry    : bond        0.00380 (13545)
  covalent geometry    : angle       0.66281 (18435)
  Misc. bond           : bond        0.00072 (    5)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 140
  time to evaluate  : 1.311 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.0660 (OUTLIER) cc_final: -0.1713 (m-80)
REVERT: A  234 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7808 (tp)
REVERT: A  318 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6325 (p90)
REVERT: B   48 TYR cc_start: 0.0788 (OUTLIER) cc_final: -0.1105 (m-80)
REVERT: B  102 ASN cc_start: 0.5667 (p0) cc_final: 0.5425 (p0)
REVERT: B  110 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6925 (mtm180)
REVERT: B  304 LYS cc_start: 0.7613 (mtmm) cc_final: 0.7193 (mtmt)
REVERT: C   48 TYR cc_start: 0.1040 (OUTLIER) cc_final: -0.1843 (m-80)
REVERT: C  110 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7014 (mtm180)
REVERT: D   48 TYR cc_start: 0.0716 (OUTLIER) cc_final: -0.0691 (m-10)
REVERT: D  110 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6933 (mtm180)
REVERT: D  318 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.6216 (p90)
REVERT: E   48 TYR cc_start: 0.1014 (OUTLIER) cc_final: -0.2131 (m-80)
REVERT: E  110 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7093 (mtt180)
REVERT: E  255 PHE cc_start: 0.5737 (OUTLIER) cc_final: 0.4890 (m-80)
REVERT: E  304 LYS cc_start: 0.7778 (mtmm) cc_final: 0.7551 (mtmm)
  outliers start: 75
  outliers final: 50
  residues processed: 200
  average time/residue: 0.2639
  time to fit residues: 78.1356
Evaluate side-chains
  202 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 139
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   48 TYR
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain C residue   48 TYR
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   68 ASP
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  110 ARG
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  248 GLU
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain C residue  432 PHE
Chi-restraints excluded: chain D residue   48 TYR
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  110 ARG
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  211 THR
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  316 PHE
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  104 SER
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  205 LEU
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  255 PHE
Chi-restraints excluded: chain E residue  316 PHE
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 104 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 131 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 95 optimal weight:    2.9990
   chunk 29 optimal weight:   20.0000
   chunk 20 optimal weight:    9.9990
   chunk 116 optimal weight:    8.9990
   chunk 35 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 102 ASN
E 204 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.238277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.216433 restraints weight = 13250.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.4325 rms_B_bonded: 1.07
r_work: 0.3962 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  13580  Z= 0.176
  Angle     :  0.684  11.245  18520  Z= 0.326
  Chirality :  0.046   0.225   2185
  Planarity :  0.003   0.028   2235
  Dihedral  :  8.107  47.539   2270
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.14 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 31.89 %
    Favored  : 63.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.22), residues: 1560
  helix:  2.69 (0.24), residues: 500
  sheet: -0.84 (0.23), residues: 385
  loop : -1.60 (0.24), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E 261 
 HIS   0.004   0.001   HIS E 204 
 PHE   0.028   0.002   PHE B  99 
 TYR   0.011   0.001   TYR C 433 
 ARG   0.003   0.000   ARG A  91 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00076 (   10)
  link_NAG-ASN         : angle       1.49092 (   30)
  link_ALPHA1-4        : bond        0.01010 (    5)
  link_ALPHA1-4        : angle       2.75096 (   15)
  link_BETA1-4         : bond        0.00565 (   10)
  link_BETA1-4         : angle       2.69365 (   30)
  hydrogen bonds       : bond        0.03656 (  625)
  hydrogen bonds       : angle       3.91246 ( 2220)
  SS BOND              : bond        0.00678 (    5)
  SS BOND              : angle       2.53242 (   10)
  covalent geometry    : bond        0.00399 (13545)
  covalent geometry    : angle       0.66723 (18435)
  Misc. bond           : bond        0.00066 (    5)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 144
  time to evaluate  : 1.430 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.0709 (OUTLIER) cc_final: -0.1570 (m-80)
REVERT: A  102 ASN cc_start: 0.5831 (p0) cc_final: 0.5557 (p0)
REVERT: A  234 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7787 (tp)
REVERT: A  318 PHE cc_start: 0.6850 (OUTLIER) cc_final: 0.6406 (p90)
REVERT: B   48 TYR cc_start: 0.0804 (OUTLIER) cc_final: -0.0860 (m-10)
REVERT: B  102 ASN cc_start: 0.5685 (p0) cc_final: 0.5450 (p0)
REVERT: B  110 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6977 (mtm180)
REVERT: B  304 LYS cc_start: 0.7644 (mtmm) cc_final: 0.7242 (mtmt)
REVERT: C   48 TYR cc_start: 0.1144 (OUTLIER) cc_final: -0.1875 (m-80)
REVERT: C  110 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7147 (mtm180)
REVERT: C  255 PHE cc_start: 0.5731 (OUTLIER) cc_final: 0.4937 (m-80)
REVERT: D   48 TYR cc_start: 0.0807 (OUTLIER) cc_final: -0.0776 (m-10)
REVERT: D  110 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7069 (mtm180)
REVERT: D  255 PHE cc_start: 0.6014 (OUTLIER) cc_final: 0.5503 (m-80)
REVERT: E   48 TYR cc_start: 0.1026 (OUTLIER) cc_final: -0.0939 (m-80)
REVERT: E  110 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7176 (mtt180)
REVERT: E  255 PHE cc_start: 0.5839 (OUTLIER) cc_final: 0.5012 (m-80)
REVERT: E  304 LYS cc_start: 0.7765 (mtmm) cc_final: 0.7549 (mtmm)
  outliers start: 73
  outliers final: 51
  residues processed: 201
  average time/residue: 0.2416
  time to fit residues: 71.4603
Evaluate side-chains
  203 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 138
  time to evaluate  : 1.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   48 TYR
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain C residue   48 TYR
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   68 ASP
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  110 ARG
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  255 PHE
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain C residue  432 PHE
Chi-restraints excluded: chain D residue   48 TYR
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  110 ARG
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  255 PHE
Chi-restraints excluded: chain D residue  312 ILE
Chi-restraints excluded: chain D residue  316 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  104 SER
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  205 LEU
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  255 PHE
Chi-restraints excluded: chain E residue  316 PHE
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 133 optimal weight:    0.9990
   chunk 145 optimal weight:    6.9990
   chunk 56 optimal weight:    0.0970
   chunk 33 optimal weight:    2.9990
   chunk 134 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 99 optimal weight:    0.0010
   chunk 124 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
E 204 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.239557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.205548 restraints weight = 13241.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.4237 rms_B_bonded: 1.20
r_work: 0.3886 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3592 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  13580  Z= 0.125
  Angle     :  0.646  11.148  18520  Z= 0.308
  Chirality :  0.044   0.213   2185
  Planarity :  0.003   0.028   2235
  Dihedral  :  7.704  44.913   2270
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  2.56 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 33.22 %
    Favored  : 63.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.22), residues: 1560
  helix:  2.68 (0.23), residues: 500
  sheet: -0.70 (0.24), residues: 385
  loop : -1.48 (0.24), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 261 
 HIS   0.004   0.000   HIS E 204 
 PHE   0.026   0.001   PHE B  99 
 TYR   0.013   0.001   TYR C 433 
 ARG   0.003   0.000   ARG D  91 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00275 (   10)
  link_NAG-ASN         : angle       1.45116 (   30)
  link_ALPHA1-4        : bond        0.01232 (    5)
  link_ALPHA1-4        : angle       2.22140 (   15)
  link_BETA1-4         : bond        0.00657 (   10)
  link_BETA1-4         : angle       2.78711 (   30)
  hydrogen bonds       : bond        0.03492 (  625)
  hydrogen bonds       : angle       3.67144 ( 2220)
  SS BOND              : bond        0.00428 (    5)
  SS BOND              : angle       1.73914 (   10)
  covalent geometry    : bond        0.00269 (13545)
  covalent geometry    : angle       0.63090 (18435)
  Misc. bond           : bond        0.00055 (    5)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 141
  time to evaluate  : 1.293 
Fit side-chains
REVERT: A   48 TYR cc_start: -0.0314 (OUTLIER) cc_final: -0.2206 (m-80)
REVERT: A  102 ASN cc_start: 0.6242 (p0) cc_final: 0.5664 (p0)
REVERT: A  318 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7229 (p90)
REVERT: B   48 TYR cc_start: -0.0215 (OUTLIER) cc_final: -0.1842 (m-80)
REVERT: B  102 ASN cc_start: 0.6084 (p0) cc_final: 0.5551 (p0)
REVERT: B  110 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.7022 (mtm180)
REVERT: C   48 TYR cc_start: -0.0033 (OUTLIER) cc_final: -0.2407 (m-80)
REVERT: C  255 PHE cc_start: 0.5513 (OUTLIER) cc_final: 0.4796 (m-80)
REVERT: D   48 TYR cc_start: -0.0262 (OUTLIER) cc_final: -0.1426 (m-10)
REVERT: D   99 PHE cc_start: 0.6818 (p90) cc_final: 0.6574 (p90)
REVERT: E   48 TYR cc_start: 0.0041 (OUTLIER) cc_final: -0.1599 (m-80)
REVERT: E  102 ASN cc_start: 0.6098 (p0) cc_final: 0.5549 (p0)
REVERT: E  110 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7175 (mtt180)
REVERT: E  255 PHE cc_start: 0.5809 (OUTLIER) cc_final: 0.5113 (m-80)
REVERT: E  304 LYS cc_start: 0.7625 (mtmm) cc_final: 0.7327 (mtmm)
  outliers start: 52
  outliers final: 36
  residues processed: 181
  average time/residue: 0.2170
  time to fit residues: 59.3304
Evaluate side-chains
  184 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 138
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   48 TYR
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain C residue   48 TYR
Chi-restraints excluded: chain C residue   68 ASP
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  255 PHE
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain D residue   48 TYR
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  211 THR
Chi-restraints excluded: chain D residue  312 ILE
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  205 LEU
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  255 PHE
Chi-restraints excluded: chain E residue  316 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 59 optimal weight:   20.0000
   chunk 1 optimal weight:    0.5980
   chunk 98 optimal weight:    0.4980
   chunk 17 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 148 optimal weight:    5.9990
   chunk 141 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   chunk 71 optimal weight:    1.9990
   chunk 123 optimal weight:   10.0000
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
E 204 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.238850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.208217 restraints weight = 13208.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.4245 rms_B_bonded: 1.07
r_work: 0.3900 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3585 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13580  Z= 0.185
  Angle     :  0.696  11.020  18520  Z= 0.333
  Chirality :  0.046   0.224   2185
  Planarity :  0.004   0.029   2235
  Dihedral  :  7.686  43.137   2270
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.72 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 32.52 %
    Favored  : 63.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.22), residues: 1560
  helix:  2.65 (0.23), residues: 500
  sheet: -0.71 (0.25), residues: 340
  loop : -1.46 (0.23), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E 261 
 HIS   0.004   0.001   HIS E 204 
 PHE   0.026   0.002   PHE B  99 
 TYR   0.010   0.001   TYR C 433 
 ARG   0.002   0.000   ARG E  91 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00114 (   10)
  link_NAG-ASN         : angle       1.35475 (   30)
  link_ALPHA1-4        : bond        0.00984 (    5)
  link_ALPHA1-4        : angle       2.93823 (   15)
  link_BETA1-4         : bond        0.00543 (   10)
  link_BETA1-4         : angle       2.62272 (   30)
  hydrogen bonds       : bond        0.03597 (  625)
  hydrogen bonds       : angle       3.91443 ( 2220)
  SS BOND              : bond        0.00689 (    5)
  SS BOND              : angle       2.30983 (   10)
  covalent geometry    : bond        0.00423 (13545)
  covalent geometry    : angle       0.68008 (18435)
  Misc. bond           : bond        0.00082 (    5)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 137
  time to evaluate  : 1.417 
Fit side-chains
REVERT: A   48 TYR cc_start: -0.0203 (OUTLIER) cc_final: -0.1979 (m-80)
REVERT: A  102 ASN cc_start: 0.6299 (p0) cc_final: 0.5771 (p0)
REVERT: A  234 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8066 (tp)
REVERT: A  255 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5909 (m-80)
REVERT: A  318 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7226 (p90)
REVERT: B   48 TYR cc_start: -0.0184 (OUTLIER) cc_final: -0.1742 (m-80)
REVERT: B  102 ASN cc_start: 0.6100 (p0) cc_final: 0.5587 (p0)
REVERT: B  110 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7160 (mtm180)
REVERT: C   48 TYR cc_start: 0.0101 (OUTLIER) cc_final: -0.2312 (m-80)
REVERT: C  110 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7280 (mtm180)
REVERT: C  255 PHE cc_start: 0.5707 (OUTLIER) cc_final: 0.4958 (m-80)
REVERT: D   48 TYR cc_start: -0.0254 (OUTLIER) cc_final: -0.1491 (m-10)
REVERT: D   99 PHE cc_start: 0.6985 (p90) cc_final: 0.6731 (p90)
REVERT: D  255 PHE cc_start: 0.6017 (OUTLIER) cc_final: 0.5488 (m-80)
REVERT: E   48 TYR cc_start: 0.0047 (OUTLIER) cc_final: -0.1468 (m-10)
REVERT: E  102 ASN cc_start: 0.6151 (p0) cc_final: 0.5637 (p0)
REVERT: E  110 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7293 (mtt180)
REVERT: E  255 PHE cc_start: 0.5944 (OUTLIER) cc_final: 0.5244 (m-80)
REVERT: E  304 LYS cc_start: 0.7663 (mtmm) cc_final: 0.7372 (mtmm)
  outliers start: 59
  outliers final: 38
  residues processed: 183
  average time/residue: 0.2272
  time to fit residues: 61.9727
Evaluate side-chains
  187 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 135
  time to evaluate  : 1.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  181 TRP
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   48 TYR
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  110 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  181 TRP
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain C residue   48 TYR
Chi-restraints excluded: chain C residue   68 ASP
Chi-restraints excluded: chain C residue  110 ARG
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  255 PHE
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain D residue   48 TYR
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  181 TRP
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  211 THR
Chi-restraints excluded: chain D residue  255 PHE
Chi-restraints excluded: chain D residue  312 ILE
Chi-restraints excluded: chain D residue  316 PHE
Chi-restraints excluded: chain E residue   48 TYR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  110 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  181 TRP
Chi-restraints excluded: chain E residue  205 LEU
Chi-restraints excluded: chain E residue  211 THR
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  255 PHE
Chi-restraints excluded: chain E residue  316 PHE
Chi-restraints excluded: chain E residue  432 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 124 optimal weight:   20.0000
   chunk 99 optimal weight:    3.9990
   chunk 29 optimal weight:   20.0000
   chunk 44 optimal weight:    3.9990
   chunk 144 optimal weight:    8.9990
   chunk 28 optimal weight:   20.0000
   chunk 39 optimal weight:    0.5980
   chunk 145 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 57 optimal weight:    7.9990
   chunk 142 optimal weight:    3.9990
   overall best weight:    2.6786

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

Flipped N/Q/H residues before XYZ refinement:
** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 204 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.235608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.204015 restraints weight = 13241.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.4220 rms_B_bonded: 1.05
r_work: 0.3847 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3524 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  13580  Z= 0.273
  Angle     :  0.792  10.871  18520  Z= 0.381
  Chirality :  0.050   0.249   2185
  Planarity :  0.005   0.042   2235
  Dihedral  :  7.943  47.386   2270
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.23 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 32.45 %
    Favored  : 63.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.22), residues: 1560
  helix:  2.56 (0.24), residues: 500
  sheet: -0.97 (0.24), residues: 335
  loop : -1.75 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP B 261 
 HIS   0.004   0.001   HIS A 131 
 PHE   0.027   0.002   PHE B  99 
 TYR   0.013   0.002   TYR B 121 
 ARG   0.005   0.001   ARG B 138 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00399 (   10)
  link_NAG-ASN         : angle       1.73143 (   30)
  link_ALPHA1-4        : bond        0.00716 (    5)
  link_ALPHA1-4        : angle       3.57625 (   15)
  link_BETA1-4         : bond        0.00493 (   10)
  link_BETA1-4         : angle       2.54621 (   30)
  hydrogen bonds       : bond        0.03847 (  625)
  hydrogen bonds       : angle       4.28812 ( 2220)
  SS BOND              : bond        0.00977 (    5)
  SS BOND              : angle       2.95634 (   10)
  covalent geometry    : bond        0.00641 (13545)
  covalent geometry    : angle       0.77406 (18435)
  Misc. bond           : bond        0.00107 (    5)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6334.57 seconds
wall clock time: 110 minutes 41.96 seconds (6641.96 seconds total)