Starting phenix.real_space_refine
on Wed Feb 12 11:59:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gn8_34157/02_2025/8gn8_34157.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gn8_34157/02_2025/8gn8_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_34157/02_2025/8gn8_34157.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gn8_34157/02_2025/8gn8_34157.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gn8_34157/02_2025/8gn8_34157.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gn8_34157/02_2025/8gn8_34157.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.87, per 1000 atoms: 0.61
  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: 1.93
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.83
  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: 2.08

  Time building geometry restraints manager: 2.28 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: 0.02
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:             1.070
  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:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.010
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
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   8120  Z= 0.160
  Angle     :  0.658   9.866  11050  Z= 0.359
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (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
 TRP   0.005   0.001   TRP C 202 
 HIS   0.003   0.001   HIS A  74 
 PHE   0.065   0.002   PHE B   9 
 TYR   0.005   0.001   TYR C 162 
 ARG   0.004   0.000   ARG E 221 

*********************** 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  : 0.913 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 85
  average time/residue: 0.1461
  time to fit residues: 18.8240
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  : 0.808 
-------------------------------------------------------------------------------
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 84 optimal weight:    3.9990
   chunk 75 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 30 optimal weight:    0.1980
   chunk 47 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 90 optimal weight:    0.0570
   overall best weight:    0.5298

-------------------------------------------------------------------------------
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 = 0.3462 r_free = 0.3462 target = 0.131921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.101902 restraints weight = 9695.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.105030 restraints weight = 5495.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.106881 restraints weight = 3966.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.0756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8120  Z= 0.157
  Angle     :  0.583   8.031  11050  Z= 0.290
  Chirality :  0.037   0.119   1310
  Planarity :  0.005   0.069   1360
  Dihedral  :  4.804  44.718   1103
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 27.59 %
    Favored  : 69.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.30), residues: 990
  helix:  1.39 (0.23), residues: 650
  sheet:  1.74 (0.75), residues: 50
  loop : -2.40 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 202 
 HIS   0.002   0.001   HIS C  74 
 PHE   0.014   0.001   PHE D   9 
 TYR   0.010   0.001   TYR D 162 
 ARG   0.003   0.000   ARG E 221 

*********************** 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
  119 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 91
  time to evaluate  : 0.823 
Fit side-chains
REVERT: B    6 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7063 (tt)
REVERT: E    9 PHE cc_start: 0.9170 (t80) cc_final: 0.8945 (t80)
REVERT: E   20 MET cc_start: 0.7307 (tpt) cc_final: 0.7000 (tpp)
  outliers start: 28
  outliers final: 18
  residues processed: 102
  average time/residue: 0.1329
  time to fit residues: 21.1215
Evaluate side-chains
  101 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   72 VAL
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  183 VAL
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   24 LEU
Chi-restraints excluded: chain B residue   72 VAL
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 C residue   72 VAL
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  183 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0570
   chunk 73 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.7700

-------------------------------------------------------------------------------
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 = 0.3455 r_free = 0.3455 target = 0.131251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.101070 restraints weight = 9869.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.104328 restraints weight = 5460.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.106231 restraints weight = 3872.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.1033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8120  Z= 0.166
  Angle     :  0.567   8.821  11050  Z= 0.281
  Chirality :  0.038   0.119   1310
  Planarity :  0.005   0.067   1360
  Dihedral  :  4.729  45.214   1100
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 27.47 %
    Favored  : 67.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.30), residues: 990
  helix:  1.38 (0.23), residues: 665
  sheet:  2.06 (0.73), residues: 50
  loop : -2.24 (0.40), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 202 
 HIS   0.003   0.001   HIS C  74 
 PHE   0.040   0.001   PHE B   9 
 TYR   0.010   0.001   TYR D 162 
 ARG   0.002   0.000   ARG C  42 

*********************** 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
  126 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 84
  time to evaluate  : 0.849 
Fit side-chains
REVERT: B    6 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7140 (tt)
REVERT: B   74 HIS cc_start: 0.6878 (OUTLIER) cc_final: 0.6175 (p-80)
  outliers start: 42
  outliers final: 27
  residues processed: 110
  average time/residue: 0.1660
  time to fit residues: 26.3268
Evaluate side-chains
  111 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 82
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
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  183 VAL
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  176 THR
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   29 THR
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 C residue   19 THR
Chi-restraints excluded: chain C residue   24 LEU
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  176 THR
Chi-restraints excluded: chain E residue    7 LEU
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   24 LEU
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  183 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    0.0670
   chunk 92 optimal weight:    4.9990
   chunk 86 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    0.9722

-------------------------------------------------------------------------------
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 = 0.126364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.096642 restraints weight = 9813.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.099688 restraints weight = 5586.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.101633 restraints weight = 4015.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8120  Z= 0.182
  Angle     :  0.568   9.180  11050  Z= 0.283
  Chirality :  0.038   0.121   1310
  Planarity :  0.005   0.066   1360
  Dihedral  :  4.743  45.569   1100
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  5.52 %
    Allowed  : 27.01 %
    Favored  : 67.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.30), residues: 990
  helix:  1.48 (0.22), residues: 660
  sheet:  2.00 (0.72), residues: 50
  loop : -2.02 (0.40), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 202 
 HIS   0.004   0.001   HIS C  74 
 PHE   0.042   0.001   PHE B   9 
 TYR   0.009   0.001   TYR D 162 
 ARG   0.002   0.000   ARG A  42 

*********************** 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
  127 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 79
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A  146 HIS cc_start: 0.8030 (OUTLIER) cc_final: 0.7559 (t-90)
REVERT: B   74 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6404 (p-80)
  outliers start: 48
  outliers final: 38
  residues processed: 109
  average time/residue: 0.1468
  time to fit residues: 24.3077
Evaluate side-chains
  115 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 75
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
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   96 VAL
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  176 THR
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain A residue   19 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   19 THR
Chi-restraints excluded: chain B residue   24 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   96 VAL
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 C residue   19 THR
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   29 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  176 THR
Chi-restraints excluded: chain E residue    7 LEU
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   24 LEU
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 65 optimal weight:    0.4980
   chunk 15 optimal weight:    6.9990
   chunk 18 optimal weight:    0.5980
   chunk 34 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 95 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3459 r_free = 0.3459 target = 0.130988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.101495 restraints weight = 9625.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.104472 restraints weight = 5652.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.106186 restraints weight = 4148.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8120  Z= 0.168
  Angle     :  0.557   9.189  11050  Z= 0.277
  Chirality :  0.038   0.119   1310
  Planarity :  0.005   0.065   1360
  Dihedral  :  4.705  45.177   1100
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 26.55 %
    Favored  : 67.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.30), residues: 990
  helix:  1.58 (0.22), residues: 665
  sheet:  1.93 (0.72), residues: 50
  loop : -2.01 (0.41), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 202 
 HIS   0.003   0.001   HIS C  74 
 PHE   0.046   0.001   PHE B   9 
 TYR   0.009   0.001   TYR D 162 
 ARG   0.002   0.000   ARG A  42 

*********************** 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
  132 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 78
  time to evaluate  : 0.874 
Fit side-chains
REVERT: A  146 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7722 (t-90)
REVERT: B   74 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6503 (p-80)
REVERT: B  190 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7573 (ptp-170)
  outliers start: 54
  outliers final: 34
  residues processed: 117
  average time/residue: 0.1469
  time to fit residues: 25.5135
Evaluate side-chains
  112 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 75
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
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   96 VAL
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  217 VAL
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   19 THR
Chi-restraints excluded: chain B residue   24 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   86 LEU
Chi-restraints excluded: chain B residue   96 VAL
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 C residue   19 THR
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   29 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  176 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   24 LEU
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  183 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 90 optimal weight:    9.9990
   chunk 2 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 70 optimal weight:    8.9990
   chunk 3 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3448 r_free = 0.3448 target = 0.129771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.100280 restraints weight = 9685.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.103181 restraints weight = 5673.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.104927 restraints weight = 4184.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8120  Z= 0.179
  Angle     :  0.563   9.636  11050  Z= 0.280
  Chirality :  0.038   0.126   1310
  Planarity :  0.005   0.065   1360
  Dihedral  :  4.720  45.592   1100
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  6.55 %
    Allowed  : 26.09 %
    Favored  : 67.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.30), residues: 990
  helix:  1.65 (0.22), residues: 665
  sheet:  1.77 (0.70), residues: 50
  loop : -1.87 (0.41), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 202 
 HIS   0.003   0.001   HIS C  74 
 PHE   0.049   0.001   PHE B   9 
 TYR   0.007   0.001   TYR D 162 
 ARG   0.002   0.000   ARG A  42 

*********************** 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
  138 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 81
  time to evaluate  : 0.819 
Fit side-chains
REVERT: D   47 ASP cc_start: 0.8754 (p0) cc_final: 0.8515 (p0)
REVERT: A  146 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7670 (t-90)
REVERT: B   74 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6609 (p-80)
REVERT: E   47 ASP cc_start: 0.8931 (p0) cc_final: 0.8720 (p0)
REVERT: E  190 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8140 (ptt180)
  outliers start: 57
  outliers final: 42
  residues processed: 120
  average time/residue: 0.1565
  time to fit residues: 27.6024
Evaluate side-chains
  121 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 76
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
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   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   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    7 LEU
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   24 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   86 LEU
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  210 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain C residue   19 THR
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   29 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  146 HIS
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   24 LEU
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  190 ARG
Chi-restraints excluded: chain E residue  195 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0870
   chunk 96 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   overall best weight:    0.7358

-------------------------------------------------------------------------------
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 = 0.123953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.095915 restraints weight = 10040.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.099310 restraints weight = 5371.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.101353 restraints weight = 3684.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8120  Z= 0.160
  Angle     :  0.552   9.369  11050  Z= 0.276
  Chirality :  0.038   0.119   1310
  Planarity :  0.005   0.064   1360
  Dihedral  :  4.669  44.851   1100
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 26.21 %
    Favored  : 67.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.30), residues: 990
  helix:  1.83 (0.22), residues: 670
  sheet:  1.69 (0.68), residues: 50
  loop : -1.83 (0.42), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 202 
 HIS   0.003   0.001   HIS C  74 
 PHE   0.052   0.001   PHE B   9 
 TYR   0.008   0.001   TYR D 162 
 ARG   0.002   0.000   ARG A  42 

*********************** 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
  135 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 81
  time to evaluate  : 0.822 
Fit side-chains
REVERT: A  146 HIS cc_start: 0.8058 (OUTLIER) cc_final: 0.7667 (t-90)
REVERT: A  190 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7891 (ptp-170)
REVERT: B   74 HIS cc_start: 0.6909 (OUTLIER) cc_final: 0.6474 (p-80)
REVERT: B  190 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7553 (ptp-170)
REVERT: C  198 MET cc_start: 0.8030 (ttm) cc_final: 0.7790 (ttm)
REVERT: E   47 ASP cc_start: 0.8910 (p0) cc_final: 0.8697 (p0)
REVERT: E  190 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8083 (ptt180)
  outliers start: 54
  outliers final: 39
  residues processed: 118
  average time/residue: 0.1747
  time to fit residues: 29.0436
Evaluate side-chains
  122 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 78
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
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   96 VAL
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   29 THR
Chi-restraints excluded: chain A residue   72 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 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   29 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   96 VAL
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 C residue   19 THR
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   29 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 E residue   19 THR
Chi-restraints excluded: chain E residue   24 LEU
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  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 63 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 97 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3339 r_free = 0.3339 target = 0.123084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.095028 restraints weight = 10136.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.098410 restraints weight = 5462.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.100415 restraints weight = 3769.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8120  Z= 0.171
  Angle     :  0.565   9.634  11050  Z= 0.280
  Chirality :  0.038   0.144   1310
  Planarity :  0.005   0.064   1360
  Dihedral  :  4.692  45.283   1100
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  5.98 %
    Allowed  : 25.86 %
    Favored  : 68.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.30), residues: 990
  helix:  1.89 (0.22), residues: 670
  sheet:  1.60 (0.67), residues: 50
  loop : -1.82 (0.42), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 202 
 HIS   0.003   0.001   HIS C  74 
 PHE   0.053   0.001   PHE B   9 
 TYR   0.006   0.001   TYR D 162 
 ARG   0.002   0.000   ARG A  42 

*********************** 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
  132 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 80
  time to evaluate  : 0.823 
Fit side-chains
REVERT: A  146 HIS cc_start: 0.8027 (OUTLIER) cc_final: 0.7584 (t-90)
REVERT: A  190 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7851 (ptp-170)
REVERT: B   74 HIS cc_start: 0.6912 (OUTLIER) cc_final: 0.6523 (p-80)
REVERT: B  190 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7507 (ptp-170)
REVERT: E   47 ASP cc_start: 0.8893 (p0) cc_final: 0.8690 (p0)
REVERT: E  190 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8049 (ptt180)
  outliers start: 52
  outliers final: 42
  residues processed: 117
  average time/residue: 0.1620
  time to fit residues: 27.4242
Evaluate side-chains
  125 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 78
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
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   96 VAL
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   29 THR
Chi-restraints excluded: chain A residue   72 VAL
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 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   29 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   96 VAL
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 C residue   19 THR
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   29 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 E residue   19 THR
Chi-restraints excluded: chain E residue   24 LEU
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  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 48 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 91 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3380 r_free = 0.3380 target = 0.126628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.096894 restraints weight = 9901.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.099978 restraints weight = 5629.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.101874 restraints weight = 4072.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8120  Z= 0.172
  Angle     :  0.567   9.709  11050  Z= 0.282
  Chirality :  0.038   0.130   1310
  Planarity :  0.005   0.063   1360
  Dihedral  :  4.689  44.728   1100
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  5.98 %
    Allowed  : 26.09 %
    Favored  : 67.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.30), residues: 990
  helix:  1.95 (0.22), residues: 670
  sheet:  1.49 (0.66), residues: 50
  loop : -1.84 (0.42), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 202 
 HIS   0.003   0.001   HIS C  74 
 PHE   0.055   0.001   PHE E   9 
 TYR   0.007   0.001   TYR D 162 
 ARG   0.002   0.000   ARG A 227 

*********************** 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
  131 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 79
  time to evaluate  : 0.811 
Fit side-chains
REVERT: A  146 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7606 (t-90)
REVERT: A  190 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7856 (ptp-170)
REVERT: B   47 ASP cc_start: 0.8679 (p0) cc_final: 0.8444 (p0)
REVERT: B   74 HIS cc_start: 0.6907 (OUTLIER) cc_final: 0.6532 (p-80)
REVERT: B  190 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7511 (ptp-170)
REVERT: E   47 ASP cc_start: 0.8891 (p0) cc_final: 0.8672 (p0)
REVERT: E  190 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8040 (ptt180)
  outliers start: 52
  outliers final: 44
  residues processed: 114
  average time/residue: 0.1810
  time to fit residues: 30.2424
Evaluate side-chains
  128 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 79
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
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   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   19 THR
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   72 VAL
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 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   29 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   96 VAL
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 C residue   19 THR
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   29 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 E residue   19 THR
Chi-restraints excluded: chain E residue   24 LEU
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  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 70 optimal weight:   10.0000
   chunk 0 optimal weight:    6.9990
   chunk 91 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0570
   chunk 32 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 80 optimal weight:    0.2980
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.5898

-------------------------------------------------------------------------------
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 = 0.3428 r_free = 0.3428 target = 0.129820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.100055 restraints weight = 9599.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.103097 restraints weight = 5428.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.105094 restraints weight = 3922.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8120  Z= 0.150
  Angle     :  0.556   9.468  11050  Z= 0.276
  Chirality :  0.038   0.127   1310
  Planarity :  0.005   0.062   1360
  Dihedral  :  4.566  43.717   1100
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 27.36 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.30), residues: 990
  helix:  2.39 (0.22), residues: 645
  sheet:  1.43 (0.65), residues: 50
  loop : -2.14 (0.39), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 202 
 HIS   0.002   0.001   HIS E  74 
 PHE   0.056   0.001   PHE E   9 
 TYR   0.007   0.001   TYR D 162 
 ARG   0.002   0.000   ARG A  42 

********************** 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
  127 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 87
  time to evaluate  : 0.841 
Fit side-chains
REVERT: A  146 HIS cc_start: 0.8108 (OUTLIER) cc_final: 0.7758 (t-90)
REVERT: A  190 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7844 (ptp-170)
REVERT: B   47 ASP cc_start: 0.8715 (p0) cc_final: 0.8492 (p0)
REVERT: B   74 HIS cc_start: 0.6881 (OUTLIER) cc_final: 0.6497 (p-80)
REVERT: B  190 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7541 (ptp-170)
REVERT: E   47 ASP cc_start: 0.8909 (p0) cc_final: 0.8704 (p0)
REVERT: E  190 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8002 (ptt180)
  outliers start: 40
  outliers final: 33
  residues processed: 114
  average time/residue: 0.1610
  time to fit residues: 27.1175
Evaluate side-chains
  121 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 83
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
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 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  103 LEU
Chi-restraints excluded: chain A residue  146 HIS
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   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 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   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 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  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 82 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 54 optimal weight:    0.4980
   chunk 98 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3417 r_free = 0.3417 target = 0.128536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.098697 restraints weight = 9659.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.101846 restraints weight = 5489.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.103620 restraints weight = 3961.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8120  Z= 0.169
  Angle     :  0.567   9.735  11050  Z= 0.281
  Chirality :  0.038   0.128   1310
  Planarity :  0.005   0.062   1360
  Dihedral  :  4.618  44.129   1100
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 27.24 %
    Favored  : 67.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.30), residues: 990
  helix:  2.34 (0.22), residues: 645
  sheet:  1.26 (0.64), residues: 50
  loop : -2.11 (0.40), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 202 
 HIS   0.003   0.001   HIS C  74 
 PHE   0.062   0.001   PHE E   9 
 TYR   0.006   0.001   TYR D 162 
 ARG   0.002   0.000   ARG A  42 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2146.91 seconds
wall clock time: 39 minutes 21.80 seconds (2361.80 seconds total)