Starting phenix.real_space_refine
on Fri Jul  3 11:19:08 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8d7e_27228/07_2026/8d7e_27228.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d7e_27228/07_2026/8d7e_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_27228/07_2026/8d7e_27228.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d7e_27228/07_2026/8d7e_27228.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d7e_27228/07_2026/8d7e_27228.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d7e_27228/07_2026/8d7e_27228.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8d7e_27228/07_2026/8d7e_27228.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8d7e_27228/07_2026/8d7e_27228.cif"
  }
  resolution = 2.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 chiralities: 2
  Time building chain proxies: 2.12, per 1000 atoms: 0.24
  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: 0.91
  Conformation dependent library (CDL) restraints added in 349.0 milliseconds
  

  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: 0.31
  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: 1.49

  Time building geometry restraints manager: 1.18 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: 5330
       33.93 -    67.86: 70
       67.86 -   101.80: 10
      101.80 -   135.73: 1
      135.73 -   169.66: 1
  Dihedral angle restraints: 5412
    sinusoidal: 2092
      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 5409 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:             3.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     9.710
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
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  : 12.139 169.662   3239
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.002   0.000   ARG D  16 
 TYR   0.018   0.001   TYR C 276 
 PHE   0.004   0.001   PHE F 126 
 TRP   0.005   0.000   TRP C 293 
 HIS   0.002   0.000   HIS D 207 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.12 ( 9194)
  covalent geometry    : angle       0.49202 /  0.26 (12533)
  SS BOND              : bond        0.00257 /  0.16 (   13)
  SS BOND              : angle       0.58746 /  0.43 (   26)
  hydrogen bonds       : bond        0.27192 / 18.57 (  274)
  hydrogen bonds       : angle      10.34248 /  7.14 (  771)
  link_BETA1-4         : bond        0.00351 /  0.18 (    4)
  link_BETA1-4         : angle       0.75390 /  0.52 (   12)
  link_NAG-ASN         : bond        0.00133 /  0.07 (    4)
  link_NAG-ASN         : angle       1.18497 /  0.73 (   12)

*********************** 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  : 0.221 
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: 0.8834 (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: 0.4549
  time to fit residues: 76.7123
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  : 0.258 
-------------------------------------------------------------------------------
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 108 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0040
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    6.9990
   overall best weight:    1.7398

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  96 HIS
C 100 GLN
C 119 ASN
C 209 ASN
G  27 GLN
F   1 GLN
F  57 ASN
F  77 ASN
F 175 GLN
F 201 ASN
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: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.148614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.114353 restraints weight = 11127.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 2.20
r_work: 0.3176 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3031
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (10 function evaluations)
r_final: 0.3031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   9215  Z= 0.214
  Angle     :  0.692   9.379  12583  Z= 0.347
  Chirality :  0.048   0.188   1418
  Planarity :  0.006   0.058   1593
  Dihedral  :  4.499  49.802   1237
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 18.02 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.24), residues: 1131
  helix: -3.48 (0.57), residues: 29
  sheet: -0.11 (0.22), residues: 519
  loop : -1.24 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  72 
 TYR   0.016   0.002   TYR F  95 
 PHE   0.016   0.002   PHE G 119 
 TRP   0.022   0.002   TRP F 101 
 HIS   0.009   0.002   HIS C 104 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00523 /  0.21 ( 9194)
  covalent geometry    : angle       0.68827 /  0.35 (12533)
  SS BOND              : bond        0.00710 /  0.49 (   13)
  SS BOND              : angle       1.22945 /  0.97 (   26)
  hydrogen bonds       : bond        0.03737 /  2.56 (  274)
  hydrogen bonds       : angle       6.50647 /  4.53 (  771)
  link_BETA1-4         : bond        0.00356 /  0.18 (    4)
  link_BETA1-4         : angle       1.30894 /  1.04 (   12)
  link_NAG-ASN         : bond        0.00414 /  0.21 (    4)
  link_NAG-ASN         : angle       1.54089 /  1.02 (   12)

*********************** 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
  162 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 108
  time to evaluate  : 0.333 
Fit side-chains
REVERT: C  169 MET cc_start: 0.6813 (mmt) cc_final: 0.6514 (mmt)
REVERT: C  283 LYS cc_start: 0.6862 (tttm) cc_final: 0.6524 (tttp)
REVERT: C  290 TRP cc_start: 0.8228 (m100) cc_final: 0.7983 (m100)
REVERT: G  148 GLN cc_start: 0.7778 (mt0) cc_final: 0.7449 (mt0)
REVERT: G  155 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7541 (mp)
REVERT: F   21 SER cc_start: 0.8923 (m) cc_final: 0.8702 (t)
REVERT: E  108 LYS cc_start: 0.8347 (tttp) cc_final: 0.7860 (ttmm)
REVERT: E  172 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.7947 (p)
REVERT: D  155 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7925 (mt-10)
REVERT: D  217 ARG cc_start: 0.6117 (tpt-90) cc_final: 0.5448 (tpp-160)
  outliers start: 54
  outliers final: 31
  residues processed: 151
  average time/residue: 0.5129
  time to fit residues: 83.0451
Evaluate side-chains
  133 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 100
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   63 ASP
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 G residue   14 SER
Chi-restraints excluded: chain G residue   49 ILE
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  102 SER
Chi-restraints excluded: chain F residue  120 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    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  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  190 THR
Chi-restraints excluded: chain D residue  200 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 43 optimal weight:    0.0980
   chunk 59 optimal weight:    0.9980
   chunk 93 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 85 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 107 optimal weight:    4.9990
   chunk 108 optimal weight:    1.9990
   chunk 71 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 119 ASN
C 256 HIS
G 148 GLN
F  77 ASN
F 201 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.145955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.111824 restraints weight = 11136.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.21
r_work: 0.3134 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3008
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    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 = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3008
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.2875

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= 0.146
  Angle     :  0.569   8.500  12583  Z= 0.287
  Chirality :  0.044   0.148   1418
  Planarity :  0.005   0.042   1593
  Dihedral  :  4.127  26.029   1233
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 19.52 %
    Favored  : 74.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.25), residues: 1131
  helix: -3.39 (0.55), residues: 29
  sheet:  0.22 (0.23), residues: 521
  loop : -0.94 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 110 
 TYR   0.017   0.001   TYR D 152 
 PHE   0.010   0.001   PHE E  99 
 TRP   0.014   0.001   TRP F 101 
 HIS   0.005   0.001   HIS D 171 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.15 ( 9194)
  covalent geometry    : angle       0.56607 /  0.29 (12533)
  SS BOND              : bond        0.00453 /  0.30 (   13)
  SS BOND              : angle       0.83834 /  0.66 (   26)
  hydrogen bonds       : bond        0.03438 /  2.38 (  274)
  hydrogen bonds       : angle       6.08845 /  4.22 (  771)
  link_BETA1-4         : bond        0.00177 /  0.09 (    4)
  link_BETA1-4         : angle       1.18545 /  0.87 (   12)
  link_NAG-ASN         : bond        0.00190 /  0.09 (    4)
  link_NAG-ASN         : angle       1.41317 /  0.92 (   12)

*********************** 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
  158 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 100
  time to evaluate  : 0.227 
Fit side-chains
REVERT: C  237 SER cc_start: 0.6029 (OUTLIER) cc_final: 0.5730 (t)
REVERT: C  283 LYS cc_start: 0.7061 (tttm) cc_final: 0.6757 (tttp)
REVERT: C  290 TRP cc_start: 0.8289 (m100) cc_final: 0.8054 (m100)
REVERT: G   71 ASP cc_start: 0.8217 (m-30) cc_final: 0.7950 (m-30)
REVERT: G  148 GLN cc_start: 0.7773 (mt0) cc_final: 0.7483 (mt0)
REVERT: G  155 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7596 (mp)
REVERT: F   21 SER cc_start: 0.8920 (m) cc_final: 0.8712 (t)
REVERT: F  196 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7270 (tttt)
REVERT: E   17 ASP cc_start: 0.8132 (m-30) cc_final: 0.7932 (t0)
REVERT: E  108 LYS cc_start: 0.8370 (tttp) cc_final: 0.7806 (ttmm)
REVERT: E  172 SER cc_start: 0.8690 (OUTLIER) cc_final: 0.8006 (p)
REVERT: D   34 MET cc_start: 0.9347 (mmt) cc_final: 0.9051 (mmm)
REVERT: D   43 LYS cc_start: 0.8550 (mttp) cc_final: 0.8261 (mttt)
REVERT: D  105 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8016 (mt-10)
REVERT: D  217 ARG cc_start: 0.6165 (tpt-90) cc_final: 0.5812 (tpp80)
  outliers start: 58
  outliers final: 36
  residues processed: 142
  average time/residue: 0.4680
  time to fit residues: 71.4579
Evaluate side-chains
  138 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 97
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   63 ASP
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  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   34 LEU
Chi-restraints excluded: chain G residue   94 SER
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   89 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   30 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   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  188 VAL
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 19 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 79 optimal weight:    0.5980
   chunk 105 optimal weight:    0.6980
   chunk 84 optimal weight:    5.9990
   chunk 99 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 90 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3667 r_free = 0.3667 target = 0.146544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.112621 restraints weight = 11187.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.23
r_work: 0.3123 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3018
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3018 r_free = 0.3018    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 = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (9 function evaluations)
r_final: 0.3017
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.3059

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= 0.111
  Angle     :  0.546   8.513  12583  Z= 0.271
  Chirality :  0.043   0.146   1418
  Planarity :  0.004   0.041   1593
  Dihedral  :  4.038  27.442   1233
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 20.42 %
    Favored  : 74.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.25), residues: 1131
  helix: -3.15 (0.58), residues: 29
  sheet:  0.49 (0.23), residues: 512
  loop : -0.74 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  18 
 TYR   0.022   0.001   TYR D 152 
 PHE   0.012   0.001   PHE C 141 
 TRP   0.014   0.001   TRP F 101 
 HIS   0.004   0.001   HIS C  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.11 ( 9194)
  covalent geometry    : angle       0.54103 /  0.27 (12533)
  SS BOND              : bond        0.00381 /  0.27 (   13)
  SS BOND              : angle       0.71362 /  0.57 (   26)
  hydrogen bonds       : bond        0.02733 /  1.91 (  274)
  hydrogen bonds       : angle       5.69853 /  3.97 (  771)
  link_BETA1-4         : bond        0.00222 /  0.11 (    4)
  link_BETA1-4         : angle       1.66107 /  0.98 (   12)
  link_NAG-ASN         : bond        0.00669 /  0.33 (    4)
  link_NAG-ASN         : angle       1.60446 /  0.96 (   12)

*********************** 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: 53
    poor density    : 95
  time to evaluate  : 0.340 
Fit side-chains
REVERT: C  237 SER cc_start: 0.6065 (OUTLIER) cc_final: 0.5864 (t)
REVERT: C  283 LYS cc_start: 0.7132 (tttm) cc_final: 0.6790 (tttp)
REVERT: C  290 TRP cc_start: 0.8308 (m100) cc_final: 0.8041 (m100)
REVERT: G   71 ASP cc_start: 0.8221 (m-30) cc_final: 0.7943 (m-30)
REVERT: G  148 GLN cc_start: 0.7750 (mt0) cc_final: 0.7532 (mt0)
REVERT: G  155 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7605 (mp)
REVERT: F   99 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7629 (tt0)
REVERT: F  184 SER cc_start: 0.9188 (m) cc_final: 0.8960 (t)
REVERT: F  196 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7284 (tttt)
REVERT: F  214 ARG cc_start: 0.8107 (tpt-90) cc_final: 0.7795 (tpt90)
REVERT: E  106 GLU cc_start: 0.8301 (pt0) cc_final: 0.8037 (pt0)
REVERT: E  108 LYS cc_start: 0.8393 (tttp) cc_final: 0.7853 (ttmm)
REVERT: E  172 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8021 (p)
REVERT: D   34 MET cc_start: 0.9351 (mmt) cc_final: 0.9100 (mmm)
REVERT: D   43 LYS cc_start: 0.8578 (mttp) cc_final: 0.8307 (mttt)
REVERT: D  163 SER cc_start: 0.7376 (OUTLIER) cc_final: 0.7062 (p)
REVERT: D  217 ARG cc_start: 0.6147 (tpt-90) cc_final: 0.5754 (tpp80)
  outliers start: 53
  outliers final: 35
  residues processed: 136
  average time/residue: 0.4434
  time to fit residues: 64.9842
Evaluate side-chains
  130 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 89
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
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   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  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   94 SER
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   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 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 D residue   50 ILE
Chi-restraints excluded: chain D residue   83 MET
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  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 75 optimal weight:    0.0170
   chunk 78 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 81 optimal weight:    3.9990
   chunk 71 optimal weight:    7.9990
   chunk 61 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 32 optimal weight:    0.2980
   chunk 76 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.7822

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3667 r_free = 0.3667 target = 0.146510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.112602 restraints weight = 11200.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 2.23
r_work: 0.3146 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3020
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    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 = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3020
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.3167

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= 0.111
  Angle     :  0.543   8.642  12583  Z= 0.270
  Chirality :  0.043   0.151   1418
  Planarity :  0.004   0.041   1593
  Dihedral  :  4.019  26.655   1233
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.25), residues: 1131
  helix: -3.03 (0.61), residues: 29
  sheet:  0.58 (0.23), residues: 512
  loop : -0.63 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  18 
 TYR   0.024   0.001   TYR D 152 
 PHE   0.008   0.001   PHE E  99 
 TRP   0.013   0.001   TRP F 101 
 HIS   0.004   0.001   HIS C  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.11 ( 9194)
  covalent geometry    : angle       0.53715 /  0.27 (12533)
  SS BOND              : bond        0.00383 /  0.27 (   13)
  SS BOND              : angle       0.76668 /  0.62 (   26)
  hydrogen bonds       : bond        0.02641 /  1.85 (  274)
  hydrogen bonds       : angle       5.56056 /  3.87 (  771)
  link_BETA1-4         : bond        0.00185 /  0.09 (    4)
  link_BETA1-4         : angle       1.38647 /  0.89 (   12)
  link_NAG-ASN         : bond        0.00774 /  0.39 (    4)
  link_NAG-ASN         : angle       2.25025 /  1.26 (   12)

*********************** 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
  149 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 93
  time to evaluate  : 0.304 
Fit side-chains
REVERT: C  237 SER cc_start: 0.6126 (OUTLIER) cc_final: 0.5925 (t)
REVERT: C  283 LYS cc_start: 0.7032 (tttm) cc_final: 0.6767 (tttp)
REVERT: C  290 TRP cc_start: 0.8298 (m100) cc_final: 0.8048 (m100)
REVERT: G   71 ASP cc_start: 0.8193 (m-30) cc_final: 0.7894 (m-30)
REVERT: G  148 GLN cc_start: 0.7724 (mt0) cc_final: 0.7510 (mt0)
REVERT: G  155 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7609 (mp)
REVERT: F   99 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7622 (tt0)
REVERT: F  184 SER cc_start: 0.9171 (m) cc_final: 0.8938 (t)
REVERT: F  196 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7274 (tttt)
REVERT: E  106 GLU cc_start: 0.8293 (pt0) cc_final: 0.7997 (pt0)
REVERT: E  108 LYS cc_start: 0.8379 (tttp) cc_final: 0.7828 (ttmm)
REVERT: E  172 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.7988 (p)
REVERT: D   34 MET cc_start: 0.9325 (mmt) cc_final: 0.9061 (mmm)
REVERT: D   43 LYS cc_start: 0.8552 (mttp) cc_final: 0.8273 (mttt)
REVERT: D  163 SER cc_start: 0.7354 (OUTLIER) cc_final: 0.7056 (p)
REVERT: D  217 ARG cc_start: 0.6090 (tpt-90) cc_final: 0.5726 (tpp80)
  outliers start: 56
  outliers final: 41
  residues processed: 138
  average time/residue: 0.4551
  time to fit residues: 67.9302
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  : 0.347 
-------------------------------------------------------------------------------
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   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  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  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   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  196 LYS
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   50 ILE
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain D residue   85 SER
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  163 SER
Chi-restraints excluded: chain D residue  188 VAL
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 92 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    1.8786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3626 r_free = 0.3626 target = 0.142554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.106880 restraints weight = 11191.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 2.17
r_work: 0.3065 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    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 = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   9215  Z= 0.214
  Angle     :  0.660  10.066  12583  Z= 0.330
  Chirality :  0.047   0.183   1418
  Planarity :  0.005   0.041   1593
  Dihedral  :  4.544  26.356   1233
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 20.32 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.25), residues: 1131
  helix: -3.11 (0.60), residues: 29
  sheet:  0.58 (0.23), residues: 523
  loop : -0.68 (0.26), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G 109 
 TYR   0.026   0.002   TYR D 152 
 PHE   0.016   0.002   PHE F 100 
 TRP   0.018   0.002   TRP F 101 
 HIS   0.008   0.001   HIS C  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00535 /  0.21 ( 9194)
  covalent geometry    : angle       0.65235 /  0.33 (12533)
  SS BOND              : bond        0.00631 /  0.45 (   13)
  SS BOND              : angle       1.21130 /  0.98 (   26)
  hydrogen bonds       : bond        0.03200 /  2.26 (  274)
  hydrogen bonds       : angle       5.80845 /  4.00 (  771)
  link_BETA1-4         : bond        0.00308 /  0.15 (    4)
  link_BETA1-4         : angle       1.90638 /  1.18 (   12)
  link_NAG-ASN         : bond        0.00843 /  0.42 (    4)
  link_NAG-ASN         : angle       2.31362 /  1.38 (   12)

*********************** 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
  152 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 88
  time to evaluate  : 0.344 
Fit side-chains
REVERT: C  283 LYS cc_start: 0.7019 (tttm) cc_final: 0.6800 (tttp)
REVERT: C  290 TRP cc_start: 0.8351 (m100) cc_final: 0.8068 (m100)
REVERT: G   71 ASP cc_start: 0.8194 (m-30) cc_final: 0.7900 (m-30)
REVERT: G  148 GLN cc_start: 0.7803 (mt0) cc_final: 0.7581 (mt0)
REVERT: G  155 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7615 (mp)
REVERT: F   99 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7806 (tt0)
REVERT: F  196 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7321 (tttt)
REVERT: E   24 ARG cc_start: 0.7407 (ttm-80) cc_final: 0.6856 (mtm110)
REVERT: E  106 GLU cc_start: 0.8352 (pt0) cc_final: 0.8036 (pt0)
REVERT: E  171 ASP cc_start: 0.8256 (m-30) cc_final: 0.8032 (m-30)
REVERT: E  172 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.7985 (p)
REVERT: E  214 GLU cc_start: 0.5402 (OUTLIER) cc_final: 0.4795 (tp30)
REVERT: D   34 MET cc_start: 0.9355 (mmt) cc_final: 0.9031 (mmm)
REVERT: D  163 SER cc_start: 0.7463 (OUTLIER) cc_final: 0.7168 (p)
REVERT: D  217 ARG cc_start: 0.6113 (tpt-90) cc_final: 0.5731 (tpp80)
  outliers start: 64
  outliers final: 40
  residues processed: 140
  average time/residue: 0.4458
  time to fit residues: 67.5761
Evaluate side-chains
  133 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 87
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
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   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  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  154 VAL
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   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   71 SER
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain D residue   85 SER
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  163 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 119 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.145099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.108606 restraints weight = 11240.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 2.32
r_work: 0.3107 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2996
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    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 = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2996
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.3585

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= 0.121
  Angle     :  0.565   8.451  12583  Z= 0.280
  Chirality :  0.044   0.200   1418
  Planarity :  0.004   0.042   1593
  Dihedral  :  4.260  26.429   1233
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 22.12 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.26), residues: 1131
  helix: -2.90 (0.65), residues: 29
  sheet:  0.65 (0.23), residues: 524
  loop : -0.55 (0.27), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  55 
 TYR   0.024   0.001   TYR D 152 
 PHE   0.009   0.001   PHE E  99 
 TRP   0.015   0.001   TRP F 101 
 HIS   0.004   0.001   HIS C  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.12 ( 9194)
  covalent geometry    : angle       0.55461 /  0.28 (12533)
  SS BOND              : bond        0.00374 /  0.26 (   13)
  SS BOND              : angle       0.75664 /  0.59 (   26)
  hydrogen bonds       : bond        0.02616 /  1.84 (  274)
  hydrogen bonds       : angle       5.51099 /  3.81 (  771)
  link_BETA1-4         : bond        0.00205 /  0.10 (    4)
  link_BETA1-4         : angle       1.56876 /  0.94 (   12)
  link_NAG-ASN         : bond        0.00971 /  0.49 (    4)
  link_NAG-ASN         : angle       3.13037 /  1.70 (   12)

*********************** 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
  143 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 93
  time to evaluate  : 0.277 
Fit side-chains
REVERT: C  283 LYS cc_start: 0.6963 (tttm) cc_final: 0.6699 (tttp)
REVERT: C  290 TRP cc_start: 0.8317 (m100) cc_final: 0.8048 (m100)
REVERT: G   71 ASP cc_start: 0.8123 (m-30) cc_final: 0.7808 (m-30)
REVERT: G  148 GLN cc_start: 0.7732 (mt0) cc_final: 0.7501 (mt0)
REVERT: G  155 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7587 (mp)
REVERT: F   99 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7643 (tt0)
REVERT: F  109 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7454 (pm20)
REVERT: F  184 SER cc_start: 0.9169 (m) cc_final: 0.8915 (t)
REVERT: F  196 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7293 (tttt)
REVERT: E  106 GLU cc_start: 0.8292 (pt0) cc_final: 0.7915 (pt0)
REVERT: E  171 ASP cc_start: 0.8269 (m-30) cc_final: 0.8048 (m-30)
REVERT: E  172 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.7914 (p)
REVERT: E  214 GLU cc_start: 0.5370 (OUTLIER) cc_final: 0.4797 (tp30)
REVERT: D   34 MET cc_start: 0.9268 (mmt) cc_final: 0.9034 (mmm)
REVERT: D   43 LYS cc_start: 0.8520 (mttp) cc_final: 0.8265 (mttt)
REVERT: D  112 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7165 (pm20)
REVERT: D  163 SER cc_start: 0.7567 (OUTLIER) cc_final: 0.7286 (p)
REVERT: D  217 ARG cc_start: 0.6001 (tpt-90) cc_final: 0.5583 (tpp80)
  outliers start: 50
  outliers final: 39
  residues processed: 133
  average time/residue: 0.4239
  time to fit residues: 61.0601
Evaluate side-chains
  133 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 86
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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   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  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  101 GLN
Chi-restraints excluded: chain G residue  147 VAL
Chi-restraints excluded: chain G residue  155 LEU
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  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  196 LYS
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   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   71 SER
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  160 SER
Chi-restraints excluded: chain D residue  163 SER
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  194 SER
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 10 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 102 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3616 r_free = 0.3616 target = 0.141740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.105883 restraints weight = 11241.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 2.28
r_work: 0.3050 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2916
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2916
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.3813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   9215  Z= 0.227
  Angle     :  0.683   9.896  12583  Z= 0.339
  Chirality :  0.048   0.211   1418
  Planarity :  0.005   0.042   1593
  Dihedral  :  4.634  26.050   1233
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 21.52 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.26), residues: 1131
  helix: -2.86 (0.66), residues: 29
  sheet:  0.46 (0.23), residues: 540
  loop : -0.55 (0.27), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  55 
 TYR   0.019   0.002   TYR D 152 
 PHE   0.016   0.002   PHE F 100 
 TRP   0.018   0.002   TRP F 101 
 HIS   0.007   0.001   HIS C  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00564 /  0.23 ( 9194)
  covalent geometry    : angle       0.66971 /  0.34 (12533)
  SS BOND              : bond        0.00618 /  0.44 (   13)
  SS BOND              : angle       1.16640 /  0.93 (   26)
  hydrogen bonds       : bond        0.03142 /  2.24 (  274)
  hydrogen bonds       : angle       5.77768 /  3.98 (  771)
  link_BETA1-4         : bond        0.00292 /  0.15 (    4)
  link_BETA1-4         : angle       2.20013 /  1.30 (   12)
  link_NAG-ASN         : bond        0.01241 /  0.62 (    4)
  link_NAG-ASN         : angle       3.60181 /  1.96 (   12)

*********************** 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
  155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 94
  time to evaluate  : 0.214 
Fit side-chains
REVERT: C  283 LYS cc_start: 0.7000 (tttm) cc_final: 0.6770 (tttp)
REVERT: C  290 TRP cc_start: 0.8379 (m100) cc_final: 0.8067 (m100)
REVERT: G   71 ASP cc_start: 0.8190 (m-30) cc_final: 0.7874 (m-30)
REVERT: G  155 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7647 (mp)
REVERT: F   99 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7787 (tt0)
REVERT: F  109 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7173 (pm20)
REVERT: F  184 SER cc_start: 0.9177 (m) cc_final: 0.8939 (t)
REVERT: F  196 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7338 (tttt)
REVERT: E   24 ARG cc_start: 0.7453 (ttm-80) cc_final: 0.6770 (mtm110)
REVERT: E  106 GLU cc_start: 0.8353 (pt0) cc_final: 0.7977 (pt0)
REVERT: E  155 LEU cc_start: 0.7684 (tm) cc_final: 0.7398 (tt)
REVERT: E  172 SER cc_start: 0.8739 (OUTLIER) cc_final: 0.7990 (p)
REVERT: E  214 GLU cc_start: 0.5431 (OUTLIER) cc_final: 0.4843 (tp30)
REVERT: D   34 MET cc_start: 0.9356 (mmt) cc_final: 0.9012 (mmm)
REVERT: D  163 SER cc_start: 0.7616 (OUTLIER) cc_final: 0.7342 (p)
REVERT: D  217 ARG cc_start: 0.6153 (tpt-90) cc_final: 0.5751 (tpp80)
  outliers start: 61
  outliers final: 46
  residues processed: 141
  average time/residue: 0.4005
  time to fit residues: 60.9874
Evaluate side-chains
  142 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 89
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
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   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  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    6 GLU
Chi-restraints excluded: chain F residue   21 SER
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  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  196 LYS
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 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   85 SER
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 105 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 13 optimal weight:    6.9990
   chunk 89 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 104 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  25 HIS
C 119 ASN
C 209 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.142500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.106572 restraints weight = 11175.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 2.31
r_work: 0.3060 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2933
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    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 = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2933
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   9215  Z= 0.186
  Angle     :  0.663  10.719  12583  Z= 0.327
  Chirality :  0.047   0.338   1418
  Planarity :  0.005   0.042   1593
  Dihedral  :  4.595  26.461   1233
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 22.02 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.26), residues: 1131
  helix: -3.02 (0.57), residues: 35
  sheet:  0.44 (0.23), residues: 540
  loop : -0.55 (0.27), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  55 
 TYR   0.019   0.002   TYR D 152 
 PHE   0.011   0.001   PHE E  99 
 TRP   0.018   0.001   TRP F 101 
 HIS   0.006   0.001   HIS C  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00458 /  0.19 ( 9194)
  covalent geometry    : angle       0.64443 /  0.32 (12533)
  SS BOND              : bond        0.00544 /  0.38 (   13)
  SS BOND              : angle       1.08438 /  0.86 (   26)
  hydrogen bonds       : bond        0.02960 /  2.12 (  274)
  hydrogen bonds       : angle       5.69932 /  3.93 (  771)
  link_BETA1-4         : bond        0.00387 /  0.19 (    4)
  link_BETA1-4         : angle       2.16070 /  1.27 (   12)
  link_NAG-ASN         : bond        0.01609 /  0.80 (    4)
  link_NAG-ASN         : angle       4.44567 /  2.35 (   12)

*********************** 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
  145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 86
  time to evaluate  : 0.316 
Fit side-chains
REVERT: C  283 LYS cc_start: 0.6989 (tttm) cc_final: 0.6760 (tttp)
REVERT: C  290 TRP cc_start: 0.8367 (m100) cc_final: 0.8056 (m100)
REVERT: G   71 ASP cc_start: 0.8137 (m-30) cc_final: 0.7821 (m-30)
REVERT: G  155 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7626 (mp)
REVERT: F   99 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7778 (tt0)
REVERT: F  184 SER cc_start: 0.9198 (m) cc_final: 0.8939 (t)
REVERT: F  196 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7366 (tttt)
REVERT: E  106 GLU cc_start: 0.8371 (pt0) cc_final: 0.8048 (pt0)
REVERT: E  155 LEU cc_start: 0.7700 (tm) cc_final: 0.7403 (tt)
REVERT: E  172 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.7990 (p)
REVERT: E  214 GLU cc_start: 0.5422 (OUTLIER) cc_final: 0.4846 (tp30)
REVERT: D   34 MET cc_start: 0.9320 (mmt) cc_final: 0.9021 (mmm)
REVERT: D  163 SER cc_start: 0.7595 (OUTLIER) cc_final: 0.7344 (p)
REVERT: D  217 ARG cc_start: 0.6020 (tpt-90) cc_final: 0.5592 (tpp80)
  outliers start: 59
  outliers final: 51
  residues processed: 134
  average time/residue: 0.4568
  time to fit residues: 66.1773
Evaluate side-chains
  143 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 86
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
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   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  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   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    6 GLU
Chi-restraints excluded: chain F residue   21 SER
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   71 SER
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   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  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  176 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 106 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 88 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    2.1388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 119 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.141075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.105393 restraints weight = 11227.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 2.16
r_work: 0.3039 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2913 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2914
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.4019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071   9215  Z= 0.247
  Angle     :  0.749  16.157  12583  Z= 0.368
  Chirality :  0.051   0.624   1418
  Planarity :  0.005   0.043   1593
  Dihedral  :  4.865  26.487   1233
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 22.32 %
    Favored  : 71.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.25), residues: 1131
  helix: -3.02 (0.56), residues: 35
  sheet:  0.37 (0.23), residues: 534
  loop : -0.60 (0.27), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  55 
 TYR   0.018   0.002   TYR F  95 
 PHE   0.015   0.002   PHE F 100 
 TRP   0.018   0.002   TRP F 101 
 HIS   0.008   0.001   HIS C  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00608 /  0.25 ( 9194)
  covalent geometry    : angle       0.72263 /  0.36 (12533)
  SS BOND              : bond        0.00667 /  0.46 (   13)
  SS BOND              : angle       1.31693 /  1.04 (   26)
  hydrogen bonds       : bond        0.03321 /  2.40 (  274)
  hydrogen bonds       : angle       5.89686 /  4.07 (  771)
  link_BETA1-4         : bond        0.00794 /  0.40 (    4)
  link_BETA1-4         : angle       2.64146 /  1.58 (   12)
  link_NAG-ASN         : bond        0.02656 /  1.33 (    4)
  link_NAG-ASN         : angle       5.64680 /  2.95 (   12)

********************** 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
  146 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 89
  time to evaluate  : 0.329 
Fit side-chains
REVERT: C  290 TRP cc_start: 0.8358 (m100) cc_final: 0.8042 (m100)
REVERT: G   71 ASP cc_start: 0.8193 (m-30) cc_final: 0.7868 (m-30)
REVERT: G  155 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7642 (mp)
REVERT: F   99 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7835 (tt0)
REVERT: F  196 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7486 (tttt)
REVERT: E   24 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.6832 (mtm110)
REVERT: E  106 GLU cc_start: 0.8422 (pt0) cc_final: 0.8072 (pt0)
REVERT: E  155 LEU cc_start: 0.7673 (tm) cc_final: 0.7359 (tt)
REVERT: E  172 SER cc_start: 0.8795 (OUTLIER) cc_final: 0.8055 (p)
REVERT: E  214 GLU cc_start: 0.5392 (OUTLIER) cc_final: 0.4825 (tp30)
REVERT: D   34 MET cc_start: 0.9378 (mmt) cc_final: 0.9024 (mmm)
REVERT: D  163 SER cc_start: 0.7593 (OUTLIER) cc_final: 0.7351 (p)
REVERT: D  217 ARG cc_start: 0.6183 (tpt-90) cc_final: 0.5770 (tpp80)
  outliers start: 57
  outliers final: 50
  residues processed: 136
  average time/residue: 0.4387
  time to fit residues: 64.5446
Evaluate side-chains
  141 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 85
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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   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   24 ARG
Chi-restraints excluded: chain G residue   34 LEU
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    6 GLU
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   71 SER
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   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  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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 46 optimal weight:    0.4980
   chunk 110 optimal weight:    5.9990
   chunk 7 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 109 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 88 optimal weight:    9.9990
   chunk 49 optimal weight:    0.0670
   overall best weight:    0.5118

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 119 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.145165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.109222 restraints weight = 11064.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.45
r_work: 0.3123 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
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 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2993
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.3904

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= 0.103
  Angle     :  0.576  11.821  12583  Z= 0.283
  Chirality :  0.044   0.327   1418
  Planarity :  0.004   0.043   1593
  Dihedral  :  4.388  26.629   1233
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 23.82 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.26), residues: 1131
  helix: -2.83 (0.59), residues: 35
  sheet:  0.55 (0.23), residues: 538
  loop : -0.47 (0.28), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  55 
 TYR   0.022   0.001   TYR D 152 
 PHE   0.010   0.001   PHE C 125 
 TRP   0.015   0.001   TRP F 101 
 HIS   0.003   0.001   HIS C  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.10 ( 9194)
  covalent geometry    : angle       0.56016 /  0.28 (12533)
  SS BOND              : bond        0.00351 /  0.22 (   13)
  SS BOND              : angle       0.76230 /  0.58 (   26)
  hydrogen bonds       : bond        0.02549 /  1.82 (  274)
  hydrogen bonds       : angle       5.43625 /  3.76 (  771)
  link_BETA1-4         : bond        0.00497 /  0.25 (    4)
  link_BETA1-4         : angle       1.49294 /  0.95 (   12)
  link_NAG-ASN         : bond        0.02046 /  1.02 (    4)
  link_NAG-ASN         : angle       4.05147 /  2.24 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3251.85 seconds
wall clock time: 56 minutes 1.92 seconds (3361.92 seconds total)