Starting phenix.real_space_refine
on Sun Jun 15 19:10:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rt9_19483/06_2025/8rt9_19483.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rt9_19483/06_2025/8rt9_19483.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rt9_19483/06_2025/8rt9_19483.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rt9_19483/06_2025/8rt9_19483.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rt9_19483/06_2025/8rt9_19483.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rt9_19483/06_2025/8rt9_19483.cif"
  }
  resolution = 2.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C   11349      2.51       5
     N    3083      2.21       5
     O    3374      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 63 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17866
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1599
          Classifications: {'peptide': 207}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 3, 'TRANS': 203}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 1599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1599
          Classifications: {'peptide': 207}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 3, 'TRANS': 203}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "C"
      Number of atoms: 1599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1599
          Classifications: {'peptide': 207}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 3, 'TRANS': 203}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "D"
      Number of atoms: 1599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1599
          Classifications: {'peptide': 207}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 3, 'TRANS': 203}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "E"
      Number of atoms: 1599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1599
          Classifications: {'peptide': 207}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 3, 'TRANS': 203}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "F"
      Number of atoms: 1963
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 272, 1963
          Classifications: {'peptide': 272}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 8, 'TRANS': 263}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 35
    Chain: "G"
      Number of atoms: 1977
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 272, 1977
          Classifications: {'peptide': 272}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 8, 'TRANS': 263}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "H"
      Number of atoms: 1977
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 272, 1977
          Classifications: {'peptide': 272}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 8, 'TRANS': 263}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "I"
      Number of atoms: 1977
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 272, 1977
          Classifications: {'peptide': 272}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 8, 'TRANS': 263}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "J"
      Number of atoms: 1977
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 272, 1977
          Classifications: {'peptide': 272}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 8, 'TRANS': 263}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 24
  Time building chain proxies: 11.26, per 1000 atoms: 0.63
  Number of scatterers: 17866
  At special positions: 0
  Unit cell: (109.901, 107.767, 234.74, 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      60     16.00
     O    3374      8.00
     N    3083      7.00
     C   11349      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.51
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4310

  Finding SS restraints...
    Secondary structure from input PDB file:
      74 helices and 0 sheets defined
      83.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 65
      removed outlier: 3.635A  pdb=" N   ALA A  33 " --> pdb=" O   ASP A  29 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   LEU A  34 " --> pdb=" O   GLY A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 83
      removed outlier: 3.505A  pdb=" N   GLU A  81 " --> pdb=" O   GLN A  78 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU A  83 " --> pdb=" O   ARG A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 93
      removed outlier: 3.748A  pdb=" N   SER A  93 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 113
      removed outlier: 3.783A  pdb=" N   GLY A 104 " --> pdb=" O   SER A 100 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   SER A 105 " --> pdb=" O   GLY A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 163
    Processing helix  chain 'A' and resid 167 through 219
      removed outlier: 3.529A  pdb=" N   ILE A 171 " --> pdb=" O   ASP A 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 65
      removed outlier: 3.636A  pdb=" N   ALA B  33 " --> pdb=" O   ASP B  29 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   LEU B  34 " --> pdb=" O   GLY B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 83
      removed outlier: 3.504A  pdb=" N   GLU B  81 " --> pdb=" O   GLN B  78 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU B  83 " --> pdb=" O   ARG B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 93
      removed outlier: 3.747A  pdb=" N   SER B  93 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 113
      removed outlier: 3.783A  pdb=" N   GLY B 104 " --> pdb=" O   SER B 100 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   SER B 105 " --> pdb=" O   GLY B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 165
      removed outlier: 3.511A  pdb=" N   SER B 163 " --> pdb=" O   MET B 159 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ARG B 164 " --> pdb=" O   ASP B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 219
      removed outlier: 3.528A  pdb=" N   ILE B 171 " --> pdb=" O   ASP B 167 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 65
      removed outlier: 3.635A  pdb=" N   ALA C  33 " --> pdb=" O   ASP C  29 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LEU C  34 " --> pdb=" O   GLY C  30 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 83
      removed outlier: 3.504A  pdb=" N   GLU C  81 " --> pdb=" O   GLN C  78 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU C  83 " --> pdb=" O   ARG C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 93
      removed outlier: 3.747A  pdb=" N   SER C  93 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 113
      removed outlier: 4.015A  pdb=" N   GLY C 104 " --> pdb=" O   SER C 100 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   SER C 105 " --> pdb=" O   GLY C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 163
      removed outlier: 3.601A  pdb=" N   SER C 163 " --> pdb=" O   MET C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 219
      removed outlier: 3.528A  pdb=" N   ILE C 171 " --> pdb=" O   ASP C 167 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 65
      removed outlier: 3.634A  pdb=" N   ALA D  33 " --> pdb=" O   ASP D  29 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   LEU D  34 " --> pdb=" O   GLY D  30 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 83
      removed outlier: 3.504A  pdb=" N   GLU D  81 " --> pdb=" O   GLN D  78 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU D  83 " --> pdb=" O   ARG D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 89 through 93
      removed outlier: 3.747A  pdb=" N   SER D  93 " --> pdb=" O   VAL D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 99 through 113
      removed outlier: 3.533A  pdb=" N   GLY D 104 " --> pdb=" O   SER D 100 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   SER D 105 " --> pdb=" O   GLY D 101 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 164
      removed outlier: 3.689A  pdb=" N   SER D 163 " --> pdb=" O   MET D 159 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ARG D 164 " --> pdb=" O   ASP D 160 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 219
      removed outlier: 3.528A  pdb=" N   ILE D 171 " --> pdb=" O   ASP D 167 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 29 through 65
      removed outlier: 3.635A  pdb=" N   ALA E  33 " --> pdb=" O   ASP E  29 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   LEU E  34 " --> pdb=" O   GLY E  30 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 78 through 83
      removed outlier: 3.505A  pdb=" N   GLU E  81 " --> pdb=" O   GLN E  78 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU E  83 " --> pdb=" O   ARG E  80 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 89 through 93
      removed outlier: 3.747A  pdb=" N   SER E  93 " --> pdb=" O   VAL E  90 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 99 through 113
      removed outlier: 3.500A  pdb=" N   GLY E 104 " --> pdb=" O   SER E 100 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   SER E 105 " --> pdb=" O   GLY E 101 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 118 through 163
      removed outlier: 3.716A  pdb=" N   SER E 163 " --> pdb=" O   MET E 159 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 167 through 219
      removed outlier: 3.529A  pdb=" N   ILE E 171 " --> pdb=" O   ASP E 167 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 5 through 22
    Processing helix  chain 'F' and resid 22 through 53
      Proline residue:  F  34  - end of helix
    Processing helix  chain 'F' and resid 61 through 80
    Processing helix  chain 'F' and resid 82 through 101
      removed outlier: 3.734A  pdb=" N   GLU F  86 " --> pdb=" O   LEU F  82 " (cutoff:3.500A)
      Proline residue:  F  95  - end of helix
      removed outlier: 3.948A  pdb=" N   SER F 100 " --> pdb=" O   ASP F  96 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 111 through 137
    Processing helix  chain 'F' and resid 141 through 185
      Proline residue:  F 181  - end of helix
    Processing helix  chain 'F' and resid 186 through 188
      No H-bonds generated for 'chain 'F' and resid 186 through 188'
    Processing helix  chain 'F' and resid 189 through 191
      No H-bonds generated for 'chain 'F' and resid 189 through 191'
    Processing helix  chain 'F' and resid 192 through 231
      removed outlier: 3.805A  pdb=" N   PHE F 196 " --> pdb=" O  ATHR F 192 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 238 through 271
      removed outlier: 3.582A  pdb=" N   LEU F 260 " --> pdb=" O   LEU F 256 " (cutoff:3.500A)
      Proline residue:  F 261  - end of helix
    Processing helix  chain 'G' and resid 5 through 20
    Processing helix  chain 'G' and resid 20 through 53
      removed outlier: 3.512A  pdb=" N   SER G  25 " --> pdb=" O   VAL G  21 " (cutoff:3.500A)
      Proline residue:  G  34  - end of helix
    Processing helix  chain 'G' and resid 61 through 79
    Processing helix  chain 'G' and resid 82 through 101
      removed outlier: 3.794A  pdb=" N   GLU G  86 " --> pdb=" O   LEU G  82 " (cutoff:3.500A)
      Proline residue:  G  95  - end of helix
      removed outlier: 4.084A  pdb=" N   SER G 100 " --> pdb=" O   ASP G  96 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA G 101 " --> pdb=" O   GLU G  97 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 111 through 137
    Processing helix  chain 'G' and resid 141 through 185
      Proline residue:  G 181  - end of helix
    Processing helix  chain 'G' and resid 186 through 188
      No H-bonds generated for 'chain 'G' and resid 186 through 188'
    Processing helix  chain 'G' and resid 192 through 231
      removed outlier: 3.793A  pdb=" N   PHE G 196 " --> pdb=" O  ATHR G 192 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 238 through 271
      removed outlier: 3.589A  pdb=" N   LEU G 260 " --> pdb=" O   LEU G 256 " (cutoff:3.500A)
      Proline residue:  G 261  - end of helix
    Processing helix  chain 'H' and resid 5 through 53
      removed outlier: 4.556A  pdb=" N   ASP H  23 " --> pdb=" O   THR H  19 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ILE H  24 " --> pdb=" O   TYR H  20 " (cutoff:3.500A)
      Proline residue:  H  34  - end of helix
    Processing helix  chain 'H' and resid 61 through 80
    Processing helix  chain 'H' and resid 82 through 101
      removed outlier: 3.994A  pdb=" N   GLU H  86 " --> pdb=" O   LEU H  82 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   VAL H  94 " --> pdb=" O   ALA H  90 " (cutoff:3.500A)
      Proline residue:  H  95  - end of helix
      removed outlier: 4.029A  pdb=" N   SER H 100 " --> pdb=" O   ASP H  96 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 111 through 137
    Processing helix  chain 'H' and resid 141 through 185
      Proline residue:  H 181  - end of helix
    Processing helix  chain 'H' and resid 186 through 188
      No H-bonds generated for 'chain 'H' and resid 186 through 188'
    Processing helix  chain 'H' and resid 189 through 191
      No H-bonds generated for 'chain 'H' and resid 189 through 191'
    Processing helix  chain 'H' and resid 192 through 231
      removed outlier: 3.811A  pdb=" N   PHE H 196 " --> pdb=" O  ATHR H 192 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 238 through 271
      Proline residue:  H 261  - end of helix
    Processing helix  chain 'I' and resid 5 through 53
      removed outlier: 3.806A  pdb=" N   THR I  22 " --> pdb=" O   ALA I  18 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   ASP I  23 " --> pdb=" O   THR I  19 " (cutoff:3.500A)
      Proline residue:  I  34  - end of helix
    Processing helix  chain 'I' and resid 61 through 79
    Processing helix  chain 'I' and resid 82 through 101
      removed outlier: 4.014A  pdb=" N   GLU I  86 " --> pdb=" O   LEU I  82 " (cutoff:3.500A)
      Proline residue:  I  95  - end of helix
      removed outlier: 3.936A  pdb=" N   SER I 100 " --> pdb=" O   ASP I  96 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 111 through 137
    Processing helix  chain 'I' and resid 141 through 186
      Proline residue:  I 181  - end of helix
    Processing helix  chain 'I' and resid 187 through 191
      removed outlier: 5.275A  pdb=" N   GLN I 190 " --> pdb=" O   LEU I 187 " (cutoff:3.500A)
      Proline residue:  I 191  - end of helix
      No H-bonds generated for 'chain 'I' and resid 187 through 191'
    Processing helix  chain 'I' and resid 192 through 230
      removed outlier: 3.950A  pdb=" N   PHE I 196 " --> pdb=" O  ATHR I 192 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 238 through 271
      Proline residue:  I 261  - end of helix
    Processing helix  chain 'J' and resid 5 through 21
    Processing helix  chain 'J' and resid 21 through 53
      Proline residue:  J  34  - end of helix
    Processing helix  chain 'J' and resid 61 through 80
    Processing helix  chain 'J' and resid 82 through 101
      removed outlier: 4.036A  pdb=" N   GLU J  86 " --> pdb=" O   LEU J  82 " (cutoff:3.500A)
      Proline residue:  J  95  - end of helix
      removed outlier: 3.991A  pdb=" N   SER J 100 " --> pdb=" O   ASP J  96 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 111 through 137
    Processing helix  chain 'J' and resid 141 through 186
      Proline residue:  J 181  - end of helix
    Processing helix  chain 'J' and resid 192 through 230
      removed outlier: 3.975A  pdb=" N   PHE J 196 " --> pdb=" O  ATHR J 192 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 238 through 271
      Proline residue:  J 261  - end of helix

    1597 hydrogen bonds defined for protein.
    4761 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: 5.11

  Time building geometry restraints manager: 5.28 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: 4797
        1.33 -     1.45: 3041
        1.45 -     1.57: 10153
        1.57 -     1.69: 0
        1.69 -     1.81: 115
  Bond restraints: 18106
  Sorted by residual:
  bond pdb=" N   PRO H  95 "
       pdb=" CD  PRO H  95 "
    ideal  model  delta    sigma   weight residual
    1.473  1.395  0.078 1.40e-02 5.10e+03 3.07e+01
  bond pdb=" N   THR H  33 "
       pdb=" CA  THR H  33 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.038 1.04e-02 9.25e+03 1.37e+01
  bond pdb=" N   ILE B 102 "
       pdb=" CA  ILE B 102 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 1.21e-02 6.83e+03 9.09e+00
  bond pdb=" N   THR A 165 "
       pdb=" CA  THR A 165 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.23e-02 6.61e+03 9.09e+00
  bond pdb=" N   SER H 100 "
       pdb=" CA  SER H 100 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 9.00e-03 1.23e+04 9.05e+00
  ... (remaining 18101 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 22951
        1.54 -     3.09: 1347
        3.09 -     4.63: 160
        4.63 -     6.17: 46
        6.17 -     7.71: 8
  Bond angle restraints: 24512
  Sorted by residual:
  angle pdb=" CA  GLY B  71 "
        pdb=" C   GLY B  71 "
        pdb=" O   GLY B  71 "
      ideal   model   delta    sigma   weight residual
     122.29  117.07    5.22 8.10e-01 1.52e+00 4.15e+01
  angle pdb=" N   GLY J  80 "
        pdb=" CA  GLY J  80 "
        pdb=" C   GLY J  80 "
      ideal   model   delta    sigma   weight residual
     114.40  108.24    6.16 1.11e+00 8.12e-01 3.08e+01
  angle pdb=" N   GLY B  71 "
        pdb=" CA  GLY B  71 "
        pdb=" C   GLY B  71 "
      ideal   model   delta    sigma   weight residual
     112.68  106.32    6.36 1.26e+00 6.30e-01 2.55e+01
  angle pdb=" C   THR I  19 "
        pdb=" N   TYR I  20 "
        pdb=" CA  TYR I  20 "
      ideal   model   delta    sigma   weight residual
     121.71  114.87    6.84 1.39e+00 5.18e-01 2.42e+01
  angle pdb=" N   LEU H 102 "
        pdb=" CA  LEU H 102 "
        pdb=" C   LEU H 102 "
      ideal   model   delta    sigma   weight residual
     114.12  107.30    6.82 1.39e+00 5.18e-01 2.41e+01
  ... (remaining 24507 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 9984
       17.70 -    35.41: 660
       35.41 -    53.11: 107
       53.11 -    70.81: 31
       70.81 -    88.52: 13
  Dihedral angle restraints: 10795
    sinusoidal: 4040
      harmonic: 6755
  Sorted by residual:
  dihedral pdb=" CA  GLY D  71 "
           pdb=" C   GLY D  71 "
           pdb=" N   ASP D  72 "
           pdb=" CA  ASP D  72 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -143.85  -36.15     0      5.00e+00 4.00e-02 5.23e+01
  dihedral pdb=" CA  GLY E  71 "
           pdb=" C   GLY E  71 "
           pdb=" N   ASP E  72 "
           pdb=" CA  ASP E  72 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -143.89  -36.11     0      5.00e+00 4.00e-02 5.21e+01
  dihedral pdb=" CA  GLY A  71 "
           pdb=" C   GLY A  71 "
           pdb=" N   ASP A  72 "
           pdb=" CA  ASP A  72 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -143.91  -36.09     0      5.00e+00 4.00e-02 5.21e+01
  ... (remaining 10792 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 2703
       0.104 -    0.209: 162
       0.209 -    0.313: 7
       0.313 -    0.417: 1
       0.417 -    0.521: 1
  Chirality restraints: 2874
  Sorted by residual:
  chirality pdb=" CA  THR H  33 "
            pdb=" N   THR H  33 "
            pdb=" C   THR H  33 "
            pdb=" CB  THR H  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.00    0.52 2.00e-01 2.50e+01 6.80e+00
  chirality pdb=" CA  LEU H  82 "
            pdb=" N   LEU H  82 "
            pdb=" C   LEU H  82 "
            pdb=" CB  LEU H  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.62e+00
  chirality pdb=" CA  LEU J  82 "
            pdb=" N   LEU J  82 "
            pdb=" C   LEU J  82 "
            pdb=" CB  LEU J  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.17e+00
  ... (remaining 2871 not shown)

  Planarity restraints: 3202
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  68 "    0.012 2.00e-02 2.50e+03   2.34e-02 5.49e+00
        pdb=" C   ARG B  68 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   ARG B  68 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLY B  69 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA H  18 "    0.011 2.00e-02 2.50e+03   2.24e-02 5.00e+00
        pdb=" C   ALA H  18 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ALA H  18 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR H  19 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA G  18 "    0.011 2.00e-02 2.50e+03   2.18e-02 4.77e+00
        pdb=" C   ALA G  18 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   ALA G  18 "    0.014 2.00e-02 2.50e+03
        pdb=" N   THR G  19 "    0.013 2.00e-02 2.50e+03
  ... (remaining 3199 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 6669
        2.88 -     3.38: 19560
        3.38 -     3.89: 31039
        3.89 -     4.39: 35013
        4.39 -     4.90: 57982
  Nonbonded interactions: 150263
  Sorted by model distance:
  nonbonded pdb=" O   ILE J 243 "
            pdb=" OG  SER J 246 "
     model   vdw
     2.370 3.040
  nonbonded pdb=" O   GLU D  81 "
            pdb=" OH  TYR D  99 "
     model   vdw
     2.390 3.040
  nonbonded pdb=" O   PRO F  34 "
            pdb=" OG  SER F  37 "
     model   vdw
     2.394 3.040
  nonbonded pdb=" OG  SER A 220 "
            pdb=" OE1 GLU J 132 "
     model   vdw
     2.417 3.040
  nonbonded pdb=" O   ASN G  89 "
            pdb=" OG1 THR G  93 "
     model   vdw
     2.420 3.040
  ... (remaining 150258 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 'C'
  selection = chain 'D'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'F'
  selection = (chain 'G' and (resid 2 through 116 or (resid 117 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 118 or (resid 119 through 122 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 123 through 154 or (resid 15 \ 
5 and (name N or name CA or name C or name O or name CB )) or resid 156 through  \ 
273))
  selection = (chain 'H' and (resid 2 through 116 or (resid 117 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 118 or (resid 119 through 122 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 123 through 154 or (resid 15 \ 
5 and (name N or name CA or name C or name O or name CB )) or resid 156 through  \ 
273))
  selection = (chain 'I' and (resid 2 through 116 or (resid 117 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 118 or (resid 119 through 122 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 123 through 154 or (resid 15 \ 
5 and (name N or name CA or name C or name O or name CB )) or resid 156 through  \ 
273))
  selection = (chain 'J' and (resid 2 through 116 or (resid 117 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 118 or (resid 119 through 122 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 123 through 154 or (resid 15 \ 
5 and (name N or name CA or name C or name O or name CB )) or resid 156 through  \ 
273))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.790
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     39.820
  Find NCS groups from input model:        0.640
  Set up NCS constraints:                  0.080
  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:10.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   58.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
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      :  0.007   0.078  18106  Z= 0.416
  Angle     :  0.790   7.714  24512  Z= 0.543
  Chirality :  0.053   0.521   2874
  Planarity :  0.004   0.046   3202
  Dihedral  : 12.660  88.516   6485
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.05 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.55 (0.17), residues: 2375
  helix:  2.52 (0.11), residues: 1905
  sheet:  None (None), residues: 0
  loop : -2.06 (0.24), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP J 199 
 HIS   0.001   0.000   HIS G 193 
 PHE   0.026   0.002   PHE F 213 
 TYR   0.018   0.002   TYR H  83 
 ARG   0.013   0.001   ARG C 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11053 ( 1597)
  hydrogen bonds       : angle       4.83168 ( 4761)
  covalent geometry    : bond        0.00728 (18106)
  covalent geometry    : angle       0.79006 (24512)

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

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

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  611 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 611
  time to evaluate  : 1.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  145 TYR cc_start: 0.9055 (t80) cc_final: 0.8759 (t80)
REVERT: H  129 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7582 (mt-10)
REVERT: H  221 MET cc_start: 0.8281 (tpt) cc_final: 0.8019 (tpt)
REVERT: J  230 ASP cc_start: 0.7794 (t0) cc_final: 0.7539 (t0)
  outliers start: 0
  outliers final: 2
  residues processed: 611
  average time/residue: 1.3416
  time to fit residues: 908.0065
Evaluate side-chains
  374 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 372
  time to evaluate  : 1.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain C residue   81 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 198 optimal weight:    0.8980
   chunk 178 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 60 optimal weight:   20.0000
   chunk 120 optimal weight:    0.5980
   chunk 95 optimal weight:    1.9990
   chunk 184 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 112 optimal weight:    1.9990
   chunk 137 optimal weight:    0.0970
   chunk 213 optimal weight:   10.0000
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  11 ASN
F 118 GLN
G  11 ASN
G 201 GLN
H  11 ASN
H 118 GLN
H 198 GLN
H 202 GLN
H 237 GLN
I  11 ASN
I  15 GLN
I 118 GLN
I 198 GLN
J  11 ASN
J 118 GLN
J 201 GLN
J 202 GLN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.080285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.062846 restraints weight = 40220.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 2.57
r_work: 0.2739 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2747
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2747
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  18106  Z= 0.173
  Angle     :  0.577  10.627  24512  Z= 0.309
  Chirality :  0.039   0.208   2874
  Planarity :  0.004   0.055   3202
  Dihedral  :  5.155 139.611   2591
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 14.39 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.06 (0.17), residues: 2375
  helix:  2.84 (0.11), residues: 1890
  sheet:  None (None), residues: 0
  loop : -1.56 (0.26), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP H 189 
 HIS   0.001   0.000   HIS G 193 
 PHE   0.030   0.001   PHE H 213 
 TYR   0.017   0.002   TYR F  83 
 ARG   0.007   0.001   ARG E  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05912 ( 1597)
  hydrogen bonds       : angle       4.39276 ( 4761)
  covalent geometry    : bond        0.00366 (18106)
  covalent geometry    : angle       0.57705 (24512)

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

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

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  520 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 445
  time to evaluate  : 1.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.9221 (pt0) cc_final: 0.8993 (pm20)
REVERT: A  125 SER cc_start: 0.9254 (m) cc_final: 0.8951 (m)
REVERT: A  212 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8895 (tp30)
REVERT: B   34 LEU cc_start: 0.9666 (mp) cc_final: 0.9464 (mm)
REVERT: B   38 GLN cc_start: 0.9413 (mm-40) cc_final: 0.9166 (mm-40)
REVERT: B  212 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8905 (tm-30)
REVERT: C   44 LYS cc_start: 0.9662 (tppp) cc_final: 0.9324 (tppp)
REVERT: D   45 GLU cc_start: 0.9163 (pt0) cc_final: 0.8666 (pm20)
REVERT: D  112 ASP cc_start: 0.9142 (m-30) cc_final: 0.8904 (m-30)
REVERT: E   44 LYS cc_start: 0.9686 (tppp) cc_final: 0.9449 (tppp)
REVERT: F    4 GLU cc_start: 0.8809 (tp30) cc_final: 0.8604 (tp30)
REVERT: F   23 ASP cc_start: 0.8536 (m-30) cc_final: 0.8330 (m-30)
REVERT: F   63 PHE cc_start: 0.8962 (t80) cc_final: 0.8691 (t80)
REVERT: F  132 GLU cc_start: 0.9035 (tt0) cc_final: 0.8606 (tt0)
REVERT: F  201 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8984 (tt0)
REVERT: F  222 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8757 (tm-30)
REVERT: F  232 ARG cc_start: 0.9147 (mtm110) cc_final: 0.8919 (mtm-85)
REVERT: G   69 ARG cc_start: 0.8224 (ttt90) cc_final: 0.8004 (ttt180)
REVERT: G  133 GLU cc_start: 0.9229 (mm-30) cc_final: 0.9013 (mm-30)
REVERT: H    4 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8998 (tp30)
REVERT: H   23 ASP cc_start: 0.8781 (m-30) cc_final: 0.8546 (m-30)
REVERT: H  230 ASP cc_start: 0.8930 (t0) cc_final: 0.8520 (t0)
REVERT: I    4 GLU cc_start: 0.8687 (tp30) cc_final: 0.8438 (tp30)
REVERT: I  129 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8937 (mt-10)
REVERT: I  189 TRP cc_start: 0.7914 (m100) cc_final: 0.7697 (m-10)
REVERT: I  228 MET cc_start: 0.9479 (mmm) cc_final: 0.9233 (mmt)
REVERT: I  230 ASP cc_start: 0.9115 (t0) cc_final: 0.8772 (t0)
REVERT: J    4 GLU cc_start: 0.8687 (tp30) cc_final: 0.8381 (tp30)
REVERT: J  222 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8767 (tm-30)
REVERT: J  230 ASP cc_start: 0.9207 (t0) cc_final: 0.8656 (t0)
  outliers start: 75
  outliers final: 18
  residues processed: 486
  average time/residue: 1.3002
  time to fit residues: 706.5387
Evaluate side-chains
  396 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 375
  time to evaluate  : 1.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain B residue  212 GLU
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain E residue  118 SER
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   67 CYS
Chi-restraints excluded: chain F residue  201 GLN
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  246 SER
Chi-restraints excluded: chain G residue   67 CYS
Chi-restraints excluded: chain H residue   67 CYS
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  246 SER
Chi-restraints excluded: chain I residue   33 THR
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain I residue   67 CYS
Chi-restraints excluded: chain I residue   68 LEU
Chi-restraints excluded: chain I residue  138 SER
Chi-restraints excluded: chain I residue  246 SER
Chi-restraints excluded: chain J residue   64 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 151 optimal weight:    1.9990
   chunk 143 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 216 optimal weight:    3.9990
   chunk 200 optimal weight:    0.5980
   chunk 60 optimal weight:    8.9990
   chunk 167 optimal weight:    0.9980
   chunk 109 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
C 116 ASN
** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  11 ASN
F  15 GLN
F 118 GLN
F 198 GLN
G  11 ASN
G 118 GLN
H  11 ASN
H 118 GLN
H 202 GLN
H 237 GLN
I  11 ASN
I  15 GLN
I 118 GLN
I 198 GLN
I 259 GLN
J 118 GLN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.077604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.059326 restraints weight = 40211.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.2841 rms_B_bonded: 2.64
r_work: 0.2694 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2694
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2694
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.2814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  18106  Z= 0.167
  Angle     :  0.557   9.823  24512  Z= 0.291
  Chirality :  0.038   0.189   2874
  Planarity :  0.004   0.069   3202
  Dihedral  :  4.010  27.404   2585
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 17.45 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.13 (0.17), residues: 2375
  helix:  2.88 (0.11), residues: 1895
  sheet:  None (None), residues: 0
  loop : -1.51 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP F 189 
 HIS   0.001   0.000   HIS H 193 
 PHE   0.023   0.001   PHE H 213 
 TYR   0.018   0.002   TYR F  83 
 ARG   0.008   0.000   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05555 ( 1597)
  hydrogen bonds       : angle       4.26385 ( 4761)
  covalent geometry    : bond        0.00356 (18106)
  covalent geometry    : angle       0.55707 (24512)

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

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

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  495 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 420
  time to evaluate  : 2.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 SER cc_start: 0.9006 (m) cc_final: 0.8751 (m)
REVERT: B   34 LEU cc_start: 0.9685 (mp) cc_final: 0.9331 (pt)
REVERT: B   38 GLN cc_start: 0.9582 (mm-40) cc_final: 0.9316 (mm-40)
REVERT: B  212 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8912 (tp30)
REVERT: C   32 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8310 (ttp80)
REVERT: C   44 LYS cc_start: 0.9664 (tppp) cc_final: 0.9299 (tppp)
REVERT: D  112 ASP cc_start: 0.9124 (m-30) cc_final: 0.8881 (m-30)
REVERT: D  197 GLN cc_start: 0.9460 (OUTLIER) cc_final: 0.9115 (tt0)
REVERT: E   44 LYS cc_start: 0.9638 (tppp) cc_final: 0.9375 (tppp)
REVERT: F    4 GLU cc_start: 0.8881 (tp30) cc_final: 0.8622 (tp30)
REVERT: F   23 ASP cc_start: 0.8557 (m-30) cc_final: 0.8318 (m-30)
REVERT: F   65 ASN cc_start: 0.9091 (t0) cc_final: 0.8660 (p0)
REVERT: F  132 GLU cc_start: 0.9054 (tt0) cc_final: 0.8647 (tt0)
REVERT: F  157 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8529 (tt)
REVERT: F  230 ASP cc_start: 0.8899 (t0) cc_final: 0.8459 (t0)
REVERT: G  230 ASP cc_start: 0.8976 (t0) cc_final: 0.8513 (t0)
REVERT: H   23 ASP cc_start: 0.8785 (m-30) cc_final: 0.8574 (m-30)
REVERT: H   87 ILE cc_start: 0.9079 (mm) cc_final: 0.8840 (mm)
REVERT: H  230 ASP cc_start: 0.8967 (t0) cc_final: 0.8446 (t0)
REVERT: I    4 GLU cc_start: 0.8738 (tp30) cc_final: 0.8435 (tp30)
REVERT: I   23 ASP cc_start: 0.8702 (m-30) cc_final: 0.8393 (m-30)
REVERT: I  189 TRP cc_start: 0.7825 (m100) cc_final: 0.7548 (m-10)
REVERT: I  230 ASP cc_start: 0.9078 (t0) cc_final: 0.8570 (t0)
REVERT: J    4 GLU cc_start: 0.8723 (tp30) cc_final: 0.8439 (tp30)
REVERT: J   62 GLU cc_start: 0.8953 (pp20) cc_final: 0.8585 (pp20)
REVERT: J  230 ASP cc_start: 0.9166 (t0) cc_final: 0.8668 (t0)
  outliers start: 75
  outliers final: 27
  residues processed: 459
  average time/residue: 1.6259
  time to fit residues: 840.4087
Evaluate side-chains
  413 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 382
  time to evaluate  : 3.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  212 GLU
Chi-restraints excluded: chain C residue   31 THR
Chi-restraints excluded: chain C residue   32 ARG
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain D residue  197 GLN
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   64 LEU
Chi-restraints excluded: chain F residue   67 CYS
Chi-restraints excluded: chain F residue  157 LEU
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  246 SER
Chi-restraints excluded: chain G residue   67 CYS
Chi-restraints excluded: chain G residue   68 LEU
Chi-restraints excluded: chain G residue   97 GLU
Chi-restraints excluded: chain G residue  157 LEU
Chi-restraints excluded: chain G residue  258 MET
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   67 CYS
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  237 GLN
Chi-restraints excluded: chain H residue  246 SER
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain I residue   67 CYS
Chi-restraints excluded: chain I residue  246 SER
Chi-restraints excluded: chain J residue   64 LEU
Chi-restraints excluded: chain J residue   67 CYS
Chi-restraints excluded: chain J residue   68 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 156 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 206 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 189 optimal weight:    0.8980
   chunk 228 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
C 116 ASN
** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  11 ASN
G  11 ASN
G 118 GLN
H  11 ASN
H 202 GLN
H 259 GLN
I  11 ASN
I 118 GLN
I 198 GLN
J  11 ASN
J 118 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.079322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.061663 restraints weight = 40428.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 2.61
r_work: 0.2728 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2734
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2734 r_free = 0.2734    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2734 r_free = 0.2734    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2734
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  18106  Z= 0.162
  Angle     :  0.547   9.632  24512  Z= 0.284
  Chirality :  0.037   0.183   2874
  Planarity :  0.003   0.044   3202
  Dihedral  :  3.909  25.743   2585
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 20.23 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.28 (0.17), residues: 2375
  helix:  2.94 (0.11), residues: 1900
  sheet:  None (None), residues: 0
  loop : -1.27 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP F 189 
 HIS   0.001   0.000   HIS H 193 
 PHE   0.020   0.001   PHE H 213 
 TYR   0.016   0.001   TYR F  83 
 ARG   0.006   0.000   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05362 ( 1597)
  hydrogen bonds       : angle       4.22058 ( 4761)
  covalent geometry    : bond        0.00347 (18106)
  covalent geometry    : angle       0.54715 (24512)

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

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

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  468 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 408
  time to evaluate  : 2.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.9278 (pt0) cc_final: 0.9019 (pm20)
REVERT: B   34 LEU cc_start: 0.9661 (mp) cc_final: 0.9311 (pt)
REVERT: B   38 GLN cc_start: 0.9584 (mm-40) cc_final: 0.9286 (mm-40)
REVERT: C   44 LYS cc_start: 0.9648 (tppp) cc_final: 0.9246 (tppp)
REVERT: D  112 ASP cc_start: 0.9089 (m-30) cc_final: 0.8834 (m-30)
REVERT: E   44 LYS cc_start: 0.9633 (tppp) cc_final: 0.9351 (tppp)
REVERT: F    4 GLU cc_start: 0.8835 (tp30) cc_final: 0.8605 (tp30)
REVERT: F   23 ASP cc_start: 0.8585 (m-30) cc_final: 0.8356 (m-30)
REVERT: F   62 GLU cc_start: 0.9000 (pp20) cc_final: 0.8449 (pp20)
REVERT: F   65 ASN cc_start: 0.9089 (t0) cc_final: 0.8656 (p0)
REVERT: F  132 GLU cc_start: 0.9050 (tt0) cc_final: 0.8635 (tt0)
REVERT: F  230 ASP cc_start: 0.8914 (t0) cc_final: 0.8514 (t0)
REVERT: G  230 ASP cc_start: 0.8998 (t0) cc_final: 0.8535 (t0)
REVERT: H    4 GLU cc_start: 0.9247 (mt-10) cc_final: 0.9046 (mm-30)
REVERT: H   23 ASP cc_start: 0.8805 (m-30) cc_final: 0.8571 (m-30)
REVERT: H   69 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7956 (ttt180)
REVERT: H   87 ILE cc_start: 0.9037 (mm) cc_final: 0.8761 (mm)
REVERT: H  230 ASP cc_start: 0.9034 (t0) cc_final: 0.8533 (t0)
REVERT: H  259 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8674 (mp10)
REVERT: H  263 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9292 (mp)
REVERT: I    4 GLU cc_start: 0.8706 (tp30) cc_final: 0.8452 (tp30)
REVERT: I   23 ASP cc_start: 0.8755 (m-30) cc_final: 0.8401 (m-30)
REVERT: I  230 ASP cc_start: 0.9124 (t0) cc_final: 0.8595 (t0)
REVERT: J    4 GLU cc_start: 0.8734 (tp30) cc_final: 0.8448 (tp30)
REVERT: J   11 ASN cc_start: 0.9073 (m-40) cc_final: 0.8815 (m-40)
REVERT: J   23 ASP cc_start: 0.8562 (m-30) cc_final: 0.8116 (m-30)
REVERT: J   62 GLU cc_start: 0.8916 (pp20) cc_final: 0.8644 (pp20)
REVERT: J  230 ASP cc_start: 0.9148 (t0) cc_final: 0.8432 (t0)
  outliers start: 60
  outliers final: 24
  residues processed: 440
  average time/residue: 1.2315
  time to fit residues: 610.6707
Evaluate side-chains
  398 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 371
  time to evaluate  : 1.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain E residue  118 SER
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   64 LEU
Chi-restraints excluded: chain F residue   67 CYS
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  246 SER
Chi-restraints excluded: chain G residue   67 CYS
Chi-restraints excluded: chain G residue  157 LEU
Chi-restraints excluded: chain G residue  208 LEU
Chi-restraints excluded: chain G residue  258 MET
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   67 CYS
Chi-restraints excluded: chain H residue   69 ARG
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  194 ARG
Chi-restraints excluded: chain H residue  259 GLN
Chi-restraints excluded: chain H residue  263 ILE
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain I residue   67 CYS
Chi-restraints excluded: chain I residue  246 SER
Chi-restraints excluded: chain J residue   64 LEU
Chi-restraints excluded: chain J residue   67 CYS
Chi-restraints excluded: chain J residue   68 LEU
Chi-restraints excluded: chain J residue  259 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 179 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 197 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 170 optimal weight:    0.9990
   chunk 224 optimal weight:    0.9990
   chunk 160 optimal weight:    2.9990
   chunk 141 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   chunk 114 optimal weight:    0.5980
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
C 116 ASN
** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 187 ASN
F  11 ASN
F  15 GLN
G  11 ASN
G 118 GLN
H  11 ASN
H 118 GLN
I  11 ASN
I 118 GLN
I 198 GLN
I 259 GLN
J  15 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.078583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.060909 restraints weight = 40994.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 2.61
r_work: 0.2712 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2720
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2720
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  18106  Z= 0.178
  Angle     :  0.559  11.184  24512  Z= 0.290
  Chirality :  0.038   0.257   2874
  Planarity :  0.003   0.045   3202
  Dihedral  :  3.848  25.274   2585
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 20.85 %
    Favored  : 75.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.29 (0.17), residues: 2375
  helix:  2.93 (0.11), residues: 1905
  sheet:  None (None), residues: 0
  loop : -1.25 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP F 189 
 HIS   0.001   0.000   HIS I 193 
 PHE   0.022   0.001   PHE B  36 
 TYR   0.016   0.001   TYR F  83 
 ARG   0.009   0.000   ARG C  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05383 ( 1597)
  hydrogen bonds       : angle       4.23926 ( 4761)
  covalent geometry    : bond        0.00389 (18106)
  covalent geometry    : angle       0.55889 (24512)

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

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

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  459 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 394
  time to evaluate  : 2.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   34 LEU cc_start: 0.9663 (mp) cc_final: 0.9320 (pt)
REVERT: B   38 GLN cc_start: 0.9606 (mm-40) cc_final: 0.9257 (mm-40)
REVERT: B  223 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8345 (mm110)
REVERT: D   45 GLU cc_start: 0.9215 (pt0) cc_final: 0.8719 (pm20)
REVERT: D  112 ASP cc_start: 0.9078 (m-30) cc_final: 0.8827 (m-30)
REVERT: D  197 GLN cc_start: 0.9465 (OUTLIER) cc_final: 0.9004 (tt0)
REVERT: F   23 ASP cc_start: 0.8633 (m-30) cc_final: 0.8367 (m-30)
REVERT: F   62 GLU cc_start: 0.9011 (pp20) cc_final: 0.8758 (pp20)
REVERT: F   65 ASN cc_start: 0.9097 (t0) cc_final: 0.8641 (p0)
REVERT: F  132 GLU cc_start: 0.9048 (tt0) cc_final: 0.8643 (tt0)
REVERT: F  230 ASP cc_start: 0.8949 (t0) cc_final: 0.8538 (t0)
REVERT: G  230 ASP cc_start: 0.8969 (t0) cc_final: 0.8503 (t0)
REVERT: H    4 GLU cc_start: 0.9257 (mt-10) cc_final: 0.9050 (mm-30)
REVERT: H   23 ASP cc_start: 0.8806 (m-30) cc_final: 0.8525 (m-30)
REVERT: H   69 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.8005 (ttt180)
REVERT: H  230 ASP cc_start: 0.9068 (t0) cc_final: 0.8575 (t0)
REVERT: H  259 GLN cc_start: 0.8820 (mp10) cc_final: 0.8567 (mp10)
REVERT: H  263 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9295 (mp)
REVERT: I    4 GLU cc_start: 0.8748 (tp30) cc_final: 0.8517 (tp30)
REVERT: I   23 ASP cc_start: 0.8764 (m-30) cc_final: 0.8389 (m-30)
REVERT: I  230 ASP cc_start: 0.9144 (t0) cc_final: 0.8531 (t0)
REVERT: J    4 GLU cc_start: 0.8747 (tp30) cc_final: 0.8448 (tp30)
REVERT: J   11 ASN cc_start: 0.9102 (m-40) cc_final: 0.8811 (m-40)
REVERT: J   23 ASP cc_start: 0.8613 (m-30) cc_final: 0.8142 (m-30)
REVERT: J  230 ASP cc_start: 0.9158 (t0) cc_final: 0.8408 (t0)
  outliers start: 65
  outliers final: 31
  residues processed: 429
  average time/residue: 1.7305
  time to fit residues: 837.2916
Evaluate side-chains
  407 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 373
  time to evaluate  : 2.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   95 ASN
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain D residue  162 ILE
Chi-restraints excluded: chain D residue  197 GLN
Chi-restraints excluded: chain E residue  118 SER
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   64 LEU
Chi-restraints excluded: chain F residue   67 CYS
Chi-restraints excluded: chain F residue  184 ILE
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain G residue   67 CYS
Chi-restraints excluded: chain G residue   68 LEU
Chi-restraints excluded: chain G residue   97 GLU
Chi-restraints excluded: chain G residue   98 LEU
Chi-restraints excluded: chain G residue  208 LEU
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   67 CYS
Chi-restraints excluded: chain H residue   69 ARG
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  194 ARG
Chi-restraints excluded: chain H residue  263 ILE
Chi-restraints excluded: chain I residue   15 GLN
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain I residue   67 CYS
Chi-restraints excluded: chain I residue   68 LEU
Chi-restraints excluded: chain I residue  246 SER
Chi-restraints excluded: chain J residue   64 LEU
Chi-restraints excluded: chain J residue   67 CYS
Chi-restraints excluded: chain J residue   68 LEU
Chi-restraints excluded: chain J residue   97 GLU
Chi-restraints excluded: chain J residue  175 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 231 optimal weight:    2.9990
   chunk 104 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 155 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 187 optimal weight:    0.9990
   chunk 122 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 171 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
C 116 ASN
C 154 GLN
** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 198 GLN
G  11 ASN
G 118 GLN
H  11 ASN
H  15 GLN
H 237 GLN
I  11 ASN
I 118 GLN
I 198 GLN
I 259 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.078923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.061398 restraints weight = 40800.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 2.59
r_work: 0.2724 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2731
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2731 r_free = 0.2731    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2731 r_free = 0.2731    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2731
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  18106  Z= 0.166
  Angle     :  0.559  10.497  24512  Z= 0.291
  Chirality :  0.038   0.215   2874
  Planarity :  0.003   0.036   3202
  Dihedral  :  3.813  24.361   2585
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 21.30 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.29 (0.17), residues: 2375
  helix:  2.96 (0.11), residues: 1900
  sheet:  None (None), residues: 0
  loop : -1.36 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP F 189 
 HIS   0.001   0.000   HIS J 193 
 PHE   0.032   0.001   PHE H 213 
 TYR   0.016   0.001   TYR F 227 
 ARG   0.003   0.000   ARG C  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05325 ( 1597)
  hydrogen bonds       : angle       4.21279 ( 4761)
  covalent geometry    : bond        0.00359 (18106)
  covalent geometry    : angle       0.55900 (24512)

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

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

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  459 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 387
  time to evaluate  : 2.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8604 (mm-30)
REVERT: B  223 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8384 (mm110)
REVERT: C   44 LYS cc_start: 0.9643 (tppp) cc_final: 0.9304 (tppp)
REVERT: D  112 ASP cc_start: 0.9098 (m-30) cc_final: 0.8864 (m-30)
REVERT: F   23 ASP cc_start: 0.8682 (m-30) cc_final: 0.8463 (m-30)
REVERT: F   65 ASN cc_start: 0.9101 (t0) cc_final: 0.8625 (p0)
REVERT: F  132 GLU cc_start: 0.9051 (tt0) cc_final: 0.8632 (tt0)
REVERT: F  230 ASP cc_start: 0.8923 (t0) cc_final: 0.8527 (t0)
REVERT: G  230 ASP cc_start: 0.8923 (t0) cc_final: 0.8478 (t0)
REVERT: H    4 GLU cc_start: 0.9253 (mt-10) cc_final: 0.9046 (mm-30)
REVERT: H   23 ASP cc_start: 0.8802 (m-30) cc_final: 0.8548 (m-30)
REVERT: H   69 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.8002 (ttt180)
REVERT: H  230 ASP cc_start: 0.9068 (t0) cc_final: 0.8537 (t0)
REVERT: H  263 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9281 (mp)
REVERT: I    4 GLU cc_start: 0.8737 (tp30) cc_final: 0.8500 (tp30)
REVERT: I   23 ASP cc_start: 0.8760 (m-30) cc_final: 0.8418 (m-30)
REVERT: J    4 GLU cc_start: 0.8770 (tp30) cc_final: 0.8500 (tp30)
REVERT: J   11 ASN cc_start: 0.9103 (m-40) cc_final: 0.8719 (m-40)
REVERT: J   23 ASP cc_start: 0.8640 (m-30) cc_final: 0.8200 (m-30)
REVERT: J   62 GLU cc_start: 0.8898 (pp20) cc_final: 0.8624 (pp20)
REVERT: J  230 ASP cc_start: 0.9143 (t0) cc_final: 0.8437 (t0)
  outliers start: 72
  outliers final: 37
  residues processed: 426
  average time/residue: 1.7263
  time to fit residues: 828.2177
Evaluate side-chains
  404 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 365
  time to evaluate  : 3.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain C residue  162 ILE
Chi-restraints excluded: chain D residue  162 ILE
Chi-restraints excluded: chain E residue   93 SER
Chi-restraints excluded: chain E residue  118 SER
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   64 LEU
Chi-restraints excluded: chain F residue   67 CYS
Chi-restraints excluded: chain F residue  194 ARG
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  246 SER
Chi-restraints excluded: chain G residue   67 CYS
Chi-restraints excluded: chain G residue   98 LEU
Chi-restraints excluded: chain G residue  182 LEU
Chi-restraints excluded: chain G residue  208 LEU
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   67 CYS
Chi-restraints excluded: chain H residue   69 ARG
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  194 ARG
Chi-restraints excluded: chain H residue  213 PHE
Chi-restraints excluded: chain H residue  237 GLN
Chi-restraints excluded: chain H residue  260 LEU
Chi-restraints excluded: chain H residue  263 ILE
Chi-restraints excluded: chain I residue   15 GLN
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain I residue   67 CYS
Chi-restraints excluded: chain I residue   68 LEU
Chi-restraints excluded: chain I residue  246 SER
Chi-restraints excluded: chain J residue   64 LEU
Chi-restraints excluded: chain J residue   67 CYS
Chi-restraints excluded: chain J residue   68 LEU
Chi-restraints excluded: chain J residue   97 GLU
Chi-restraints excluded: chain J residue  175 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 5 optimal weight:    0.0030
   chunk 64 optimal weight:    4.9990
   chunk 166 optimal weight:    2.9990
   chunk 180 optimal weight:    0.6980
   chunk 139 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 150 optimal weight:    0.9990
   chunk 212 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 184 optimal weight:    0.9990
   chunk 79 optimal weight:    0.4980
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
C 116 ASN
** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  15 GLN
F 198 GLN
G  11 ASN
G 118 GLN
I  11 ASN
I 118 GLN
I 198 GLN
I 259 GLN
J 259 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.079841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.062259 restraints weight = 40502.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.2894 rms_B_bonded: 2.58
r_work: 0.2749 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2751
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2751
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
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      :  0.003   0.057  18106  Z= 0.149
  Angle     :  0.565   9.710  24512  Z= 0.292
  Chirality :  0.037   0.184   2874
  Planarity :  0.003   0.036   3202
  Dihedral  :  3.769  23.777   2585
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 21.98 %
    Favored  : 74.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.32 (0.17), residues: 2375
  helix:  2.98 (0.11), residues: 1900
  sheet:  None (None), residues: 0
  loop : -1.32 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP I 189 
 HIS   0.001   0.000   HIS H 193 
 PHE   0.030   0.001   PHE H 213 
 TYR   0.016   0.001   TYR F 227 
 ARG   0.003   0.000   ARG G 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05149 ( 1597)
  hydrogen bonds       : angle       4.16391 ( 4761)
  covalent geometry    : bond        0.00309 (18106)
  covalent geometry    : angle       0.56497 (24512)

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

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

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  457 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 392
  time to evaluate  : 1.915 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8581 (mm-30)
REVERT: B  223 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8462 (mm110)
REVERT: C   44 LYS cc_start: 0.9614 (tppp) cc_final: 0.9280 (tppp)
REVERT: C  138 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8785 (tttm)
REVERT: C  215 MET cc_start: 0.9225 (mmt) cc_final: 0.8961 (mmm)
REVERT: D   45 GLU cc_start: 0.9219 (pt0) cc_final: 0.8688 (pm20)
REVERT: D  112 ASP cc_start: 0.9078 (m-30) cc_final: 0.8854 (m-30)
REVERT: D  197 GLN cc_start: 0.9447 (OUTLIER) cc_final: 0.8971 (tt0)
REVERT: E   44 LYS cc_start: 0.9631 (tppp) cc_final: 0.9340 (tppp)
REVERT: F   23 ASP cc_start: 0.8681 (m-30) cc_final: 0.8456 (m-30)
REVERT: F   62 GLU cc_start: 0.8905 (pp20) cc_final: 0.8545 (pp20)
REVERT: F  132 GLU cc_start: 0.9015 (tt0) cc_final: 0.8592 (tt0)
REVERT: F  189 TRP cc_start: 0.8644 (m-90) cc_final: 0.8196 (m-10)
REVERT: F  230 ASP cc_start: 0.8859 (t0) cc_final: 0.8459 (t0)
REVERT: G  132 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8641 (mt-10)
REVERT: G  142 LEU cc_start: 0.8946 (mp) cc_final: 0.8565 (mp)
REVERT: G  230 ASP cc_start: 0.8872 (t0) cc_final: 0.8410 (t0)
REVERT: H    4 GLU cc_start: 0.9239 (mt-10) cc_final: 0.9032 (mm-30)
REVERT: H   23 ASP cc_start: 0.8800 (m-30) cc_final: 0.8505 (m-30)
REVERT: H   69 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7938 (ttt180)
REVERT: H   87 ILE cc_start: 0.8997 (mm) cc_final: 0.8737 (mm)
REVERT: H  230 ASP cc_start: 0.9017 (t0) cc_final: 0.8546 (t0)
REVERT: H  263 ILE cc_start: 0.9481 (OUTLIER) cc_final: 0.9279 (mp)
REVERT: I   23 ASP cc_start: 0.8747 (m-30) cc_final: 0.8389 (m-30)
REVERT: I  132 GLU cc_start: 0.9013 (tt0) cc_final: 0.8749 (tt0)
REVERT: J    4 GLU cc_start: 0.8755 (tp30) cc_final: 0.8495 (tp30)
REVERT: J   11 ASN cc_start: 0.9108 (m-40) cc_final: 0.8719 (m-40)
REVERT: J   23 ASP cc_start: 0.8625 (m-30) cc_final: 0.8188 (m-30)
REVERT: J  230 ASP cc_start: 0.9126 (t0) cc_final: 0.8468 (t0)
  outliers start: 65
  outliers final: 34
  residues processed: 430
  average time/residue: 1.2357
  time to fit residues: 600.6323
Evaluate side-chains
  414 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 376
  time to evaluate  : 1.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain C residue  138 LYS
Chi-restraints excluded: chain D residue  162 ILE
Chi-restraints excluded: chain D residue  197 GLN
Chi-restraints excluded: chain E residue   93 SER
Chi-restraints excluded: chain E residue  118 SER
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   64 LEU
Chi-restraints excluded: chain F residue   67 CYS
Chi-restraints excluded: chain F residue  213 PHE
Chi-restraints excluded: chain F residue  246 SER
Chi-restraints excluded: chain F residue  260 LEU
Chi-restraints excluded: chain G residue   67 CYS
Chi-restraints excluded: chain G residue   98 LEU
Chi-restraints excluded: chain G residue  182 LEU
Chi-restraints excluded: chain G residue  208 LEU
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   67 CYS
Chi-restraints excluded: chain H residue   69 ARG
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  194 ARG
Chi-restraints excluded: chain H residue  259 GLN
Chi-restraints excluded: chain H residue  260 LEU
Chi-restraints excluded: chain H residue  263 ILE
Chi-restraints excluded: chain I residue   15 GLN
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain I residue   67 CYS
Chi-restraints excluded: chain I residue  246 SER
Chi-restraints excluded: chain J residue   64 LEU
Chi-restraints excluded: chain J residue   68 LEU
Chi-restraints excluded: chain J residue   70 ILE
Chi-restraints excluded: chain J residue   97 GLU
Chi-restraints excluded: chain J residue  175 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 63 optimal weight:    0.5980
   chunk 95 optimal weight:    0.7980
   chunk 121 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9980
   chunk 181 optimal weight:    0.0770
   chunk 70 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 150 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 143 optimal weight:    0.7980
   chunk 101 optimal weight:    0.7980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
C 116 ASN
** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 198 GLN
G  11 ASN
G 118 GLN
G 122 GLN
H  11 ASN
I  11 ASN
I 118 GLN
I 198 GLN
I 259 GLN
J 118 GLN
J 259 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.080004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.062432 restraints weight = 40669.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 2.57
r_work: 0.2749 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2752
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2752 r_free = 0.2752    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2752 r_free = 0.2752    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2752
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.3650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  18106  Z= 0.155
  Angle     :  0.588  11.654  24512  Z= 0.300
  Chirality :  0.038   0.240   2874
  Planarity :  0.003   0.037   3202
  Dihedral  :  3.760  24.353   2585
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 22.38 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.31 (0.17), residues: 2375
  helix:  2.97 (0.11), residues: 1900
  sheet:  None (None), residues: 0
  loop : -1.31 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP I 189 
 HIS   0.001   0.000   HIS J 193 
 PHE   0.030   0.001   PHE D  36 
 TYR   0.017   0.001   TYR F 227 
 ARG   0.006   0.000   ARG H 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05139 ( 1597)
  hydrogen bonds       : angle       4.18046 ( 4761)
  covalent geometry    : bond        0.00329 (18106)
  covalent geometry    : angle       0.58785 (24512)

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

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

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  445 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 385
  time to evaluate  : 2.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8571 (mm-30)
REVERT: B  223 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8494 (mm110)
REVERT: C   34 LEU cc_start: 0.9701 (mp) cc_final: 0.9482 (pt)
REVERT: C   44 LYS cc_start: 0.9623 (tppp) cc_final: 0.9274 (tppp)
REVERT: C  138 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8774 (tttm)
REVERT: C  159 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8029 (mtp)
REVERT: C  215 MET cc_start: 0.9198 (mmt) cc_final: 0.8946 (mmm)
REVERT: D   45 GLU cc_start: 0.9215 (pt0) cc_final: 0.8674 (pm20)
REVERT: D  112 ASP cc_start: 0.9078 (m-30) cc_final: 0.8845 (m-30)
REVERT: D  197 GLN cc_start: 0.9460 (OUTLIER) cc_final: 0.8974 (tt0)
REVERT: E   44 LYS cc_start: 0.9634 (tppp) cc_final: 0.9339 (tppp)
REVERT: F   23 ASP cc_start: 0.8682 (m-30) cc_final: 0.8462 (m-30)
REVERT: F   62 GLU cc_start: 0.8843 (pp20) cc_final: 0.8412 (pp20)
REVERT: F   65 ASN cc_start: 0.9063 (t0) cc_final: 0.8612 (p0)
REVERT: F  132 GLU cc_start: 0.9019 (tt0) cc_final: 0.8656 (tt0)
REVERT: F  230 ASP cc_start: 0.8836 (t0) cc_final: 0.8437 (t0)
REVERT: G  230 ASP cc_start: 0.8858 (t0) cc_final: 0.8436 (t0)
REVERT: H    4 GLU cc_start: 0.9216 (mt-10) cc_final: 0.9011 (mm-30)
REVERT: H   23 ASP cc_start: 0.8754 (m-30) cc_final: 0.8427 (m-30)
REVERT: H   69 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7939 (ttt180)
REVERT: H  230 ASP cc_start: 0.9065 (t0) cc_final: 0.8603 (t0)
REVERT: I   23 ASP cc_start: 0.8736 (m-30) cc_final: 0.8394 (m-30)
REVERT: I  132 GLU cc_start: 0.9023 (tt0) cc_final: 0.8731 (tt0)
REVERT: J    4 GLU cc_start: 0.8756 (tp30) cc_final: 0.8485 (tp30)
REVERT: J   11 ASN cc_start: 0.9090 (m-40) cc_final: 0.8819 (m-40)
REVERT: J   23 ASP cc_start: 0.8636 (m-30) cc_final: 0.8380 (m-30)
REVERT: J  230 ASP cc_start: 0.9116 (t0) cc_final: 0.8464 (t0)
  outliers start: 60
  outliers final: 40
  residues processed: 421
  average time/residue: 1.2121
  time to fit residues: 573.8236
Evaluate side-chains
  411 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 367
  time to evaluate  : 1.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain C residue  138 LYS
Chi-restraints excluded: chain C residue  159 MET
Chi-restraints excluded: chain C residue  162 ILE
Chi-restraints excluded: chain D residue  162 ILE
Chi-restraints excluded: chain D residue  197 GLN
Chi-restraints excluded: chain E residue   93 SER
Chi-restraints excluded: chain E residue  118 SER
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   67 CYS
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue  182 LEU
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  213 PHE
Chi-restraints excluded: chain F residue  260 LEU
Chi-restraints excluded: chain G residue   67 CYS
Chi-restraints excluded: chain G residue   68 LEU
Chi-restraints excluded: chain G residue   98 LEU
Chi-restraints excluded: chain G residue  157 LEU
Chi-restraints excluded: chain G residue  182 LEU
Chi-restraints excluded: chain G residue  208 LEU
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   67 CYS
Chi-restraints excluded: chain H residue   69 ARG
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  194 ARG
Chi-restraints excluded: chain H residue  213 PHE
Chi-restraints excluded: chain H residue  259 GLN
Chi-restraints excluded: chain H residue  260 LEU
Chi-restraints excluded: chain I residue   15 GLN
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain I residue   67 CYS
Chi-restraints excluded: chain I residue   68 LEU
Chi-restraints excluded: chain I residue  185 LEU
Chi-restraints excluded: chain I residue  246 SER
Chi-restraints excluded: chain J residue   64 LEU
Chi-restraints excluded: chain J residue   67 CYS
Chi-restraints excluded: chain J residue   97 GLU
Chi-restraints excluded: chain J residue  175 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 104 optimal weight:    5.9990
   chunk 186 optimal weight:    9.9990
   chunk 155 optimal weight:    3.9990
   chunk 132 optimal weight:    0.7980
   chunk 210 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 231 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 185 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
C 116 ASN
** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 187 ASN
** E  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  15 GLN
F 198 GLN
G  11 ASN
G 118 GLN
I  11 ASN
I 118 GLN
I 198 GLN
I 259 GLN
J 118 GLN
J 259 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.077050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.059089 restraints weight = 40911.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 2.76
r_work: 0.2721 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2697
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2697 r_free = 0.2697    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2697 r_free = 0.2697    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2697
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.3700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  18106  Z= 0.189
  Angle     :  0.620  11.533  24512  Z= 0.314
  Chirality :  0.039   0.250   2874
  Planarity :  0.003   0.038   3202
  Dihedral  :  3.799  27.927   2585
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 23.29 %
    Favored  : 73.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.20 (0.17), residues: 2375
  helix:  2.89 (0.11), residues: 1905
  sheet:  None (None), residues: 0
  loop : -1.40 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP I 189 
 HIS   0.000   0.000   HIS J 193 
 PHE   0.027   0.002   PHE H 213 
 TYR   0.019   0.002   TYR F 227 
 ARG   0.011   0.000   ARG G 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05369 ( 1597)
  hydrogen bonds       : angle       4.23218 ( 4761)
  covalent geometry    : bond        0.00420 (18106)
  covalent geometry    : angle       0.61994 (24512)

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

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

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  427 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 371
  time to evaluate  : 2.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  223 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8532 (mm110)
REVERT: C   34 LEU cc_start: 0.9696 (mp) cc_final: 0.9476 (pt)
REVERT: C   44 LYS cc_start: 0.9613 (tppp) cc_final: 0.9239 (tppp)
REVERT: C  159 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8201 (mtp)
REVERT: D   45 GLU cc_start: 0.9234 (pt0) cc_final: 0.8698 (pm20)
REVERT: D  112 ASP cc_start: 0.9087 (m-30) cc_final: 0.8866 (m-30)
REVERT: D  197 GLN cc_start: 0.9464 (OUTLIER) cc_final: 0.8982 (tt0)
REVERT: E   44 LYS cc_start: 0.9637 (tppp) cc_final: 0.9338 (tppp)
REVERT: F   23 ASP cc_start: 0.8717 (m-30) cc_final: 0.8494 (m-30)
REVERT: F   62 GLU cc_start: 0.8866 (pp20) cc_final: 0.8448 (pp20)
REVERT: F   65 ASN cc_start: 0.9070 (t0) cc_final: 0.8606 (p0)
REVERT: F  132 GLU cc_start: 0.9054 (tt0) cc_final: 0.8697 (tt0)
REVERT: F  230 ASP cc_start: 0.8912 (t0) cc_final: 0.8500 (t0)
REVERT: G  132 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8719 (mt-10)
REVERT: G  230 ASP cc_start: 0.8918 (t0) cc_final: 0.8475 (t0)
REVERT: H    4 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8986 (mm-30)
REVERT: H   20 TYR cc_start: 0.8574 (m-80) cc_final: 0.8350 (m-80)
REVERT: H   23 ASP cc_start: 0.8758 (m-30) cc_final: 0.8450 (m-30)
REVERT: H   69 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.8018 (ttt180)
REVERT: H   83 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7272 (t80)
REVERT: H  133 GLU cc_start: 0.9308 (mm-30) cc_final: 0.9065 (mm-30)
REVERT: H  179 LEU cc_start: 0.9086 (mm) cc_final: 0.8787 (mt)
REVERT: H  230 ASP cc_start: 0.9101 (t0) cc_final: 0.8612 (t0)
REVERT: I   23 ASP cc_start: 0.8755 (m-30) cc_final: 0.8410 (m-30)
REVERT: I  132 GLU cc_start: 0.9049 (tt0) cc_final: 0.8747 (tt0)
REVERT: I  142 LEU cc_start: 0.8608 (pt) cc_final: 0.7982 (tt)
REVERT: I  230 ASP cc_start: 0.9014 (t0) cc_final: 0.8513 (t0)
REVERT: J    4 GLU cc_start: 0.8745 (tp30) cc_final: 0.8467 (tp30)
REVERT: J   11 ASN cc_start: 0.9093 (m-40) cc_final: 0.8822 (m-40)
REVERT: J   20 TYR cc_start: 0.9000 (m-80) cc_final: 0.8744 (m-10)
REVERT: J   23 ASP cc_start: 0.8647 (m-30) cc_final: 0.8399 (m-30)
REVERT: J  230 ASP cc_start: 0.9134 (t0) cc_final: 0.8463 (t0)
  outliers start: 56
  outliers final: 38
  residues processed: 404
  average time/residue: 1.1920
  time to fit residues: 542.3101
Evaluate side-chains
  407 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 365
  time to evaluate  : 1.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain C residue  159 MET
Chi-restraints excluded: chain C residue  162 ILE
Chi-restraints excluded: chain D residue  162 ILE
Chi-restraints excluded: chain D residue  197 GLN
Chi-restraints excluded: chain E residue   93 SER
Chi-restraints excluded: chain E residue  118 SER
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   64 LEU
Chi-restraints excluded: chain F residue   67 CYS
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue  173 LEU
Chi-restraints excluded: chain F residue  182 LEU
Chi-restraints excluded: chain F residue  184 ILE
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  213 PHE
Chi-restraints excluded: chain G residue   67 CYS
Chi-restraints excluded: chain G residue   68 LEU
Chi-restraints excluded: chain G residue   98 LEU
Chi-restraints excluded: chain G residue  182 LEU
Chi-restraints excluded: chain G residue  208 LEU
Chi-restraints excluded: chain H residue   15 GLN
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   67 CYS
Chi-restraints excluded: chain H residue   69 ARG
Chi-restraints excluded: chain H residue   83 TYR
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  194 ARG
Chi-restraints excluded: chain H residue  259 GLN
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain I residue   67 CYS
Chi-restraints excluded: chain I residue   68 LEU
Chi-restraints excluded: chain I residue  185 LEU
Chi-restraints excluded: chain I residue  246 SER
Chi-restraints excluded: chain J residue   64 LEU
Chi-restraints excluded: chain J residue   67 CYS
Chi-restraints excluded: chain J residue  175 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 221 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9980
   chunk 139 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 113 optimal weight:    0.7980
   chunk 173 optimal weight:    0.0030
   chunk 98 optimal weight:    0.8980
   chunk 126 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.5590

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
C 116 ASN
** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 198 GLN
G  11 ASN
G 118 GLN
H  11 ASN
I  11 ASN
I 118 GLN
I 198 GLN
I 259 GLN
J 259 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.078309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.060574 restraints weight = 40406.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.2891 rms_B_bonded: 2.73
r_work: 0.2754 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2732
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2732 r_free = 0.2732    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2732 r_free = 0.2732    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2732
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  18106  Z= 0.157
  Angle     :  0.612  10.549  24512  Z= 0.311
  Chirality :  0.038   0.261   2874
  Planarity :  0.003   0.046   3202
  Dihedral  :  3.824  27.332   2585
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 23.85 %
    Favored  : 73.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.16 (0.17), residues: 2375
  helix:  2.87 (0.11), residues: 1905
  sheet:  None (None), residues: 0
  loop : -1.45 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP I 189 
 HIS   0.001   0.000   HIS H 193 
 PHE   0.026   0.001   PHE B  36 
 TYR   0.028   0.001   TYR F  83 
 ARG   0.011   0.000   ARG G 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05185 ( 1597)
  hydrogen bonds       : angle       4.21225 ( 4761)
  covalent geometry    : bond        0.00333 (18106)
  covalent geometry    : angle       0.61181 (24512)

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

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

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4750 Ramachandran restraints generated.
    2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  422 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 375
  time to evaluate  : 1.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 GLU cc_start: 0.8180 (pp20) cc_final: 0.7975 (pp20)
REVERT: B  223 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8631 (mm110)
REVERT: C   34 LEU cc_start: 0.9686 (mp) cc_final: 0.9474 (pt)
REVERT: C   44 LYS cc_start: 0.9617 (tppp) cc_final: 0.9247 (tppp)
REVERT: C  159 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8055 (mtp)
REVERT: C  215 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8909 (mmm)
REVERT: D  112 ASP cc_start: 0.9075 (m-30) cc_final: 0.8864 (m-30)
REVERT: D  197 GLN cc_start: 0.9453 (OUTLIER) cc_final: 0.8971 (tt0)
REVERT: E   44 LYS cc_start: 0.9646 (tppp) cc_final: 0.9347 (tppp)
REVERT: F   23 ASP cc_start: 0.8747 (m-30) cc_final: 0.8454 (m-30)
REVERT: F   62 GLU cc_start: 0.8852 (pp20) cc_final: 0.8472 (pp20)
REVERT: F   65 ASN cc_start: 0.9041 (t0) cc_final: 0.8689 (p0)
REVERT: F  132 GLU cc_start: 0.9046 (tt0) cc_final: 0.8695 (tt0)
REVERT: F  230 ASP cc_start: 0.8847 (t0) cc_final: 0.8432 (t0)
REVERT: G  230 ASP cc_start: 0.8865 (t0) cc_final: 0.8458 (t0)
REVERT: H    4 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8961 (mm-30)
REVERT: H   20 TYR cc_start: 0.8592 (m-80) cc_final: 0.8368 (m-80)
REVERT: H   23 ASP cc_start: 0.8739 (m-30) cc_final: 0.8439 (m-30)
REVERT: H   69 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7983 (ttt180)
REVERT: H   83 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.7032 (t80)
REVERT: H  179 LEU cc_start: 0.9017 (mm) cc_final: 0.8723 (mt)
REVERT: H  230 ASP cc_start: 0.9058 (t0) cc_final: 0.8567 (t0)
REVERT: I   23 ASP cc_start: 0.8748 (m-30) cc_final: 0.8404 (m-30)
REVERT: I  132 GLU cc_start: 0.9039 (tt0) cc_final: 0.8766 (tt0)
REVERT: I  230 ASP cc_start: 0.8998 (t0) cc_final: 0.8355 (t0)
REVERT: J    4 GLU cc_start: 0.8761 (tp30) cc_final: 0.8392 (tp30)
REVERT: J   11 ASN cc_start: 0.9087 (m-40) cc_final: 0.8810 (m-40)
REVERT: J   20 TYR cc_start: 0.8984 (m-80) cc_final: 0.8724 (m-10)
REVERT: J   23 ASP cc_start: 0.8664 (m-30) cc_final: 0.8420 (m-30)
REVERT: J  230 ASP cc_start: 0.9115 (t0) cc_final: 0.8471 (t0)
  outliers start: 47
  outliers final: 35
  residues processed: 401
  average time/residue: 1.1947
  time to fit residues: 551.3606
Evaluate side-chains
  407 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 367
  time to evaluate  : 2.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain C residue  159 MET
Chi-restraints excluded: chain C residue  162 ILE
Chi-restraints excluded: chain C residue  215 MET
Chi-restraints excluded: chain D residue  162 ILE
Chi-restraints excluded: chain D residue  197 GLN
Chi-restraints excluded: chain E residue   93 SER
Chi-restraints excluded: chain E residue  118 SER
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue  173 LEU
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  213 PHE
Chi-restraints excluded: chain F residue  260 LEU
Chi-restraints excluded: chain G residue   67 CYS
Chi-restraints excluded: chain G residue   68 LEU
Chi-restraints excluded: chain G residue   98 LEU
Chi-restraints excluded: chain G residue  182 LEU
Chi-restraints excluded: chain G residue  208 LEU
Chi-restraints excluded: chain H residue   15 GLN
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   67 CYS
Chi-restraints excluded: chain H residue   69 ARG
Chi-restraints excluded: chain H residue   83 TYR
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  194 ARG
Chi-restraints excluded: chain H residue  259 GLN
Chi-restraints excluded: chain I residue   67 CYS
Chi-restraints excluded: chain I residue   68 LEU
Chi-restraints excluded: chain I residue  115 LEU
Chi-restraints excluded: chain I residue  185 LEU
Chi-restraints excluded: chain I residue  246 SER
Chi-restraints excluded: chain J residue   64 LEU
Chi-restraints excluded: chain J residue   67 CYS
Chi-restraints excluded: chain J residue  175 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 235
   random chunks:
   chunk 137 optimal weight:    7.9990
   chunk 157 optimal weight:    0.6980
   chunk 183 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 174 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 231 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 133 optimal weight:    0.8980
   chunk 164 optimal weight:    0.1980
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
C 116 ASN
** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  15 GLN
F 198 GLN
G  11 ASN
G 118 GLN
H 259 GLN
I  11 ASN
I 118 GLN
I 198 GLN
I 259 GLN
J 259 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.080099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.062532 restraints weight = 40442.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.2899 rms_B_bonded: 2.62
r_work: 0.2751 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.3905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  18106  Z= 0.158
  Angle     :  0.629  12.083  24512  Z= 0.316
  Chirality :  0.039   0.259   2874
  Planarity :  0.003   0.047   3202
  Dihedral  :  3.805  27.101   2585
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 24.31 %
    Favored  : 73.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.14 (0.17), residues: 2375
  helix:  2.81 (0.11), residues: 1915
  sheet:  None (None), residues: 0
  loop : -1.35 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP I 189 
 HIS   0.001   0.000   HIS J 193 
 PHE   0.029   0.001   PHE A  28 
 TYR   0.019   0.001   TYR F 227 
 ARG   0.010   0.000   ARG G 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05128 ( 1597)
  hydrogen bonds       : angle       4.18592 ( 4761)
  covalent geometry    : bond        0.00339 (18106)
  covalent geometry    : angle       0.62884 (24512)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 15627.92 seconds
wall clock time: 274 minutes 31.39 seconds (16471.39 seconds total)