Starting phenix.real_space_refine
on Tue Mar  3 18:08:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gn8_34157/03_2026/8gn8_34157.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gn8_34157/03_2026/8gn8_34157.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/8gn8_34157/03_2026/8gn8_34157.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gn8_34157/03_2026/8gn8_34157.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gn8_34157/03_2026/8gn8_34157.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gn8_34157/03_2026/8gn8_34157.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 sd=   0.116
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      70      5.16       5
     C    5230      2.51       5
     N    1340      2.21       5
     O    1280      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7920
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "D"
      Number of atoms: 1584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1584
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 12, 'TRANS': 189}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1584
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 12, 'TRANS': 189}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1584
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 12, 'TRANS': 189}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1584
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 12, 'TRANS': 189}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1584
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 12, 'TRANS': 189}
          Chain breaks: 1
  Time building chain proxies: 1.69, per 1000 atoms: 0.21
  Number of scatterers: 7920
  At special positions: 0
  Unit cell: (90.16, 90.16, 95.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      70     16.00
     O    1280      8.00
     N    1340      7.00
     C    5230      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  54 " - pdb=" SG  CYS D 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  61 " - pdb=" SG  CYS D 180 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  65 " - pdb=" SG  CYS D 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  61 " - pdb=" SG  CYS A 180 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  65 " - pdb=" SG  CYS A 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  54 " - pdb=" SG  CYS B 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  61 " - pdb=" SG  CYS B 180 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  65 " - pdb=" SG  CYS B 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  54 " - pdb=" SG  CYS C 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  61 " - pdb=" SG  CYS C 180 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  65 " - pdb=" SG  CYS C 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  54 " - pdb=" SG  CYS E 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  61 " - pdb=" SG  CYS E 180 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  65 " - pdb=" SG  CYS E 175 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 230.1 milliseconds
  

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1880

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 5 sheets defined
      70.5% alpha, 3.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'D' and resid 11 through 16
    Processing helix  chain 'D' and resid 19 through 32
    Processing helix  chain 'D' and resid 35 through 42
      removed outlier: 3.959A  pdb=" N   ARG D  42 " --> pdb=" O   VAL D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 43 through 48
      removed outlier: 4.408A  pdb=" N   ASP D  47 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   GLU D  48 " --> pdb=" O   TYR D  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 60 through 70
    Processing helix  chain 'D' and resid 73 through 102
      removed outlier: 3.713A  pdb=" N   PHE D  77 " --> pdb=" O   SER D  73 " (cutoff:3.500A)
      Proline residue:  D  88  - end of helix
      removed outlier: 3.867A  pdb=" N   SER D  93 " --> pdb=" O   SER D  89 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THR D 102 " --> pdb=" O   HIS D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 107
      removed outlier: 4.198A  pdb=" N   LEU D 106 " --> pdb=" O   THR D 102 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLY D 107 " --> pdb=" O   LEU D 103 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 102 through 107'
    Processing helix  chain 'D' and resid 140 through 166
      removed outlier: 3.728A  pdb=" N   ILE D 144 " --> pdb=" O   SER D 140 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ILE D 145 " --> pdb=" O   ALA D 141 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   HIS D 146 " --> pdb=" O   GLY D 142 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLU D 154 " --> pdb=" O   ARG D 150 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA D 155 " --> pdb=" O   THR D 151 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ALA D 156 " --> pdb=" O   LEU D 152 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   PHE D 157 " --> pdb=" O   LEU D 153 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 219
      removed outlier: 3.657A  pdb=" N   LYS D 194 " --> pdb=" O   ARG D 190 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU D 210 " --> pdb=" O   ALA D 206 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LEU D 216 " --> pdb=" O   GLY D 212 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL D 217 " --> pdb=" O   LEU D 213 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 223 through 227
      removed outlier: 3.691A  pdb=" N   ARG D 227 " --> pdb=" O   MET D 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 11 through 16
    Processing helix  chain 'A' and resid 19 through 32
    Processing helix  chain 'A' and resid 35 through 41
    Processing helix  chain 'A' and resid 43 through 48
      removed outlier: 4.423A  pdb=" N   ASP A  47 " --> pdb=" O   VAL A  44 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   GLU A  48 " --> pdb=" O   TYR A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 70
    Processing helix  chain 'A' and resid 73 through 107
      removed outlier: 3.724A  pdb=" N   PHE A  77 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
      Proline residue:  A  88  - end of helix
      removed outlier: 3.835A  pdb=" N   SER A  93 " --> pdb=" O   SER A  89 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR A 102 " --> pdb=" O   HIS A  98 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LEU A 103 " --> pdb=" O   ARG A  99 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ALA A 104 " --> pdb=" O   GLY A 100 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   ALA A 105 " --> pdb=" O   ALA A 101 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   LEU A 106 " --> pdb=" O   THR A 102 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLY A 107 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 166
      removed outlier: 3.739A  pdb=" N   ILE A 144 " --> pdb=" O   SER A 140 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ILE A 145 " --> pdb=" O   ALA A 141 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   HIS A 146 " --> pdb=" O   GLY A 142 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A 154 " --> pdb=" O   ARG A 150 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA A 155 " --> pdb=" O   THR A 151 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ALA A 156 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   PHE A 157 " --> pdb=" O   LEU A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 225
      removed outlier: 3.648A  pdb=" N   LYS A 194 " --> pdb=" O   ARG A 190 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A 210 " --> pdb=" O   ALA A 206 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LEU A 216 " --> pdb=" O   GLY A 212 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL A 217 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ARG A 221 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ARG A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   MET A 224 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ARG A 225 " --> pdb=" O   ARG A 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 16
    Processing helix  chain 'B' and resid 19 through 32
    Processing helix  chain 'B' and resid 35 through 41
    Processing helix  chain 'B' and resid 43 through 47
      removed outlier: 4.389A  pdb=" N   ASP B  47 " --> pdb=" O   VAL B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 70
    Processing helix  chain 'B' and resid 73 through 102
      removed outlier: 3.718A  pdb=" N   PHE B  77 " --> pdb=" O   SER B  73 " (cutoff:3.500A)
      Proline residue:  B  88  - end of helix
      removed outlier: 3.892A  pdb=" N   SER B  93 " --> pdb=" O   SER B  89 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR B 102 " --> pdb=" O   HIS B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 107
      removed outlier: 4.214A  pdb=" N   LEU B 106 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLY B 107 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 102 through 107'
    Processing helix  chain 'B' and resid 140 through 166
      removed outlier: 3.730A  pdb=" N   ILE B 144 " --> pdb=" O   SER B 140 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   ILE B 145 " --> pdb=" O   ALA B 141 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   HIS B 146 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLU B 154 " --> pdb=" O   ARG B 150 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA B 155 " --> pdb=" O   THR B 151 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ALA B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   PHE B 157 " --> pdb=" O   LEU B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 225
      removed outlier: 3.647A  pdb=" N   LYS B 194 " --> pdb=" O   ARG B 190 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU B 210 " --> pdb=" O   ALA B 206 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LEU B 216 " --> pdb=" O   GLY B 212 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL B 217 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ARG B 221 " --> pdb=" O   VAL B 217 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   ARG B 223 " --> pdb=" O   SER B 219 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   MET B 224 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ARG B 225 " --> pdb=" O   ARG B 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 11 through 16
    Processing helix  chain 'C' and resid 19 through 32
    Processing helix  chain 'C' and resid 35 through 42
      removed outlier: 3.967A  pdb=" N   ARG C  42 " --> pdb=" O   VAL C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 47
      removed outlier: 4.411A  pdb=" N   ASP C  47 " --> pdb=" O   VAL C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 70
    Processing helix  chain 'C' and resid 73 through 102
      removed outlier: 3.711A  pdb=" N   PHE C  77 " --> pdb=" O   SER C  73 " (cutoff:3.500A)
      Proline residue:  C  88  - end of helix
      removed outlier: 3.898A  pdb=" N   SER C  93 " --> pdb=" O   SER C  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 107
      removed outlier: 4.198A  pdb=" N   LEU C 106 " --> pdb=" O   THR C 102 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLY C 107 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 102 through 107'
    Processing helix  chain 'C' and resid 140 through 166
      removed outlier: 3.761A  pdb=" N   ILE C 144 " --> pdb=" O   SER C 140 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   ILE C 145 " --> pdb=" O   ALA C 141 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   HIS C 146 " --> pdb=" O   GLY C 142 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLU C 154 " --> pdb=" O   ARG C 150 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA C 155 " --> pdb=" O   THR C 151 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ALA C 156 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   PHE C 157 " --> pdb=" O   LEU C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 225
      removed outlier: 3.649A  pdb=" N   LYS C 194 " --> pdb=" O   ARG C 190 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU C 210 " --> pdb=" O   ALA C 206 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU C 211 " --> pdb=" O   LEU C 207 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LEU C 216 " --> pdb=" O   GLY C 212 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL C 217 " --> pdb=" O   LEU C 213 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ARG C 221 " --> pdb=" O   VAL C 217 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   ARG C 223 " --> pdb=" O   SER C 219 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   MET C 224 " --> pdb=" O   LEU C 220 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ARG C 225 " --> pdb=" O   ARG C 221 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 11 through 16
    Processing helix  chain 'E' and resid 19 through 32
    Processing helix  chain 'E' and resid 35 through 42
      removed outlier: 3.943A  pdb=" N   ARG E  42 " --> pdb=" O   VAL E  38 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 43 through 47
      removed outlier: 4.404A  pdb=" N   ASP E  47 " --> pdb=" O   VAL E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 60 through 70
    Processing helix  chain 'E' and resid 73 through 107
      removed outlier: 3.713A  pdb=" N   PHE E  77 " --> pdb=" O   SER E  73 " (cutoff:3.500A)
      Proline residue:  E  88  - end of helix
      removed outlier: 3.991A  pdb=" N   SER E  93 " --> pdb=" O   SER E  89 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR E 102 " --> pdb=" O   HIS E  98 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU E 103 " --> pdb=" O   ARG E  99 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ALA E 104 " --> pdb=" O   GLY E 100 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   ALA E 105 " --> pdb=" O   ALA E 101 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   LEU E 106 " --> pdb=" O   THR E 102 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLY E 107 " --> pdb=" O   LEU E 103 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 140 through 166
      removed outlier: 3.725A  pdb=" N   ILE E 144 " --> pdb=" O   SER E 140 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ILE E 145 " --> pdb=" O   ALA E 141 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   HIS E 146 " --> pdb=" O   GLY E 142 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLU E 154 " --> pdb=" O   ARG E 150 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA E 155 " --> pdb=" O   THR E 151 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ALA E 156 " --> pdb=" O   LEU E 152 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   PHE E 157 " --> pdb=" O   LEU E 153 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 225
      removed outlier: 3.650A  pdb=" N   LYS E 194 " --> pdb=" O   ARG E 190 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LEU E 210 " --> pdb=" O   ALA E 206 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU E 216 " --> pdb=" O   GLY E 212 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL E 217 " --> pdb=" O   LEU E 213 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ARG E 221 " --> pdb=" O   VAL E 217 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   ARG E 223 " --> pdb=" O   SER E 219 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   MET E 224 " --> pdb=" O   LEU E 220 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ARG E 225 " --> pdb=" O   ARG E 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 172 through 175
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54
      removed outlier: 3.889A  pdb=" N   VAL A  53 " --> pdb=" O   TYR A 187 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54
      removed outlier: 3.854A  pdb=" N   VAL B  53 " --> pdb=" O   TYR B 187 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 172 through 175
    Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54
      removed outlier: 3.860A  pdb=" N   VAL E  53 " --> pdb=" O   TYR E 187 " (cutoff:3.500A)

    437 hydrogen bonds defined for protein.
    1278 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.13

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2450
        1.35 -     1.46: 1954
        1.46 -     1.58: 3621
        1.58 -     1.70: 0
        1.70 -     1.82: 95
  Bond restraints: 8120
  Sorted by residual:
  bond pdb=" CA  PHE D   9 "
       pdb=" C   PHE D   9 "
    ideal  model  delta    sigma   weight residual
    1.523  1.539 -0.016 1.34e-02 5.57e+03 1.41e+00
  bond pdb=" CA  PHE E   9 "
       pdb=" C   PHE E   9 "
    ideal  model  delta    sigma   weight residual
    1.523  1.539 -0.016 1.34e-02 5.57e+03 1.35e+00
  bond pdb=" CA  PHE A   9 "
       pdb=" C   PHE A   9 "
    ideal  model  delta    sigma   weight residual
    1.523  1.538 -0.015 1.34e-02 5.57e+03 1.28e+00
  bond pdb=" CA  PHE C   9 "
       pdb=" C   PHE C   9 "
    ideal  model  delta    sigma   weight residual
    1.523  1.538 -0.015 1.34e-02 5.57e+03 1.24e+00
  bond pdb=" CA  PHE B   9 "
       pdb=" C   PHE B   9 "
    ideal  model  delta    sigma   weight residual
    1.523  1.536 -0.013 1.34e-02 5.57e+03 9.51e-01
  ... (remaining 8115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 10846
        1.97 -     3.95: 160
        3.95 -     5.92: 30
        5.92 -     7.89: 9
        7.89 -     9.87: 5
  Bond angle restraints: 11050
  Sorted by residual:
  angle pdb=" N   GLY A   8 "
        pdb=" CA  GLY A   8 "
        pdb=" C   GLY A   8 "
      ideal   model   delta    sigma   weight residual
     110.21  107.14    3.07 9.10e-01 1.21e+00 1.13e+01
  angle pdb=" N   GLY B   8 "
        pdb=" CA  GLY B   8 "
        pdb=" C   GLY B   8 "
      ideal   model   delta    sigma   weight residual
     110.21  107.16    3.05 9.10e-01 1.21e+00 1.12e+01
  angle pdb=" C   PHE B   9 "
        pdb=" CA  PHE B   9 "
        pdb=" CB  PHE B   9 "
      ideal   model   delta    sigma   weight residual
     110.42  116.63   -6.21 1.99e+00 2.53e-01 9.74e+00
  angle pdb=" C   PHE E   9 "
        pdb=" CA  PHE E   9 "
        pdb=" CB  PHE E   9 "
      ideal   model   delta    sigma   weight residual
     110.42  116.55   -6.13 1.99e+00 2.53e-01 9.49e+00
  angle pdb=" C   PHE A   9 "
        pdb=" CA  PHE A   9 "
        pdb=" CB  PHE A   9 "
      ideal   model   delta    sigma   weight residual
     110.42  116.42   -6.00 1.99e+00 2.53e-01 9.09e+00
  ... (remaining 11045 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.82: 3806
       11.82 -    23.65: 530
       23.65 -    35.47: 313
       35.47 -    47.29: 124
       47.29 -    59.12: 52
  Dihedral angle restraints: 4825
    sinusoidal: 1915
      harmonic: 2910
  Sorted by residual:
  dihedral pdb=" CA  PRO D 178 "
           pdb=" C   PRO D 178 "
           pdb=" N   PRO D 179 "
           pdb=" CA  PRO D 179 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  133.93   46.07     0      5.00e+00 4.00e-02 8.49e+01
  dihedral pdb=" CA  PRO E 178 "
           pdb=" C   PRO E 178 "
           pdb=" N   PRO E 179 "
           pdb=" CA  PRO E 179 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  133.94   46.06     0      5.00e+00 4.00e-02 8.49e+01
  dihedral pdb=" CA  PRO A 178 "
           pdb=" C   PRO A 178 "
           pdb=" N   PRO A 179 "
           pdb=" CA  PRO A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.14   45.86     0      5.00e+00 4.00e-02 8.41e+01
  ... (remaining 4822 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 676
       0.024 -    0.048: 311
       0.048 -    0.072: 223
       0.072 -    0.096: 74
       0.096 -    0.120: 26
  Chirality restraints: 1310
  Sorted by residual:
  chirality pdb=" CA  VAL E 183 "
            pdb=" N   VAL E 183 "
            pdb=" C   VAL E 183 "
            pdb=" CB  VAL E 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.58e-01
  chirality pdb=" CA  VAL C 183 "
            pdb=" N   VAL C 183 "
            pdb=" C   VAL C 183 "
            pdb=" CB  VAL C 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.54e-01
  chirality pdb=" CA  VAL A 183 "
            pdb=" N   VAL A 183 "
            pdb=" C   VAL A 183 "
            pdb=" CB  VAL A 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.48e-01
  ... (remaining 1307 not shown)

  Planarity restraints: 1360
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B   9 "    0.021 2.00e-02 2.50e+03   2.82e-02 1.40e+01
        pdb=" CG  PHE B   9 "   -0.065 2.00e-02 2.50e+03
        pdb=" CD1 PHE B   9 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 PHE B   9 "    0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE B   9 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B   9 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B   9 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E   9 "    0.020 2.00e-02 2.50e+03   2.73e-02 1.31e+01
        pdb=" CG  PHE E   9 "   -0.063 2.00e-02 2.50e+03
        pdb=" CD1 PHE E   9 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 PHE E   9 "    0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE E   9 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE E   9 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE E   9 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 178 "   -0.049 5.00e-02 4.00e+02   7.38e-02 8.72e+00
        pdb=" N   PRO C 179 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO C 179 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO C 179 "   -0.041 5.00e-02 4.00e+02
  ... (remaining 1357 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1853
        2.80 -     3.32: 6851
        3.32 -     3.85: 12089
        3.85 -     4.37: 12711
        4.37 -     4.90: 23595
  Nonbonded interactions: 57099
  Sorted by model distance:
  nonbonded pdb=" O   SER A  70 "
            pdb=" OG  SER A  70 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" O   SER B  70 "
            pdb=" OG  SER B  70 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   SER C  70 "
            pdb=" OG  SER C  70 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   SER D  70 "
            pdb=" OG  SER D  70 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   SER E  70 "
            pdb=" OG  SER E  70 "
     model   vdw
     2.275 3.040
  ... (remaining 57094 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             0.990
  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:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.460
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
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      :  0.003   0.029   8135  Z= 0.128
  Angle     :  0.662   9.866  11080  Z= 0.361
  Chirality :  0.039   0.120   1310
  Planarity :  0.006   0.074   1360
  Dihedral  : 16.612  58.699   2900
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 31.61 %
    Favored  : 68.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.30), residues: 990
  helix:  1.09 (0.23), residues: 645
  sheet:  1.60 (0.79), residues: 50
  loop : -2.18 (0.38), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 221 
 TYR   0.005   0.001   TYR C 162 
 PHE   0.065   0.002   PHE B   9 
 TRP   0.005   0.001   TRP C 202 
 HIS   0.003   0.001   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8120)
  covalent geometry    : angle       0.65834 (11050)
  SS BOND              : bond        0.00362 (   15)
  SS BOND              : angle       1.54242 (   30)
  hydrogen bonds       : bond        0.18466 (  437)
  hydrogen bonds       : angle       6.92062 ( 1278)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.290 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 85
  average time/residue: 0.0593
  time to fit residues: 7.9028
Evaluate side-chains
  79 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   96 VAL
Chi-restraints excluded: chain E residue  185 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** B  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  98 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.122932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.092252 restraints weight = 10142.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.095273 restraints weight = 5836.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.096999 restraints weight = 4252.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.098079 restraints weight = 3578.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.098576 restraints weight = 3257.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.1153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8135  Z= 0.222
  Angle     :  0.698  10.569  11080  Z= 0.350
  Chirality :  0.044   0.160   1310
  Planarity :  0.006   0.074   1360
  Dihedral  :  5.333  48.612   1103
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 27.70 %
    Favored  : 67.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.29), residues: 990
  helix:  0.66 (0.22), residues: 670
  sheet:  1.56 (0.77), residues: 50
  loop : -2.25 (0.40), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 221 
 TYR   0.009   0.002   TYR D 162 
 PHE   0.014   0.001   PHE D   9 
 TRP   0.004   0.001   TRP C  78 
 HIS   0.009   0.003   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 ( 8120)
  covalent geometry    : angle       0.69636 (11050)
  SS BOND              : bond        0.00406 (   15)
  SS BOND              : angle       1.11877 (   30)
  hydrogen bonds       : bond        0.06697 (  437)
  hydrogen bonds       : angle       4.72587 ( 1278)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 70
  time to evaluate  : 0.263 
Fit side-chains
REVERT: D   74 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6372 (p-80)
REVERT: A    6 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7427 (mm)
REVERT: B    6 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7348 (mm)
REVERT: B   74 HIS cc_start: 0.7222 (OUTLIER) cc_final: 0.6304 (p-80)
  outliers start: 45
  outliers final: 32
  residues processed: 107
  average time/residue: 0.0582
  time to fit residues: 9.6358
Evaluate side-chains
  98 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 62
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   19 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   72 VAL
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   74 HIS
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  195 SER
Chi-restraints excluded: chain C residue   19 THR
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   29 THR
Chi-restraints excluded: chain E residue   74 HIS
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  183 VAL
Chi-restraints excluded: chain E residue  195 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 97 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** B  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.126867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.096940 restraints weight = 9762.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.099980 restraints weight = 5593.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.101875 restraints weight = 4052.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.102790 restraints weight = 3378.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.103501 restraints weight = 3083.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8135  Z= 0.124
  Angle     :  0.569   7.650  11080  Z= 0.287
  Chirality :  0.038   0.121   1310
  Planarity :  0.005   0.069   1360
  Dihedral  :  5.021  46.719   1100
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 29.20 %
    Favored  : 66.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.30), residues: 990
  helix:  1.05 (0.22), residues: 670
  sheet:  1.77 (0.76), residues: 50
  loop : -2.12 (0.41), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 221 
 TYR   0.012   0.001   TYR D 162 
 PHE   0.040   0.001   PHE B   9 
 TRP   0.005   0.001   TRP C 202 
 HIS   0.003   0.001   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8120)
  covalent geometry    : angle       0.56836 (11050)
  SS BOND              : bond        0.00272 (   15)
  SS BOND              : angle       0.86422 (   30)
  hydrogen bonds       : bond        0.04878 (  437)
  hydrogen bonds       : angle       4.31904 ( 1278)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 79
  time to evaluate  : 0.219 
Fit side-chains
REVERT: D   74 HIS cc_start: 0.6914 (OUTLIER) cc_final: 0.6221 (p-80)
REVERT: A  146 HIS cc_start: 0.8023 (OUTLIER) cc_final: 0.7633 (t-90)
REVERT: B    6 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7237 (mm)
REVERT: B   74 HIS cc_start: 0.7030 (OUTLIER) cc_final: 0.6143 (p-80)
  outliers start: 39
  outliers final: 22
  residues processed: 105
  average time/residue: 0.0804
  time to fit residues: 12.0549
Evaluate side-chains
  101 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   72 VAL
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   74 HIS
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain E residue   29 THR
Chi-restraints excluded: chain E residue   74 HIS
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain E residue  183 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0670
   chunk 32 optimal weight:    4.9990
   chunk 24 optimal weight:    0.1980
   chunk 61 optimal weight:    0.2980
   chunk 45 optimal weight:    0.1980
   chunk 44 optimal weight:    0.0870
   chunk 88 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   overall best weight:    0.1696

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

Flipped N/Q/H residues before XYZ refinement:
** B  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.132206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.102828 restraints weight = 9846.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.106056 restraints weight = 5470.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.107997 restraints weight = 3886.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.109062 restraints weight = 3217.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.109484 restraints weight = 2903.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8135  Z= 0.102
  Angle     :  0.548   7.671  11080  Z= 0.276
  Chirality :  0.037   0.121   1310
  Planarity :  0.005   0.064   1360
  Dihedral  :  4.624  43.741   1100
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 28.97 %
    Favored  : 65.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.30), residues: 990
  helix:  1.67 (0.23), residues: 660
  sheet:  1.93 (0.72), residues: 50
  loop : -2.04 (0.40), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 221 
 TYR   0.013   0.001   TYR D 162 
 PHE   0.040   0.001   PHE E   9 
 TRP   0.006   0.001   TRP C 202 
 HIS   0.001   0.000   HIS D 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 8120)
  covalent geometry    : angle       0.54605 (11050)
  SS BOND              : bond        0.00247 (   15)
  SS BOND              : angle       1.03901 (   30)
  hydrogen bonds       : bond        0.03227 (  437)
  hydrogen bonds       : angle       3.92689 ( 1278)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 94
  time to evaluate  : 0.297 
Fit side-chains
REVERT: D   74 HIS cc_start: 0.6533 (OUTLIER) cc_final: 0.5980 (p-80)
REVERT: A  190 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7792 (ptp-170)
REVERT: B    6 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7067 (tt)
REVERT: B   47 ASP cc_start: 0.8713 (p0) cc_final: 0.8492 (p0)
REVERT: B  190 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7390 (ptp-170)
REVERT: C  190 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7854 (ptp-170)
REVERT: C  198 MET cc_start: 0.7850 (ttm) cc_final: 0.7551 (ttm)
REVERT: E   47 ASP cc_start: 0.8802 (p0) cc_final: 0.8520 (p0)
REVERT: E  190 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7889 (ptt180)
  outliers start: 45
  outliers final: 17
  residues processed: 128
  average time/residue: 0.0725
  time to fit residues: 13.3383
Evaluate side-chains
  111 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   19 THR
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue  146 HIS
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  190 ARG
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  190 ARG
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   19 THR
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  190 ARG
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue  183 VAL
Chi-restraints excluded: chain E residue  190 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 77 optimal weight:    0.6980
   chunk 85 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 93 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 70 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** B  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.123478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.093901 restraints weight = 9906.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.096826 restraints weight = 5685.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.098683 restraints weight = 4129.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.099601 restraints weight = 3464.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.100245 restraints weight = 3155.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8135  Z= 0.147
  Angle     :  0.601  10.364  11080  Z= 0.298
  Chirality :  0.040   0.135   1310
  Planarity :  0.005   0.067   1360
  Dihedral  :  4.818  46.590   1100
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 28.28 %
    Favored  : 66.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.30), residues: 990
  helix:  1.45 (0.22), residues: 670
  sheet:  1.86 (0.73), residues: 50
  loop : -1.92 (0.42), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  42 
 TYR   0.006   0.001   TYR D 162 
 PHE   0.056   0.002   PHE E   9 
 TRP   0.003   0.001   TRP A  78 
 HIS   0.006   0.002   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 8120)
  covalent geometry    : angle       0.59990 (11050)
  SS BOND              : bond        0.00278 (   15)
  SS BOND              : angle       0.86817 (   30)
  hydrogen bonds       : bond        0.04944 (  437)
  hydrogen bonds       : angle       4.10046 ( 1278)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 79
  time to evaluate  : 0.228 
Fit side-chains
REVERT: D   74 HIS cc_start: 0.6957 (OUTLIER) cc_final: 0.6163 (p-80)
REVERT: A    6 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7609 (mm)
REVERT: A  146 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.7490 (t-90)
REVERT: B    6 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7290 (mm)
REVERT: B   74 HIS cc_start: 0.7085 (OUTLIER) cc_final: 0.6529 (p-80)
  outliers start: 45
  outliers final: 31
  residues processed: 111
  average time/residue: 0.0670
  time to fit residues: 11.1133
Evaluate side-chains
  110 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 74
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   19 THR
Chi-restraints excluded: chain D residue   72 VAL
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue   96 VAL
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  146 HIS
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   74 HIS
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain C residue   19 THR
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  146 HIS
Chi-restraints excluded: chain C residue  171 LYS
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   74 HIS
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  146 HIS
Chi-restraints excluded: chain E residue  183 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    0.0020
   chunk 47 optimal weight:    4.9990
   chunk 50 optimal weight:    9.9990
   chunk 87 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 16 optimal weight:    0.3980
   chunk 75 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 84 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
** B  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.124252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.096148 restraints weight = 10087.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.099596 restraints weight = 5402.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.101679 restraints weight = 3700.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.102780 restraints weight = 2984.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.103590 restraints weight = 2658.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8135  Z= 0.106
  Angle     :  0.559   9.229  11080  Z= 0.278
  Chirality :  0.038   0.120   1310
  Planarity :  0.005   0.065   1360
  Dihedral  :  4.698  44.914   1100
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 28.51 %
    Favored  : 66.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.30), residues: 990
  helix:  1.74 (0.22), residues: 670
  sheet:  1.86 (0.71), residues: 50
  loop : -1.91 (0.42), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 221 
 TYR   0.009   0.001   TYR D 162 
 PHE   0.048   0.001   PHE B   9 
 TRP   0.004   0.001   TRP A 202 
 HIS   0.002   0.000   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 8120)
  covalent geometry    : angle       0.55831 (11050)
  SS BOND              : bond        0.00223 (   15)
  SS BOND              : angle       0.85215 (   30)
  hydrogen bonds       : bond        0.03821 (  437)
  hydrogen bonds       : angle       3.88501 ( 1278)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 84
  time to evaluate  : 0.250 
Fit side-chains
REVERT: D   74 HIS cc_start: 0.6842 (OUTLIER) cc_final: 0.6181 (p-80)
REVERT: B    6 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7105 (tt)
REVERT: B   74 HIS cc_start: 0.6849 (OUTLIER) cc_final: 0.6368 (p-80)
REVERT: B  190 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7557 (ptp-170)
  outliers start: 44
  outliers final: 29
  residues processed: 112
  average time/residue: 0.0639
  time to fit residues: 10.8902
Evaluate side-chains
  113 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 80
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   19 THR
Chi-restraints excluded: chain D residue   72 VAL
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  146 HIS
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   74 HIS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  190 ARG
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain C residue   19 THR
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  146 HIS
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   29 THR
Chi-restraints excluded: chain E residue   74 HIS
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  146 HIS
Chi-restraints excluded: chain E residue  183 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0010
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 71 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 29 optimal weight:    0.1980
   chunk 10 optimal weight:   20.0000
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
** B  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.125319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.097383 restraints weight = 10005.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.100791 restraints weight = 5332.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.102889 restraints weight = 3664.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.104013 restraints weight = 2950.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.104485 restraints weight = 2628.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8135  Z= 0.104
  Angle     :  0.559   9.623  11080  Z= 0.276
  Chirality :  0.038   0.118   1310
  Planarity :  0.005   0.064   1360
  Dihedral  :  4.597  44.414   1100
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 28.05 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.30), residues: 990
  helix:  1.95 (0.22), residues: 670
  sheet:  1.79 (0.69), residues: 50
  loop : -1.87 (0.42), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 221 
 TYR   0.008   0.001   TYR D 162 
 PHE   0.052   0.001   PHE B   9 
 TRP   0.004   0.001   TRP C 202 
 HIS   0.003   0.001   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 8120)
  covalent geometry    : angle       0.55746 (11050)
  SS BOND              : bond        0.00244 (   15)
  SS BOND              : angle       0.98846 (   30)
  hydrogen bonds       : bond        0.03638 (  437)
  hydrogen bonds       : angle       3.79260 ( 1278)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 83
  time to evaluate  : 0.269 
Fit side-chains
REVERT: D   74 HIS cc_start: 0.6740 (OUTLIER) cc_final: 0.6093 (p-80)
REVERT: B   74 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.6334 (p-80)
REVERT: C  190 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7850 (ptp-170)
REVERT: E  190 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7961 (ptt180)
  outliers start: 43
  outliers final: 30
  residues processed: 111
  average time/residue: 0.0685
  time to fit residues: 11.2165
Evaluate side-chains
  113 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 79
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   19 THR
Chi-restraints excluded: chain D residue   72 VAL
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue  146 HIS
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   74 HIS
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain C residue   19 THR
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  146 HIS
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  190 ARG
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   29 THR
Chi-restraints excluded: chain E residue   74 HIS
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  146 HIS
Chi-restraints excluded: chain E residue  183 VAL
Chi-restraints excluded: chain E residue  190 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 81 optimal weight:    0.4980
   chunk 54 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 90 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.123748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.095682 restraints weight = 10063.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.098994 restraints weight = 5395.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.101060 restraints weight = 3735.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.102229 restraints weight = 3021.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.102691 restraints weight = 2684.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8135  Z= 0.113
  Angle     :  0.568   9.675  11080  Z= 0.280
  Chirality :  0.038   0.120   1310
  Planarity :  0.005   0.064   1360
  Dihedral  :  4.631  44.895   1100
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 27.82 %
    Favored  : 66.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.30), residues: 990
  helix:  1.98 (0.22), residues: 670
  sheet:  1.63 (0.68), residues: 50
  loop : -1.80 (0.43), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 221 
 TYR   0.007   0.001   TYR D 162 
 PHE   0.052   0.001   PHE E   9 
 TRP   0.003   0.001   TRP C 202 
 HIS   0.003   0.001   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8120)
  covalent geometry    : angle       0.56674 (11050)
  SS BOND              : bond        0.00264 (   15)
  SS BOND              : angle       0.96320 (   30)
  hydrogen bonds       : bond        0.03958 (  437)
  hydrogen bonds       : angle       3.82036 ( 1278)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 79
  time to evaluate  : 0.287 
Fit side-chains
REVERT: D   74 HIS cc_start: 0.6869 (OUTLIER) cc_final: 0.6223 (p-80)
REVERT: A  190 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7907 (ptp-170)
REVERT: B   74 HIS cc_start: 0.6917 (OUTLIER) cc_final: 0.6466 (p-80)
REVERT: B  190 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7588 (ptp-170)
REVERT: C  190 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7909 (ptp-170)
REVERT: E  190 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8063 (ptt180)
  outliers start: 47
  outliers final: 37
  residues processed: 112
  average time/residue: 0.0808
  time to fit residues: 12.7544
Evaluate side-chains
  122 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 79
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   19 THR
Chi-restraints excluded: chain D residue   72 VAL
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue   96 VAL
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  146 HIS
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  190 ARG
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   74 HIS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  190 ARG
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain C residue   19 THR
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  146 HIS
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  190 ARG
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   29 THR
Chi-restraints excluded: chain E residue   74 HIS
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  146 HIS
Chi-restraints excluded: chain E residue  183 VAL
Chi-restraints excluded: chain E residue  190 ARG
Chi-restraints excluded: chain E residue  195 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 71 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0020
   overall best weight:    1.3992

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

Flipped N/Q/H residues before XYZ refinement:
** B  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.122888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.093165 restraints weight = 9823.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.096118 restraints weight = 5699.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.097866 restraints weight = 4165.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.098927 restraints weight = 3497.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.099132 restraints weight = 3173.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8135  Z= 0.147
  Angle     :  0.603  10.556  11080  Z= 0.298
  Chirality :  0.040   0.132   1310
  Planarity :  0.005   0.065   1360
  Dihedral  :  4.821  46.118   1100
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 28.05 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.30), residues: 990
  helix:  1.80 (0.22), residues: 670
  sheet:  1.39 (0.66), residues: 50
  loop : -1.79 (0.43), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 221 
 TYR   0.006   0.001   TYR A  66 
 PHE   0.056   0.002   PHE B   9 
 TRP   0.002   0.001   TRP A  25 
 HIS   0.005   0.001   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8120)
  covalent geometry    : angle       0.60133 (11050)
  SS BOND              : bond        0.00317 (   15)
  SS BOND              : angle       1.09399 (   30)
  hydrogen bonds       : bond        0.04897 (  437)
  hydrogen bonds       : angle       4.01581 ( 1278)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 77
  time to evaluate  : 0.282 
Fit side-chains
REVERT: B   74 HIS cc_start: 0.7156 (OUTLIER) cc_final: 0.6690 (p-80)
REVERT: C  190 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7992 (ptp-170)
REVERT: E  190 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8078 (ptt180)
  outliers start: 43
  outliers final: 36
  residues processed: 107
  average time/residue: 0.0724
  time to fit residues: 11.3466
Evaluate side-chains
  116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 77
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   19 THR
Chi-restraints excluded: chain D residue   72 VAL
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue   96 VAL
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  146 HIS
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   74 HIS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain C residue   19 THR
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  146 HIS
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  190 ARG
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   29 THR
Chi-restraints excluded: chain E residue   74 HIS
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  146 HIS
Chi-restraints excluded: chain E residue  183 VAL
Chi-restraints excluded: chain E residue  190 ARG
Chi-restraints excluded: chain E residue  195 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 94 optimal weight:    0.0030
   chunk 53 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 93 optimal weight:    0.5980
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
** B  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.126089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.096532 restraints weight = 9699.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.099569 restraints weight = 5573.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.101367 restraints weight = 4053.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.102514 restraints weight = 3390.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.102770 restraints weight = 3055.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8135  Z= 0.111
  Angle     :  0.570   9.784  11080  Z= 0.283
  Chirality :  0.038   0.125   1310
  Planarity :  0.005   0.063   1360
  Dihedral  :  4.695  44.796   1100
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 28.28 %
    Favored  : 66.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.30), residues: 990
  helix:  2.00 (0.22), residues: 670
  sheet:  1.37 (0.65), residues: 50
  loop : -1.77 (0.43), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 221 
 TYR   0.007   0.001   TYR D 162 
 PHE   0.057   0.001   PHE B   9 
 TRP   0.005   0.001   TRP C 202 
 HIS   0.003   0.001   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8120)
  covalent geometry    : angle       0.56820 (11050)
  SS BOND              : bond        0.00275 (   15)
  SS BOND              : angle       1.07376 (   30)
  hydrogen bonds       : bond        0.04034 (  437)
  hydrogen bonds       : angle       3.83581 ( 1278)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 81
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A  190 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7884 (ptp-170)
REVERT: B   74 HIS cc_start: 0.6920 (OUTLIER) cc_final: 0.6483 (p-80)
REVERT: B  190 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7590 (ptp-170)
REVERT: C  190 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7921 (ptp-170)
REVERT: E  190 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8058 (ptt180)
  outliers start: 42
  outliers final: 36
  residues processed: 109
  average time/residue: 0.0669
  time to fit residues: 10.5200
Evaluate side-chains
  121 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 80
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   19 THR
Chi-restraints excluded: chain D residue   72 VAL
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue   96 VAL
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  146 HIS
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  190 ARG
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   74 HIS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  190 ARG
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain C residue   19 THR
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  146 HIS
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  190 ARG
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   29 THR
Chi-restraints excluded: chain E residue   74 HIS
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  146 HIS
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain E residue  183 VAL
Chi-restraints excluded: chain E residue  190 ARG
Chi-restraints excluded: chain E residue  195 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:    0.5980
   chunk 73 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0770
   chunk 53 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 11 optimal weight:    0.4980
   chunk 47 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
** B  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.128580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.099113 restraints weight = 9624.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.102189 restraints weight = 5497.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.104117 restraints weight = 3961.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.105064 restraints weight = 3307.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.105499 restraints weight = 3008.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8135  Z= 0.103
  Angle     :  0.565  10.077  11080  Z= 0.277
  Chirality :  0.037   0.119   1310
  Planarity :  0.005   0.062   1360
  Dihedral  :  4.558  44.220   1100
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 28.39 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.30), residues: 990
  helix:  2.16 (0.22), residues: 665
  sheet:  1.27 (0.64), residues: 50
  loop : -1.65 (0.42), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 221 
 TYR   0.008   0.001   TYR D 162 
 PHE   0.056   0.001   PHE E   9 
 TRP   0.004   0.001   TRP C 202 
 HIS   0.002   0.001   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 8120)
  covalent geometry    : angle       0.56236 (11050)
  SS BOND              : bond        0.00276 (   15)
  SS BOND              : angle       1.10240 (   30)
  hydrogen bonds       : bond        0.03536 (  437)
  hydrogen bonds       : angle       3.70012 ( 1278)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1127.54 seconds
wall clock time: 20 minutes 11.84 seconds (1211.84 seconds total)