Starting phenix.real_space_refine
on Thu Mar 13 10:50:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7upn_26673/03_2025/7upn_26673.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7upn_26673/03_2025/7upn_26673.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7upn_26673/03_2025/7upn_26673.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7upn_26673/03_2025/7upn_26673.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7upn_26673/03_2025/7upn_26673.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7upn_26673/03_2025/7upn_26673.cif"
  }
  resolution = 3.5
  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=   0.003 sd=   0.027
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: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      58      5.16       5
     C    5698      2.51       5
     N    1526      2.21       5
     O    1588      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8872
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 163, 1248
          Classifications: {'peptide': 163}
          Link IDs: {'PTRANS': 6, 'TRANS': 156}
    Chain: "C"
      Number of atoms: 1771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1771
          Classifications: {'peptide': 208}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 9, 'TRANS': 198}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 16
    Chain: "E"
      Number of atoms: 684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 684
          Classifications: {'peptide': 86}
          Link IDs: {'PTRANS': 4, 'TRANS': 81}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 732
          Classifications: {'peptide': 93}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 86}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 1248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 163, 1248
          Classifications: {'peptide': 163}
          Link IDs: {'PTRANS': 6, 'TRANS': 156}
    Chain: "F"
      Number of atoms: 1771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1771
          Classifications: {'peptide': 208}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 9, 'TRANS': 198}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 16
    Chain: "G"
      Number of atoms: 684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 684
          Classifications: {'peptide': 86}
          Link IDs: {'PTRANS': 4, 'TRANS': 81}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 732
          Classifications: {'peptide': 93}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 86}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2218  SG  CYS C 135      91.948  47.665  47.487  1.00 94.84           S
  ATOM   2230  SG  CYS C 137      95.347  47.388  45.860  1.00 97.86           S
  ATOM   2412  SG  CYS C 157      94.166  50.756  46.865  1.00 93.10           S
  ATOM   2433  SG  CYS C 160      95.075  48.157  49.582  1.00 84.53           S
  ATOM   6653  SG  CYS F 135      55.449  44.735  47.627  1.00 94.28           S
  ATOM   6665  SG  CYS F 137      52.062  45.021  45.976  1.00100.38           S
  ATOM   6847  SG  CYS F 157      53.228  41.650  46.990  1.00 93.43           S
  ATOM   6868  SG  CYS F 160      52.307  44.252  49.701  1.00 84.59           S

  Time building chain proxies: 5.85, per 1000 atoms: 0.66
  Number of scatterers: 8872
  At special positions: 0
  Unit cell: (148.5, 94.6, 106.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      58     16.00
     O    1588      8.00
     N    1526      7.00
     C    5698      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.27
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C 301 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C 137 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C 135 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C 157 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C 160 "
      pdb="  ZN F 301 "
        pdb="ZN    ZN F 301 " - pdb=" SG  CYS F 137 "
        pdb="ZN    ZN F 301 " - pdb=" SG  CYS F 135 "
        pdb="ZN    ZN F 301 " - pdb=" SG  CYS F 157 "
        pdb="ZN    ZN F 301 " - pdb=" SG  CYS F 160 "
      Number of angles added : 12


  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2028

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      26.2% alpha, 14.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 42
      removed outlier: 3.918A  pdb=" N   ALA A  33 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 144
    Processing helix  chain 'C' and resid 41 through 52
    Processing helix  chain 'C' and resid 115 through 120
    Processing helix  chain 'C' and resid 123 through 135
      removed outlier: 3.593A  pdb=" N   TRP C 127 " --> pdb=" O   GLU C 123 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ILE C 132 " --> pdb=" O   PHE C 128 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   CYS C 135 " --> pdb=" O   ARG C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 157 through 169
      removed outlier: 3.516A  pdb=" N   GLN C 162 " --> pdb=" O   LYS C 158 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLY C 163 " --> pdb=" O   SER C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 183
    Processing helix  chain 'C' and resid 218 through 223
    Processing helix  chain 'E' and resid 33 through 37
    Processing helix  chain 'E' and resid 39 through 48
    Processing helix  chain 'E' and resid 66 through 83
      removed outlier: 3.698A  pdb=" N   MET E  75 " --> pdb=" O   SER E  71 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   TYR E  76 " --> pdb=" O   LYS E  72 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   PHE E  77 " --> pdb=" O   VAL E  73 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   THR E  78 " --> pdb=" O   CYS E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 96 through 111
      removed outlier: 4.231A  pdb=" N   LEU E 101 " --> pdb=" O   PRO E  97 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   GLU E 102 " --> pdb=" O   GLU E  98 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU E 104 " --> pdb=" O   ALA E 100 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   MET E 105 " --> pdb=" O   LEU E 101 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ALA E 106 " --> pdb=" O   GLU E 102 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   PHE E 109 " --> pdb=" O   MET E 105 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 23 through 36
      removed outlier: 4.233A  pdb=" N   LEU H  27 " --> pdb=" O   THR H  23 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY H  33 " --> pdb=" O   ARG H  29 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ILE H  34 " --> pdb=" O   ILE H  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 42
      removed outlier: 3.919A  pdb=" N   ALA B  33 " --> pdb=" O   VAL B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 144
    Processing helix  chain 'F' and resid 41 through 52
    Processing helix  chain 'F' and resid 115 through 120
    Processing helix  chain 'F' and resid 123 through 135
      removed outlier: 3.592A  pdb=" N   TRP F 127 " --> pdb=" O   GLU F 123 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ILE F 132 " --> pdb=" O   PHE F 128 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   CYS F 135 " --> pdb=" O   ARG F 131 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 157 through 169
      removed outlier: 3.516A  pdb=" N   GLN F 162 " --> pdb=" O   LYS F 158 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLY F 163 " --> pdb=" O   SER F 159 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 177 through 183
    Processing helix  chain 'F' and resid 218 through 223
    Processing helix  chain 'G' and resid 33 through 37
    Processing helix  chain 'G' and resid 39 through 48
    Processing helix  chain 'G' and resid 66 through 83
      removed outlier: 3.698A  pdb=" N   MET G  75 " --> pdb=" O   SER G  71 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   TYR G  76 " --> pdb=" O   LYS G  72 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   PHE G  77 " --> pdb=" O   VAL G  73 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   THR G  78 " --> pdb=" O   CYS G  74 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 96 through 111
      removed outlier: 4.231A  pdb=" N   LEU G 101 " --> pdb=" O   PRO G  97 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   GLU G 102 " --> pdb=" O   GLU G  98 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU G 104 " --> pdb=" O   ALA G 100 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   MET G 105 " --> pdb=" O   LEU G 101 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ALA G 106 " --> pdb=" O   GLU G 102 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   PHE G 109 " --> pdb=" O   MET G 105 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 23 through 36
      removed outlier: 4.233A  pdb=" N   LEU I  27 " --> pdb=" O   THR I  23 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY I  33 " --> pdb=" O   ARG I  29 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ILE I  34 " --> pdb=" O   ILE I  30 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 57
      removed outlier: 3.699A  pdb=" N   ARG A  55 " --> pdb=" O   GLN A  63 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   GLN A 111 " --> pdb=" O   ALA A 101 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   MET A 100 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   VAL A 128 " --> pdb=" O   MET A 100 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   SER A  21 " --> pdb=" O   LYS A 133 " (cutoff:3.500A)
      removed outlier: 5.637A  pdb=" N   VAL A  12 " --> pdb=" O   PRO A  16 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   GLY A  18 " --> pdb=" O   ILE A  10 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   THR A   5 " --> pdb=" O   GLN A 163 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   GLN A 163 " --> pdb=" O   THR A   5 " (cutoff:3.500A)
      removed outlier: 7.352A  pdb=" N   PHE A   7 " --> pdb=" O   CYS A 161 " (cutoff:3.500A)
      removed outlier: 4.955A  pdb=" N   CYS A 161 " --> pdb=" O   PHE A   7 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ASP A   9 " --> pdb=" O   ALA A 159 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 61 through 64
      removed outlier: 4.263A  pdb=" N   GLU C  69 " --> pdb=" O   VAL C  62 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 28 through 32
      removed outlier: 8.382A  pdb=" N   VAL E  60 " --> pdb=" O   TYR E  18 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   LYS E  20 " --> pdb=" O   VAL E  60 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 12 through 18
      removed outlier: 3.867A  pdb=" N   ALA H  73 " --> pdb=" O   PHE H   4 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 45 through 46
    Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 57
      removed outlier: 3.698A  pdb=" N   ARG B  55 " --> pdb=" O   GLN B  63 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   GLN B 111 " --> pdb=" O   ALA B 101 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   MET B 100 " --> pdb=" O   VAL B 128 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   VAL B 128 " --> pdb=" O   MET B 100 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   SER B  21 " --> pdb=" O   LYS B 133 " (cutoff:3.500A)
      removed outlier: 5.637A  pdb=" N   VAL B  12 " --> pdb=" O   PRO B  16 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   GLY B  18 " --> pdb=" O   ILE B  10 " (cutoff:3.500A)
      removed outlier: 7.772A  pdb=" N   THR B   5 " --> pdb=" O   GLN B 163 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   GLN B 163 " --> pdb=" O   THR B   5 " (cutoff:3.500A)
      removed outlier: 7.352A  pdb=" N   PHE B   7 " --> pdb=" O   CYS B 161 " (cutoff:3.500A)
      removed outlier: 4.955A  pdb=" N   CYS B 161 " --> pdb=" O   PHE B   7 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ASP B   9 " --> pdb=" O   ALA B 159 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 61 through 64
      removed outlier: 4.265A  pdb=" N   GLU F  69 " --> pdb=" O   VAL F  62 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 28 through 32
      removed outlier: 8.382A  pdb=" N   VAL G  60 " --> pdb=" O   TYR G  18 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   LYS G  20 " --> pdb=" O   VAL G  60 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'I' and resid 12 through 18
      removed outlier: 3.867A  pdb=" N   ALA I  73 " --> pdb=" O   PHE I   4 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'I' and resid 45 through 46

    248 hydrogen bonds defined for protein.
    690 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: 2.08

  Time building geometry restraints manager: 2.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2515
        1.33 -     1.45: 1621
        1.45 -     1.57: 4878
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 9104
  Sorted by residual:
  bond pdb=" CA  GLU F  64 "
       pdb=" C   GLU F  64 "
    ideal  model  delta    sigma   weight residual
    1.533  1.507  0.026 9.60e-03 1.09e+04 7.50e+00
  bond pdb=" CA  ASN F  65 "
       pdb=" C   ASN F  65 "
    ideal  model  delta    sigma   weight residual
    1.522  1.497  0.025 1.18e-02 7.18e+03 4.49e+00
  bond pdb=" CA  ASN C  65 "
       pdb=" C   ASN C  65 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.022 1.17e-02 7.31e+03 3.48e+00
  bond pdb=" C   TYR C  68 "
       pdb=" O   TYR C  68 "
    ideal  model  delta    sigma   weight residual
    1.235  1.216  0.020 1.21e-02 6.83e+03 2.61e+00
  bond pdb=" C   LEU C  23 "
       pdb=" N   PRO C  24 "
    ideal  model  delta    sigma   weight residual
    1.334  1.371 -0.037 2.34e-02 1.83e+03 2.56e+00
  ... (remaining 9099 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 11978
        1.46 -     2.91: 253
        2.91 -     4.37: 35
        4.37 -     5.82: 12
        5.82 -     7.28: 6
  Bond angle restraints: 12284
  Sorted by residual:
  angle pdb=" C   HIS I  10 "
        pdb=" CA  HIS I  10 "
        pdb=" CB  HIS I  10 "
      ideal   model   delta    sigma   weight residual
     110.42  116.96   -6.54 1.99e+00 2.53e-01 1.08e+01
  angle pdb=" C   HIS H  10 "
        pdb=" CA  HIS H  10 "
        pdb=" CB  HIS H  10 "
      ideal   model   delta    sigma   weight residual
     110.42  116.92   -6.50 1.99e+00 2.53e-01 1.07e+01
  angle pdb=" CA  PRO F  24 "
        pdb=" N   PRO F  24 "
        pdb=" CD  PRO F  24 "
      ideal   model   delta    sigma   weight residual
     112.00  107.59    4.41 1.40e+00 5.10e-01 9.93e+00
  angle pdb=" CA  PRO C  24 "
        pdb=" N   PRO C  24 "
        pdb=" CD  PRO C  24 "
      ideal   model   delta    sigma   weight residual
     112.00  107.66    4.34 1.40e+00 5.10e-01 9.62e+00
  angle pdb=" N   PRO C  24 "
        pdb=" CA  PRO C  24 "
        pdb=" C   PRO C  24 "
      ideal   model   delta    sigma   weight residual
     112.47  118.61   -6.14 2.06e+00 2.36e-01 8.89e+00
  ... (remaining 12279 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.61: 4765
       17.61 -    35.22: 485
       35.22 -    52.83: 78
       52.83 -    70.44: 18
       70.44 -    88.05: 12
  Dihedral angle restraints: 5358
    sinusoidal: 2214
      harmonic: 3144
  Sorted by residual:
  dihedral pdb=" CA  LEU C  23 "
           pdb=" C   LEU C  23 "
           pdb=" N   PRO C  24 "
           pdb=" CA  PRO C  24 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.42  -23.58     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  LEU F  23 "
           pdb=" C   LEU F  23 "
           pdb=" N   PRO F  24 "
           pdb=" CA  PRO F  24 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.47  -23.53     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CB  GLU E  59 "
           pdb=" CG  GLU E  59 "
           pdb=" CD  GLU E  59 "
           pdb=" OE1 GLU E  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.05   88.05     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 5355 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 987
       0.044 -    0.088: 231
       0.088 -    0.132: 56
       0.132 -    0.176: 6
       0.176 -    0.220: 2
  Chirality restraints: 1282
  Sorted by residual:
  chirality pdb=" CA  PRO C  24 "
            pdb=" N   PRO C  24 "
            pdb=" C   PRO C  24 "
            pdb=" CB  PRO C  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  PRO F  24 "
            pdb=" N   PRO F  24 "
            pdb=" C   PRO F  24 "
            pdb=" CB  PRO F  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  GLN C  66 "
            pdb=" N   GLN C  66 "
            pdb=" C   GLN C  66 "
            pdb=" CB  GLN C  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.21e-01
  ... (remaining 1279 not shown)

  Planarity restraints: 1562
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C  23 "    0.069 5.00e-02 4.00e+02   1.04e-01 1.73e+01
        pdb=" N   PRO C  24 "   -0.180 5.00e-02 4.00e+02
        pdb=" CA  PRO C  24 "    0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO C  24 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU F  23 "    0.069 5.00e-02 4.00e+02   1.04e-01 1.73e+01
        pdb=" N   PRO F  24 "   -0.180 5.00e-02 4.00e+02
        pdb=" CA  PRO F  24 "    0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO F  24 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H  91 "    0.021 5.00e-02 4.00e+02   3.10e-02 1.54e+00
        pdb=" N   PRO H  92 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO H  92 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO H  92 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1559 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2443
        2.81 -     3.33: 7770
        3.33 -     3.85: 13561
        3.85 -     4.38: 14798
        4.38 -     4.90: 26239
  Nonbonded interactions: 64811
  Sorted by model distance:
  nonbonded pdb=" O   LYS G  80 "
            pdb=" OG1 THR G  84 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   LYS E  80 "
            pdb=" OG1 THR E  84 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   ASP F  87 "
            pdb=" N   ARG F  95 "
     model   vdw
     2.329 3.120
  nonbonded pdb=" O   ASP C  87 "
            pdb=" N   ARG C  95 "
     model   vdw
     2.329 3.120
  nonbonded pdb=" OE2 GLU C 123 "
            pdb=" NE1 TRP C 127 "
     model   vdw
     2.347 3.120
  ... (remaining 64806 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'I'
  selection = chain 'H'
}

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 group one per residue
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:             0.720
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.100
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.059   9104  Z= 0.162
  Angle     :  0.529   7.278  12284  Z= 0.282
  Chirality :  0.041   0.220   1282
  Planarity :  0.005   0.104   1562
  Dihedral  : 14.658  88.054   3330
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  7.37 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  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: -1.27 (0.25), residues: 1072
  helix:  0.49 (0.32), residues: 270
  sheet:  0.85 (0.66), residues: 72
  loop : -1.66 (0.22), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  28 
 HIS   0.005   0.001   HIS H  10 
 PHE   0.012   0.001   PHE B 113 
 TYR   0.006   0.001   TYR C 213 
 ARG   0.002   0.000   ARG E  33 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.7820 (ppp) cc_final: 0.7067 (ppp)
REVERT: C  225 MET cc_start: 0.7755 (ttm) cc_final: 0.7341 (ttm)
REVERT: E   70 LEU cc_start: 0.8979 (tp) cc_final: 0.8751 (tt)
REVERT: E   76 TYR cc_start: 0.7799 (t80) cc_final: 0.7497 (t80)
REVERT: E   99 ILE cc_start: 0.8069 (tp) cc_final: 0.7748 (tt)
REVERT: H   52 ASP cc_start: 0.9406 (p0) cc_final: 0.9179 (p0)
REVERT: H   55 LYS cc_start: 0.8768 (tmmt) cc_final: 0.8357 (ptmm)
REVERT: B   61 MET cc_start: 0.7656 (ppp) cc_final: 0.7052 (ppp)
REVERT: F  225 MET cc_start: 0.7752 (ttm) cc_final: 0.7343 (ttm)
REVERT: I   55 LYS cc_start: 0.8866 (tmmt) cc_final: 0.8575 (ptmm)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1851
  time to fit residues: 39.7708
Evaluate side-chains
  116 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 80 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 27 optimal weight:    0.2980
   chunk 54 optimal weight:    7.9990
   chunk 42 optimal weight:    6.9990
   chunk 83 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0980
   chunk 61 optimal weight:    5.9990
   chunk 96 optimal weight:    4.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
C 220 GLN
** H  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 106 ASN
F 220 GLN
** I  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.084541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.063791 restraints weight = 36394.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.065673 restraints weight = 18781.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.066841 restraints weight = 12923.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9104  Z= 0.225
  Angle     :  0.557   6.825  12284  Z= 0.296
  Chirality :  0.044   0.216   1282
  Planarity :  0.005   0.107   1562
  Dihedral  :  4.074  23.121   1176
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  8.40 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  9.11 %
    Favored  : 89.41 %
  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: -1.37 (0.25), residues: 1072
  helix:  0.70 (0.31), residues: 282
  sheet:  0.18 (0.56), residues: 96
  loop : -1.89 (0.22), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 130 
 HIS   0.005   0.001   HIS H  10 
 PHE   0.011   0.001   PHE A 113 
 TYR   0.015   0.001   TYR G  76 
 ARG   0.004   0.000   ARG G  63 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 1.078 
Fit side-chains
REVERT: A   61 MET cc_start: 0.8137 (ppp) cc_final: 0.7509 (ppp)
REVERT: H   26 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8253 (pm20)
REVERT: H   52 ASP cc_start: 0.9495 (p0) cc_final: 0.9233 (p0)
REVERT: H   55 LYS cc_start: 0.8865 (tmmt) cc_final: 0.8367 (ptmm)
REVERT: B   61 MET cc_start: 0.8079 (ppp) cc_final: 0.7475 (ppp)
REVERT: I   26 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8458 (pm20)
REVERT: I   55 LYS cc_start: 0.9003 (tmmt) cc_final: 0.8649 (ptmm)
  outliers start: 14
  outliers final: 3
  residues processed: 127
  average time/residue: 0.1765
  time to fit residues: 33.1736
Evaluate side-chains
  110 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 GLU
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain H residue   26 GLU
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain I residue   26 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 87 optimal weight:    0.0020
   chunk 39 optimal weight:   10.0000
   chunk 104 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   overall best weight:    2.3794

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

Flipped N/Q/H residues before XYZ refinement:
C 181 HIS
C 220 GLN
H  49 GLN
F 181 HIS
F 186 HIS
F 220 GLN
** I  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.087542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.065711 restraints weight = 37686.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.067453 restraints weight = 19636.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.068627 restraints weight = 13736.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9104  Z= 0.290
  Angle     :  0.588  12.066  12284  Z= 0.315
  Chirality :  0.044   0.210   1282
  Planarity :  0.006   0.113   1562
  Dihedral  :  4.433  24.472   1176
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  8.96 %
    Favored  : 90.49 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 10.91 %
    Favored  : 87.39 %
  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: -1.70 (0.24), residues: 1072
  helix:  0.22 (0.31), residues: 310
  sheet: -0.55 (0.51), residues: 106
  loop : -2.02 (0.22), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  78 
 HIS   0.004   0.002   HIS B  92 
 PHE   0.013   0.002   PHE A   8 
 TYR   0.009   0.001   TYR G  76 
 ARG   0.005   0.000   ARG H   9 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8320 (ppp) cc_final: 0.7495 (ppp)
REVERT: C   71 TRP cc_start: 0.6012 (p-90) cc_final: 0.5142 (p-90)
REVERT: E   75 MET cc_start: 0.8184 (mtp) cc_final: 0.7890 (mtp)
REVERT: H   52 ASP cc_start: 0.9641 (p0) cc_final: 0.9390 (p0)
REVERT: H   55 LYS cc_start: 0.8850 (tmmt) cc_final: 0.8321 (ptmm)
REVERT: B   61 MET cc_start: 0.8297 (ppp) cc_final: 0.7405 (ppp)
REVERT: F   71 TRP cc_start: 0.6285 (p-90) cc_final: 0.5705 (p-90)
REVERT: G   75 MET cc_start: 0.8285 (mtp) cc_final: 0.7816 (mtm)
REVERT: I   52 ASP cc_start: 0.9365 (p0) cc_final: 0.9160 (p0)
REVERT: I   55 LYS cc_start: 0.8921 (tmmt) cc_final: 0.8492 (ptmm)
  outliers start: 16
  outliers final: 6
  residues processed: 118
  average time/residue: 0.1735
  time to fit residues: 30.0328
Evaluate side-chains
  99 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 CYS
Chi-restraints excluded: chain A residue  143 GLU
Chi-restraints excluded: chain B residue  115 CYS
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  142 MET
Chi-restraints excluded: chain B residue  143 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 77 optimal weight:    8.9990
   chunk 98 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   chunk 47 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9980
   chunk 99 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0370
   overall best weight:    1.4064

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

Flipped N/Q/H residues before XYZ refinement:
F 181 HIS
F 186 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.082875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.062223 restraints weight = 36795.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.064095 restraints weight = 18820.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.065258 restraints weight = 12981.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9104  Z= 0.211
  Angle     :  0.571  12.625  12284  Z= 0.295
  Chirality :  0.044   0.214   1282
  Planarity :  0.005   0.112   1562
  Dihedral  :  4.303  24.300   1176
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  8.58 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 11.44 %
    Favored  : 86.97 %
  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: -1.60 (0.24), residues: 1072
  helix:  0.36 (0.32), residues: 300
  sheet: -0.15 (0.47), residues: 128
  loop : -2.07 (0.22), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  78 
 HIS   0.004   0.001   HIS H  10 
 PHE   0.010   0.001   PHE B 113 
 TYR   0.014   0.001   TYR I  45 
 ARG   0.003   0.000   ARG I   9 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8292 (ppp) cc_final: 0.7446 (ppp)
REVERT: C   78 TRP cc_start: 0.7528 (m-10) cc_final: 0.7317 (m-10)
REVERT: C   80 MET cc_start: 0.7252 (mtt) cc_final: 0.7020 (mtt)
REVERT: E  105 MET cc_start: 0.9115 (mmm) cc_final: 0.8839 (mmm)
REVERT: H   52 ASP cc_start: 0.9528 (p0) cc_final: 0.9276 (p0)
REVERT: H   55 LYS cc_start: 0.8802 (tmmt) cc_final: 0.8248 (ptmm)
REVERT: B   61 MET cc_start: 0.8309 (ppp) cc_final: 0.7453 (ppp)
REVERT: F   71 TRP cc_start: 0.5835 (p-90) cc_final: 0.5373 (p-90)
REVERT: I   55 LYS cc_start: 0.8934 (tmmt) cc_final: 0.8452 (ptmm)
  outliers start: 15
  outliers final: 9
  residues processed: 113
  average time/residue: 0.1752
  time to fit residues: 29.1243
Evaluate side-chains
  106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue  115 CYS
Chi-restraints excluded: chain A residue  143 GLU
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue  115 CYS
Chi-restraints excluded: chain B residue  142 MET
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain F residue  109 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 86 optimal weight:    9.9990
   chunk 96 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 51 optimal weight:   10.0000
   chunk 93 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 92 optimal weight:   10.0000
   chunk 3 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** C  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 181 HIS
F 186 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.082807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.062266 restraints weight = 36688.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.064129 restraints weight = 18807.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.065303 restraints weight = 12996.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.3009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9104  Z= 0.208
  Angle     :  0.573  11.633  12284  Z= 0.292
  Chirality :  0.044   0.219   1282
  Planarity :  0.005   0.114   1562
  Dihedral  :  4.232  26.543   1176
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  8.77 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 12.92 %
    Favored  : 85.28 %
  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: -1.60 (0.25), residues: 1072
  helix:  0.44 (0.32), residues: 298
  sheet: -0.20 (0.46), residues: 128
  loop : -2.10 (0.21), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  78 
 HIS   0.004   0.001   HIS B 126 
 PHE   0.011   0.001   PHE B 113 
 TYR   0.009   0.001   TYR G  79 
 ARG   0.004   0.000   ARG I   9 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 1.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8303 (ppp) cc_final: 0.7484 (ppp)
REVERT: C   60 MET cc_start: 0.7694 (ptp) cc_final: 0.7490 (ptt)
REVERT: H   26 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8291 (pm20)
REVERT: H   52 ASP cc_start: 0.9575 (p0) cc_final: 0.9215 (p0)
REVERT: H   55 LYS cc_start: 0.8863 (tmmt) cc_final: 0.8582 (tttt)
REVERT: B   61 MET cc_start: 0.8328 (ppp) cc_final: 0.7450 (ppp)
REVERT: F   71 TRP cc_start: 0.6407 (p-90) cc_final: 0.6145 (p-90)
REVERT: G   63 ARG cc_start: 0.8477 (mmm160) cc_final: 0.8167 (mmm160)
REVERT: I   26 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8327 (pm20)
REVERT: I   55 LYS cc_start: 0.8830 (tmmt) cc_final: 0.8425 (ptmm)
  outliers start: 17
  outliers final: 11
  residues processed: 114
  average time/residue: 0.1816
  time to fit residues: 30.7053
Evaluate side-chains
  108 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue  115 CYS
Chi-restraints excluded: chain A residue  143 GLU
Chi-restraints excluded: chain C residue   74 SER
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain H residue   26 GLU
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue  115 CYS
Chi-restraints excluded: chain B residue  142 MET
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain F residue  109 ILE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain I residue   26 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 47 optimal weight:   20.0000
   chunk 16 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 60 optimal weight:   20.0000
   chunk 17 optimal weight:    6.9990
   chunk 94 optimal weight:    4.9990
   chunk 45 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** C  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 186 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.081438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.059846 restraints weight = 36397.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.061767 restraints weight = 18756.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.062985 restraints weight = 12932.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   9104  Z= 0.197
  Angle     :  0.575  12.533  12284  Z= 0.289
  Chirality :  0.044   0.263   1282
  Planarity :  0.005   0.116   1562
  Dihedral  :  4.158  26.995   1176
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  8.30 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 13.67 %
    Favored  : 84.53 %
  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: -1.67 (0.24), residues: 1072
  helix:  0.38 (0.31), residues: 310
  sheet: -0.48 (0.53), residues: 96
  loop : -2.06 (0.21), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  78 
 HIS   0.004   0.001   HIS H  10 
 PHE   0.011   0.001   PHE B 113 
 TYR   0.009   0.001   TYR G  79 
 ARG   0.004   0.000   ARG E  63 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8249 (ppp) cc_final: 0.7464 (ppp)
REVERT: E  105 MET cc_start: 0.9195 (mmm) cc_final: 0.8844 (mmm)
REVERT: H   26 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8272 (pm20)
REVERT: H   52 ASP cc_start: 0.9512 (p0) cc_final: 0.9301 (p0)
REVERT: H   55 LYS cc_start: 0.8831 (tmmt) cc_final: 0.8259 (ptmm)
REVERT: B   61 MET cc_start: 0.8274 (ppp) cc_final: 0.7469 (ppp)
REVERT: G   63 ARG cc_start: 0.8439 (mmm160) cc_final: 0.8159 (mmm160)
REVERT: I   26 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8293 (pm20)
REVERT: I   55 LYS cc_start: 0.8815 (ttmt) cc_final: 0.8394 (ptmm)
  outliers start: 17
  outliers final: 10
  residues processed: 109
  average time/residue: 0.2091
  time to fit residues: 33.2513
Evaluate side-chains
  103 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue  115 CYS
Chi-restraints excluded: chain A residue  143 GLU
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain H residue   26 GLU
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue  115 CYS
Chi-restraints excluded: chain B residue  142 MET
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain F residue  109 ILE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain I residue   26 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 78 optimal weight:    9.9990
   chunk 93 optimal weight:    0.9980
   chunk 50 optimal weight:    9.9990
   chunk 7 optimal weight:    0.0670
   chunk 31 optimal weight:    1.9990
   chunk 96 optimal weight:    0.3980
   chunk 55 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 48 optimal weight:   20.0000
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.0922

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

Flipped N/Q/H residues before XYZ refinement:
** C  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 186 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.081483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.059717 restraints weight = 36820.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.061609 restraints weight = 19068.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.062886 restraints weight = 13285.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.3184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   9104  Z= 0.194
  Angle     :  0.573  11.845  12284  Z= 0.289
  Chirality :  0.044   0.271   1282
  Planarity :  0.005   0.117   1562
  Dihedral  :  4.130  27.522   1176
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  8.40 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.67 %
    Favored  : 84.43 %
  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: -1.66 (0.24), residues: 1072
  helix:  0.39 (0.31), residues: 310
  sheet: -0.45 (0.53), residues: 96
  loop : -2.06 (0.21), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F  71 
 HIS   0.004   0.001   HIS B 126 
 PHE   0.010   0.001   PHE B 113 
 TYR   0.009   0.001   TYR G  79 
 ARG   0.003   0.000   ARG I   9 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8302 (ppp) cc_final: 0.7780 (ppp)
REVERT: C   96 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7578 (p0)
REVERT: E  105 MET cc_start: 0.9239 (mmm) cc_final: 0.8955 (mmm)
REVERT: H   26 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8252 (pm20)
REVERT: H   52 ASP cc_start: 0.9580 (p0) cc_final: 0.9372 (p0)
REVERT: H   55 LYS cc_start: 0.8902 (tmmt) cc_final: 0.8331 (ptmm)
REVERT: B   61 MET cc_start: 0.8313 (ppp) cc_final: 0.7791 (ppp)
REVERT: G   63 ARG cc_start: 0.8477 (mmm160) cc_final: 0.8199 (mmm160)
REVERT: I   55 LYS cc_start: 0.8839 (ttmt) cc_final: 0.8613 (tttt)
  outliers start: 18
  outliers final: 10
  residues processed: 110
  average time/residue: 0.1770
  time to fit residues: 28.5929
Evaluate side-chains
  106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue  115 CYS
Chi-restraints excluded: chain A residue  143 GLU
Chi-restraints excluded: chain C residue   96 ASN
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain H residue   26 GLU
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue  115 CYS
Chi-restraints excluded: chain B residue  142 MET
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain F residue  109 ILE
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 52 optimal weight:    0.2980
   chunk 61 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 102 optimal weight:    1.9990
   chunk 47 optimal weight:   10.0000
   chunk 49 optimal weight:   20.0000
   chunk 85 optimal weight:    0.9980
   chunk 68 optimal weight:    6.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    2.6586

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

Flipped N/Q/H residues before XYZ refinement:
** C  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 181 HIS
** F  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  96 ASN
F 181 HIS
F 186 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.079708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.058510 restraints weight = 36924.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.060263 restraints weight = 19005.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.061319 restraints weight = 13165.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.3687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   9104  Z= 0.317
  Angle     :  0.641  11.125  12284  Z= 0.332
  Chirality :  0.046   0.266   1282
  Planarity :  0.006   0.122   1562
  Dihedral  :  4.535  27.540   1176
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  9.33 %
    Favored  : 90.11 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 14.72 %
    Favored  : 83.26 %
  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 (0.24), residues: 1072
  helix:  0.16 (0.31), residues: 300
  sheet: -0.18 (0.48), residues: 116
  loop : -2.11 (0.21), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  78 
 HIS   0.008   0.002   HIS A 126 
 PHE   0.012   0.002   PHE A   8 
 TYR   0.010   0.001   TYR G  79 
 ARG   0.014   0.000   ARG E  63 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8459 (ppp) cc_final: 0.7733 (ppp)
REVERT: C   96 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7827 (p0)
REVERT: E   75 MET cc_start: 0.8256 (mtp) cc_final: 0.8014 (mtm)
REVERT: H   26 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8234 (pm20)
REVERT: H   52 ASP cc_start: 0.9602 (p0) cc_final: 0.9201 (p0)
REVERT: H   55 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8771 (tttt)
REVERT: B   61 MET cc_start: 0.8475 (ppp) cc_final: 0.7743 (ppp)
REVERT: G  105 MET cc_start: 0.9079 (mmm) cc_final: 0.8784 (mmm)
REVERT: I   26 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8363 (pm20)
REVERT: I   55 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8694 (tttt)
REVERT: I   74 THR cc_start: 0.9049 (m) cc_final: 0.8741 (t)
  outliers start: 19
  outliers final: 12
  residues processed: 109
  average time/residue: 0.1880
  time to fit residues: 30.1045
Evaluate side-chains
  107 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue  115 CYS
Chi-restraints excluded: chain A residue  143 GLU
Chi-restraints excluded: chain C residue   96 ASN
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain H residue   26 GLU
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue  115 CYS
Chi-restraints excluded: chain B residue  142 MET
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain F residue   61 PHE
Chi-restraints excluded: chain F residue   96 ASN
Chi-restraints excluded: chain F residue  109 ILE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain I residue   26 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 51 optimal weight:    0.3980
   chunk 9 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 76 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 29 optimal weight:    0.2980
   chunk 37 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** C  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 181 HIS
F 186 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.081425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.060421 restraints weight = 36623.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.062216 restraints weight = 18603.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.063423 restraints weight = 12813.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.3577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9104  Z= 0.203
  Angle     :  0.606  10.913  12284  Z= 0.304
  Chirality :  0.044   0.267   1282
  Planarity :  0.006   0.122   1562
  Dihedral  :  4.392  28.929   1176
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  8.21 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.04 %
    Favored  : 83.16 %
  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: -1.64 (0.24), residues: 1072
  helix:  0.38 (0.32), residues: 286
  sheet: -0.13 (0.48), residues: 116
  loop : -2.06 (0.21), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP F  71 
 HIS   0.004   0.001   HIS B 126 
 PHE   0.010   0.001   PHE A 113 
 TYR   0.009   0.001   TYR E  79 
 ARG   0.007   0.000   ARG E  63 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 1.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8353 (ppp) cc_final: 0.7719 (ppp)
REVERT: C   96 ASN cc_start: 0.7879 (OUTLIER) cc_final: 0.7617 (p0)
REVERT: H   26 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8203 (pm20)
REVERT: H   52 ASP cc_start: 0.9567 (p0) cc_final: 0.9144 (p0)
REVERT: H   55 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8703 (tttt)
REVERT: B   61 MET cc_start: 0.8372 (ppp) cc_final: 0.7723 (ppp)
REVERT: G   63 ARG cc_start: 0.8474 (mmm160) cc_final: 0.8187 (mmm160)
REVERT: G  105 MET cc_start: 0.9147 (mmm) cc_final: 0.8932 (mmm)
REVERT: I   26 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8301 (pm20)
REVERT: I   55 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8659 (tttt)
REVERT: I   74 THR cc_start: 0.8971 (m) cc_final: 0.8660 (t)
  outliers start: 17
  outliers final: 9
  residues processed: 110
  average time/residue: 0.2187
  time to fit residues: 35.1398
Evaluate side-chains
  106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 1.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue  115 CYS
Chi-restraints excluded: chain A residue  143 GLU
Chi-restraints excluded: chain C residue   96 ASN
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain H residue   26 GLU
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue  115 CYS
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain F residue   60 MET
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain I residue   26 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 38 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   chunk 65 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** C  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  96 ASN
F 186 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.080550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.059273 restraints weight = 36255.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.061101 restraints weight = 18833.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.062283 restraints weight = 13164.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.3751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   9104  Z= 0.243
  Angle     :  0.621  10.701  12284  Z= 0.314
  Chirality :  0.045   0.265   1282
  Planarity :  0.006   0.124   1562
  Dihedral  :  4.443  28.197   1176
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  9.51 %
    Favored  : 89.93 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 15.57 %
    Favored  : 83.05 %
  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: -1.67 (0.24), residues: 1072
  helix:  0.36 (0.32), residues: 286
  sheet: -0.16 (0.48), residues: 116
  loop : -2.07 (0.21), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP F  71 
 HIS   0.007   0.001   HIS B 126 
 PHE   0.011   0.001   PHE B  46 
 TYR   0.010   0.001   TYR G  79 
 ARG   0.007   0.000   ARG E  63 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8314 (ppp) cc_final: 0.7795 (ppp)
REVERT: C   96 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7598 (p0)
REVERT: E   75 MET cc_start: 0.8189 (mtp) cc_final: 0.7902 (mtm)
REVERT: H   26 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8175 (pm20)
REVERT: H   52 ASP cc_start: 0.9536 (p0) cc_final: 0.9113 (p0)
REVERT: H   55 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8734 (tttt)
REVERT: H   74 THR cc_start: 0.8936 (m) cc_final: 0.8544 (t)
REVERT: B   61 MET cc_start: 0.8347 (ppp) cc_final: 0.7809 (ppp)
REVERT: G  105 MET cc_start: 0.9106 (mmm) cc_final: 0.8853 (mmm)
REVERT: I   26 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8283 (pm20)
REVERT: I   55 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8665 (tttt)
REVERT: I   74 THR cc_start: 0.8990 (m) cc_final: 0.8677 (t)
  outliers start: 13
  outliers final: 10
  residues processed: 106
  average time/residue: 0.1839
  time to fit residues: 28.4667
Evaluate side-chains
  108 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue  115 CYS
Chi-restraints excluded: chain A residue  143 GLU
Chi-restraints excluded: chain C residue   96 ASN
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain H residue   26 GLU
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue  115 CYS
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain F residue   61 PHE
Chi-restraints excluded: chain F residue   96 ASN
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain I residue   26 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 53 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 38 optimal weight:    9.9990
   chunk 104 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
** C  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  96 ASN
** F 186 HIS ** 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 = 0.3835 r_free = 0.3835 target = 0.083157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.060450 restraints weight = 37525.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.062378 restraints weight = 19432.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.063556 restraints weight = 13539.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.3754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.115   9104  Z= 0.324
  Angle     :  0.929  59.199  12284  Z= 0.534
  Chirality :  0.046   0.328   1282
  Planarity :  0.006   0.125   1562
  Dihedral  :  4.479  28.519   1176
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  9.51 %
    Favored  : 89.93 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 16.00 %
    Favored  : 82.52 %
  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: -1.67 (0.24), residues: 1072
  helix:  0.35 (0.32), residues: 286
  sheet: -0.16 (0.48), residues: 116
  loop : -2.07 (0.21), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP C  78 
 HIS   0.006   0.001   HIS B 126 
 PHE   0.011   0.001   PHE B 113 
 TYR   0.011   0.001   TYR G  79 
 ARG   0.006   0.000   ARG E  63 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3097.55 seconds
wall clock time: 54 minutes 56.27 seconds (3296.27 seconds total)