Starting phenix.real_space_refine
on Sat Aug 23 06:43:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f6f_28882/08_2025/8f6f_28882.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f6f_28882/08_2025/8f6f_28882.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f6f_28882/08_2025/8f6f_28882.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f6f_28882/08_2025/8f6f_28882.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f6f_28882/08_2025/8f6f_28882.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f6f_28882/08_2025/8f6f_28882.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.061
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      6      6.06       5
     S      28      5.16       5
     C    6608      2.51       5
     N    1736      2.21       5
     O    1966      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10344
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2150
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2150
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 6, 'TRANS': 271}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1474
          Classifications: {'peptide': 192}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1545
          Classifications: {'peptide': 202}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 189}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2150
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2150
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 6, 'TRANS': 271}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1474
          Classifications: {'peptide': 192}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1545
          Classifications: {'peptide': 202}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 189}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' ZN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' ZN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.56, per 1000 atoms: 0.25
  Number of scatterers: 10344
  At special positions: 0
  Unit cell: (72.293, 156.455, 146.744, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      6     29.99
     S      28     16.00
     O    1966      8.00
     N    1736      7.00
     C    6608      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  24 " - pdb=" SG  CYS C  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 136 " - pdb=" SG  CYS C 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  25 " - pdb=" SG  CYS D  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 157 " - pdb=" SG  CYS D 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  24 " - pdb=" SG  CYS E  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 136 " - pdb=" SG  CYS E 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  25 " - pdb=" SG  CYS F  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 157 " - pdb=" SG  CYS F 213 " 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: 1.02
  Conformation dependent library (CDL) restraints added in 434.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 301 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A 234 "
        pdb="ZN    ZN A 301 " - pdb=" ND1 HIS A 250 "
      pdb="  ZN A 302 "
        pdb="ZN    ZN A 302 " - pdb=" NE2 HIS A  77 "
        pdb="ZN    ZN A 302 " - pdb=" ND1 HIS A  73 "
      pdb="  ZN A 303 "
        pdb="ZN    ZN A 303 " - pdb=" NE2 HIS B 263 "
        pdb="ZN    ZN A 303 " - pdb=" NE2 HIS A 285 "
      pdb="  ZN B 301 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS A 263 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B 285 "
      pdb="  ZN B 302 "
        pdb="ZN    ZN B 302 " - pdb=" NE2 HIS B 234 "
        pdb="ZN    ZN B 302 " - pdb=" ND1 HIS B 250 "
      pdb="  ZN B 303 "
        pdb="ZN    ZN B 303 " - pdb=" NE2 HIS B  77 "
        pdb="ZN    ZN B 303 " - pdb=" ND1 HIS B  73 "


  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2520

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 22 sheets defined
      30.7% alpha, 21.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 36
      removed outlier: 3.690A  pdb=" N   LYS A  29 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 67
      removed outlier: 3.799A  pdb=" N   SER A  48 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER A  55 " --> pdb=" O   ALA A  51 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ILE A  56 " --> pdb=" O   THR A  52 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   VAL A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 108
      removed outlier: 3.898A  pdb=" N   ALA A  85 " --> pdb=" O   GLU A  81 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LEU A  86 " --> pdb=" O   PRO A  82 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   PHE A 101 " --> pdb=" O   PHE A  97 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLY A 104 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLU A 105 " --> pdb=" O   PHE A 101 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ARG A 106 " --> pdb=" O   TYR A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 140
      removed outlier: 3.541A  pdb=" N   THR A 130 " --> pdb=" O   ALA A 126 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA A 132 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A 135 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LYS A 138 " --> pdb=" O   VAL A 134 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ARG A 139 " --> pdb=" O   LEU A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 158
      removed outlier: 3.821A  pdb=" N   SER A 153 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   TYR A 156 " --> pdb=" O   ASP A 152 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LYS A 157 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 174
      removed outlier: 3.630A  pdb=" N   LEU A 162 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ALA A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 208
      removed outlier: 4.235A  pdb=" N   ALA A 185 " --> pdb=" O   ASP A 181 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LEU A 187 " --> pdb=" O   LEU A 183 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLN A 195 " --> pdb=" O   TYR A 191 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ALA A 196 " --> pdb=" O   ILE A 192 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ARG A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLN A 205 " --> pdb=" O   TYR A 201 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ALA A 206 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU A 208 " --> pdb=" O   ILE A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 225
    Processing helix  chain 'A' and resid 258 through 277
      removed outlier: 3.569A  pdb=" N   PHE A 277 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 130
      removed outlier: 3.668A  pdb=" N   LEU C 127 " --> pdb=" O   SER C 123 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LYS C 128 " --> pdb=" O   ASP C 124 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLY C 130 " --> pdb=" O   GLN C 126 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 185 through 189
      removed outlier: 4.398A  pdb=" N   GLU C 189 " --> pdb=" O   LYS C 185 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 185 through 189'
    Processing helix  chain 'B' and resid 11 through 36
    Processing helix  chain 'B' and resid 40 through 66
      removed outlier: 4.141A  pdb=" N   SER B  44 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   SER B  48 " --> pdb=" O   SER B  44 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE B  66 " --> pdb=" O   ILE B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 102
      removed outlier: 3.679A  pdb=" N   ALA B  85 " --> pdb=" O   GLU B  81 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   PHE B 101 " --> pdb=" O   PHE B  97 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   TYR B 102 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 108
    Processing helix  chain 'B' and resid 118 through 140
      removed outlier: 3.523A  pdb=" N   THR B 130 " --> pdb=" O   ALA B 126 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA B 132 " --> pdb=" O   VAL B 128 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLN B 137 " --> pdb=" O   LEU B 133 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   LYS B 138 " --> pdb=" O   VAL B 134 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   ARG B 139 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 158
      removed outlier: 3.814A  pdb=" N   SER B 153 " --> pdb=" O   VAL B 149 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   HIS B 155 " --> pdb=" O   ALA B 151 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   TYR B 156 " --> pdb=" O   ASP B 152 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   LYS B 157 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 174
      removed outlier: 3.645A  pdb=" N   LEU B 162 " --> pdb=" O   SER B 158 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA B 164 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 208
      removed outlier: 3.930A  pdb=" N   ALA B 185 " --> pdb=" O   ASP B 181 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   LEU B 187 " --> pdb=" O   LEU B 183 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   GLN B 205 " --> pdb=" O   TYR B 201 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ALA B 206 " --> pdb=" O   ARG B 202 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU B 208 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 225
    Processing helix  chain 'B' and resid 258 through 277
      removed outlier: 3.574A  pdb=" N   PHE B 277 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 123 through 130
      removed outlier: 3.669A  pdb=" N   LEU E 127 " --> pdb=" O   SER E 123 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LYS E 128 " --> pdb=" O   ASP E 124 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLY E 130 " --> pdb=" O   GLN E 126 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 187 through 191
      removed outlier: 3.586A  pdb=" N   HIS E 191 " --> pdb=" O   TYR E 188 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 234
      removed outlier: 3.980A  pdb=" N   GLY A 232 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLU A 252 " --> pdb=" O   GLY A 232 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 238 through 241
      removed outlier: 6.301A  pdb=" N   VAL A 245 " --> pdb=" O   GLU A 281 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 25
      removed outlier: 3.613A  pdb=" N   VAL C  20 " --> pdb=" O   ILE C  76 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   PHE C  72 " --> pdb=" O   CYS C  24 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55
      removed outlier: 3.534A  pdb=" N   TYR C  50 " --> pdb=" O   SER C  54 " (cutoff:3.500A)
      removed outlier: 5.672A  pdb=" N   LEU C  47 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   GLN C  38 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE C  49 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 120
      removed outlier: 3.827A  pdb=" N   VAL C 135 " --> pdb=" O   PHE C 120 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   VAL C 134 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   TYR C 175 " --> pdb=" O   ASN C 140 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 6 through 10
      removed outlier: 3.515A  pdb=" N   VAL D   8 " --> pdb=" O   ALA D  26 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU D  23 " --> pdb=" O   LEU D  84 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 60 through 63
      removed outlier: 3.588A  pdb=" N   SER D  60 " --> pdb=" O   TYR D  55 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   TRP D  39 " --> pdb=" O   VAL D  51 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   SER D  53 " --> pdb=" O   ILE D  37 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   ILE D  37 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 106 through 107
    Processing sheet with id=AA9, first strand: chain 'D' and resid 137 through 141
      removed outlier: 3.672A  pdb=" N   LEU D 141 " --> pdb=" O   GLY D 156 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   GLY D 156 " --> pdb=" O   LEU D 141 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ASP D 161 " --> pdb=" O   TYR D 193 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   TYR D 193 " --> pdb=" O   ASP D 161 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 137 through 141
      removed outlier: 3.672A  pdb=" N   LEU D 141 " --> pdb=" O   GLY D 156 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   GLY D 156 " --> pdb=" O   LEU D 141 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ASP D 161 " --> pdb=" O   TYR D 193 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   TYR D 193 " --> pdb=" O   ASP D 161 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 168 through 170
      removed outlier: 3.803A  pdb=" N   CYS D 213 " --> pdb=" O   LYS D 226 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   LYS D 226 " --> pdb=" O   CYS D 213 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   VAL D 224 " --> pdb=" O   VAL D 215 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   HIS D 217 " --> pdb=" O   THR D 222 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   THR D 222 " --> pdb=" O   HIS D 217 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.963A  pdb=" N   GLY B 232 " --> pdb=" O   GLU B 252 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLU B 252 " --> pdb=" O   GLY B 232 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 238 through 241
      removed outlier: 6.369A  pdb=" N   VAL B 245 " --> pdb=" O   GLU B 281 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 20 through 23
      removed outlier: 3.622A  pdb=" N   VAL E  20 " --> pdb=" O   ILE E  76 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 54 through 55
      removed outlier: 3.501A  pdb=" N   TYR E  50 " --> pdb=" O   SER E  54 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   LEU E  47 " --> pdb=" O   GLN E  38 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   GLN E  38 " --> pdb=" O   LEU E  47 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 90 through 91
      removed outlier: 3.851A  pdb=" N   THR E  99 " --> pdb=" O   GLN E  91 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 118 through 120
      removed outlier: 3.875A  pdb=" N   VAL E 135 " --> pdb=" O   PHE E 120 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   VAL E 134 " --> pdb=" O   LEU E 181 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   TYR E 175 " --> pdb=" O   ASN E 140 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 6 through 10
      removed outlier: 3.595A  pdb=" N   LEU F  23 " --> pdb=" O   LEU F  84 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 60 through 63
      removed outlier: 7.065A  pdb=" N   TRP F  39 " --> pdb=" O   VAL F  51 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   SER F  53 " --> pdb=" O   ILE F  37 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   ILE F  37 " --> pdb=" O   SER F  53 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 106 through 107
    Processing sheet with id=AC3, first strand: chain 'F' and resid 137 through 141
      removed outlier: 3.563A  pdb=" N   LEU F 141 " --> pdb=" O   GLY F 156 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   GLY F 156 " --> pdb=" O   LEU F 141 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   TYR F 193 " --> pdb=" O   ASP F 161 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'F' and resid 168 through 170
      removed outlier: 3.767A  pdb=" N   CYS F 213 " --> pdb=" O   LYS F 226 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LYS F 226 " --> pdb=" O   CYS F 213 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   VAL F 224 " --> pdb=" O   VAL F 215 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   HIS F 217 " --> pdb=" O   THR F 222 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR F 222 " --> pdb=" O   HIS F 217 " (cutoff:3.500A)

    435 hydrogen bonds defined for protein.
    1209 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3288
        1.34 -     1.46: 2546
        1.46 -     1.58: 4694
        1.58 -     1.70: 0
        1.70 -     1.82: 38
  Bond restraints: 10566
  Sorted by residual:
  bond pdb=" C   LYS E  40 "
       pdb=" N   PRO E  41 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.38e-02 5.25e+03 3.14e+00
  bond pdb=" C   LYS C  40 "
       pdb=" N   PRO C  41 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.36e-02 5.41e+03 3.13e+00
  bond pdb=" CA  ASP B 227 "
       pdb=" CB  ASP B 227 "
    ideal  model  delta    sigma   weight residual
    1.524  1.539 -0.014 1.55e-02 4.16e+03 8.32e-01
  bond pdb=" N   VAL E  59 "
       pdb=" CA  VAL E  59 "
    ideal  model  delta    sigma   weight residual
    1.468  1.460  0.008 1.05e-02 9.07e+03 6.44e-01
  bond pdb=" C   PHE D 139 "
       pdb=" O   PHE D 139 "
    ideal  model  delta    sigma   weight residual
    1.240  1.248 -0.009 1.16e-02 7.43e+03 5.72e-01
  ... (remaining 10561 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.16: 13828
        1.16 -     2.31: 425
        2.31 -     3.47: 93
        3.47 -     4.62: 26
        4.62 -     5.78: 4
  Bond angle restraints: 14376
  Sorted by residual:
  angle pdb=" N   ILE C  92 "
        pdb=" CA  ILE C  92 "
        pdb=" C   ILE C  92 "
      ideal   model   delta    sigma   weight residual
     111.88  109.07    2.81 1.06e+00 8.90e-01 7.02e+00
  angle pdb=" C   GLY B 242 "
        pdb=" N   LYS B 243 "
        pdb=" CA  LYS B 243 "
      ideal   model   delta    sigma   weight residual
     121.54  125.80   -4.26 1.91e+00 2.74e-01 4.96e+00
  angle pdb=" N   ILE E  92 "
        pdb=" CA  ILE E  92 "
        pdb=" C   ILE E  92 "
      ideal   model   delta    sigma   weight residual
     111.88  109.60    2.28 1.06e+00 8.90e-01 4.64e+00
  angle pdb=" N   GLU E 145 "
        pdb=" CA  GLU E 145 "
        pdb=" C   GLU E 145 "
      ideal   model   delta    sigma   weight residual
     108.58  112.12   -3.54 1.82e+00 3.02e-01 3.78e+00
  angle pdb=" CA  GLU B 226 "
        pdb=" CB  GLU B 226 "
        pdb=" CG  GLU B 226 "
      ideal   model   delta    sigma   weight residual
     114.10  117.97   -3.87 2.00e+00 2.50e-01 3.74e+00
  ... (remaining 14371 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 5682
       17.51 -    35.03: 492
       35.03 -    52.54: 73
       52.54 -    70.05: 11
       70.05 -    87.57: 10
  Dihedral angle restraints: 6268
    sinusoidal: 2360
      harmonic: 3908
  Sorted by residual:
  dihedral pdb=" CB  CYS C  24 "
           pdb=" SG  CYS C  24 "
           pdb=" SG  CYS C  89 "
           pdb=" CB  CYS C  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.40  -74.40     1      1.00e+01 1.00e-02 7.02e+01
  dihedral pdb=" CB  CYS F  25 "
           pdb=" SG  CYS F  25 "
           pdb=" SG  CYS F  99 "
           pdb=" CB  CYS F  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.09  -72.09     1      1.00e+01 1.00e-02 6.65e+01
  dihedral pdb=" CB  CYS D  25 "
           pdb=" SG  CYS D  25 "
           pdb=" SG  CYS D  99 "
           pdb=" CB  CYS D  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  164.82  -71.82     1      1.00e+01 1.00e-02 6.60e+01
  ... (remaining 6265 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 977
       0.027 -    0.054: 450
       0.054 -    0.080: 108
       0.080 -    0.107: 107
       0.107 -    0.134: 24
  Chirality restraints: 1666
  Sorted by residual:
  chirality pdb=" CA  ILE E  49 "
            pdb=" N   ILE E  49 "
            pdb=" C   ILE E  49 "
            pdb=" CB  ILE E  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.49e-01
  chirality pdb=" CA  VAL A  67 "
            pdb=" N   VAL A  67 "
            pdb=" C   VAL A  67 "
            pdb=" CB  VAL A  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.37e-01
  chirality pdb=" CA  VAL B  67 "
            pdb=" N   VAL B  67 "
            pdb=" C   VAL B  67 "
            pdb=" CB  VAL B  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 1663 not shown)

  Planarity restraints: 1804
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E  40 "   -0.032 5.00e-02 4.00e+02   4.96e-02 3.94e+00
        pdb=" N   PRO E  41 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO E  41 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO E  41 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  40 "    0.025 5.00e-02 4.00e+02   3.81e-02 2.33e+00
        pdb=" N   PRO C  41 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO C  41 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C  41 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 184 "    0.009 2.00e-02 2.50e+03   1.14e-02 2.26e+00
        pdb=" CG  PHE B 184 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 184 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 184 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 184 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 184 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 184 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1801 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 87
        2.59 -     3.17: 8525
        3.17 -     3.74: 15219
        3.74 -     4.32: 20115
        4.32 -     4.90: 34061
  Nonbonded interactions: 78007
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 287 "
            pdb="ZN    ZN B 302 "
     model   vdw
     2.011 2.230
  nonbonded pdb=" OD1 ASP B 287 "
            pdb="ZN    ZN B 301 "
     model   vdw
     2.037 2.230
  nonbonded pdb=" OD1 ASP A 287 "
            pdb="ZN    ZN A 303 "
     model   vdw
     2.051 2.230
  nonbonded pdb=" OD2 ASP A 287 "
            pdb="ZN    ZN A 301 "
     model   vdw
     2.060 2.230
  nonbonded pdb=" OD1 ASN D 216 "
            pdb=" NZ  LYS D 223 "
     model   vdw
     2.241 3.120
  ... (remaining 78002 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}

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:             2.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.880
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
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  10586  Z= 0.117
  Angle     :  0.516   5.781  14392  Z= 0.269
  Chirality :  0.039   0.134   1666
  Planarity :  0.004   0.050   1804
  Dihedral  : 13.451  87.567   3724
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.57 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.35 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.24), residues: 1312
  helix:  0.98 (0.28), residues: 370
  sheet: -0.20 (0.29), residues: 366
  loop : -1.03 (0.25), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  90 
 TYR   0.010   0.001   TYR B 156 
 PHE   0.026   0.001   PHE B 184 
 TRP   0.019   0.001   TRP B 178 
 HIS   0.003   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (10566)
  covalent geometry    : angle       0.51576 (14376)
  SS BOND              : bond        0.00117 (    8)
  SS BOND              : angle       0.88293 (   16)
  hydrogen bonds       : bond        0.28456 (  427)
  hydrogen bonds       : angle       8.91149 ( 1209)
  metal coordination   : bond        0.00186 (   12)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 192
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.7970 (ppp) cc_final: 0.7154 (ppp)
REVERT: B  195 GLN cc_start: 0.7625 (mt0) cc_final: 0.7148 (mt0)
  outliers start: 1
  outliers final: 0
  residues processed: 193
  average time/residue: 0.0975
  time to fit residues: 26.7749
Evaluate side-chains
  157 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 66 optimal weight:   30.0000
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
B 109 ASN
B 137 GLN
B 195 GLN
E 102 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.174640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.121403 restraints weight = 14087.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.122018 restraints weight = 9764.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.120999 restraints weight = 7019.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.121366 restraints weight = 8336.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.121757 restraints weight = 7065.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10586  Z= 0.169
  Angle     :  0.607  10.083  14392  Z= 0.320
  Chirality :  0.043   0.185   1666
  Planarity :  0.004   0.036   1804
  Dihedral  :  4.162  16.964   1440
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.80 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  9.47 %
    Favored  : 89.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.23), residues: 1312
  helix:  1.54 (0.27), residues: 380
  sheet: -0.51 (0.28), residues: 366
  loop : -1.14 (0.24), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  90 
 TYR   0.019   0.001   TYR A 191 
 PHE   0.012   0.001   PHE B 184 
 TRP   0.015   0.001   TRP D  50 
 HIS   0.004   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (10566)
  covalent geometry    : angle       0.60615 (14376)
  SS BOND              : bond        0.00495 (    8)
  SS BOND              : angle       1.23620 (   16)
  hydrogen bonds       : bond        0.06089 (  427)
  hydrogen bonds       : angle       5.71798 ( 1209)
  metal coordination   : bond        0.00470 (   12)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 170
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.7759 (ppp) cc_final: 0.6877 (ppp)
REVERT: A  174 GLN cc_start: 0.5846 (tt0) cc_final: 0.5598 (tm-30)
REVERT: C  189 GLU cc_start: 0.5728 (mp0) cc_final: 0.5481 (mp0)
REVERT: D  118 MET cc_start: 0.8427 (mtt) cc_final: 0.8172 (mtt)
REVERT: E  189 GLU cc_start: 0.5593 (mp0) cc_final: 0.5372 (mp0)
REVERT: F  118 MET cc_start: 0.8431 (mtt) cc_final: 0.8135 (mtt)
  outliers start: 13
  outliers final: 7
  residues processed: 178
  average time/residue: 0.1096
  time to fit residues: 27.2822
Evaluate side-chains
  159 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 152
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain B residue  101 PHE
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain F residue   60 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 124 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 110 optimal weight:    0.4980
   chunk 131 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   chunk 130 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 97 optimal weight:    0.1980
   chunk 113 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C   7 GLN
** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 102 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.174963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.119721 restraints weight = 14041.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.121075 restraints weight = 10185.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.120948 restraints weight = 8176.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.121200 restraints weight = 7480.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.121787 restraints weight = 6874.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10586  Z= 0.137
  Angle     :  0.552   8.976  14392  Z= 0.287
  Chirality :  0.041   0.159   1666
  Planarity :  0.004   0.036   1804
  Dihedral  :  4.076  17.841   1440
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.96 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 13.27 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.24 (0.23), residues: 1312
  helix:  1.64 (0.27), residues: 376
  sheet: -0.48 (0.27), residues: 364
  loop : -1.12 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  90 
 TYR   0.014   0.001   TYR B 191 
 PHE   0.022   0.001   PHE B  97 
 TRP   0.012   0.001   TRP B 178 
 HIS   0.004   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (10566)
  covalent geometry    : angle       0.55185 (14376)
  SS BOND              : bond        0.00298 (    8)
  SS BOND              : angle       0.94752 (   16)
  hydrogen bonds       : bond        0.04820 (  427)
  hydrogen bonds       : angle       5.06049 ( 1209)
  metal coordination   : bond        0.00352 (   12)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 167
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.7706 (ppp) cc_final: 0.6892 (ppp)
REVERT: A   59 PHE cc_start: 0.8815 (t80) cc_final: 0.8592 (t80)
REVERT: D  118 MET cc_start: 0.8452 (mtt) cc_final: 0.8226 (mtt)
REVERT: B   58 ASN cc_start: 0.8171 (m-40) cc_final: 0.7814 (m110)
REVERT: B  201 TYR cc_start: 0.8119 (t80) cc_final: 0.7762 (t80)
REVERT: E  119 ILE cc_start: 0.7330 (mt) cc_final: 0.7120 (mm)
REVERT: F  118 MET cc_start: 0.8434 (mtt) cc_final: 0.8176 (mtt)
  outliers start: 12
  outliers final: 8
  residues processed: 174
  average time/residue: 0.1143
  time to fit residues: 27.4847
Evaluate side-chains
  156 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 148
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain F residue   60 SER
Chi-restraints excluded: chain F residue   94 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 89 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 119 optimal weight:    0.8980
   chunk 63 optimal weight:    0.5980
   chunk 120 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0010
   chunk 43 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0570
   overall best weight:    0.4904

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 163 ASN
C 140 ASN
** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 102 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.168512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.114657 restraints weight = 14010.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.113778 restraints weight = 10144.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.114082 restraints weight = 7942.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.114856 restraints weight = 6959.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.115051 restraints weight = 6449.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10586  Z= 0.120
  Angle     :  0.556   8.794  14392  Z= 0.282
  Chirality :  0.041   0.178   1666
  Planarity :  0.004   0.037   1804
  Dihedral  :  3.998  16.921   1440
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 14.34 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.23), residues: 1312
  helix:  1.72 (0.27), residues: 372
  sheet: -0.45 (0.28), residues: 364
  loop : -1.07 (0.25), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  90 
 TYR   0.013   0.001   TYR A 191 
 PHE   0.014   0.001   PHE A  97 
 TRP   0.013   0.001   TRP B 178 
 HIS   0.003   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (10566)
  covalent geometry    : angle       0.55532 (14376)
  SS BOND              : bond        0.00252 (    8)
  SS BOND              : angle       0.84346 (   16)
  hydrogen bonds       : bond        0.04199 (  427)
  hydrogen bonds       : angle       4.69995 ( 1209)
  metal coordination   : bond        0.00268 (   12)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 161
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.7610 (ppp) cc_final: 0.6726 (ppp)
REVERT: C  119 ILE cc_start: 0.7757 (mt) cc_final: 0.7389 (mm)
REVERT: D  118 MET cc_start: 0.8420 (mtt) cc_final: 0.8180 (mtt)
REVERT: B   58 ASN cc_start: 0.8125 (m-40) cc_final: 0.7760 (m-40)
REVERT: B  201 TYR cc_start: 0.8122 (t80) cc_final: 0.7793 (t80)
REVERT: E  119 ILE cc_start: 0.7468 (mt) cc_final: 0.7250 (mm)
REVERT: F  118 MET cc_start: 0.8461 (mtt) cc_final: 0.8163 (mtt)
REVERT: F  132 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6788 (pp30)
  outliers start: 19
  outliers final: 12
  residues processed: 174
  average time/residue: 0.1179
  time to fit residues: 28.4015
Evaluate side-chains
  161 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 148
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain B residue  101 PHE
Chi-restraints excluded: chain F residue   60 SER
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  132 GLN
Chi-restraints excluded: chain F residue  212 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   chunk 110 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9980
   chunk 38 optimal weight:   30.0000
   chunk 100 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 44 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 234 HIS
C 168 GLN
E 140 ASN
F 123 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.161830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.102451 restraints weight = 14068.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.105960 restraints weight = 10229.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.106553 restraints weight = 6720.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.107048 restraints weight = 6796.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.107126 restraints weight = 6529.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.317  10586  Z= 0.231
  Angle     :  0.615   8.658  14392  Z= 0.314
  Chirality :  0.043   0.263   1666
  Planarity :  0.004   0.038   1804
  Dihedral  :  4.299  17.873   1440
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.84 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.23), residues: 1312
  helix:  1.73 (0.27), residues: 372
  sheet: -0.43 (0.27), residues: 372
  loop : -1.21 (0.25), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  90 
 TYR   0.013   0.001   TYR B 191 
 PHE   0.020   0.001   PHE B  97 
 TRP   0.019   0.001   TRP A 178 
 HIS   0.006   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 (10566)
  covalent geometry    : angle       0.61493 (14376)
  SS BOND              : bond        0.00323 (    8)
  SS BOND              : angle       0.88704 (   16)
  hydrogen bonds       : bond        0.04388 (  427)
  hydrogen bonds       : angle       4.78739 ( 1209)
  metal coordination   : bond        0.09161 (   12)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 157
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.7763 (ppp) cc_final: 0.6819 (ppp)
REVERT: A  133 LEU cc_start: 0.9217 (mm) cc_final: 0.8997 (mm)
REVERT: C   82 GLU cc_start: 0.7774 (pm20) cc_final: 0.7336 (pm20)
REVERT: C  119 ILE cc_start: 0.7914 (mt) cc_final: 0.7571 (mm)
REVERT: D  132 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6959 (pp30)
REVERT: B  201 TYR cc_start: 0.8230 (t80) cc_final: 0.7850 (t80)
REVERT: E  119 ILE cc_start: 0.7474 (mt) cc_final: 0.7232 (mm)
REVERT: F  118 MET cc_start: 0.8622 (mtt) cc_final: 0.8342 (mtt)
REVERT: F  132 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6442 (pp30)
  outliers start: 26
  outliers final: 21
  residues processed: 174
  average time/residue: 0.1167
  time to fit residues: 27.9882
Evaluate side-chains
  169 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  132 GLN
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  101 PHE
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  286 GLN
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue   60 SER
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  123 GLN
Chi-restraints excluded: chain F residue  132 GLN
Chi-restraints excluded: chain F residue  212 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 97 optimal weight:    0.0040
   chunk 13 optimal weight:   20.0000
   chunk 28 optimal weight:    6.9990
   chunk 114 optimal weight:    0.6980
   chunk 116 optimal weight:    2.9990
   overall best weight:    1.7396

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 195 GLN
B 163 ASN
B 234 HIS
E 102 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.159924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.098515 restraints weight = 14171.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.101684 restraints weight = 9205.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.103790 restraints weight = 7101.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.104980 restraints weight = 6046.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.105922 restraints weight = 5476.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.304  10586  Z= 0.290
  Angle     :  0.682  14.801  14392  Z= 0.344
  Chirality :  0.046   0.310   1666
  Planarity :  0.004   0.039   1804
  Dihedral  :  4.568  17.759   1440
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 17.43 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.23), residues: 1312
  helix:  1.45 (0.27), residues: 384
  sheet: -0.60 (0.27), residues: 372
  loop : -1.45 (0.24), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  90 
 TYR   0.014   0.002   TYR A 191 
 PHE   0.015   0.002   PHE A  97 
 TRP   0.018   0.002   TRP F  50 
 HIS   0.007   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00645 (10566)
  covalent geometry    : angle       0.68143 (14376)
  SS BOND              : bond        0.00362 (    8)
  SS BOND              : angle       0.87031 (   16)
  hydrogen bonds       : bond        0.04537 (  427)
  hydrogen bonds       : angle       4.90562 ( 1209)
  metal coordination   : bond        0.08859 (   12)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 154
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.7776 (ppp) cc_final: 0.6807 (ppp)
REVERT: A  133 LEU cc_start: 0.9231 (mm) cc_final: 0.9030 (pp)
REVERT: C  119 ILE cc_start: 0.7926 (mt) cc_final: 0.7616 (mm)
REVERT: D  132 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6817 (pp30)
REVERT: B   58 ASN cc_start: 0.8078 (m-40) cc_final: 0.7794 (m110)
REVERT: B  174 GLN cc_start: 0.5214 (tt0) cc_final: 0.4993 (tm-30)
REVERT: B  201 TYR cc_start: 0.8250 (t80) cc_final: 0.7801 (t80)
REVERT: F  132 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6535 (pp30)
  outliers start: 36
  outliers final: 28
  residues processed: 178
  average time/residue: 0.1126
  time to fit residues: 27.9547
Evaluate side-chains
  175 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 145
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  286 GLN
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  132 GLN
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  101 PHE
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  286 GLN
Chi-restraints excluded: chain E residue   73 THR
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain F residue   36 SER
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue   60 SER
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  132 GLN
Chi-restraints excluded: chain F residue  212 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   chunk 66 optimal weight:   30.0000
   chunk 57 optimal weight:    0.7980
   chunk 130 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 85 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.159962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.105243 restraints weight = 14050.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.104956 restraints weight = 9238.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.103753 restraints weight = 8249.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.104672 restraints weight = 7780.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.104648 restraints weight = 7314.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  10586  Z= 0.239
  Angle     :  0.673  12.092  14392  Z= 0.335
  Chirality :  0.044   0.168   1666
  Planarity :  0.004   0.043   1804
  Dihedral  :  4.618  17.288   1440
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.41 %
    Favored  : 78.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.23), residues: 1312
  helix:  1.49 (0.27), residues: 388
  sheet: -0.65 (0.27), residues: 372
  loop : -1.56 (0.25), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  90 
 TYR   0.011   0.001   TYR E  50 
 PHE   0.022   0.002   PHE B  97 
 TRP   0.017   0.002   TRP D  50 
 HIS   0.008   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 (10566)
  covalent geometry    : angle       0.67255 (14376)
  SS BOND              : bond        0.00357 (    8)
  SS BOND              : angle       0.85885 (   16)
  hydrogen bonds       : bond        0.04385 (  427)
  hydrogen bonds       : angle       4.84213 ( 1209)
  metal coordination   : bond        0.00861 (   12)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 155
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.7704 (ppp) cc_final: 0.6770 (ppp)
REVERT: C   82 GLU cc_start: 0.7854 (pm20) cc_final: 0.7401 (pm20)
REVERT: C  119 ILE cc_start: 0.7903 (mt) cc_final: 0.7577 (mm)
REVERT: B   58 ASN cc_start: 0.8123 (m-40) cc_final: 0.7816 (m110)
REVERT: B  174 GLN cc_start: 0.5414 (tt0) cc_final: 0.5192 (tm-30)
REVERT: B  201 TYR cc_start: 0.8289 (t80) cc_final: 0.7838 (t80)
  outliers start: 34
  outliers final: 26
  residues processed: 177
  average time/residue: 0.1124
  time to fit residues: 27.7801
Evaluate side-chains
  172 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 146
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  286 GLN
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  212 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  101 PHE
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  286 GLN
Chi-restraints excluded: chain E residue   73 THR
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue   60 SER
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  212 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 0 optimal weight:   30.0000
   chunk 125 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0470
   chunk 6 optimal weight:    0.9990
   chunk 89 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 195 GLN
B 109 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.163048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.108037 restraints weight = 13957.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.108077 restraints weight = 8938.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.106525 restraints weight = 7894.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.107650 restraints weight = 7898.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.107930 restraints weight = 6893.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10586  Z= 0.141
  Angle     :  0.664  11.846  14392  Z= 0.318
  Chirality :  0.044   0.237   1666
  Planarity :  0.004   0.045   1804
  Dihedral  :  4.377  18.207   1440
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 19.73 %
    Favored  : 78.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.24), residues: 1312
  helix:  1.82 (0.28), residues: 368
  sheet: -0.56 (0.27), residues: 376
  loop : -1.33 (0.25), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  90 
 TYR   0.017   0.001   TYR A 191 
 PHE   0.016   0.001   PHE A 184 
 TRP   0.025   0.001   TRP A 178 
 HIS   0.013   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (10566)
  covalent geometry    : angle       0.66339 (14376)
  SS BOND              : bond        0.00277 (    8)
  SS BOND              : angle       0.80976 (   16)
  hydrogen bonds       : bond        0.03973 (  427)
  hydrogen bonds       : angle       4.67294 ( 1209)
  metal coordination   : bond        0.00228 (   12)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 156
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.7591 (ppp) cc_final: 0.6711 (ppp)
REVERT: C   82 GLU cc_start: 0.7812 (pm20) cc_final: 0.7376 (pm20)
REVERT: C  119 ILE cc_start: 0.7905 (mt) cc_final: 0.7557 (mm)
REVERT: B  174 GLN cc_start: 0.5340 (tt0) cc_final: 0.5077 (tm-30)
REVERT: B  201 TYR cc_start: 0.8294 (t80) cc_final: 0.7860 (t80)
REVERT: E   82 GLU cc_start: 0.7636 (pm20) cc_final: 0.7223 (pm20)
  outliers start: 25
  outliers final: 24
  residues processed: 174
  average time/residue: 0.1153
  time to fit residues: 27.8614
Evaluate side-chains
  167 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  286 GLN
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  101 PHE
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  286 GLN
Chi-restraints excluded: chain E residue   73 THR
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain F residue   60 SER
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  212 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 129 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 97 optimal weight:    0.1980
   chunk 88 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0870
   chunk 125 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 93 optimal weight:    0.5980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.163898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.102025 restraints weight = 14017.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.105396 restraints weight = 8963.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.107641 restraints weight = 6869.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.109137 restraints weight = 5801.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.109964 restraints weight = 5222.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10586  Z= 0.133
  Angle     :  0.642  12.105  14392  Z= 0.311
  Chirality :  0.043   0.251   1666
  Planarity :  0.004   0.044   1804
  Dihedral  :  4.219  17.430   1440
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.82 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.24), residues: 1312
  helix:  1.63 (0.28), residues: 388
  sheet: -0.52 (0.27), residues: 378
  loop : -1.45 (0.25), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  90 
 TYR   0.021   0.001   TYR A 191 
 PHE   0.022   0.001   PHE B  97 
 TRP   0.026   0.001   TRP A 178 
 HIS   0.003   0.001   HIS B 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (10566)
  covalent geometry    : angle       0.64225 (14376)
  SS BOND              : bond        0.00251 (    8)
  SS BOND              : angle       0.76633 (   16)
  hydrogen bonds       : bond        0.03797 (  427)
  hydrogen bonds       : angle       4.54549 ( 1209)
  metal coordination   : bond        0.00187 (   12)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 150
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.7639 (ppp) cc_final: 0.6683 (ppp)
REVERT: A  133 LEU cc_start: 0.9387 (tp) cc_final: 0.9119 (pp)
REVERT: C  119 ILE cc_start: 0.7975 (mt) cc_final: 0.7633 (mm)
REVERT: B  174 GLN cc_start: 0.5375 (tt0) cc_final: 0.5060 (tm-30)
REVERT: B  201 TYR cc_start: 0.8327 (t80) cc_final: 0.7933 (t80)
REVERT: E   82 GLU cc_start: 0.7589 (pm20) cc_final: 0.7235 (pm20)
REVERT: E  175 TYR cc_start: 0.7551 (m-10) cc_final: 0.7327 (m-10)
  outliers start: 26
  outliers final: 24
  residues processed: 169
  average time/residue: 0.1158
  time to fit residues: 27.1563
Evaluate side-chains
  165 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  286 GLN
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  101 PHE
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  286 GLN
Chi-restraints excluded: chain E residue   73 THR
Chi-restraints excluded: chain E residue  108 ILE
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain F residue   31 THR
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue   60 SER
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  212 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 113 optimal weight:    3.9990
   chunk 99 optimal weight:    0.0570
   chunk 100 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 110 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 52 optimal weight:    0.1980
   chunk 85 optimal weight:    0.9980
   chunk 16 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.5698

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.164453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.108900 restraints weight = 13965.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.106696 restraints weight = 8915.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.108172 restraints weight = 7196.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.108559 restraints weight = 7107.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.108972 restraints weight = 6102.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10586  Z= 0.132
  Angle     :  0.648  12.386  14392  Z= 0.315
  Chirality :  0.043   0.269   1666
  Planarity :  0.004   0.038   1804
  Dihedral  :  4.156  17.519   1440
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 20.27 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.24), residues: 1312
  helix:  1.68 (0.28), residues: 384
  sheet: -0.38 (0.28), residues: 370
  loop : -1.45 (0.25), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  90 
 TYR   0.020   0.001   TYR B 191 
 PHE   0.019   0.001   PHE A 184 
 TRP   0.029   0.001   TRP A 178 
 HIS   0.003   0.001   HIS B 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (10566)
  covalent geometry    : angle       0.64817 (14376)
  SS BOND              : bond        0.00225 (    8)
  SS BOND              : angle       0.72822 (   16)
  hydrogen bonds       : bond        0.03735 (  427)
  hydrogen bonds       : angle       4.46627 ( 1209)
  metal coordination   : bond        0.00192 (   12)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 148
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.7503 (ppp) cc_final: 0.6568 (ppp)
REVERT: A  133 LEU cc_start: 0.9253 (tp) cc_final: 0.9045 (pp)
REVERT: C   82 GLU cc_start: 0.7825 (pm20) cc_final: 0.7366 (pm20)
REVERT: C  119 ILE cc_start: 0.7940 (mt) cc_final: 0.7588 (mm)
REVERT: B  174 GLN cc_start: 0.5419 (tt0) cc_final: 0.5166 (tm-30)
REVERT: B  201 TYR cc_start: 0.8313 (t80) cc_final: 0.7930 (t80)
REVERT: E   82 GLU cc_start: 0.7669 (pm20) cc_final: 0.7347 (pm20)
  outliers start: 27
  outliers final: 23
  residues processed: 168
  average time/residue: 0.1141
  time to fit residues: 26.7129
Evaluate side-chains
  163 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  286 GLN
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  101 PHE
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  286 GLN
Chi-restraints excluded: chain E residue   73 THR
Chi-restraints excluded: chain E residue  108 ILE
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain F residue   31 THR
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue   60 SER
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  212 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0970
   chunk 110 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 33 optimal weight:    0.1980
   chunk 17 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.4978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.164973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.109580 restraints weight = 14110.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.106749 restraints weight = 9978.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.107265 restraints weight = 8428.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.107796 restraints weight = 7476.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.108388 restraints weight = 6752.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10586  Z= 0.127
  Angle     :  0.655  12.198  14392  Z= 0.315
  Chirality :  0.043   0.265   1666
  Planarity :  0.004   0.038   1804
  Dihedral  :  4.163  25.324   1440
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 20.35 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.24), residues: 1312
  helix:  1.70 (0.28), residues: 384
  sheet: -0.33 (0.28), residues: 370
  loop : -1.42 (0.25), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  90 
 TYR   0.022   0.001   TYR A 191 
 PHE   0.022   0.001   PHE B  97 
 TRP   0.037   0.001   TRP A 178 
 HIS   0.003   0.001   HIS B 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10566)
  covalent geometry    : angle       0.65401 (14376)
  SS BOND              : bond        0.00187 (    8)
  SS BOND              : angle       1.40010 (   16)
  hydrogen bonds       : bond        0.03657 (  427)
  hydrogen bonds       : angle       4.43772 ( 1209)
  metal coordination   : bond        0.00163 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2012.48 seconds
wall clock time: 35 minutes 43.84 seconds (2143.84 seconds total)