Starting phenix.real_space_refine
on Fri May 16 01:59:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d7e_27228/05_2025/8d7e_27228.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d7e_27228/05_2025/8d7e_27228.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d7e_27228/05_2025/8d7e_27228.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d7e_27228/05_2025/8d7e_27228.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d7e_27228/05_2025/8d7e_27228.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d7e_27228/05_2025/8d7e_27228.cif"
  }
  resolution = 2.93
  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=   0.000 sd=   0.036
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6044 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    5654      2.51       5
     N    1512      2.21       5
     O    1759      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Residue "G GLU  166": not complete - not flipped    Residue "G GLU  166": not complete - not flipped    Residue "E GLU  166": not complete - not flipped    Residue "E GLU  166": not complete - not flipped  Time to flip 79 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8959
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "C"
      Number of atoms: 2259
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2259
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 24, 'TRANS': 257}
    Chain: "G"
      Number of atoms: 1649
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 215, 1649
          Classifications: {'peptide': 215}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 202}
    Chain: "F"
      Number of atoms: 1654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1654
          Classifications: {'peptide': 217}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 206}
    Chain: "E"
      Number of atoms: 1646
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 215, 1646
          Classifications: {'peptide': 215}
          Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 202}
    Chain: "D"
      Number of atoms: 1639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1639
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "I"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 6.40, per 1000 atoms: 0.71
  Number of scatterers: 8959
  At special positions: 0
  Unit cell: (84.15, 125.8, 165.75, 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      34     16.00
     O    1759      8.00
     N    1512      7.00
     C    5654      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  46 " - pdb=" SG  CYS C  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 116 " - pdb=" SG  CYS C 127 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 154 " - pdb=" SG  CYS C 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G  23 " - pdb=" SG  CYS G  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 135 " - pdb=" SG  CYS G 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 215 " - pdb=" SG  CYS F 131 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 144 " - pdb=" SG  CYS F 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  23 " - pdb=" SG  CYS E  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 135 " - pdb=" SG  CYS E 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 215 " - pdb=" SG  CYS D 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 147 " - pdb=" SG  CYS D 203 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG B   1 " - " NAG B   2 "
      " NAG H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
    NAG-ASN
      " NAG A   1 " - " ASN C 190 "
      " NAG B   1 " - " ASN C  70 "
      " NAG H   1 " - " ASN C  60 "
      " NAG I   1 " - " ASN C 142 "
  Time building additional restraints: 2.35
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2134

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 26 sheets defined
      6.4% alpha, 40.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.42
  Creating SS restraints...
    Processing helix  chain 'C' and resid 65 through 67
      No H-bonds generated for 'chain 'C' and resid 65 through 67'
    Processing helix  chain 'G' and resid 29 through 32
      removed outlier: 3.925A  pdb=" N   SER G  32 " --> pdb=" O   VAL G  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 29 through 32'
    Processing helix  chain 'G' and resid 80 through 84
      removed outlier: 4.205A  pdb=" N   PHE G  84 " --> pdb=" O   PRO G  81 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 122 through 129
    Processing helix  chain 'G' and resid 184 through 188
      removed outlier: 3.631A  pdb=" N   GLU G 188 " --> pdb=" O   LYS G 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 184 through 188'
    Processing helix  chain 'F' and resid 28 through 32
      removed outlier: 3.590A  pdb=" N   THR F  31 " --> pdb=" O   THR F  28 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER F  32 " --> pdb=" O   PHE F  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 28 through 32'
    Processing helix  chain 'F' and resid 87 through 91
      removed outlier: 3.856A  pdb=" N   THR F  91 " --> pdb=" O   ALA F  88 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 191 through 194
      removed outlier: 4.055A  pdb=" N   GLY F 194 " --> pdb=" O   SER F 191 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 191 through 194'
    Processing helix  chain 'E' and resid 79 through 83
      removed outlier: 4.059A  pdb=" N   PHE E  83 " --> pdb=" O   PRO E  80 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 127
      removed outlier: 3.602A  pdb=" N   LEU E 126 " --> pdb=" O   SER E 122 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   LYS E 127 " --> pdb=" O   ASP E 123 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 122 through 127'
    Processing helix  chain 'E' and resid 184 through 190
      removed outlier: 3.560A  pdb=" N   HIS E 190 " --> pdb=" O   ASP E 186 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.576A  pdb=" N   TYR D  32 " --> pdb=" O   PHE D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 91
    Processing helix  chain 'D' and resid 163 through 165
      No H-bonds generated for 'chain 'D' and resid 163 through 165'
    Processing helix  chain 'D' and resid 194 through 196
      No H-bonds generated for 'chain 'D' and resid 194 through 196'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 32 through 37
      removed outlier: 6.108A  pdb=" N   HIS C  32 " --> pdb=" O   LEU C 102 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   HIS C 104 " --> pdb=" O   HIS C  32 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   GLN C  34 " --> pdb=" O   HIS C 104 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   GLY C 106 " --> pdb=" O   GLN C  34 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   GLU C  36 " --> pdb=" O   GLY C 106 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   LEU C  97 " --> pdb=" O   HIS C  91 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   HIS C  91 " --> pdb=" O   LEU C  97 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   HIS C  99 " --> pdb=" O   CYS C  89 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 44
      removed outlier: 3.682A  pdb=" N   VAL C  42 " --> pdb=" O   LEU C  76 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN C  73 " --> pdb=" O   ASN C  70 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 113 through 117
      removed outlier: 3.544A  pdb=" N   HIS C 130 " --> pdb=" O   VAL C 113 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 150 through 151
      removed outlier: 3.699A  pdb=" N   HIS C 147 " --> pdb=" O   LYS C 150 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   THR C 140 " --> pdb=" O   SER C 184 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 211 through 213
      removed outlier: 3.569A  pdb=" N   VAL C 211 " --> pdb=" O   THR C 225 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   THR C 225 " --> pdb=" O   VAL C 211 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   VAL C 224 " --> pdb=" O   HIS C 265 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   HIS C 265 " --> pdb=" O   VAL C 224 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 240 through 241
    Processing sheet with id=AA7, first strand: chain 'C' and resid 257 through 258
    Processing sheet with id=AA8, first strand: chain 'G' and resid 5 through 7
      removed outlier: 3.547A  pdb=" N   SER G  22 " --> pdb=" O   SER G   7 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ALA G  19 " --> pdb=" O   ILE G  76 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   PHE G  72 " --> pdb=" O   CYS G  23 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ASP G  71 " --> pdb=" O   SER G  68 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 10 through 13
      removed outlier: 3.583A  pdb=" N   TYR G  88 " --> pdb=" O   TYR G  37 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   LEU G  34 " --> pdb=" O   TYR G  50 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   TYR G  50 " --> pdb=" O   LEU G  34 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   TRP G  36 " --> pdb=" O   LEU G  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'G' and resid 10 through 13
    Processing sheet with id=AB2, first strand: chain 'G' and resid 115 through 119
      removed outlier: 3.557A  pdb=" N   ASN G 138 " --> pdb=" O   SER G 115 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   TYR G 174 " --> pdb=" O   ASN G 139 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'G' and resid 146 through 150
      removed outlier: 4.099A  pdb=" N   LYS G 146 " --> pdb=" O   THR G 198 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   THR G 198 " --> pdb=" O   LYS G 146 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 3 through 7
    Processing sheet with id=AB5, first strand: chain 'F' and resid 11 through 12
      removed outlier: 3.562A  pdb=" N   ALA F  92 " --> pdb=" O   VAL F 113 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA F  97 " --> pdb=" O   HIS F  35 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   HIS F  35 " --> pdb=" O   ALA F  97 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   MET F  34 " --> pdb=" O   ASN F  50 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   ASN F  50 " --> pdb=" O   MET F  34 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   TRP F  36 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 124 through 128
      removed outlier: 6.474A  pdb=" N   TYR F 180 " --> pdb=" O   ASP F 148 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 124 through 128
      removed outlier: 6.474A  pdb=" N   TYR F 180 " --> pdb=" O   ASP F 148 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 155 through 158
      removed outlier: 3.784A  pdb=" N   THR F 155 " --> pdb=" O   ASP F 203 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ASP F 203 " --> pdb=" O   THR F 155 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   CYS F 200 " --> pdb=" O   LYS F 213 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 5 through 7
      removed outlier: 11.818A  pdb=" N   CYS E  23 " --> pdb=" O   THR E  74 " (cutoff:3.500A)
      removed outlier: 11.059A  pdb=" N   THR E  74 " --> pdb=" O   CYS E  23 " (cutoff:3.500A)
      removed outlier: 12.176A  pdb=" N   ALA E  25 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
      removed outlier: 12.016A  pdb=" N   THR E  72 " --> pdb=" O   ALA E  25 " (cutoff:3.500A)
      removed outlier: 10.829A  pdb=" N   GLN E  27 " --> pdb=" O   ASP E  70 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   ASP E  70 " --> pdb=" O   GLN E  27 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 13
      removed outlier: 6.576A  pdb=" N   LEU E  11 " --> pdb=" O   GLU E 106 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   LEU E  33 " --> pdb=" O   TYR E  49 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   TYR E  49 " --> pdb=" O   LEU E  33 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   TRP E  35 " --> pdb=" O   LEU E  47 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 117 through 119
      removed outlier: 3.511A  pdb=" N   VAL E 134 " --> pdb=" O   PHE E 119 " (cutoff:3.500A)
      removed outlier: 5.801A  pdb=" N   TYR E 174 " --> pdb=" O   ASN E 139 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'E' and resid 146 through 150
      removed outlier: 3.763A  pdb=" N   LYS E 150 " --> pdb=" O   ALA E 194 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AC5, first strand: chain 'D' and resid 58 through 60
      removed outlier: 6.930A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   ILE D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   MET D  34 " --> pdb=" O   ILE D  50 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   CYS D  96 " --> pdb=" O   TRP D 110 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   TRP D 110 " --> pdb=" O   CYS D  96 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ALA D  98 " --> pdb=" O   GLN D 108 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 58 through 60
      removed outlier: 6.930A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   ILE D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   MET D  34 " --> pdb=" O   ILE D  50 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY D  92 " --> pdb=" O   VAL D 116 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'D' and resid 127 through 131
      removed outlier: 3.652A  pdb=" N   SER D 187 " --> pdb=" O   CYS D 147 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   TYR D 183 " --> pdb=" O   ASP D 151 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'D' and resid 158 through 161
      removed outlier: 4.231A  pdb=" N   TYR D 201 " --> pdb=" O   VAL D 218 " (cutoff:3.500A)

    305 hydrogen bonds defined for protein.
    771 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.84

  Time building geometry restraints manager: 2.73 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2662
        1.33 -     1.46: 1935
        1.46 -     1.58: 4555
        1.58 -     1.70: 0
        1.70 -     1.82: 42
  Bond restraints: 9194
  Sorted by residual:
  bond pdb=" C   ILE C 278 "
       pdb=" O   ILE C 278 "
    ideal  model  delta    sigma   weight residual
    1.236  1.211  0.025 1.04e-02 9.25e+03 5.72e+00
  bond pdb=" C1  NAG I   1 "
       pdb=" O5  NAG I   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.38e+00
  bond pdb=" C1  NAG H   1 "
       pdb=" O5  NAG H   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.37e+00
  bond pdb=" C   ARG D  16 "
       pdb=" O   ARG D  16 "
    ideal  model  delta    sigma   weight residual
    1.234  1.215  0.020 1.28e-02 6.10e+03 2.36e+00
  bond pdb=" C1  NAG I   2 "
       pdb=" O5  NAG I   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.25e+00
  ... (remaining 9189 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 12276
        1.50 -     3.00: 227
        3.00 -     4.50: 25
        4.50 -     6.00: 2
        6.00 -     7.50: 3
  Bond angle restraints: 12533
  Sorted by residual:
  angle pdb=" N   ALA C 296 "
        pdb=" CA  ALA C 296 "
        pdb=" C   ALA C 296 "
      ideal   model   delta    sigma   weight residual
     107.88  112.34   -4.46 1.41e+00 5.03e-01 1.00e+01
  angle pdb=" CA  CYS C 154 "
        pdb=" CB  CYS C 154 "
        pdb=" SG  CYS C 154 "
      ideal   model   delta    sigma   weight residual
     114.40  121.59   -7.19 2.30e+00 1.89e-01 9.77e+00
  angle pdb=" N   LYS D 208 "
        pdb=" CA  LYS D 208 "
        pdb=" C   LYS D 208 "
      ideal   model   delta    sigma   weight residual
     109.81  116.48   -6.67 2.21e+00 2.05e-01 9.11e+00
  angle pdb=" C   HIS F 204 "
        pdb=" N   LYS F 205 "
        pdb=" CA  LYS F 205 "
      ideal   model   delta    sigma   weight residual
     120.09  123.47   -3.38 1.25e+00 6.40e-01 7.31e+00
  angle pdb=" C   LYS D 208 "
        pdb=" N   PRO D 209 "
        pdb=" CA  PRO D 209 "
      ideal   model   delta    sigma   weight residual
     118.97  116.39    2.58 1.04e+00 9.25e-01 6.15e+00
  ... (remaining 12528 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.93: 5495
       33.93 -    67.86: 73
       67.86 -   101.80: 10
      101.80 -   135.73: 1
      135.73 -   169.66: 1
  Dihedral angle restraints: 5580
    sinusoidal: 2260
      harmonic: 3320
  Sorted by residual:
  dihedral pdb=" CB  GLU E 166 "
           pdb=" CG  GLU E 166 "
           pdb=" CD  GLU E 166 "
           pdb=" OE1 GLU E 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  169.66 -169.66     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" CB  CYS G 215 "
           pdb=" SG  CYS G 215 "
           pdb=" SG  CYS F 131 "
           pdb=" CB  CYS F 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -49.68  -36.32     1      1.00e+01 1.00e-02 1.86e+01
  dihedral pdb=" CB  GLU G 166 "
           pdb=" CG  GLU G 166 "
           pdb=" CD  GLU G 166 "
           pdb=" OE1 GLU G 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  104.32 -104.32     1      3.00e+01 1.11e-03 1.33e+01
  ... (remaining 5577 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1230
       0.057 -    0.113: 177
       0.113 -    0.170: 9
       0.170 -    0.226: 0
       0.226 -    0.283: 2
  Chirality restraints: 1418
  Sorted by residual:
  chirality pdb=" CA  LYS D 208 "
            pdb=" N   LYS D 208 "
            pdb=" C   LYS D 208 "
            pdb=" CB  LYS D 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CA  ILE C 278 "
            pdb=" N   ILE C 278 "
            pdb=" C   ILE C 278 "
            pdb=" CB  ILE C 278 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  VAL E  58 "
            pdb=" N   VAL E  58 "
            pdb=" C   VAL E  58 "
            pdb=" CB  VAL E  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 1415 not shown)

  Planarity restraints: 1597
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO E  95 "    0.025 5.00e-02 4.00e+02   3.82e-02 2.34e+00
        pdb=" N   PRO E  96 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO E  96 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO E  96 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 153 "   -0.024 5.00e-02 4.00e+02   3.61e-02 2.08e+00
        pdb=" N   PRO D 154 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO D 154 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 154 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER G  95 "   -0.021 5.00e-02 4.00e+02   3.13e-02 1.57e+00
        pdb=" N   PRO G  96 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO G  96 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO G  96 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1594 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1916
        2.79 -     3.31: 7168
        3.31 -     3.84: 14328
        3.84 -     4.37: 16082
        4.37 -     4.90: 29061
  Nonbonded interactions: 68555
  Sorted by model distance:
  nonbonded pdb=" OH  TYR G  37 "
            pdb=" OE1 GLN G  90 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OD1 ASP F  73 "
            pdb=" OG  SER F  75 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   HIS C  83 "
            pdb=" OH  TYR C  87 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   PRO D 192 "
            pdb=" OG  SER D 195 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OD1 ASP D  54 "
            pdb=" OG  SER D  56 "
     model   vdw
     2.334 3.040
  ... (remaining 68550 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'H'
  selection = chain 'I'
}
ncs_group {
  reference = (chain 'D' and (resid 1 through 9 or resid 11 through 22 or resid 24 through 30  \ 
or resid 34 through 39 or resid 41 through 48 or resid 51 or resid 54 through 55 \ 
 or resid 58 or resid 60 or resid 62 through 78 or resid 81 through 87 or resid  \ 
89 through 91 or resid 94 through 97 or resid 103 or resid 107 or resid 110 thro \ 
ugh 114 or resid 116 through 220))
  selection = (chain 'F' and (resid 1 through 9 or resid 11 through 22 or resid 24 through 30  \ 
or resid 34 through 39 or resid 41 through 48 or resid 51 or resid 54 through 55 \ 
 or resid 58 or resid 60 or resid 62 through 78 or resid 81 through 87 or resid  \ 
89 through 91 or resid 94 through 97 or resid 101 or resid 104 or resid 107 thro \ 
ugh 111 or resid 113 through 132 or resid 139 through 217))
}
ncs_group {
  reference = (chain 'E' and (resid 2 or resid 5 through 8 or resid 11 through 12 or resid 14  \ 
or resid 16 or resid 18 or resid 20 or resid 23 through 28 or resid 30 through 3 \ 
3 or resid 35 through 41 or resid 43 through 44 or resid 46 through 49 or resid  \ 
51 through 53 or resid 57 or resid 59 or resid 61 through 76 or resid 78 or resi \ 
d 80 through 84 or resid 86 through 90 or resid 93 or resid 95 or resid 98 throu \ 
gh 103 or resid 106 through 215))
  selection = (chain 'G' and (resid 2 or resid 5 through 8 or resid 11 through 12 or resid 14  \ 
or resid 16 or resid 18 or resid 20 or resid 23 through 28 or resid 30 through 3 \ 
1 or resid 33 through 34 or resid 36 through 42 or resid 44 through 45 or resid  \ 
47 through 50 or resid 52 through 54 or resid 58 or resid 60 or resid 62 through \ 
 77 or resid 79 or resid 81 through 85 or resid 87 through 91 or resid 94 or res \ 
id 96 or resid 98 through 103 or resid 106 through 215))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     24.830
  Find NCS groups from input model:        0.300
  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:             0.010
  Load rotamer database and sin/cos tables:11.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
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      :  0.002   0.047   9215  Z= 0.123
  Angle     :  0.494   7.496  12583  Z= 0.264
  Chirality :  0.041   0.283   1418
  Planarity :  0.004   0.038   1593
  Dihedral  : 11.955 169.662   3407
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 16.62 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    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: -2.25 (0.23), residues: 1131
  helix: -4.06 (0.45), residues: 28
  sheet: -0.79 (0.23), residues: 494
  loop : -1.98 (0.22), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP C 293 
 HIS   0.002   0.000   HIS D 207 
 PHE   0.004   0.001   PHE F 126 
 TYR   0.018   0.001   TYR C 276 
 ARG   0.002   0.000   ARG D  16 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00133 (    4)
  link_NAG-ASN         : angle       1.18497 (   12)
  link_BETA1-4         : bond        0.00351 (    4)
  link_BETA1-4         : angle       0.75390 (   12)
  hydrogen bonds       : bond        0.27192 (  274)
  hydrogen bonds       : angle      10.34248 (  771)
  SS BOND              : bond        0.00257 (   13)
  SS BOND              : angle       0.58746 (   26)
  covalent geometry    : bond        0.00235 ( 9194)
  covalent geometry    : angle       0.49202 (12533)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 152
  time to evaluate  : 0.895 
Fit side-chains
REVERT: C  169 MET cc_start: 0.6823 (mmt) cc_final: 0.6535 (mmt)
REVERT: C  243 PHE cc_start: 0.7714 (t80) cc_final: 0.7507 (t80)
REVERT: G  104 LYS cc_start: 0.8835 (tttt) cc_final: 0.8570 (tttp)
REVERT: G  148 GLN cc_start: 0.7470 (mt0) cc_final: 0.7252 (mt0)
REVERT: E  108 LYS cc_start: 0.8203 (tttp) cc_final: 0.7838 (ttmm)
REVERT: D  152 TYR cc_start: 0.7418 (p90) cc_final: 0.7206 (p90)
REVERT: D  160 SER cc_start: 0.8110 (p) cc_final: 0.7870 (t)
REVERT: D  183 TYR cc_start: 0.8060 (m-80) cc_final: 0.7828 (m-80)
REVERT: D  188 VAL cc_start: 0.8354 (t) cc_final: 0.8135 (m)
  outliers start: 7
  outliers final: 3
  residues processed: 157
  average time/residue: 1.0419
  time to fit residues: 176.1622
Evaluate side-chains
  104 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  277 ILE
Chi-restraints excluded: chain G residue  147 VAL
Chi-restraints excluded: chain E residue   78 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 101 optimal weight:    2.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
C  96 HIS
C 100 GLN
C 119 ASN
C 209 ASN
G  27 GLN
G 148 GLN
F  57 ASN
F  77 ASN
F 175 GLN
E  27 GLN
E  34 ASN
E 148 GLN
D  77 ASN
D  99 GLN
D 178 GLN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.144316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.108915 restraints weight = 11126.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.30
r_work: 0.3114 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2985
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2985
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067   9215  Z= 0.288
  Angle     :  0.750  10.137  12583  Z= 0.380
  Chirality :  0.051   0.201   1418
  Planarity :  0.006   0.055   1593
  Dihedral  :  4.819  47.034   1405
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 17.32 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.24), residues: 1131
  helix: -3.56 (0.55), residues: 29
  sheet: -0.19 (0.22), residues: 519
  loop : -1.36 (0.24), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP F 101 
 HIS   0.010   0.003   HIS C  99 
 PHE   0.020   0.002   PHE F 100 
 TYR   0.019   0.003   TYR F  95 
 ARG   0.006   0.001   ARG G 109 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00406 (    4)
  link_NAG-ASN         : angle       1.84835 (   12)
  link_BETA1-4         : bond        0.00401 (    4)
  link_BETA1-4         : angle       1.45605 (   12)
  hydrogen bonds       : bond        0.04795 (  274)
  hydrogen bonds       : angle       6.84184 (  771)
  SS BOND              : bond        0.00799 (   13)
  SS BOND              : angle       1.37710 (   26)
  covalent geometry    : bond        0.00709 ( 9194)
  covalent geometry    : angle       0.74567 (12533)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 109
  time to evaluate  : 1.072 
Fit side-chains
REVERT: C  283 LYS cc_start: 0.6899 (tttm) cc_final: 0.6634 (tttp)
REVERT: C  290 TRP cc_start: 0.8252 (m100) cc_final: 0.7956 (m100)
REVERT: G   18 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8088 (ttm170)
REVERT: G  148 GLN cc_start: 0.7829 (mt0) cc_final: 0.7457 (mt0)
REVERT: G  155 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7626 (mp)
REVERT: F   21 SER cc_start: 0.8912 (m) cc_final: 0.8668 (t)
REVERT: E   79 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8203 (mp10)
REVERT: E  108 LYS cc_start: 0.8341 (tttp) cc_final: 0.7840 (ttmm)
REVERT: E  172 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.7953 (p)
REVERT: D  155 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8054 (mt-10)
REVERT: D  187 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8567 (t)
  outliers start: 60
  outliers final: 35
  residues processed: 158
  average time/residue: 1.0612
  time to fit residues: 180.6387
Evaluate side-chains
  137 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 98
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  237 SER
Chi-restraints excluded: chain C residue  289 THR
Chi-restraints excluded: chain G residue   14 SER
Chi-restraints excluded: chain G residue   18 ARG
Chi-restraints excluded: chain G residue   95 SER
Chi-restraints excluded: chain G residue  147 VAL
Chi-restraints excluded: chain G residue  155 LEU
Chi-restraints excluded: chain G residue  157 SER
Chi-restraints excluded: chain G residue  181 THR
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   89 GLU
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain F residue  120 THR
Chi-restraints excluded: chain F residue  135 THR
Chi-restraints excluded: chain F residue  138 SER
Chi-restraints excluded: chain F residue  197 THR
Chi-restraints excluded: chain F residue  200 CYS
Chi-restraints excluded: chain F residue  211 VAL
Chi-restraints excluded: chain E residue   12 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   76 SER
Chi-restraints excluded: chain E residue  111 VAL
Chi-restraints excluded: chain E residue  172 SER
Chi-restraints excluded: chain E residue  177 SER
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue   85 SER
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  187 SER
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  195 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 98 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 94 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9980
   chunk 79 optimal weight:    0.0060
   chunk 97 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
C 119 ASN
C 256 HIS
F  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.147393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.113396 restraints weight = 11150.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.20
r_work: 0.3142 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2990
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2990 r_free = 0.2990    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2990 r_free = 0.2990    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2990
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9215  Z= 0.101
  Angle     :  0.536   8.029  12583  Z= 0.271
  Chirality :  0.043   0.146   1418
  Planarity :  0.004   0.040   1593
  Dihedral  :  4.080  24.639   1401
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 20.42 %
    Favored  : 75.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    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: -0.76 (0.25), residues: 1131
  helix: -3.48 (0.54), residues: 29
  sheet:  0.20 (0.23), residues: 519
  loop : -0.97 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F 101 
 HIS   0.003   0.001   HIS D 171 
 PHE   0.009   0.001   PHE C 125 
 TYR   0.020   0.001   TYR D 152 
 ARG   0.003   0.000   ARG G 143 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00082 (    4)
  link_NAG-ASN         : angle       1.30459 (   12)
  link_BETA1-4         : bond        0.00253 (    4)
  link_BETA1-4         : angle       1.22015 (   12)
  hydrogen bonds       : bond        0.03129 (  274)
  hydrogen bonds       : angle       6.07224 (  771)
  SS BOND              : bond        0.00345 (   13)
  SS BOND              : angle       0.69159 (   26)
  covalent geometry    : bond        0.00237 ( 9194)
  covalent geometry    : angle       0.53340 (12533)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 101
  time to evaluate  : 0.949 
Fit side-chains
REVERT: C  237 SER cc_start: 0.5976 (OUTLIER) cc_final: 0.5699 (t)
REVERT: C  283 LYS cc_start: 0.7071 (tttm) cc_final: 0.6765 (tttp)
REVERT: C  290 TRP cc_start: 0.8286 (m100) cc_final: 0.8082 (m100)
REVERT: G   18 ARG cc_start: 0.8470 (ttm110) cc_final: 0.8143 (ttm170)
REVERT: G  148 GLN cc_start: 0.7799 (mt0) cc_final: 0.7504 (mt0)
REVERT: G  155 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7608 (mp)
REVERT: F   99 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7601 (tt0)
REVERT: F  184 SER cc_start: 0.9178 (m) cc_final: 0.8933 (t)
REVERT: F  196 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7259 (tttt)
REVERT: E   79 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8211 (mp10)
REVERT: E  108 LYS cc_start: 0.8359 (tttp) cc_final: 0.7797 (ttmm)
REVERT: E  172 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8011 (p)
REVERT: E  196 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.6062 (mp0)
REVERT: D   43 LYS cc_start: 0.8548 (mttp) cc_final: 0.8334 (mttt)
REVERT: D  105 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7966 (mt-10)
REVERT: D  163 SER cc_start: 0.7348 (OUTLIER) cc_final: 0.7033 (p)
REVERT: D  217 ARG cc_start: 0.6116 (tpt-90) cc_final: 0.5761 (tpp80)
  outliers start: 44
  outliers final: 22
  residues processed: 135
  average time/residue: 1.1751
  time to fit residues: 169.5453
Evaluate side-chains
  122 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 92
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue  211 VAL
Chi-restraints excluded: chain C residue  237 SER
Chi-restraints excluded: chain C residue  289 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue  101 GLN
Chi-restraints excluded: chain G residue  147 VAL
Chi-restraints excluded: chain G residue  155 LEU
Chi-restraints excluded: chain G residue  157 SER
Chi-restraints excluded: chain G residue  181 THR
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   99 GLU
Chi-restraints excluded: chain F residue  120 THR
Chi-restraints excluded: chain F residue  135 THR
Chi-restraints excluded: chain F residue  196 LYS
Chi-restraints excluded: chain F residue  211 VAL
Chi-restraints excluded: chain E residue    9 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   76 SER
Chi-restraints excluded: chain E residue  172 SER
Chi-restraints excluded: chain E residue  177 SER
Chi-restraints excluded: chain E residue  196 GLU
Chi-restraints excluded: chain D residue  105 GLU
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  163 SER
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  203 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 89 optimal weight:   10.0000
   chunk 101 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 105 optimal weight:    7.9990
   chunk 96 optimal weight:    0.0670
   chunk 95 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.9520

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

Flipped N/Q/H residues before XYZ refinement:
C 119 ASN
F  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.145656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.111632 restraints weight = 11117.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.22
r_work: 0.3131 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3006
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.3006
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9215  Z= 0.127
  Angle     :  0.563   8.831  12583  Z= 0.280
  Chirality :  0.044   0.152   1418
  Planarity :  0.004   0.040   1593
  Dihedral  :  4.148  26.596   1401
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 20.52 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    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: -0.40 (0.25), residues: 1131
  helix: -3.29 (0.56), residues: 29
  sheet:  0.43 (0.23), residues: 525
  loop : -0.73 (0.26), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP F 101 
 HIS   0.005   0.001   HIS C  99 
 PHE   0.012   0.001   PHE C 141 
 TYR   0.024   0.001   TYR D 152 
 ARG   0.002   0.000   ARG C 110 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00608 (    4)
  link_NAG-ASN         : angle       1.61831 (   12)
  link_BETA1-4         : bond        0.00386 (    4)
  link_BETA1-4         : angle       1.69059 (   12)
  hydrogen bonds       : bond        0.02837 (  274)
  hydrogen bonds       : angle       5.75871 (  771)
  SS BOND              : bond        0.00432 (   13)
  SS BOND              : angle       0.79374 (   26)
  covalent geometry    : bond        0.00309 ( 9194)
  covalent geometry    : angle       0.55807 (12533)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 92
  time to evaluate  : 0.999 
Fit side-chains
REVERT: C  237 SER cc_start: 0.6010 (OUTLIER) cc_final: 0.5791 (t)
REVERT: C  283 LYS cc_start: 0.7130 (tttm) cc_final: 0.6835 (tttp)
REVERT: C  290 TRP cc_start: 0.8256 (m100) cc_final: 0.7973 (m100)
REVERT: G   71 ASP cc_start: 0.8202 (m-30) cc_final: 0.7924 (m-30)
REVERT: G  148 GLN cc_start: 0.7781 (mt0) cc_final: 0.7563 (mt0)
REVERT: G  155 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7625 (mp)
REVERT: F   99 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7641 (tt0)
REVERT: F  184 SER cc_start: 0.9184 (m) cc_final: 0.8952 (t)
REVERT: F  196 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7286 (tttt)
REVERT: E  108 LYS cc_start: 0.8364 (tttp) cc_final: 0.7795 (ttmm)
REVERT: E  172 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.7966 (p)
REVERT: D   43 LYS cc_start: 0.8547 (mttp) cc_final: 0.8272 (mttt)
REVERT: D  105 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7990 (mt-10)
REVERT: D  163 SER cc_start: 0.7386 (OUTLIER) cc_final: 0.7072 (p)
REVERT: D  217 ARG cc_start: 0.6099 (tpt-90) cc_final: 0.5705 (tpp80)
  outliers start: 56
  outliers final: 35
  residues processed: 137
  average time/residue: 1.0491
  time to fit residues: 154.6344
Evaluate side-chains
  132 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 90
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  211 VAL
Chi-restraints excluded: chain C residue  237 SER
Chi-restraints excluded: chain G residue   24 ARG
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue  147 VAL
Chi-restraints excluded: chain G residue  155 LEU
Chi-restraints excluded: chain G residue  157 SER
Chi-restraints excluded: chain G residue  181 THR
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   89 GLU
Chi-restraints excluded: chain F residue   99 GLU
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain F residue  120 THR
Chi-restraints excluded: chain F residue  131 CYS
Chi-restraints excluded: chain F residue  196 LYS
Chi-restraints excluded: chain F residue  200 CYS
Chi-restraints excluded: chain E residue    9 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   76 SER
Chi-restraints excluded: chain E residue  111 VAL
Chi-restraints excluded: chain E residue  172 SER
Chi-restraints excluded: chain E residue  177 SER
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue   85 SER
Chi-restraints excluded: chain D residue  105 GLU
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  163 SER
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  194 SER
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  203 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 88 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
C 119 ASN
F  77 ASN
E 190 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.142424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.106673 restraints weight = 11167.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 2.28
r_work: 0.3060 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2937
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2937 r_free = 0.2937    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2937 r_free = 0.2937    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2937
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   9215  Z= 0.217
  Angle     :  0.660  10.368  12583  Z= 0.331
  Chirality :  0.047   0.201   1418
  Planarity :  0.005   0.042   1593
  Dihedral  :  4.846  26.351   1401
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 20.62 %
    Favored  : 73.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    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: -0.41 (0.25), residues: 1131
  helix: -3.22 (0.61), residues: 29
  sheet:  0.47 (0.23), residues: 523
  loop : -0.78 (0.26), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP F 101 
 HIS   0.009   0.001   HIS C  99 
 PHE   0.016   0.002   PHE C 141 
 TYR   0.025   0.002   TYR D 152 
 ARG   0.005   0.001   ARG G 109 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00754 (    4)
  link_NAG-ASN         : angle       1.94001 (   12)
  link_BETA1-4         : bond        0.00371 (    4)
  link_BETA1-4         : angle       1.93721 (   12)
  hydrogen bonds       : bond        0.03272 (  274)
  hydrogen bonds       : angle       5.94744 (  771)
  SS BOND              : bond        0.00608 (   13)
  SS BOND              : angle       1.16049 (   26)
  covalent geometry    : bond        0.00538 ( 9194)
  covalent geometry    : angle       0.65369 (12533)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 90
  time to evaluate  : 1.006 
Fit side-chains
REVERT: C   28 GLN cc_start: 0.6779 (OUTLIER) cc_final: 0.6575 (tp-100)
REVERT: C  283 LYS cc_start: 0.6955 (tttm) cc_final: 0.6713 (tttp)
REVERT: C  290 TRP cc_start: 0.8329 (m100) cc_final: 0.8027 (m100)
REVERT: G   71 ASP cc_start: 0.8190 (m-30) cc_final: 0.7880 (m-30)
REVERT: G  148 GLN cc_start: 0.7845 (mt0) cc_final: 0.7614 (mt0)
REVERT: G  155 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7644 (mp)
REVERT: F   99 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7746 (tt0)
REVERT: F  196 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7265 (tttt)
REVERT: E   24 ARG cc_start: 0.7413 (ttm-80) cc_final: 0.6819 (mtm110)
REVERT: E  141 TYR cc_start: 0.8528 (t80) cc_final: 0.8201 (t80)
REVERT: E  171 ASP cc_start: 0.8260 (m-30) cc_final: 0.8004 (m-30)
REVERT: E  172 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.7948 (p)
REVERT: E  214 GLU cc_start: 0.5453 (OUTLIER) cc_final: 0.4815 (tp30)
REVERT: D  163 SER cc_start: 0.7435 (OUTLIER) cc_final: 0.7130 (p)
REVERT: D  217 ARG cc_start: 0.6101 (tpt-90) cc_final: 0.5726 (tpp80)
  outliers start: 63
  outliers final: 44
  residues processed: 141
  average time/residue: 0.9892
  time to fit residues: 150.6404
Evaluate side-chains
  138 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 87
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   28 GLN
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  211 VAL
Chi-restraints excluded: chain C residue  289 THR
Chi-restraints excluded: chain G residue   14 SER
Chi-restraints excluded: chain G residue   24 ARG
Chi-restraints excluded: chain G residue   95 SER
Chi-restraints excluded: chain G residue  147 VAL
Chi-restraints excluded: chain G residue  155 LEU
Chi-restraints excluded: chain G residue  181 THR
Chi-restraints excluded: chain G residue  192 VAL
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   89 GLU
Chi-restraints excluded: chain F residue   99 GLU
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain F residue  120 THR
Chi-restraints excluded: chain F residue  131 CYS
Chi-restraints excluded: chain F residue  135 THR
Chi-restraints excluded: chain F residue  196 LYS
Chi-restraints excluded: chain F residue  200 CYS
Chi-restraints excluded: chain F residue  211 VAL
Chi-restraints excluded: chain E residue    9 SER
Chi-restraints excluded: chain E residue   12 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   76 SER
Chi-restraints excluded: chain E residue  111 VAL
Chi-restraints excluded: chain E residue  172 SER
Chi-restraints excluded: chain E residue  177 SER
Chi-restraints excluded: chain E residue  214 GLU
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue   85 SER
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  163 SER
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  194 SER
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  203 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0670
   chunk 27 optimal weight:    9.9990
   chunk 6 optimal weight:    0.4980
   chunk 39 optimal weight:    0.6980
   chunk 83 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 109 optimal weight:    7.9990
   overall best weight:    0.8520

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

Flipped N/Q/H residues before XYZ refinement:
C 119 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.144669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.108509 restraints weight = 11088.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.37
r_work: 0.3115 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2994
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       25 |
|-----------------------------------------------------------------------------|
r_final: 0.2994
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9215  Z= 0.120
  Angle     :  0.571   8.990  12583  Z= 0.284
  Chirality :  0.044   0.161   1418
  Planarity :  0.004   0.042   1593
  Dihedral  :  4.619  26.798   1401
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 22.02 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    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: -0.24 (0.26), residues: 1131
  helix: -3.17 (0.62), residues: 29
  sheet:  0.55 (0.23), residues: 524
  loop : -0.63 (0.27), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP F 101 
 HIS   0.004   0.001   HIS C  99 
 PHE   0.009   0.001   PHE E  99 
 TYR   0.022   0.001   TYR D 152 
 ARG   0.006   0.000   ARG G  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01144 (    4)
  link_NAG-ASN         : angle       2.70762 (   12)
  link_BETA1-4         : bond        0.00294 (    4)
  link_BETA1-4         : angle       1.79317 (   12)
  hydrogen bonds       : bond        0.02704 (  274)
  hydrogen bonds       : angle       5.60366 (  771)
  SS BOND              : bond        0.00399 (   13)
  SS BOND              : angle       0.82143 (   26)
  covalent geometry    : bond        0.00290 ( 9194)
  covalent geometry    : angle       0.56173 (12533)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 90
  time to evaluate  : 1.038 
Fit side-chains
REVERT: C   28 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6560 (tp-100)
REVERT: C  283 LYS cc_start: 0.6939 (tttm) cc_final: 0.6695 (tttp)
REVERT: C  290 TRP cc_start: 0.8307 (m100) cc_final: 0.8047 (m100)
REVERT: G   71 ASP cc_start: 0.8127 (m-30) cc_final: 0.7824 (m-30)
REVERT: G  148 GLN cc_start: 0.7807 (mt0) cc_final: 0.7585 (mt0)
REVERT: G  155 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7597 (mp)
REVERT: F   99 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7633 (tt0)
REVERT: F  184 SER cc_start: 0.9155 (m) cc_final: 0.8900 (t)
REVERT: F  196 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7283 (tttt)
REVERT: E  106 GLU cc_start: 0.8271 (pt0) cc_final: 0.7828 (pt0)
REVERT: E  171 ASP cc_start: 0.8258 (m-30) cc_final: 0.8018 (m-30)
REVERT: E  172 SER cc_start: 0.8670 (OUTLIER) cc_final: 0.7920 (p)
REVERT: D   43 LYS cc_start: 0.8522 (mttp) cc_final: 0.8264 (mttt)
REVERT: D  112 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7181 (pm20)
REVERT: D  163 SER cc_start: 0.7468 (OUTLIER) cc_final: 0.7173 (p)
REVERT: D  217 ARG cc_start: 0.6010 (tpt-90) cc_final: 0.5616 (tpp80)
  outliers start: 53
  outliers final: 39
  residues processed: 133
  average time/residue: 0.9630
  time to fit residues: 138.8733
Evaluate side-chains
  131 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 85
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   28 GLN
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  211 VAL
Chi-restraints excluded: chain C residue  289 THR
Chi-restraints excluded: chain G residue   14 SER
Chi-restraints excluded: chain G residue   24 ARG
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue  147 VAL
Chi-restraints excluded: chain G residue  155 LEU
Chi-restraints excluded: chain G residue  181 THR
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   89 GLU
Chi-restraints excluded: chain F residue   99 GLU
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain F residue  120 THR
Chi-restraints excluded: chain F residue  131 CYS
Chi-restraints excluded: chain F residue  135 THR
Chi-restraints excluded: chain F residue  154 VAL
Chi-restraints excluded: chain F residue  176 SER
Chi-restraints excluded: chain F residue  196 LYS
Chi-restraints excluded: chain F residue  199 THR
Chi-restraints excluded: chain F residue  200 CYS
Chi-restraints excluded: chain F residue  211 VAL
Chi-restraints excluded: chain E residue    9 SER
Chi-restraints excluded: chain E residue   12 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   76 SER
Chi-restraints excluded: chain E residue  172 SER
Chi-restraints excluded: chain E residue  177 SER
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain D residue   85 SER
Chi-restraints excluded: chain D residue  112 GLN
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  160 SER
Chi-restraints excluded: chain D residue  163 SER
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  194 SER
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  203 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 88 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0870
   chunk 10 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0000
   chunk 32 optimal weight:    0.6980
   chunk 94 optimal weight:    4.9990
   chunk 73 optimal weight:    8.9990
   chunk 43 optimal weight:    0.4980
   chunk 93 optimal weight:    0.5980
   overall best weight:    0.3762

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

Flipped N/Q/H residues before XYZ refinement:
C 119 ASN
F 201 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.146747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.112946 restraints weight = 11161.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.24
r_work: 0.3128 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       25 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.3021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.3548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   9215  Z= 0.090
  Angle     :  0.539   8.261  12583  Z= 0.267
  Chirality :  0.043   0.268   1418
  Planarity :  0.004   0.042   1593
  Dihedral  :  4.345  27.685   1401
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 22.12 %
    Favored  : 72.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    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: -0.02 (0.26), residues: 1131
  helix: -2.92 (0.65), residues: 29
  sheet:  0.67 (0.23), residues: 524
  loop : -0.46 (0.27), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F 101 
 HIS   0.002   0.000   HIS C  99 
 PHE   0.009   0.001   PHE C 141 
 TYR   0.022   0.001   TYR D 152 
 ARG   0.005   0.000   ARG G  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01006 (    4)
  link_NAG-ASN         : angle       3.09202 (   12)
  link_BETA1-4         : bond        0.00215 (    4)
  link_BETA1-4         : angle       1.69413 (   12)
  hydrogen bonds       : bond        0.02446 (  274)
  hydrogen bonds       : angle       5.27540 (  771)
  SS BOND              : bond        0.00300 (   13)
  SS BOND              : angle       0.61477 (   26)
  covalent geometry    : bond        0.00207 ( 9194)
  covalent geometry    : angle       0.52817 (12533)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 91
  time to evaluate  : 1.051 
Fit side-chains
REVERT: C  283 LYS cc_start: 0.7214 (tttm) cc_final: 0.6868 (tttp)
REVERT: C  290 TRP cc_start: 0.8330 (m100) cc_final: 0.8072 (m100)
REVERT: G   71 ASP cc_start: 0.8181 (m-30) cc_final: 0.7914 (m-30)
REVERT: G  155 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7592 (mp)
REVERT: F   99 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7603 (tt0)
REVERT: F  184 SER cc_start: 0.9143 (m) cc_final: 0.8930 (t)
REVERT: E  106 GLU cc_start: 0.8345 (pt0) cc_final: 0.7989 (pt0)
REVERT: D   43 LYS cc_start: 0.8598 (mttp) cc_final: 0.8326 (mttt)
REVERT: D  112 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7163 (pm20)
REVERT: D  163 SER cc_start: 0.7431 (OUTLIER) cc_final: 0.7145 (p)
REVERT: D  217 ARG cc_start: 0.6086 (tpt-90) cc_final: 0.5681 (tpp80)
  outliers start: 51
  outliers final: 36
  residues processed: 130
  average time/residue: 1.0197
  time to fit residues: 143.5825
Evaluate side-chains
  127 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 87
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  211 VAL
Chi-restraints excluded: chain C residue  289 THR
Chi-restraints excluded: chain G residue   14 SER
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue  147 VAL
Chi-restraints excluded: chain G residue  155 LEU
Chi-restraints excluded: chain G residue  157 SER
Chi-restraints excluded: chain G residue  181 THR
Chi-restraints excluded: chain G residue  192 VAL
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue    6 GLU
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   89 GLU
Chi-restraints excluded: chain F residue   99 GLU
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain F residue  131 CYS
Chi-restraints excluded: chain F residue  135 THR
Chi-restraints excluded: chain F residue  154 VAL
Chi-restraints excluded: chain F residue  176 SER
Chi-restraints excluded: chain F residue  199 THR
Chi-restraints excluded: chain F residue  200 CYS
Chi-restraints excluded: chain F residue  211 VAL
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   76 SER
Chi-restraints excluded: chain E residue  111 VAL
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue  112 GLN
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  163 SER
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  203 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 60 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0980
   chunk 18 optimal weight:    0.0370
   chunk 9 optimal weight:    0.3980
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.6660

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

Flipped N/Q/H residues before XYZ refinement:
C 119 ASN
F  77 ASN
F 201 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.146101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.112193 restraints weight = 11235.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.22
r_work: 0.3104 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3019
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.3019
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9215  Z= 0.106
  Angle     :  0.564   9.636  12583  Z= 0.278
  Chirality :  0.044   0.335   1418
  Planarity :  0.004   0.042   1593
  Dihedral  :  4.472  32.747   1401
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 22.72 %
    Favored  : 72.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    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:  0.04 (0.26), residues: 1131
  helix: -2.84 (0.67), residues: 29
  sheet:  0.62 (0.23), residues: 533
  loop : -0.32 (0.28), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F 101 
 HIS   0.004   0.001   HIS C  99 
 PHE   0.008   0.001   PHE E  99 
 TYR   0.029   0.001   TYR D 152 
 ARG   0.005   0.000   ARG G  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01070 (    4)
  link_NAG-ASN         : angle       3.76704 (   12)
  link_BETA1-4         : bond        0.00216 (    4)
  link_BETA1-4         : angle       1.73119 (   12)
  hydrogen bonds       : bond        0.02471 (  274)
  hydrogen bonds       : angle       5.23730 (  771)
  SS BOND              : bond        0.00356 (   13)
  SS BOND              : angle       0.71474 (   26)
  covalent geometry    : bond        0.00252 ( 9194)
  covalent geometry    : angle       0.54918 (12533)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 86
  time to evaluate  : 1.012 
Fit side-chains
REVERT: C  283 LYS cc_start: 0.7259 (tttm) cc_final: 0.6953 (tttp)
REVERT: C  290 TRP cc_start: 0.8337 (m100) cc_final: 0.8092 (m100)
REVERT: G   71 ASP cc_start: 0.8188 (m-30) cc_final: 0.7935 (m-30)
REVERT: G  155 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7593 (mp)
REVERT: F   99 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7614 (tt0)
REVERT: F  184 SER cc_start: 0.9150 (m) cc_final: 0.8935 (t)
REVERT: E  106 GLU cc_start: 0.8353 (pt0) cc_final: 0.7989 (pt0)
REVERT: E  214 GLU cc_start: 0.5280 (OUTLIER) cc_final: 0.4500 (tp30)
REVERT: D   43 LYS cc_start: 0.8571 (mttp) cc_final: 0.8315 (mttt)
REVERT: D  112 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7147 (pm20)
REVERT: D  163 SER cc_start: 0.7513 (OUTLIER) cc_final: 0.7244 (p)
REVERT: D  217 ARG cc_start: 0.6142 (tpt-90) cc_final: 0.5732 (tpp80)
  outliers start: 48
  outliers final: 39
  residues processed: 122
  average time/residue: 1.0130
  time to fit residues: 133.8244
Evaluate side-chains
  126 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 82
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  211 VAL
Chi-restraints excluded: chain C residue  237 SER
Chi-restraints excluded: chain C residue  289 THR
Chi-restraints excluded: chain G residue   14 SER
Chi-restraints excluded: chain G residue   24 ARG
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue  147 VAL
Chi-restraints excluded: chain G residue  155 LEU
Chi-restraints excluded: chain G residue  181 THR
Chi-restraints excluded: chain G residue  192 VAL
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue    6 GLU
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   89 GLU
Chi-restraints excluded: chain F residue   99 GLU
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain F residue  131 CYS
Chi-restraints excluded: chain F residue  135 THR
Chi-restraints excluded: chain F residue  154 VAL
Chi-restraints excluded: chain F residue  176 SER
Chi-restraints excluded: chain F residue  199 THR
Chi-restraints excluded: chain F residue  200 CYS
Chi-restraints excluded: chain F residue  211 VAL
Chi-restraints excluded: chain E residue    9 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   76 SER
Chi-restraints excluded: chain E residue  111 VAL
Chi-restraints excluded: chain E residue  214 GLU
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue  112 GLN
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  163 SER
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  203 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0980
   chunk 11 optimal weight:    0.5980
   chunk 99 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C 119 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.146608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.112204 restraints weight = 11096.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 2.21
r_work: 0.3118 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2998 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3030
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.3030
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.3656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   9215  Z= 0.106
  Angle     :  0.577  12.415  12583  Z= 0.282
  Chirality :  0.045   0.522   1418
  Planarity :  0.004   0.042   1593
  Dihedral  :  4.607  40.713   1401
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 22.62 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    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:  0.06 (0.26), residues: 1131
  helix: -2.74 (0.69), residues: 29
  sheet:  0.58 (0.23), residues: 535
  loop : -0.26 (0.28), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F 101 
 HIS   0.003   0.001   HIS C  99 
 PHE   0.007   0.001   PHE C 125 
 TYR   0.029   0.001   TYR D 152 
 ARG   0.005   0.000   ARG G  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.02407 (    4)
  link_NAG-ASN         : angle       4.94903 (   12)
  link_BETA1-4         : bond        0.00435 (    4)
  link_BETA1-4         : angle       1.79078 (   12)
  hydrogen bonds       : bond        0.02448 (  274)
  hydrogen bonds       : angle       5.19203 (  771)
  SS BOND              : bond        0.00341 (   13)
  SS BOND              : angle       0.66792 (   26)
  covalent geometry    : bond        0.00244 ( 9194)
  covalent geometry    : angle       0.55431 (12533)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 88
  time to evaluate  : 1.014 
Fit side-chains
REVERT: C  283 LYS cc_start: 0.7245 (tttm) cc_final: 0.6912 (tttp)
REVERT: C  290 TRP cc_start: 0.8332 (m100) cc_final: 0.8089 (m100)
REVERT: G   71 ASP cc_start: 0.8174 (m-30) cc_final: 0.7902 (m-30)
REVERT: G  155 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7618 (mp)
REVERT: F   99 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7609 (tt0)
REVERT: F  109 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7293 (pm20)
REVERT: F  184 SER cc_start: 0.9139 (m) cc_final: 0.8925 (t)
REVERT: E  106 GLU cc_start: 0.8332 (pt0) cc_final: 0.7970 (pt0)
REVERT: E  172 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8010 (p)
REVERT: E  214 GLU cc_start: 0.5214 (OUTLIER) cc_final: 0.4425 (tp30)
REVERT: D   43 LYS cc_start: 0.8571 (mttp) cc_final: 0.8317 (mttt)
REVERT: D  112 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7106 (pm20)
REVERT: D  163 SER cc_start: 0.7536 (OUTLIER) cc_final: 0.7267 (p)
REVERT: D  217 ARG cc_start: 0.6089 (tpt-90) cc_final: 0.5655 (tpp80)
  outliers start: 47
  outliers final: 40
  residues processed: 125
  average time/residue: 0.9987
  time to fit residues: 134.9302
Evaluate side-chains
  134 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 87
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  211 VAL
Chi-restraints excluded: chain C residue  237 SER
Chi-restraints excluded: chain C residue  289 THR
Chi-restraints excluded: chain G residue   14 SER
Chi-restraints excluded: chain G residue   24 ARG
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue  147 VAL
Chi-restraints excluded: chain G residue  155 LEU
Chi-restraints excluded: chain G residue  181 THR
Chi-restraints excluded: chain G residue  192 VAL
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue    6 GLU
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   89 GLU
Chi-restraints excluded: chain F residue   99 GLU
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain F residue  109 GLN
Chi-restraints excluded: chain F residue  131 CYS
Chi-restraints excluded: chain F residue  135 THR
Chi-restraints excluded: chain F residue  154 VAL
Chi-restraints excluded: chain F residue  176 SER
Chi-restraints excluded: chain F residue  199 THR
Chi-restraints excluded: chain F residue  200 CYS
Chi-restraints excluded: chain F residue  211 VAL
Chi-restraints excluded: chain E residue    9 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   76 SER
Chi-restraints excluded: chain E residue  111 VAL
Chi-restraints excluded: chain E residue  172 SER
Chi-restraints excluded: chain E residue  177 SER
Chi-restraints excluded: chain E residue  214 GLU
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue  112 GLN
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  163 SER
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  203 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 102 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0980
   chunk 75 optimal weight:    0.9990
   chunk 108 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 24 optimal weight:    0.3980
   chunk 107 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C 119 ASN
F  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.146520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.110710 restraints weight = 11196.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.33
r_work: 0.3131 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2993
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2993 r_free = 0.2993    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2993 r_free = 0.2993    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2993
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9215  Z= 0.101
  Angle     :  0.556  13.253  12583  Z= 0.271
  Chirality :  0.043   0.170   1418
  Planarity :  0.004   0.042   1593
  Dihedral  :  4.408  40.295   1401
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 22.82 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    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 (0.26), residues: 1131
  helix: -2.65 (0.69), residues: 29
  sheet:  0.64 (0.23), residues: 535
  loop : -0.22 (0.28), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F 101 
 HIS   0.003   0.001   HIS C  99 
 PHE   0.007   0.001   PHE E  99 
 TYR   0.032   0.001   TYR D 152 
 ARG   0.005   0.000   ARG G  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01011 (    4)
  link_NAG-ASN         : angle       4.62811 (   12)
  link_BETA1-4         : bond        0.00223 (    4)
  link_BETA1-4         : angle       1.69323 (   12)
  hydrogen bonds       : bond        0.02460 (  274)
  hydrogen bonds       : angle       5.14278 (  771)
  SS BOND              : bond        0.00341 (   13)
  SS BOND              : angle       0.67902 (   26)
  covalent geometry    : bond        0.00240 ( 9194)
  covalent geometry    : angle       0.53506 (12533)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 86
  time to evaluate  : 0.937 
Fit side-chains
REVERT: C  283 LYS cc_start: 0.7113 (tttm) cc_final: 0.6725 (tttp)
REVERT: C  290 TRP cc_start: 0.8295 (m100) cc_final: 0.8024 (m100)
REVERT: G   71 ASP cc_start: 0.8135 (m-30) cc_final: 0.7840 (m-30)
REVERT: G  155 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7689 (mp)
REVERT: G  156 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8255 (mm-40)
REVERT: F   99 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7615 (tt0)
REVERT: F  109 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7231 (pm20)
REVERT: F  135 THR cc_start: 0.6849 (OUTLIER) cc_final: 0.6503 (m)
REVERT: F  184 SER cc_start: 0.9149 (m) cc_final: 0.8937 (t)
REVERT: E  106 GLU cc_start: 0.8334 (pt0) cc_final: 0.7944 (pt0)
REVERT: E  155 LEU cc_start: 0.7701 (tm) cc_final: 0.7454 (tt)
REVERT: E  172 SER cc_start: 0.8615 (OUTLIER) cc_final: 0.7915 (p)
REVERT: E  214 GLU cc_start: 0.5218 (OUTLIER) cc_final: 0.4443 (tp30)
REVERT: D   43 LYS cc_start: 0.8498 (mttp) cc_final: 0.8240 (mttt)
REVERT: D  112 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7097 (pm20)
REVERT: D  163 SER cc_start: 0.7570 (OUTLIER) cc_final: 0.7295 (p)
REVERT: D  217 ARG cc_start: 0.5979 (tpt-90) cc_final: 0.5569 (tpp80)
  outliers start: 48
  outliers final: 40
  residues processed: 123
  average time/residue: 1.0061
  time to fit residues: 133.5013
Evaluate side-chains
  131 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 83
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  211 VAL
Chi-restraints excluded: chain C residue  237 SER
Chi-restraints excluded: chain C residue  289 THR
Chi-restraints excluded: chain G residue   14 SER
Chi-restraints excluded: chain G residue   24 ARG
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue  147 VAL
Chi-restraints excluded: chain G residue  155 LEU
Chi-restraints excluded: chain G residue  181 THR
Chi-restraints excluded: chain G residue  192 VAL
Chi-restraints excluded: chain F residue    2 VAL
Chi-restraints excluded: chain F residue    6 GLU
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   89 GLU
Chi-restraints excluded: chain F residue   99 GLU
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain F residue  109 GLN
Chi-restraints excluded: chain F residue  131 CYS
Chi-restraints excluded: chain F residue  135 THR
Chi-restraints excluded: chain F residue  154 VAL
Chi-restraints excluded: chain F residue  176 SER
Chi-restraints excluded: chain F residue  199 THR
Chi-restraints excluded: chain F residue  200 CYS
Chi-restraints excluded: chain F residue  211 VAL
Chi-restraints excluded: chain E residue    9 SER
Chi-restraints excluded: chain E residue   12 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   76 SER
Chi-restraints excluded: chain E residue  111 VAL
Chi-restraints excluded: chain E residue  172 SER
Chi-restraints excluded: chain E residue  177 SER
Chi-restraints excluded: chain E residue  214 GLU
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue  112 GLN
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  163 SER
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain D residue  203 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 27 optimal weight:    0.4980
   chunk 79 optimal weight:    0.2980
   chunk 99 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 4 optimal weight:    6.9990
   chunk 110 optimal weight:   10.0000
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
F  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.143931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.108415 restraints weight = 11217.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 2.21
r_work: 0.3052 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2965
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.3823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9215  Z= 0.145
  Angle     :  0.598  12.169  12583  Z= 0.294
  Chirality :  0.045   0.212   1418
  Planarity :  0.005   0.042   1593
  Dihedral  :  4.585  33.210   1401
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 22.22 %
    Favored  : 72.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    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:  0.02 (0.26), residues: 1131
  helix: -2.85 (0.58), residues: 35
  sheet:  0.61 (0.23), residues: 534
  loop : -0.31 (0.28), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP F 101 
 HIS   0.005   0.001   HIS C  99 
 PHE   0.013   0.001   PHE C 141 
 TYR   0.029   0.002   TYR D 152 
 ARG   0.005   0.000   ARG G  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01364 (    4)
  link_NAG-ASN         : angle       4.31722 (   12)
  link_BETA1-4         : bond        0.00279 (    4)
  link_BETA1-4         : angle       1.61738 (   12)
  hydrogen bonds       : bond        0.02653 (  274)
  hydrogen bonds       : angle       5.38465 (  771)
  SS BOND              : bond        0.00474 (   13)
  SS BOND              : angle       0.89193 (   26)
  covalent geometry    : bond        0.00357 ( 9194)
  covalent geometry    : angle       0.58083 (12533)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6936.80 seconds
wall clock time: 120 minutes 19.23 seconds (7219.23 seconds total)