Starting phenix.real_space_refine
on Tue May 13 08:09:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ito_60873/05_2025/9ito_60873.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ito_60873/05_2025/9ito_60873.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ito_60873/05_2025/9ito_60873.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ito_60873/05_2025/9ito_60873.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ito_60873/05_2025/9ito_60873.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ito_60873/05_2025/9ito_60873.cif"
  }
  resolution = 3.3
  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=  -0.001 sd=   0.011
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      32      5.16       5
     C    6648      2.51       5
     N    1605      2.21       5
     O    1702      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9987
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "H"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "I"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "J"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "K"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "L"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "M"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "N"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "O"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "P"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "Q"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "Z"
      Number of atoms: 2028
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 260, 2028
          Classifications: {'peptide': 260}
          Link IDs: {'PTRANS': 14, 'TRANS': 245}
          Chain breaks: 1
    Chain: "Y"
      Number of atoms: 423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 423
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 2, 'TRANS': 47}
    Chain: "V"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 407
          Classifications: {'peptide': 49}
          Link IDs: {'PTRANS': 2, 'TRANS': 46}
    Chain: "X"
      Number of atoms: 179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 179
          Classifications: {'peptide': 36}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 2, 'TRANS': 33}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 125
          Unresolved non-hydrogen angles: 162
          Unresolved non-hydrogen dihedrals: 99
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 60
    Chain: "U"
      Number of atoms: 190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 190
          Classifications: {'peptide': 38}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 1, 'TRANS': 36}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 140
          Unresolved non-hydrogen angles: 180
          Unresolved non-hydrogen dihedrals: 111
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 71
    Chain: "T"
      Number of atoms: 1630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1630
          Classifications: {'peptide': 225}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 10, 'TRANS': 214}
          Chain breaks: 1
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 148
          Unresolved non-hydrogen angles: 190
          Unresolved non-hydrogen dihedrals: 127
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 74
  Time building chain proxies: 6.86, per 1000 atoms: 0.69
  Number of scatterers: 9987
  At special positions: 0
  Unit cell: (106.95, 106.95, 93, 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      32     16.00
     O    1702      8.00
     N    1605      7.00
     C    6648      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS Z 135 " - pdb=" SG  CYS Z 173 " distance=2.69

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.55
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2440

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 1 sheets defined
      85.1% alpha, 0.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'H' and resid 3 through 38
      removed outlier: 3.539A  pdb=" N   VAL H   7 " --> pdb=" O   GLY H   3 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   GLY H  19 " --> pdb=" O   LEU H  15 " (cutoff:3.500A)
      Proline residue:  H  20  - end of helix
    Processing helix  chain 'H' and resid 41 through 72
      removed outlier: 4.444A  pdb=" N   THR H  47 " --> pdb=" O   ASN H  43 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   PHE H  55 " --> pdb=" O   ILE H  51 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LEU H  59 " --> pdb=" O   PHE H  55 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA H  60 " --> pdb=" O   THR H  56 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE H  62 " --> pdb=" O   ALA H  58 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 3 through 17
      removed outlier: 3.529A  pdb=" N   VAL I  13 " --> pdb=" O   THR I   9 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 18 through 38
      removed outlier: 3.535A  pdb=" N   VAL I  22 " --> pdb=" O   ILE I  18 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY I  25 " --> pdb=" O   GLY I  21 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 41 through 72
      removed outlier: 4.562A  pdb=" N   TYR I  48 " --> pdb=" O   ARG I  44 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 3 through 38
      removed outlier: 4.192A  pdb=" N   GLY J  19 " --> pdb=" O   LEU J  15 " (cutoff:3.500A)
      Proline residue:  J  20  - end of helix
    Processing helix  chain 'J' and resid 41 through 71
      removed outlier: 3.900A  pdb=" N   TYR J  48 " --> pdb=" O   ARG J  44 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE J  51 " --> pdb=" O   THR J  47 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   PHE J  55 " --> pdb=" O   ILE J  51 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LEU J  59 " --> pdb=" O   PHE J  55 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ALA J  60 " --> pdb=" O   THR J  56 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 3 through 16
      removed outlier: 3.885A  pdb=" N   VAL K   7 " --> pdb=" O   GLY K   3 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 19 through 38
    Processing helix  chain 'K' and resid 41 through 72
      removed outlier: 4.183A  pdb=" N   THR K  47 " --> pdb=" O   ASN K  43 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   TYR K  48 " --> pdb=" O   ARG K  44 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ILE K  51 " --> pdb=" O   THR K  47 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   LEU K  59 " --> pdb=" O   PHE K  55 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA K  60 " --> pdb=" O   THR K  56 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE K  66 " --> pdb=" O   PHE K  62 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 3 through 16
    Processing helix  chain 'L' and resid 18 through 38
      removed outlier: 4.065A  pdb=" N   VAL L  22 " --> pdb=" O   ILE L  18 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 41 through 72
      removed outlier: 4.082A  pdb=" N   THR L  47 " --> pdb=" O   ASN L  43 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   TYR L  48 " --> pdb=" O   ARG L  44 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 3 through 17
      removed outlier: 3.504A  pdb=" N   VAL M   7 " --> pdb=" O   GLY M   3 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA M  17 " --> pdb=" O   VAL M  13 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 17 through 38
      removed outlier: 3.521A  pdb=" N   VAL M  22 " --> pdb=" O   ILE M  18 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 41 through 71
      removed outlier: 3.509A  pdb=" N   THR M  56 " --> pdb=" O   GLY M  52 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLY M  63 " --> pdb=" O   LEU M  59 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ILE M  66 " --> pdb=" O   PHE M  62 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 3 through 15
    Processing helix  chain 'N' and resid 18 through 38
      removed outlier: 5.198A  pdb=" N   ILE N  24 " --> pdb=" O   PRO N  20 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   GLY N  25 " --> pdb=" O   GLY N  21 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 41 through 72
      removed outlier: 4.300A  pdb=" N   TYR N  48 " --> pdb=" O   ARG N  44 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU N  59 " --> pdb=" O   PHE N  55 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 3 through 38
      removed outlier: 3.715A  pdb=" N   VAL O   7 " --> pdb=" O   GLY O   3 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   GLY O  19 " --> pdb=" O   LEU O  15 " (cutoff:3.500A)
      Proline residue:  O  20  - end of helix
    Processing helix  chain 'O' and resid 42 through 72
      removed outlier: 4.659A  pdb=" N   TYR O  48 " --> pdb=" O   ARG O  44 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE O  70 " --> pdb=" O   ILE O  66 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 3 through 15
      removed outlier: 3.739A  pdb=" N   VAL P   7 " --> pdb=" O   GLY P   3 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   VAL P  13 " --> pdb=" O   THR P   9 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 18 through 38
    Processing helix  chain 'P' and resid 41 through 72
      removed outlier: 5.071A  pdb=" N   THR P  47 " --> pdb=" O   ASN P  43 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   TYR P  48 " --> pdb=" O   ARG P  44 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ALA P  54 " --> pdb=" O   PHE P  50 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE P  66 " --> pdb=" O   PHE P  62 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 3 through 16
      removed outlier: 3.760A  pdb=" N   VAL Q   7 " --> pdb=" O   GLY Q   3 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 17 through 38
      removed outlier: 4.094A  pdb=" N   VAL Q  22 " --> pdb=" O   ILE Q  18 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 44 through 72
      removed outlier: 3.845A  pdb=" N   TYR Q  48 " --> pdb=" O   ARG Q  44 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLY Q  63 " --> pdb=" O   LEU Q  59 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 49 through 71
    Processing helix  chain 'Z' and resid 79 through 97
    Processing helix  chain 'Z' and resid 102 through 124
      Proline residue:  Z 108  - end of helix
      removed outlier: 3.611A  pdb=" N   THR Z 112 " --> pdb=" O   PRO Z 108 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   PHE Z 119 " --> pdb=" O   LEU Z 115 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 172 through 176
    Processing helix  chain 'Z' and resid 186 through 189
    Processing helix  chain 'Z' and resid 190 through 211
      removed outlier: 3.625A  pdb=" N   PHE Z 195 " --> pdb=" O   LEU Z 191 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA Z 196 " --> pdb=" O   ASN Z 192 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 227 through 267
      removed outlier: 3.847A  pdb=" N   ILE Z 233 " --> pdb=" O   SER Z 229 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ILE Z 234 " --> pdb=" O   PHE Z 230 " (cutoff:3.500A)
      Proline residue:  Z 243  - end of helix
      removed outlier: 4.022A  pdb=" N   GLY Z 257 " --> pdb=" O   ASN Z 253 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 273 through 304
      removed outlier: 3.592A  pdb=" N   ALA Z 292 " --> pdb=" O   ALA Z 288 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 10 through 29
    Processing helix  chain 'Y' and resid 29 through 56
    Processing helix  chain 'V' and resid 7 through 29
    Processing helix  chain 'V' and resid 29 through 50
      removed outlier: 3.550A  pdb=" N   ASP V  50 " --> pdb=" O   GLU V  46 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 7 through 40
      removed outlier: 4.572A  pdb=" N   ARG X  31 " --> pdb=" O   ALA X  27 " (cutoff:3.500A)
      Proline residue:  X  32  - end of helix
    Processing helix  chain 'U' and resid 9 through 45
      removed outlier: 3.879A  pdb=" N   LEU U  28 " --> pdb=" O   ILE U  24 " (cutoff:3.500A)
      Proline residue:  U  32  - end of helix
      removed outlier: 3.768A  pdb=" N   GLU U  45 " --> pdb=" O   THR U  41 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 49 through 72
      removed outlier: 3.915A  pdb=" N   VAL T  53 " --> pdb=" O   THR T  49 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   VAL T  54 " --> pdb=" O   ASN T  50 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   ASN T  72 " --> pdb=" O   ALA T  68 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 79 through 99
      removed outlier: 3.823A  pdb=" N   ILE T  98 " --> pdb=" O   LEU T  94 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 106 through 124
      removed outlier: 3.876A  pdb=" N   PHE T 119 " --> pdb=" O   LEU T 115 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY T 124 " --> pdb=" O   GLY T 120 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 171 through 175
      removed outlier: 4.561A  pdb=" N   ALA T 175 " --> pdb=" O   THR T 172 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 186 through 190
      removed outlier: 3.955A  pdb=" N   ASP T 190 " --> pdb=" O   PRO T 187 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 192 through 210
      removed outlier: 3.605A  pdb=" N   ALA T 196 " --> pdb=" O   ASN T 192 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ILE T 197 " --> pdb=" O   PHE T 193 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 213 through 217
    Processing helix  chain 'T' and resid 228 through 268
      removed outlier: 4.008A  pdb=" N   PHE T 236 " --> pdb=" O   GLY T 232 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ILE T 237 " --> pdb=" O   ILE T 233 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER T 238 " --> pdb=" O   ILE T 234 " (cutoff:3.500A)
      Proline residue:  T 243  - end of helix
    Processing helix  chain 'T' and resid 273 through 304
      removed outlier: 3.679A  pdb=" N   GLY T 278 " --> pdb=" O   LEU T 274 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   PHE T 279 " --> pdb=" O   PRO T 275 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ALA T 292 " --> pdb=" O   ALA T 288 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'Z' and resid 133 through 134

    876 hydrogen bonds defined for protein.
    2604 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.83

  Time building geometry restraints manager: 2.94 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3172
        1.34 -     1.46: 2228
        1.46 -     1.58: 4704
        1.58 -     1.70: 0
        1.70 -     1.81: 60
  Bond restraints: 10164
  Sorted by residual:
  bond pdb=" N   ILE Z  39 "
       pdb=" CA  ILE Z  39 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.19e-02 7.06e+03 1.03e+01
  bond pdb=" N   ILE I  70 "
       pdb=" CA  ILE I  70 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.035 1.21e-02 6.83e+03 8.29e+00
  bond pdb=" N   ILE K  70 "
       pdb=" CA  ILE K  70 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.22e-02 6.72e+03 8.22e+00
  bond pdb=" N   ILE H  70 "
       pdb=" CA  ILE H  70 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.19e-02 7.06e+03 8.22e+00
  bond pdb=" N   VAL T 231 "
       pdb=" CA  VAL T 231 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.21e-02 6.83e+03 7.97e+00
  ... (remaining 10159 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 13330
        1.39 -     2.78: 395
        2.78 -     4.17: 78
        4.17 -     5.56: 28
        5.56 -     6.95: 2
  Bond angle restraints: 13833
  Sorted by residual:
  angle pdb=" N   VAL N  22 "
        pdb=" CA  VAL N  22 "
        pdb=" C   VAL N  22 "
      ideal   model   delta    sigma   weight residual
     112.96  108.02    4.94 1.00e+00 1.00e+00 2.44e+01
  angle pdb=" N   ILE P  70 "
        pdb=" CA  ILE P  70 "
        pdb=" C   ILE P  70 "
      ideal   model   delta    sigma   weight residual
     111.67  107.08    4.59 9.50e-01 1.11e+00 2.33e+01
  angle pdb=" C   CYS T 135 "
        pdb=" CA  CYS T 135 "
        pdb=" CB  CYS T 135 "
      ideal   model   delta    sigma   weight residual
     111.86  106.55    5.31 1.34e+00 5.57e-01 1.57e+01
  angle pdb=" N   ILE Q  70 "
        pdb=" CA  ILE Q  70 "
        pdb=" C   ILE Q  70 "
      ideal   model   delta    sigma   weight residual
     110.72  106.75    3.97 1.01e+00 9.80e-01 1.55e+01
  angle pdb=" C   ASP Z  41 "
        pdb=" CA  ASP Z  41 "
        pdb=" CB  ASP Z  41 "
      ideal   model   delta    sigma   weight residual
     116.63  112.11    4.52 1.16e+00 7.43e-01 1.52e+01
  ... (remaining 13828 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.35: 5045
       17.35 -    34.69: 576
       34.69 -    52.04: 162
       52.04 -    69.38: 27
       69.38 -    86.73: 11
  Dihedral angle restraints: 5821
    sinusoidal: 1996
      harmonic: 3825
  Sorted by residual:
  dihedral pdb=" CB  CYS Z 135 "
           pdb=" SG  CYS Z 135 "
           pdb=" SG  CYS Z 173 "
           pdb=" CB  CYS Z 173 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  147.08  -54.08     1      1.00e+01 1.00e-02 3.97e+01
  dihedral pdb=" CA  MET Z 264 "
           pdb=" C   MET Z 264 "
           pdb=" N   ALA Z 265 "
           pdb=" CA  ALA Z 265 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.38   19.62     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  ARG H  44 "
           pdb=" C   ARG H  44 "
           pdb=" N   VAL H  45 "
           pdb=" CA  VAL H  45 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.47  -17.53     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 5818 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1300
       0.047 -    0.093: 336
       0.093 -    0.140: 57
       0.140 -    0.187: 14
       0.187 -    0.233: 9
  Chirality restraints: 1716
  Sorted by residual:
  chirality pdb=" CA  ILE M  70 "
            pdb=" N   ILE M  70 "
            pdb=" C   ILE M  70 "
            pdb=" CB  ILE M  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CA  ILE H  70 "
            pdb=" N   ILE H  70 "
            pdb=" C   ILE H  70 "
            pdb=" CB  ILE H  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  ILE O  70 "
            pdb=" N   ILE O  70 "
            pdb=" C   ILE O  70 "
            pdb=" CB  ILE O  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 1713 not shown)

  Planarity restraints: 1745
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY O  19 "    0.046 5.00e-02 4.00e+02   7.01e-02 7.85e+00
        pdb=" N   PRO O  20 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO O  20 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO O  20 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY L  19 "   -0.045 5.00e-02 4.00e+02   6.85e-02 7.50e+00
        pdb=" N   PRO L  20 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO L  20 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO L  20 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY J  19 "   -0.041 5.00e-02 4.00e+02   6.12e-02 6.00e+00
        pdb=" N   PRO J  20 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO J  20 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO J  20 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1742 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2506
        2.79 -     3.32: 10665
        3.32 -     3.85: 17494
        3.85 -     4.37: 18894
        4.37 -     4.90: 32880
  Nonbonded interactions: 82439
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN V   7 "
            pdb=" OG1 THR V   9 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OE2 GLU H  42 "
            pdb=" OH  TYR Q  48 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   GLU T 235 "
            pdb=" OG  SER T 238 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   ASN T  99 "
            pdb=" OH  TYR T 296 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   ARG T 249 "
            pdb=" ND2 ASN T 253 "
     model   vdw
     2.325 3.120
  ... (remaining 82434 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 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
}
ncs_group {
  reference = (chain 'T' and (resid 47 through 135 or resid 170 through 304))
  selection = (chain 'Z' and ((resid 47 through 48 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 49 through 66 or (resid 67 through 78 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 79 through 120 or (resid 121 thro \ 
ugh 123 and (name N or name CA or name C or name O or name CB )) or resid 124 or \ 
 (resid 125 through 127 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 128 or (resid 129 and (name N or name CA or name C or name O or name C \ 
B )) or resid 130 or (resid 131 through 132 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 133 or (resid 134 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 135 or resid 170 through 175 or (resid 176 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 177 through 182 o \ 
r (resid 183 through 189 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 190 through 217 or (resid 218 through 225 and (name N or name CA or n \ 
ame C or name O or name CB )) or resid 226 or (resid 227 through 230 and (name N \ 
 or name CA or name C or name O or name CB )) or resid 231 through 304))
}
ncs_group {
  reference = (chain 'U' and resid 8 through 40)
  selection = (chain 'X' and resid 8 through 40)
}
ncs_group {
  reference = (chain 'V' and resid 7 through 50)
  selection = (chain 'Y' and resid 7 through 50)
}

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:             4.190
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.690
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
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      :  0.008   0.661  10165  Z= 0.409
  Angle     :  0.695  41.274  13835  Z= 0.415
  Chirality :  0.045   0.233   1716
  Planarity :  0.005   0.070   1745
  Dihedral  : 16.525  86.729   3378
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 30.17 %
    Favored  : 68.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.23), residues: 1342
  helix:  0.92 (0.15), residues: 1131
  sheet:  None (None), residues: 0
  loop : -2.42 (0.41), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP T 208 
 HIS   0.001   0.000   HIS Z 170 
 PHE   0.026   0.001   PHE Z 276 
 TYR   0.013   0.001   TYR V  30 
 ARG   0.002   0.000   ARG Y  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14185 (  876)
  hydrogen bonds       : angle       6.16134 ( 2604)
  SS BOND              : bond        0.66080 (    1)
  SS BOND              : angle      29.25561 (    2)
  covalent geometry    : bond        0.00448 (10164)
  covalent geometry    : angle       0.59998 (13833)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 325
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   41 ILE cc_start: 0.9101 (tp) cc_final: 0.8788 (tp)
REVERT: H   51 ILE cc_start: 0.9566 (pt) cc_final: 0.9346 (pt)
REVERT: I    2 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8235 (mm-30)
REVERT: I    5 ASN cc_start: 0.8688 (p0) cc_final: 0.8483 (p0)
REVERT: I   38 ASN cc_start: 0.9028 (t0) cc_final: 0.8716 (t0)
REVERT: I   40 GLU cc_start: 0.8662 (tp30) cc_final: 0.8295 (tp30)
REVERT: I   48 TYR cc_start: 0.9176 (m-80) cc_final: 0.8956 (m-80)
REVERT: J   38 ASN cc_start: 0.9256 (t0) cc_final: 0.9051 (t0)
REVERT: K    1 MET cc_start: 0.6821 (mpt) cc_final: 0.5842 (mpt)
REVERT: K   41 ILE cc_start: 0.9541 (tp) cc_final: 0.9304 (tp)
REVERT: L    1 MET cc_start: 0.7649 (mtp) cc_final: 0.7329 (mtm)
REVERT: N   41 ILE cc_start: 0.9175 (tp) cc_final: 0.8866 (tp)
REVERT: P    4 LEU cc_start: 0.9374 (tp) cc_final: 0.9135 (tp)
REVERT: P   42 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8567 (tm-30)
REVERT: Z   23 PHE cc_start: 0.7247 (m-80) cc_final: 0.7015 (m-80)
REVERT: Z   71 ARG cc_start: 0.7926 (ttt90) cc_final: 0.7572 (ttm-80)
REVERT: Z  239 GLU cc_start: 0.9273 (tp30) cc_final: 0.8561 (tp30)
REVERT: Z  242 LYS cc_start: 0.9259 (tttt) cc_final: 0.8745 (mttm)
REVERT: Y   31 ARG cc_start: 0.9010 (tpp-160) cc_final: 0.8568 (tpp80)
REVERT: Y   34 MET cc_start: 0.8891 (mmp) cc_final: 0.8575 (tpp)
REVERT: T  246 LEU cc_start: 0.9252 (mt) cc_final: 0.9023 (mt)
REVERT: T  254 ILE cc_start: 0.9036 (mm) cc_final: 0.8440 (tt)
REVERT: T  264 MET cc_start: 0.4659 (tpp) cc_final: 0.4288 (tpp)
REVERT: T  291 PHE cc_start: 0.9115 (t80) cc_final: 0.8798 (t80)
  outliers start: 9
  outliers final: 4
  residues processed: 329
  average time/residue: 0.2113
  time to fit residues: 97.3661
Evaluate side-chains
  275 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 271
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   68 PHE
Chi-restraints excluded: chain Z residue  109 LEU
Chi-restraints excluded: chain V residue   17 ASN
Chi-restraints excluded: chain T residue  135 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 112 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 55 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0870
   chunk 53 optimal weight:    0.5980
   chunk 104 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 120 optimal weight:    7.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** Y  17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 253 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.123688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.087747 restraints weight = 19289.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.89
r_work: 0.3139 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10165  Z= 0.149
  Angle     :  0.530   8.019  13835  Z= 0.282
  Chirality :  0.041   0.185   1716
  Planarity :  0.005   0.066   1745
  Dihedral  :  3.958  35.547   1435
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 29.22 %
    Favored  : 66.14 %
  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:  1.41 (0.23), residues: 1342
  helix:  1.62 (0.15), residues: 1090
  sheet:  None (None), residues: 0
  loop : -2.17 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP T 208 
 HIS   0.001   0.001   HIS T 136 
 PHE   0.028   0.001   PHE J  62 
 TYR   0.016   0.002   TYR T 277 
 ARG   0.007   0.000   ARG T  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04451 (  876)
  hydrogen bonds       : angle       3.86920 ( 2604)
  SS BOND              : bond        0.01592 (    1)
  SS BOND              : angle       2.33468 (    2)
  covalent geometry    : bond        0.00337 (10164)
  covalent geometry    : angle       0.52892 (13833)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 307
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   41 ILE cc_start: 0.9170 (tp) cc_final: 0.8847 (tp)
REVERT: I    2 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8369 (mm-30)
REVERT: I    5 ASN cc_start: 0.8753 (p0) cc_final: 0.8501 (p0)
REVERT: I   38 ASN cc_start: 0.9035 (t0) cc_final: 0.8701 (t0)
REVERT: I   40 GLU cc_start: 0.9005 (tp30) cc_final: 0.8598 (tp30)
REVERT: I   48 TYR cc_start: 0.9311 (m-80) cc_final: 0.9102 (m-80)
REVERT: J    4 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8692 (mp)
REVERT: J   18 ILE cc_start: 0.9019 (mt) cc_final: 0.8803 (mp)
REVERT: J   38 ASN cc_start: 0.9208 (t0) cc_final: 0.8979 (t0)
REVERT: J   48 TYR cc_start: 0.9108 (m-80) cc_final: 0.8880 (m-80)
REVERT: K    1 MET cc_start: 0.7058 (mpt) cc_final: 0.6155 (mpt)
REVERT: K   41 ILE cc_start: 0.9539 (tp) cc_final: 0.9280 (tp)
REVERT: K   43 ASN cc_start: 0.9183 (p0) cc_final: 0.8912 (p0)
REVERT: L    1 MET cc_start: 0.8285 (mtp) cc_final: 0.7791 (mtm)
REVERT: M   57 GLU cc_start: 0.8756 (tp30) cc_final: 0.8530 (tp30)
REVERT: Q    1 MET cc_start: 0.7648 (tpt) cc_final: 0.6956 (tpt)
REVERT: Q   37 ARG cc_start: 0.8487 (tpp80) cc_final: 0.8015 (mtm-85)
REVERT: Q   38 ASN cc_start: 0.9093 (t0) cc_final: 0.8464 (t0)
REVERT: Z   23 PHE cc_start: 0.7480 (m-80) cc_final: 0.7199 (m-80)
REVERT: Z   78 ARG cc_start: 0.4597 (tmt170) cc_final: 0.4342 (tmt170)
REVERT: Z  239 GLU cc_start: 0.9219 (tp30) cc_final: 0.8491 (tp30)
REVERT: Z  242 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8668 (mttm)
REVERT: Y   31 ARG cc_start: 0.9106 (tpp-160) cc_final: 0.8682 (tpp80)
REVERT: Y   56 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6436 (mm-30)
REVERT: T   59 ASP cc_start: 0.5225 (OUTLIER) cc_final: 0.4615 (m-30)
REVERT: T  136 HIS cc_start: 0.5966 (OUTLIER) cc_final: 0.5546 (m170)
REVERT: T  191 LEU cc_start: 0.7294 (mm) cc_final: 0.5774 (pt)
REVERT: T  254 ILE cc_start: 0.8953 (mm) cc_final: 0.8481 (tt)
REVERT: T  264 MET cc_start: 0.5411 (tpp) cc_final: 0.5058 (tpp)
REVERT: T  272 LEU cc_start: 0.7453 (tp) cc_final: 0.6975 (tt)
REVERT: T  291 PHE cc_start: 0.9262 (t80) cc_final: 0.8928 (t80)
  outliers start: 44
  outliers final: 23
  residues processed: 328
  average time/residue: 0.1994
  time to fit residues: 92.5162
Evaluate side-chains
  313 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 285
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain I residue   56 THR
Chi-restraints excluded: chain I residue   65 VAL
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain J residue   64 LEU
Chi-restraints excluded: chain K residue   13 VAL
Chi-restraints excluded: chain K residue   18 ILE
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain L residue   38 ASN
Chi-restraints excluded: chain L residue   65 VAL
Chi-restraints excluded: chain M residue   53 ILE
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain O residue   45 VAL
Chi-restraints excluded: chain P residue   45 VAL
Chi-restraints excluded: chain P residue   47 THR
Chi-restraints excluded: chain P residue   64 LEU
Chi-restraints excluded: chain Q residue    7 VAL
Chi-restraints excluded: chain Q residue   68 PHE
Chi-restraints excluded: chain Z residue   26 TYR
Chi-restraints excluded: chain Z residue  126 LEU
Chi-restraints excluded: chain Z residue  240 LEU
Chi-restraints excluded: chain Z residue  242 LYS
Chi-restraints excluded: chain Y residue   33 VAL
Chi-restraints excluded: chain Y residue   56 GLU
Chi-restraints excluded: chain T residue   59 ASP
Chi-restraints excluded: chain T residue   97 ASN
Chi-restraints excluded: chain T residue  136 HIS
Chi-restraints excluded: chain T residue  231 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 78 optimal weight:    0.7980
   chunk 108 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 86 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** Y  17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.122482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.086943 restraints weight = 19410.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 2.88
r_work: 0.3120 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  10165  Z= 0.160
  Angle     :  0.522   7.920  13835  Z= 0.279
  Chirality :  0.041   0.237   1716
  Planarity :  0.005   0.066   1745
  Dihedral  :  3.607  19.852   1428
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 30.59 %
    Favored  : 63.82 %
  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:  1.62 (0.23), residues: 1342
  helix:  1.71 (0.15), residues: 1098
  sheet:  None (None), residues: 0
  loop : -1.90 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP T 208 
 HIS   0.002   0.001   HIS Z 170 
 PHE   0.020   0.001   PHE J  62 
 TYR   0.020   0.002   TYR M  48 
 ARG   0.007   0.000   ARG T  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04275 (  876)
  hydrogen bonds       : angle       3.71814 ( 2604)
  SS BOND              : bond        0.00494 (    1)
  SS BOND              : angle       0.98407 (    2)
  covalent geometry    : bond        0.00372 (10164)
  covalent geometry    : angle       0.52238 (13833)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 296
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I    2 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8429 (mm-30)
REVERT: I    5 ASN cc_start: 0.8743 (p0) cc_final: 0.8506 (p0)
REVERT: I   38 ASN cc_start: 0.9059 (t0) cc_final: 0.8699 (t0)
REVERT: I   40 GLU cc_start: 0.9031 (tp30) cc_final: 0.8614 (tp30)
REVERT: I   48 TYR cc_start: 0.9310 (m-80) cc_final: 0.9083 (m-80)
REVERT: J    4 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8695 (mp)
REVERT: J   38 ASN cc_start: 0.9227 (t0) cc_final: 0.8965 (t0)
REVERT: N   41 ILE cc_start: 0.9140 (tp) cc_final: 0.8728 (tp)
REVERT: Q   37 ARG cc_start: 0.8580 (tpp80) cc_final: 0.8166 (mtm-85)
REVERT: Q   38 ASN cc_start: 0.9038 (t0) cc_final: 0.8380 (t0)
REVERT: Z   23 PHE cc_start: 0.7568 (m-80) cc_final: 0.7273 (m-80)
REVERT: Z   78 ARG cc_start: 0.4471 (tmt170) cc_final: 0.4242 (tmt170)
REVERT: Z  239 GLU cc_start: 0.9220 (tp30) cc_final: 0.8534 (tp30)
REVERT: Y   31 ARG cc_start: 0.9103 (tpp-160) cc_final: 0.8696 (tpp80)
REVERT: Y   56 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6425 (mm-30)
REVERT: T   59 ASP cc_start: 0.5279 (OUTLIER) cc_final: 0.4839 (m-30)
REVERT: T  136 HIS cc_start: 0.5952 (OUTLIER) cc_final: 0.5560 (m170)
REVERT: T  254 ILE cc_start: 0.8976 (mm) cc_final: 0.8527 (tt)
REVERT: T  264 MET cc_start: 0.5556 (tpp) cc_final: 0.5164 (tpp)
REVERT: T  272 LEU cc_start: 0.7446 (tp) cc_final: 0.6963 (tt)
REVERT: T  291 PHE cc_start: 0.9279 (t80) cc_final: 0.8964 (t80)
  outliers start: 53
  outliers final: 34
  residues processed: 321
  average time/residue: 0.2022
  time to fit residues: 91.7387
Evaluate side-chains
  316 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 278
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain I residue   56 THR
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain I residue   65 VAL
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain K residue   18 ILE
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain K residue   53 ILE
Chi-restraints excluded: chain L residue   65 VAL
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   68 PHE
Chi-restraints excluded: chain O residue   45 VAL
Chi-restraints excluded: chain O residue   59 LEU
Chi-restraints excluded: chain O residue   68 PHE
Chi-restraints excluded: chain P residue   45 VAL
Chi-restraints excluded: chain P residue   53 ILE
Chi-restraints excluded: chain P residue   64 LEU
Chi-restraints excluded: chain Q residue   49 MET
Chi-restraints excluded: chain Q residue   68 PHE
Chi-restraints excluded: chain Z residue   26 TYR
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   54 VAL
Chi-restraints excluded: chain Z residue   76 VAL
Chi-restraints excluded: chain Z residue  126 LEU
Chi-restraints excluded: chain Z residue  224 THR
Chi-restraints excluded: chain Z residue  240 LEU
Chi-restraints excluded: chain Z residue  266 PHE
Chi-restraints excluded: chain Z residue  286 ILE
Chi-restraints excluded: chain Y residue   20 LEU
Chi-restraints excluded: chain Y residue   56 GLU
Chi-restraints excluded: chain V residue   36 LEU
Chi-restraints excluded: chain T residue   59 ASP
Chi-restraints excluded: chain T residue   82 ASN
Chi-restraints excluded: chain T residue   97 ASN
Chi-restraints excluded: chain T residue  136 HIS
Chi-restraints excluded: chain T residue  231 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 52 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 100 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 93 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 130 optimal weight:    0.0870
   chunk 29 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
** Y  17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 300 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.122923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.087617 restraints weight = 19264.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.83
r_work: 0.3143 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  10165  Z= 0.146
  Angle     :  0.516   7.360  13835  Z= 0.275
  Chirality :  0.041   0.210   1716
  Planarity :  0.005   0.065   1745
  Dihedral  :  3.590  20.138   1428
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 32.28 %
    Favored  : 62.24 %
  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:  1.75 (0.23), residues: 1342
  helix:  1.80 (0.15), residues: 1098
  sheet:  None (None), residues: 0
  loop : -1.86 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP T 208 
 HIS   0.001   0.000   HIS Z 170 
 PHE   0.023   0.001   PHE J  62 
 TYR   0.014   0.002   TYR Z 296 
 ARG   0.005   0.000   ARG K  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04125 (  876)
  hydrogen bonds       : angle       3.63487 ( 2604)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       1.14170 (    2)
  covalent geometry    : bond        0.00340 (10164)
  covalent geometry    : angle       0.51607 (13833)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 293
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I    2 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8482 (mm-30)
REVERT: I    5 ASN cc_start: 0.8781 (p0) cc_final: 0.8542 (p0)
REVERT: I   38 ASN cc_start: 0.9024 (t0) cc_final: 0.8666 (t0)
REVERT: I   48 TYR cc_start: 0.9280 (m-80) cc_final: 0.9070 (m-80)
REVERT: J    4 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8686 (mp)
REVERT: J   18 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8848 (mp)
REVERT: J   38 ASN cc_start: 0.9207 (t0) cc_final: 0.8946 (t0)
REVERT: K   41 ILE cc_start: 0.9500 (OUTLIER) cc_final: 0.9267 (tp)
REVERT: K   43 ASN cc_start: 0.9132 (p0) cc_final: 0.8887 (p0)
REVERT: M   48 TYR cc_start: 0.9134 (m-80) cc_final: 0.8834 (m-80)
REVERT: N   41 ILE cc_start: 0.9072 (tp) cc_final: 0.8742 (tp)
REVERT: N   57 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8484 (mm-30)
REVERT: Q   37 ARG cc_start: 0.8496 (tpp80) cc_final: 0.8114 (mtm-85)
REVERT: Q   38 ASN cc_start: 0.9027 (t0) cc_final: 0.8392 (t0)
REVERT: Q   48 TYR cc_start: 0.8780 (m-80) cc_final: 0.8492 (m-80)
REVERT: Z   23 PHE cc_start: 0.7519 (m-80) cc_final: 0.7224 (m-80)
REVERT: Z   78 ARG cc_start: 0.4425 (tmt170) cc_final: 0.4180 (tmt170)
REVERT: Z  239 GLU cc_start: 0.9212 (tp30) cc_final: 0.8476 (tp30)
REVERT: Z  242 LYS cc_start: 0.9156 (mttp) cc_final: 0.8569 (mtpp)
REVERT: Y   31 ARG cc_start: 0.9044 (tpp-160) cc_final: 0.8646 (tpp80)
REVERT: Y   56 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6450 (mm-30)
REVERT: T   59 ASP cc_start: 0.5394 (OUTLIER) cc_final: 0.4953 (m-30)
REVERT: T  136 HIS cc_start: 0.5971 (OUTLIER) cc_final: 0.5605 (m170)
REVERT: T  254 ILE cc_start: 0.8945 (mm) cc_final: 0.8477 (tt)
REVERT: T  264 MET cc_start: 0.5539 (tpp) cc_final: 0.5122 (tpp)
REVERT: T  272 LEU cc_start: 0.7488 (tp) cc_final: 0.7018 (tt)
REVERT: T  291 PHE cc_start: 0.9236 (t80) cc_final: 0.8930 (t80)
  outliers start: 52
  outliers final: 31
  residues processed: 318
  average time/residue: 0.1948
  time to fit residues: 88.0456
Evaluate side-chains
  320 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 283
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain I residue   56 THR
Chi-restraints excluded: chain I residue   65 VAL
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain J residue   18 ILE
Chi-restraints excluded: chain K residue   18 ILE
Chi-restraints excluded: chain K residue   41 ILE
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain L residue   38 ASN
Chi-restraints excluded: chain L residue   65 VAL
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   68 PHE
Chi-restraints excluded: chain O residue   45 VAL
Chi-restraints excluded: chain O residue   59 LEU
Chi-restraints excluded: chain O residue   68 PHE
Chi-restraints excluded: chain P residue   45 VAL
Chi-restraints excluded: chain P residue   53 ILE
Chi-restraints excluded: chain P residue   64 LEU
Chi-restraints excluded: chain Q residue    7 VAL
Chi-restraints excluded: chain Q residue   68 PHE
Chi-restraints excluded: chain Z residue   26 TYR
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   54 VAL
Chi-restraints excluded: chain Z residue   76 VAL
Chi-restraints excluded: chain Z residue   80 LEU
Chi-restraints excluded: chain Z residue  126 LEU
Chi-restraints excluded: chain Z residue  224 THR
Chi-restraints excluded: chain Z residue  266 PHE
Chi-restraints excluded: chain Y residue   20 LEU
Chi-restraints excluded: chain Y residue   56 GLU
Chi-restraints excluded: chain V residue   36 LEU
Chi-restraints excluded: chain T residue   59 ASP
Chi-restraints excluded: chain T residue   84 MET
Chi-restraints excluded: chain T residue  136 HIS
Chi-restraints excluded: chain T residue  231 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 130 optimal weight:    0.0670
   chunk 69 optimal weight:    1.9990
   chunk 122 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 116 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
** Y  17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 300 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.123891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.088451 restraints weight = 19213.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.84
r_work: 0.3154 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  10165  Z= 0.139
  Angle     :  0.513   7.059  13835  Z= 0.273
  Chirality :  0.041   0.211   1716
  Planarity :  0.005   0.064   1745
  Dihedral  :  3.578  22.497   1428
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 31.75 %
    Favored  : 62.55 %
  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:  1.84 (0.23), residues: 1342
  helix:  1.88 (0.15), residues: 1099
  sheet:  None (None), residues: 0
  loop : -1.90 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP T 208 
 HIS   0.001   0.000   HIS Z 170 
 PHE   0.025   0.001   PHE J  62 
 TYR   0.014   0.002   TYR Z 296 
 ARG   0.007   0.000   ARG K  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04034 (  876)
  hydrogen bonds       : angle       3.57845 ( 2604)
  SS BOND              : bond        0.00040 (    1)
  SS BOND              : angle       0.86299 (    2)
  covalent geometry    : bond        0.00319 (10164)
  covalent geometry    : angle       0.51278 (13833)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 293
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I    2 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8483 (mm-30)
REVERT: I    5 ASN cc_start: 0.8786 (p0) cc_final: 0.8550 (p0)
REVERT: I   38 ASN cc_start: 0.9005 (t0) cc_final: 0.8636 (t0)
REVERT: J    4 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8710 (mp)
REVERT: J   38 ASN cc_start: 0.9202 (t0) cc_final: 0.8927 (t0)
REVERT: K   41 ILE cc_start: 0.9447 (OUTLIER) cc_final: 0.9198 (tp)
REVERT: M   48 TYR cc_start: 0.9123 (m-80) cc_final: 0.8828 (m-80)
REVERT: N   41 ILE cc_start: 0.9072 (tp) cc_final: 0.8753 (tp)
REVERT: Q   37 ARG cc_start: 0.8506 (tpp80) cc_final: 0.8143 (mtm-85)
REVERT: Q   38 ASN cc_start: 0.9036 (t0) cc_final: 0.8402 (t0)
REVERT: Q   48 TYR cc_start: 0.8816 (m-80) cc_final: 0.8523 (m-80)
REVERT: Z   23 PHE cc_start: 0.7484 (m-80) cc_final: 0.7183 (m-80)
REVERT: Z   78 ARG cc_start: 0.4713 (tmt170) cc_final: 0.4349 (tmt170)
REVERT: Z  101 LYS cc_start: 0.9289 (tttm) cc_final: 0.8881 (tttm)
REVERT: Z  239 GLU cc_start: 0.9227 (tp30) cc_final: 0.8530 (tp30)
REVERT: Z  242 LYS cc_start: 0.9147 (mttp) cc_final: 0.8646 (mtpp)
REVERT: Y   31 ARG cc_start: 0.9034 (tpp-160) cc_final: 0.8646 (tpp80)
REVERT: T   59 ASP cc_start: 0.5388 (OUTLIER) cc_final: 0.4947 (m-30)
REVERT: T  136 HIS cc_start: 0.5978 (OUTLIER) cc_final: 0.5606 (m170)
REVERT: T  254 ILE cc_start: 0.8957 (mm) cc_final: 0.8552 (tt)
REVERT: T  264 MET cc_start: 0.5620 (tpp) cc_final: 0.5204 (tpp)
REVERT: T  272 LEU cc_start: 0.7527 (tp) cc_final: 0.7032 (tt)
REVERT: T  291 PHE cc_start: 0.9231 (t80) cc_final: 0.8933 (t80)
  outliers start: 54
  outliers final: 41
  residues processed: 324
  average time/residue: 0.1955
  time to fit residues: 89.8642
Evaluate side-chains
  325 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 280
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   29 SER
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain I residue   56 THR
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain I residue   65 VAL
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain K residue   13 VAL
Chi-restraints excluded: chain K residue   18 ILE
Chi-restraints excluded: chain K residue   41 ILE
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain K residue   56 THR
Chi-restraints excluded: chain L residue   38 ASN
Chi-restraints excluded: chain L residue   65 VAL
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   68 PHE
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain O residue   45 VAL
Chi-restraints excluded: chain O residue   68 PHE
Chi-restraints excluded: chain P residue   45 VAL
Chi-restraints excluded: chain P residue   47 THR
Chi-restraints excluded: chain P residue   53 ILE
Chi-restraints excluded: chain Q residue    7 VAL
Chi-restraints excluded: chain Q residue   68 PHE
Chi-restraints excluded: chain Z residue   26 TYR
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   54 VAL
Chi-restraints excluded: chain Z residue   76 VAL
Chi-restraints excluded: chain Z residue  103 VAL
Chi-restraints excluded: chain Z residue  126 LEU
Chi-restraints excluded: chain Z residue  224 THR
Chi-restraints excluded: chain Z residue  240 LEU
Chi-restraints excluded: chain Z residue  266 PHE
Chi-restraints excluded: chain Z residue  286 ILE
Chi-restraints excluded: chain Y residue   20 LEU
Chi-restraints excluded: chain Y residue   35 ASN
Chi-restraints excluded: chain Y residue   56 GLU
Chi-restraints excluded: chain V residue   25 LEU
Chi-restraints excluded: chain V residue   36 LEU
Chi-restraints excluded: chain T residue   59 ASP
Chi-restraints excluded: chain T residue   82 ASN
Chi-restraints excluded: chain T residue   84 MET
Chi-restraints excluded: chain T residue  136 HIS
Chi-restraints excluded: chain T residue  231 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 32 optimal weight:    0.4980
   chunk 121 optimal weight:    0.0370
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** Y  17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 300 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.124125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.088646 restraints weight = 19449.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.88
r_work: 0.3155 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10165  Z= 0.140
  Angle     :  0.528   6.642  13835  Z= 0.280
  Chirality :  0.042   0.256   1716
  Planarity :  0.005   0.064   1745
  Dihedral  :  3.598  21.051   1428
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 32.59 %
    Favored  : 62.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.23), residues: 1342
  helix:  1.92 (0.15), residues: 1100
  sheet:  None (None), residues: 0
  loop : -1.85 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP T 208 
 HIS   0.001   0.000   HIS Z 170 
 PHE   0.016   0.001   PHE T 202 
 TYR   0.015   0.001   TYR Z 296 
 ARG   0.007   0.000   ARG K  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04006 (  876)
  hydrogen bonds       : angle       3.58875 ( 2604)
  SS BOND              : bond        0.00013 (    1)
  SS BOND              : angle       0.80551 (    2)
  covalent geometry    : bond        0.00323 (10164)
  covalent geometry    : angle       0.52829 (13833)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  343 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 292
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I    2 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8488 (mm-30)
REVERT: I    5 ASN cc_start: 0.8750 (p0) cc_final: 0.8535 (p0)
REVERT: I   38 ASN cc_start: 0.9038 (t0) cc_final: 0.8658 (t0)
REVERT: I   57 GLU cc_start: 0.8705 (mm-30) cc_final: 0.7771 (tt0)
REVERT: J    4 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8700 (mp)
REVERT: J   38 ASN cc_start: 0.9211 (t0) cc_final: 0.8921 (t0)
REVERT: M   48 TYR cc_start: 0.9117 (m-80) cc_final: 0.8809 (m-80)
REVERT: N   41 ILE cc_start: 0.9054 (tp) cc_final: 0.8745 (tp)
REVERT: Q   37 ARG cc_start: 0.8532 (tpp80) cc_final: 0.8172 (mtm-85)
REVERT: Q   38 ASN cc_start: 0.9028 (t0) cc_final: 0.8407 (t0)
REVERT: Q   44 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7865 (tmm-80)
REVERT: Q   48 TYR cc_start: 0.8752 (m-80) cc_final: 0.8484 (m-80)
REVERT: Z   23 PHE cc_start: 0.7622 (m-80) cc_final: 0.7294 (m-80)
REVERT: Z   78 ARG cc_start: 0.4652 (tmt170) cc_final: 0.4307 (tmt170)
REVERT: Z  101 LYS cc_start: 0.9318 (tttm) cc_final: 0.8930 (tttm)
REVERT: Z  239 GLU cc_start: 0.9232 (tp30) cc_final: 0.8535 (tp30)
REVERT: Z  242 LYS cc_start: 0.9121 (mttp) cc_final: 0.8563 (mtpp)
REVERT: Z  264 MET cc_start: 0.8514 (mmm) cc_final: 0.8282 (mtt)
REVERT: Y   31 ARG cc_start: 0.9039 (tpp-160) cc_final: 0.8653 (tpp80)
REVERT: Y   43 ARG cc_start: 0.7494 (tmm-80) cc_final: 0.7224 (ttp-170)
REVERT: T   59 ASP cc_start: 0.5380 (OUTLIER) cc_final: 0.4946 (m-30)
REVERT: T  136 HIS cc_start: 0.5953 (OUTLIER) cc_final: 0.5628 (m170)
REVERT: T  239 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8750 (mm-30)
REVERT: T  254 ILE cc_start: 0.9043 (mm) cc_final: 0.8574 (tt)
REVERT: T  264 MET cc_start: 0.5567 (tpp) cc_final: 0.5120 (tpp)
REVERT: T  272 LEU cc_start: 0.7463 (tp) cc_final: 0.6981 (tt)
REVERT: T  291 PHE cc_start: 0.9261 (t80) cc_final: 0.8996 (t80)
  outliers start: 51
  outliers final: 39
  residues processed: 320
  average time/residue: 0.1940
  time to fit residues: 88.1195
Evaluate side-chains
  323 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 281
  time to evaluate  : 1.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   29 SER
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain I residue   56 THR
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain I residue   65 VAL
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain K residue   18 ILE
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain K residue   56 THR
Chi-restraints excluded: chain L residue   38 ASN
Chi-restraints excluded: chain L residue   65 VAL
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   68 PHE
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain O residue   45 VAL
Chi-restraints excluded: chain O residue   68 PHE
Chi-restraints excluded: chain P residue   45 VAL
Chi-restraints excluded: chain P residue   47 THR
Chi-restraints excluded: chain Q residue   68 PHE
Chi-restraints excluded: chain Z residue   26 TYR
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   54 VAL
Chi-restraints excluded: chain Z residue   76 VAL
Chi-restraints excluded: chain Z residue   80 LEU
Chi-restraints excluded: chain Z residue  103 VAL
Chi-restraints excluded: chain Z residue  126 LEU
Chi-restraints excluded: chain Z residue  224 THR
Chi-restraints excluded: chain Z residue  240 LEU
Chi-restraints excluded: chain Z residue  266 PHE
Chi-restraints excluded: chain Z residue  294 LEU
Chi-restraints excluded: chain Y residue   20 LEU
Chi-restraints excluded: chain Y residue   35 ASN
Chi-restraints excluded: chain Y residue   56 GLU
Chi-restraints excluded: chain V residue   25 LEU
Chi-restraints excluded: chain V residue   36 LEU
Chi-restraints excluded: chain T residue   59 ASP
Chi-restraints excluded: chain T residue   82 ASN
Chi-restraints excluded: chain T residue   84 MET
Chi-restraints excluded: chain T residue  136 HIS
Chi-restraints excluded: chain T residue  231 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 58 optimal weight:    0.5980
   chunk 117 optimal weight:    5.9990
   chunk 26 optimal weight:    0.5980
   chunk 93 optimal weight:    0.6980
   chunk 104 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** Y  17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  97 ASN
T 300 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.123645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.088156 restraints weight = 19780.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.91
r_work: 0.3148 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  10165  Z= 0.150
  Angle     :  0.545   8.152  13835  Z= 0.288
  Chirality :  0.042   0.232   1716
  Planarity :  0.005   0.064   1745
  Dihedral  :  3.631  24.247   1428
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 32.91 %
    Favored  : 62.24 %
  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:  1.91 (0.23), residues: 1342
  helix:  1.97 (0.15), residues: 1092
  sheet:  None (None), residues: 0
  loop : -2.02 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP T 208 
 HIS   0.001   0.000   HIS Z 170 
 PHE   0.018   0.001   PHE T 114 
 TYR   0.016   0.002   TYR T 277 
 ARG   0.007   0.000   ARG K  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04004 (  876)
  hydrogen bonds       : angle       3.61824 ( 2604)
  SS BOND              : bond        0.00038 (    1)
  SS BOND              : angle       0.74501 (    2)
  covalent geometry    : bond        0.00354 (10164)
  covalent geometry    : angle       0.54485 (13833)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 288
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I    2 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8458 (mm-30)
REVERT: I    5 ASN cc_start: 0.8774 (p0) cc_final: 0.8543 (p0)
REVERT: I   38 ASN cc_start: 0.9049 (t0) cc_final: 0.8663 (t0)
REVERT: J    4 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8713 (mp)
REVERT: J   38 ASN cc_start: 0.9214 (t0) cc_final: 0.8917 (t0)
REVERT: M   48 TYR cc_start: 0.9131 (m-80) cc_final: 0.8760 (m-80)
REVERT: N   41 ILE cc_start: 0.9075 (tp) cc_final: 0.8758 (tp)
REVERT: Q   37 ARG cc_start: 0.8555 (tpp80) cc_final: 0.8189 (mtm-85)
REVERT: Q   38 ASN cc_start: 0.9024 (t0) cc_final: 0.8412 (t0)
REVERT: Q   44 ARG cc_start: 0.8312 (ttp80) cc_final: 0.7884 (tmm-80)
REVERT: Q   48 TYR cc_start: 0.8799 (m-80) cc_final: 0.8481 (m-80)
REVERT: Z   23 PHE cc_start: 0.7612 (m-80) cc_final: 0.7282 (m-80)
REVERT: Z   78 ARG cc_start: 0.4634 (tmt170) cc_final: 0.4266 (tmt170)
REVERT: Z  101 LYS cc_start: 0.9320 (tttm) cc_final: 0.8936 (tttm)
REVERT: Z  102 TYR cc_start: 0.8453 (m-80) cc_final: 0.8024 (m-80)
REVERT: Z  239 GLU cc_start: 0.9252 (tp30) cc_final: 0.8581 (tp30)
REVERT: Y   31 ARG cc_start: 0.9019 (tpp-160) cc_final: 0.8641 (tpp80)
REVERT: T   59 ASP cc_start: 0.5288 (OUTLIER) cc_final: 0.4870 (m-30)
REVERT: T  136 HIS cc_start: 0.5976 (OUTLIER) cc_final: 0.5645 (m170)
REVERT: T  239 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8729 (mm-30)
REVERT: T  254 ILE cc_start: 0.9060 (mm) cc_final: 0.8594 (tt)
REVERT: T  264 MET cc_start: 0.5626 (tpp) cc_final: 0.5185 (tpp)
REVERT: T  272 LEU cc_start: 0.7516 (tp) cc_final: 0.7034 (tt)
REVERT: T  291 PHE cc_start: 0.9266 (t80) cc_final: 0.9025 (t80)
  outliers start: 46
  outliers final: 40
  residues processed: 314
  average time/residue: 0.1958
  time to fit residues: 86.9267
Evaluate side-chains
  323 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 280
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   64 LEU
Chi-restraints excluded: chain I residue   29 SER
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain I residue   56 THR
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain I residue   65 VAL
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain K residue   18 ILE
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain K residue   56 THR
Chi-restraints excluded: chain L residue   38 ASN
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   68 PHE
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain O residue   45 VAL
Chi-restraints excluded: chain O residue   68 PHE
Chi-restraints excluded: chain P residue   45 VAL
Chi-restraints excluded: chain Q residue    7 VAL
Chi-restraints excluded: chain Q residue   68 PHE
Chi-restraints excluded: chain Z residue   26 TYR
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   54 VAL
Chi-restraints excluded: chain Z residue   76 VAL
Chi-restraints excluded: chain Z residue   80 LEU
Chi-restraints excluded: chain Z residue  103 VAL
Chi-restraints excluded: chain Z residue  126 LEU
Chi-restraints excluded: chain Z residue  224 THR
Chi-restraints excluded: chain Z residue  240 LEU
Chi-restraints excluded: chain Z residue  266 PHE
Chi-restraints excluded: chain Z residue  286 ILE
Chi-restraints excluded: chain Z residue  294 LEU
Chi-restraints excluded: chain Y residue   20 LEU
Chi-restraints excluded: chain Y residue   35 ASN
Chi-restraints excluded: chain Y residue   56 GLU
Chi-restraints excluded: chain V residue   17 ASN
Chi-restraints excluded: chain V residue   25 LEU
Chi-restraints excluded: chain V residue   36 LEU
Chi-restraints excluded: chain T residue   59 ASP
Chi-restraints excluded: chain T residue   84 MET
Chi-restraints excluded: chain T residue  136 HIS
Chi-restraints excluded: chain T residue  231 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 73 optimal weight:    0.0010
   chunk 88 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 71 optimal weight:    0.3980
   chunk 83 optimal weight:    0.9990
   chunk 114 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9990
   chunk 126 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 105 optimal weight:    0.3980
   overall best weight:    0.4586

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

Flipped N/Q/H residues before XYZ refinement:
** Y  17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.124562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.089372 restraints weight = 19665.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.90
r_work: 0.3168 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10165  Z= 0.139
  Angle     :  0.557   7.645  13835  Z= 0.293
  Chirality :  0.043   0.288   1716
  Planarity :  0.005   0.063   1745
  Dihedral  :  3.612  22.227   1428
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 33.33 %
    Favored  : 61.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.23), residues: 1342
  helix:  2.00 (0.15), residues: 1092
  sheet:  None (None), residues: 0
  loop : -2.03 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP T 208 
 HIS   0.001   0.000   HIS Z 170 
 PHE   0.027   0.001   PHE Z 276 
 TYR   0.014   0.001   TYR Z 296 
 ARG   0.008   0.000   ARG K  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03971 (  876)
  hydrogen bonds       : angle       3.60144 ( 2604)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       0.72855 (    2)
  covalent geometry    : bond        0.00322 (10164)
  covalent geometry    : angle       0.55731 (13833)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 296
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I    2 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8421 (mm-30)
REVERT: I    5 ASN cc_start: 0.8785 (p0) cc_final: 0.8544 (p0)
REVERT: I   38 ASN cc_start: 0.9028 (t0) cc_final: 0.8637 (t0)
REVERT: J    4 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8695 (mp)
REVERT: J   38 ASN cc_start: 0.9203 (t0) cc_final: 0.8904 (t0)
REVERT: K   41 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9199 (tp)
REVERT: M   48 TYR cc_start: 0.9149 (m-80) cc_final: 0.8760 (m-80)
REVERT: N   41 ILE cc_start: 0.9062 (tp) cc_final: 0.8765 (tp)
REVERT: P   70 ILE cc_start: 0.9327 (mm) cc_final: 0.9115 (mm)
REVERT: Q   37 ARG cc_start: 0.8524 (tpp80) cc_final: 0.8228 (mtm-85)
REVERT: Q   38 ASN cc_start: 0.9046 (t0) cc_final: 0.8438 (t0)
REVERT: Q   44 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7859 (tmm-80)
REVERT: Q   48 TYR cc_start: 0.8750 (m-80) cc_final: 0.8439 (m-80)
REVERT: Z   23 PHE cc_start: 0.7627 (m-80) cc_final: 0.7324 (m-80)
REVERT: Z   71 ARG cc_start: 0.7922 (ttt90) cc_final: 0.7569 (ttm-80)
REVERT: Z   78 ARG cc_start: 0.4602 (tmt170) cc_final: 0.4226 (tmt170)
REVERT: Z  101 LYS cc_start: 0.9314 (tttm) cc_final: 0.8931 (tttm)
REVERT: Z  102 TYR cc_start: 0.8437 (m-80) cc_final: 0.8008 (m-80)
REVERT: Z  239 GLU cc_start: 0.9233 (tp30) cc_final: 0.8680 (tp30)
REVERT: Z  242 LYS cc_start: 0.9160 (mttt) cc_final: 0.8743 (mttt)
REVERT: Y   31 ARG cc_start: 0.9046 (tpp-160) cc_final: 0.8677 (tpp80)
REVERT: T   59 ASP cc_start: 0.5289 (OUTLIER) cc_final: 0.4825 (m-30)
REVERT: T  136 HIS cc_start: 0.6017 (OUTLIER) cc_final: 0.5694 (m170)
REVERT: T  239 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8714 (mm-30)
REVERT: T  254 ILE cc_start: 0.9065 (mm) cc_final: 0.8607 (tt)
REVERT: T  264 MET cc_start: 0.5601 (tpp) cc_final: 0.5319 (tpp)
REVERT: T  272 LEU cc_start: 0.7479 (tp) cc_final: 0.7012 (tt)
REVERT: T  291 PHE cc_start: 0.9261 (t80) cc_final: 0.9033 (t80)
  outliers start: 49
  outliers final: 39
  residues processed: 323
  average time/residue: 0.2024
  time to fit residues: 92.5252
Evaluate side-chains
  325 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 282
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   64 LEU
Chi-restraints excluded: chain I residue   29 SER
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain I residue   56 THR
Chi-restraints excluded: chain I residue   65 VAL
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain K residue   41 ILE
Chi-restraints excluded: chain K residue   42 GLU
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain K residue   56 THR
Chi-restraints excluded: chain L residue   38 ASN
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain O residue   45 VAL
Chi-restraints excluded: chain O residue   66 ILE
Chi-restraints excluded: chain O residue   68 PHE
Chi-restraints excluded: chain P residue   45 VAL
Chi-restraints excluded: chain P residue   59 LEU
Chi-restraints excluded: chain Q residue    7 VAL
Chi-restraints excluded: chain Q residue   68 PHE
Chi-restraints excluded: chain Z residue   26 TYR
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   54 VAL
Chi-restraints excluded: chain Z residue   76 VAL
Chi-restraints excluded: chain Z residue   80 LEU
Chi-restraints excluded: chain Z residue  103 VAL
Chi-restraints excluded: chain Z residue  126 LEU
Chi-restraints excluded: chain Z residue  224 THR
Chi-restraints excluded: chain Z residue  240 LEU
Chi-restraints excluded: chain Z residue  266 PHE
Chi-restraints excluded: chain Z residue  286 ILE
Chi-restraints excluded: chain Y residue   20 LEU
Chi-restraints excluded: chain Y residue   35 ASN
Chi-restraints excluded: chain Y residue   56 GLU
Chi-restraints excluded: chain V residue   17 ASN
Chi-restraints excluded: chain V residue   25 LEU
Chi-restraints excluded: chain V residue   36 LEU
Chi-restraints excluded: chain T residue   59 ASP
Chi-restraints excluded: chain T residue   84 MET
Chi-restraints excluded: chain T residue  118 LEU
Chi-restraints excluded: chain T residue  136 HIS
Chi-restraints excluded: chain T residue  231 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 111 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9980
   chunk 131 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 121 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 126 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** Y  17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  97 ASN
** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.123581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.088604 restraints weight = 19695.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.88
r_work: 0.3156 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  10165  Z= 0.157
  Angle     :  0.580   8.414  13835  Z= 0.304
  Chirality :  0.044   0.306   1716
  Planarity :  0.005   0.063   1745
  Dihedral  :  3.636  22.014   1428
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 34.70 %
    Favored  : 60.55 %
  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:  1.87 (0.23), residues: 1342
  helix:  1.95 (0.15), residues: 1092
  sheet:  None (None), residues: 0
  loop : -2.06 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP T 208 
 HIS   0.001   0.000   HIS Z 170 
 PHE   0.027   0.001   PHE J  62 
 TYR   0.017   0.002   TYR T 277 
 ARG   0.011   0.001   ARG K  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04048 (  876)
  hydrogen bonds       : angle       3.64548 ( 2604)
  SS BOND              : bond        0.00108 (    1)
  SS BOND              : angle       0.55226 (    2)
  covalent geometry    : bond        0.00375 (10164)
  covalent geometry    : angle       0.57971 (13833)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 287
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I    2 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8440 (mm-30)
REVERT: I    5 ASN cc_start: 0.8809 (p0) cc_final: 0.8565 (p0)
REVERT: I   38 ASN cc_start: 0.9060 (t0) cc_final: 0.8677 (t0)
REVERT: J    4 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8724 (mp)
REVERT: J   37 ARG cc_start: 0.8653 (mtt180) cc_final: 0.8372 (mtm-85)
REVERT: J   38 ASN cc_start: 0.9235 (t0) cc_final: 0.8926 (t0)
REVERT: K   41 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.9231 (tp)
REVERT: N   41 ILE cc_start: 0.9079 (tp) cc_final: 0.8775 (tp)
REVERT: Q   37 ARG cc_start: 0.8584 (tpp80) cc_final: 0.8174 (mtm-85)
REVERT: Q   38 ASN cc_start: 0.9054 (t0) cc_final: 0.8443 (t0)
REVERT: Q   44 ARG cc_start: 0.8256 (ttp80) cc_final: 0.7834 (tmm-80)
REVERT: Q   48 TYR cc_start: 0.8780 (m-80) cc_final: 0.8446 (m-80)
REVERT: Z   23 PHE cc_start: 0.7607 (m-80) cc_final: 0.7336 (m-80)
REVERT: Z   71 ARG cc_start: 0.7937 (ttt90) cc_final: 0.7584 (ttm-80)
REVERT: Z   78 ARG cc_start: 0.4762 (tmt170) cc_final: 0.4341 (tmt170)
REVERT: Z  201 SER cc_start: 0.9043 (t) cc_final: 0.8805 (t)
REVERT: Z  239 GLU cc_start: 0.9243 (tp30) cc_final: 0.8537 (tp30)
REVERT: Z  242 LYS cc_start: 0.9167 (mttt) cc_final: 0.8755 (mttt)
REVERT: Y   31 ARG cc_start: 0.9039 (tpp-160) cc_final: 0.8672 (tpp80)
REVERT: T  136 HIS cc_start: 0.6092 (OUTLIER) cc_final: 0.5755 (m170)
REVERT: T  239 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8817 (mm-30)
REVERT: T  254 ILE cc_start: 0.9026 (mm) cc_final: 0.8532 (tt)
REVERT: T  272 LEU cc_start: 0.7569 (tp) cc_final: 0.7238 (tt)
REVERT: T  291 PHE cc_start: 0.9289 (t80) cc_final: 0.9054 (t80)
  outliers start: 45
  outliers final: 40
  residues processed: 314
  average time/residue: 0.1968
  time to fit residues: 88.0581
Evaluate side-chains
  326 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 283
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   64 LEU
Chi-restraints excluded: chain I residue   29 SER
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain I residue   56 THR
Chi-restraints excluded: chain I residue   65 VAL
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain K residue   18 ILE
Chi-restraints excluded: chain K residue   41 ILE
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain K residue   56 THR
Chi-restraints excluded: chain L residue   38 ASN
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain O residue   45 VAL
Chi-restraints excluded: chain O residue   66 ILE
Chi-restraints excluded: chain O residue   68 PHE
Chi-restraints excluded: chain P residue   45 VAL
Chi-restraints excluded: chain P residue   59 LEU
Chi-restraints excluded: chain Q residue    7 VAL
Chi-restraints excluded: chain Q residue   68 PHE
Chi-restraints excluded: chain Z residue   26 TYR
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   54 VAL
Chi-restraints excluded: chain Z residue   76 VAL
Chi-restraints excluded: chain Z residue   80 LEU
Chi-restraints excluded: chain Z residue  103 VAL
Chi-restraints excluded: chain Z residue  126 LEU
Chi-restraints excluded: chain Z residue  224 THR
Chi-restraints excluded: chain Z residue  240 LEU
Chi-restraints excluded: chain Z residue  266 PHE
Chi-restraints excluded: chain Z residue  286 ILE
Chi-restraints excluded: chain Y residue   20 LEU
Chi-restraints excluded: chain Y residue   35 ASN
Chi-restraints excluded: chain Y residue   56 GLU
Chi-restraints excluded: chain V residue   17 ASN
Chi-restraints excluded: chain V residue   25 LEU
Chi-restraints excluded: chain V residue   36 LEU
Chi-restraints excluded: chain T residue   84 MET
Chi-restraints excluded: chain T residue  118 LEU
Chi-restraints excluded: chain T residue  136 HIS
Chi-restraints excluded: chain T residue  231 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 131 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 102 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:
** Y  17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.123125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.087980 restraints weight = 19756.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.88
r_work: 0.3141 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  10165  Z= 0.169
  Angle     :  0.611  13.464  13835  Z= 0.316
  Chirality :  0.046   0.437   1716
  Planarity :  0.005   0.064   1745
  Dihedral  :  3.640  21.067   1428
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 34.49 %
    Favored  : 60.86 %
  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:  1.80 (0.23), residues: 1342
  helix:  1.89 (0.15), residues: 1093
  sheet:  None (None), residues: 0
  loop : -2.04 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP T 208 
 HIS   0.001   0.000   HIS Z 170 
 PHE   0.027   0.001   PHE O  62 
 TYR   0.018   0.002   TYR M  48 
 ARG   0.009   0.000   ARG K  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04133 (  876)
  hydrogen bonds       : angle       3.69137 ( 2604)
  SS BOND              : bond        0.00096 (    1)
  SS BOND              : angle       0.60004 (    2)
  covalent geometry    : bond        0.00404 (10164)
  covalent geometry    : angle       0.61113 (13833)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 286
  time to evaluate  : 1.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I    2 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8422 (mm-30)
REVERT: I    5 ASN cc_start: 0.8841 (p0) cc_final: 0.8582 (p0)
REVERT: I   38 ASN cc_start: 0.9073 (t0) cc_final: 0.8691 (t0)
REVERT: J    4 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8739 (mp)
REVERT: J   38 ASN cc_start: 0.9282 (t0) cc_final: 0.8958 (t0)
REVERT: K   41 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9250 (tp)
REVERT: N   41 ILE cc_start: 0.9083 (tp) cc_final: 0.8786 (tp)
REVERT: P   70 ILE cc_start: 0.9347 (mm) cc_final: 0.9145 (mm)
REVERT: Q   38 ASN cc_start: 0.9052 (t0) cc_final: 0.8429 (t0)
REVERT: Q   44 ARG cc_start: 0.8308 (ttp80) cc_final: 0.7855 (tmm-80)
REVERT: Q   48 TYR cc_start: 0.8805 (m-80) cc_final: 0.8457 (m-80)
REVERT: Z   23 PHE cc_start: 0.7623 (m-80) cc_final: 0.7370 (m-80)
REVERT: Z   71 ARG cc_start: 0.7923 (ttt90) cc_final: 0.7574 (ttm-80)
REVERT: Z   78 ARG cc_start: 0.4701 (tmt170) cc_final: 0.4278 (tmt170)
REVERT: Z  201 SER cc_start: 0.9033 (t) cc_final: 0.8789 (t)
REVERT: Z  239 GLU cc_start: 0.9246 (tp30) cc_final: 0.8532 (tp30)
REVERT: Z  242 LYS cc_start: 0.9172 (mttt) cc_final: 0.8622 (mttm)
REVERT: Y   31 ARG cc_start: 0.9047 (tpp-160) cc_final: 0.8677 (tpp80)
REVERT: T  136 HIS cc_start: 0.6200 (OUTLIER) cc_final: 0.5846 (m170)
REVERT: T  239 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8742 (mm-30)
REVERT: T  254 ILE cc_start: 0.9042 (mm) cc_final: 0.8592 (tt)
REVERT: T  272 LEU cc_start: 0.7441 (tp) cc_final: 0.7147 (tt)
REVERT: T  291 PHE cc_start: 0.9309 (t80) cc_final: 0.9083 (t80)
  outliers start: 44
  outliers final: 39
  residues processed: 312
  average time/residue: 0.1956
  time to fit residues: 86.6813
Evaluate side-chains
  325 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 283
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   64 LEU
Chi-restraints excluded: chain I residue   29 SER
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain I residue   56 THR
Chi-restraints excluded: chain I residue   65 VAL
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain K residue   18 ILE
Chi-restraints excluded: chain K residue   41 ILE
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain K residue   56 THR
Chi-restraints excluded: chain L residue   38 ASN
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain O residue   45 VAL
Chi-restraints excluded: chain O residue   68 PHE
Chi-restraints excluded: chain P residue   45 VAL
Chi-restraints excluded: chain P residue   47 THR
Chi-restraints excluded: chain P residue   59 LEU
Chi-restraints excluded: chain Q residue    7 VAL
Chi-restraints excluded: chain Q residue   68 PHE
Chi-restraints excluded: chain Z residue   26 TYR
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   54 VAL
Chi-restraints excluded: chain Z residue   76 VAL
Chi-restraints excluded: chain Z residue   80 LEU
Chi-restraints excluded: chain Z residue  103 VAL
Chi-restraints excluded: chain Z residue  126 LEU
Chi-restraints excluded: chain Z residue  224 THR
Chi-restraints excluded: chain Z residue  240 LEU
Chi-restraints excluded: chain Z residue  266 PHE
Chi-restraints excluded: chain Z residue  286 ILE
Chi-restraints excluded: chain Y residue   20 LEU
Chi-restraints excluded: chain Y residue   35 ASN
Chi-restraints excluded: chain Y residue   56 GLU
Chi-restraints excluded: chain V residue   17 ASN
Chi-restraints excluded: chain V residue   25 LEU
Chi-restraints excluded: chain V residue   36 LEU
Chi-restraints excluded: chain T residue   84 MET
Chi-restraints excluded: chain T residue  118 LEU
Chi-restraints excluded: chain T residue  136 HIS
Chi-restraints excluded: chain T residue  231 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 121 optimal weight:    0.0030
   chunk 6 optimal weight:    0.9980
   chunk 93 optimal weight:    0.4980
   chunk 29 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0000
   chunk 85 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 78 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   overall best weight:    0.3394

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

Flipped N/Q/H residues before XYZ refinement:
** Y  17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  97 ASN
** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.125037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.090095 restraints weight = 19468.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.85
r_work: 0.3191 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  10165  Z= 0.139
  Angle     :  0.604  13.497  13835  Z= 0.309
  Chirality :  0.045   0.457   1716
  Planarity :  0.005   0.062   1745
  Dihedral  :  3.639  21.170   1428
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 34.70 %
    Favored  : 61.08 %
  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:  1.83 (0.23), residues: 1342
  helix:  1.92 (0.15), residues: 1092
  sheet:  None (None), residues: 0
  loop : -2.05 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP T 208 
 HIS   0.001   0.000   HIS Z 170 
 PHE   0.038   0.001   PHE M  62 
 TYR   0.015   0.002   TYR T 277 
 ARG   0.008   0.001   ARG K  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04008 (  876)
  hydrogen bonds       : angle       3.64222 ( 2604)
  SS BOND              : bond        0.00030 (    1)
  SS BOND              : angle       0.64038 (    2)
  covalent geometry    : bond        0.00322 (10164)
  covalent geometry    : angle       0.60367 (13833)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5009.70 seconds
wall clock time: 87 minutes 18.39 seconds (5238.39 seconds total)