Starting phenix.real_space_refine
on Wed Jan 14 19:13:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7via_32005/01_2026/7via_32005.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7via_32005/01_2026/7via_32005.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7via_32005/01_2026/7via_32005.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7via_32005/01_2026/7via_32005.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7via_32005/01_2026/7via_32005.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7via_32005/01_2026/7via_32005.cif"
  }
  resolution = 3.88
  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=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      84      5.16       5
     C   11620      2.51       5
     N    3171      2.21       5
     O    3570      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18445
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2635
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 18, 'TRANS': 316}
    Chain: "B"
      Number of atoms: 2635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2635
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 18, 'TRANS': 316}
    Chain: "C"
      Number of atoms: 2635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2635
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 18, 'TRANS': 316}
    Chain: "D"
      Number of atoms: 2635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2635
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 18, 'TRANS': 316}
    Chain: "E"
      Number of atoms: 2635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2635
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 18, 'TRANS': 316}
    Chain: "F"
      Number of atoms: 2635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2635
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 18, 'TRANS': 316}
    Chain: "G"
      Number of atoms: 2635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2635
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 18, 'TRANS': 316}
  Time building chain proxies: 4.21, per 1000 atoms: 0.23
  Number of scatterers: 18445
  At special positions: 0
  Unit cell: (126.734, 145.026, 171.157, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      84     16.00
     O    3570      8.00
     N    3171      7.00
     C   11620      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.68
  Conformation dependent library (CDL) restraints added in 816.3 milliseconds
  

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4368

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 48 sheets defined
      28.0% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 44
      No H-bonds generated for 'chain 'A' and resid 42 through 44'
    Processing helix  chain 'A' and resid 97 through 102
      removed outlier: 3.793A  pdb=" N   ALA A 102 " --> pdb=" O   GLN A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 138
      removed outlier: 3.602A  pdb=" N   MET A 113 " --> pdb=" O   ARG A 109 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLN A 125 " --> pdb=" O   LEU A 121 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   VAL A 126 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU A 127 " --> pdb=" O   ILE A 123 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   SER A 133 " --> pdb=" O   MET A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 161
      removed outlier: 3.563A  pdb=" N   ASN A 160 " --> pdb=" O   SER A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 190
      removed outlier: 4.173A  pdb=" N   ASN A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 218
      removed outlier: 3.626A  pdb=" N   GLU A 216 " --> pdb=" O   LYS A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 235
      removed outlier: 3.674A  pdb=" N   VAL A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 296
      removed outlier: 3.893A  pdb=" N   ARG A 295 " --> pdb=" O   ALA A 291 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU A 296 " --> pdb=" O   ASP A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 335
      removed outlier: 3.768A  pdb=" N   PHE A 335 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 138
      removed outlier: 3.734A  pdb=" N   ARG B 109 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   MET B 113 " --> pdb=" O   ARG B 109 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   LYS B 137 " --> pdb=" O   SER B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 161
      removed outlier: 3.642A  pdb=" N   ASN B 161 " --> pdb=" O   GLU B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 189
    Processing helix  chain 'B' and resid 203 through 211
      removed outlier: 4.288A  pdb=" N   LEU B 207 " --> pdb=" O   LYS B 203 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   PHE B 208 " --> pdb=" O   GLY B 204 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   PHE B 211 " --> pdb=" O   LEU B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 218
      removed outlier: 3.998A  pdb=" N   LYS B 215 " --> pdb=" O   PHE B 211 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   GLU B 216 " --> pdb=" O   LYS B 212 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   LYS B 217 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 234
      removed outlier: 3.835A  pdb=" N   ASP B 234 " --> pdb=" O   THR B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 296
    Processing helix  chain 'B' and resid 331 through 335
      removed outlier: 3.928A  pdb=" N   PHE B 335 " --> pdb=" O   PRO B 332 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 44
      No H-bonds generated for 'chain 'C' and resid 42 through 44'
    Processing helix  chain 'C' and resid 97 through 103
      removed outlier: 4.142A  pdb=" N   LEU C 101 " --> pdb=" O   ASP C  97 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA C 102 " --> pdb=" O   PRO C  98 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ASP C 103 " --> pdb=" O   GLN C  99 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 97 through 103'
    Processing helix  chain 'C' and resid 103 through 138
      removed outlier: 4.053A  pdb=" N   GLN C 125 " --> pdb=" O   LEU C 121 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   VAL C 126 " --> pdb=" O   ALA C 122 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ALA C 131 " --> pdb=" O   GLU C 127 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LYS C 137 " --> pdb=" O   SER C 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 180 through 190
      removed outlier: 4.543A  pdb=" N   ASN C 190 " --> pdb=" O   ALA C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 210
      removed outlier: 4.038A  pdb=" N   LEU C 207 " --> pdb=" O   LYS C 203 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   PHE C 208 " --> pdb=" O   GLY C 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 216
    Processing helix  chain 'C' and resid 227 through 233
    Processing helix  chain 'C' and resid 290 through 296
    Processing helix  chain 'C' and resid 331 through 335
      removed outlier: 3.839A  pdb=" N   PHE C 335 " --> pdb=" O   PRO C 332 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 42 through 44
      No H-bonds generated for 'chain 'D' and resid 42 through 44'
    Processing helix  chain 'D' and resid 98 through 102
    Processing helix  chain 'D' and resid 103 through 138
      removed outlier: 3.931A  pdb=" N   ARG D 107 " --> pdb=" O   ASP D 103 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   MET D 113 " --> pdb=" O   ARG D 109 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   VAL D 126 " --> pdb=" O   ALA D 122 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   LYS D 137 " --> pdb=" O   SER D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 161
    Processing helix  chain 'D' and resid 180 through 188
    Processing helix  chain 'D' and resid 189 through 192
      removed outlier: 4.308A  pdb=" N   SER D 192 " --> pdb=" O   LEU D 189 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 189 through 192'
    Processing helix  chain 'D' and resid 201 through 206
    Processing helix  chain 'D' and resid 211 through 218
      removed outlier: 3.569A  pdb=" N   LYS D 215 " --> pdb=" O   PHE D 211 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   GLU D 216 " --> pdb=" O   LYS D 212 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 235
      removed outlier: 3.636A  pdb=" N   ALA D 231 " --> pdb=" O   GLU D 227 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASP D 234 " --> pdb=" O   THR D 230 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU D 235 " --> pdb=" O   ALA D 231 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 290 through 296
    Processing helix  chain 'D' and resid 331 through 333
      No H-bonds generated for 'chain 'D' and resid 331 through 333'
    Processing helix  chain 'E' and resid 40 through 44
    Processing helix  chain 'E' and resid 97 through 102
      removed outlier: 4.002A  pdb=" N   ASN E 100 " --> pdb=" O   ASP E  97 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU E 101 " --> pdb=" O   PRO E  98 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ALA E 102 " --> pdb=" O   GLN E  99 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 97 through 102'
    Processing helix  chain 'E' and resid 103 through 138
      removed outlier: 3.567A  pdb=" N   ARG E 107 " --> pdb=" O   ASP E 103 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ARG E 109 " --> pdb=" O   ALA E 105 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   MET E 113 " --> pdb=" O   ARG E 109 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL E 126 " --> pdb=" O   ALA E 122 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LYS E 137 " --> pdb=" O   SER E 133 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 157 through 161
      removed outlier: 3.626A  pdb=" N   ASN E 160 " --> pdb=" O   SER E 157 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 180 through 185
    Processing helix  chain 'E' and resid 188 through 192
      removed outlier: 3.593A  pdb=" N   ALA E 191 " --> pdb=" O   ALA E 188 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   SER E 192 " --> pdb=" O   LEU E 189 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 188 through 192'
    Processing helix  chain 'E' and resid 201 through 211
      removed outlier: 3.628A  pdb=" N   ALA E 206 " --> pdb=" O   PRO E 202 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU E 207 " --> pdb=" O   LYS E 203 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   PHE E 208 " --> pdb=" O   GLY E 204 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   PHE E 211 " --> pdb=" O   LEU E 207 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 211 through 218
      removed outlier: 4.055A  pdb=" N   LYS E 215 " --> pdb=" O   PHE E 211 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   GLU E 216 " --> pdb=" O   LYS E 212 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   LYS E 217 " --> pdb=" O   ALA E 213 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 228 through 235
    Processing helix  chain 'E' and resid 290 through 296
    Processing helix  chain 'F' and resid 40 through 44
    Processing helix  chain 'F' and resid 99 through 102
    Processing helix  chain 'F' and resid 103 through 138
      removed outlier: 3.955A  pdb=" N   LEU F 121 " --> pdb=" O   ARG F 117 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ALA F 122 " --> pdb=" O   ASP F 118 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE F 123 " --> pdb=" O   GLU F 119 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   VAL F 126 " --> pdb=" O   ALA F 122 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LYS F 137 " --> pdb=" O   SER F 133 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 157 through 161
    Processing helix  chain 'F' and resid 180 through 187
    Processing helix  chain 'F' and resid 201 through 211
      removed outlier: 4.124A  pdb=" N   LEU F 207 " --> pdb=" O   LYS F 203 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   PHE F 208 " --> pdb=" O   GLY F 204 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   PHE F 211 " --> pdb=" O   LEU F 207 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 211 through 218
      removed outlier: 3.525A  pdb=" N   LYS F 215 " --> pdb=" O   PHE F 211 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 227 through 236
      removed outlier: 4.263A  pdb=" N   LYS F 233 " --> pdb=" O   THR F 230 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   ASP F 234 " --> pdb=" O   ALA F 231 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 290 through 296
    Processing helix  chain 'G' and resid 40 through 44
    Processing helix  chain 'G' and resid 98 through 102
      removed outlier: 3.618A  pdb=" N   ALA G 102 " --> pdb=" O   GLN G  99 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 103 through 133
      removed outlier: 3.744A  pdb=" N   MET G 113 " --> pdb=" O   ARG G 109 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ASP G 118 " --> pdb=" O   GLN G 114 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   VAL G 126 " --> pdb=" O   ALA G 122 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   SER G 133 " --> pdb=" O   MET G 129 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 133 through 138
      removed outlier: 3.823A  pdb=" N   LYS G 137 " --> pdb=" O   SER G 133 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 157 through 161
      removed outlier: 3.562A  pdb=" N   ASN G 161 " --> pdb=" O   GLU G 158 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 180 through 190
      removed outlier: 4.377A  pdb=" N   ASN G 190 " --> pdb=" O   ALA G 186 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 201 through 210
      removed outlier: 4.414A  pdb=" N   LEU G 207 " --> pdb=" O   LYS G 203 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   PHE G 208 " --> pdb=" O   GLY G 204 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 211 through 218
      removed outlier: 3.693A  pdb=" N   GLU G 216 " --> pdb=" O   LYS G 212 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 228 through 235
      removed outlier: 3.797A  pdb=" N   VAL G 232 " --> pdb=" O   LEU G 228 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ASP G 234 " --> pdb=" O   THR G 230 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU G 235 " --> pdb=" O   ALA G 231 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 290 through 296
    Processing helix  chain 'G' and resid 331 through 335
      removed outlier: 3.581A  pdb=" N   GLU G 334 " --> pdb=" O   ASP G 331 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   PHE G 335 " --> pdb=" O   PRO G 332 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 331 through 335'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33
      removed outlier: 7.541A  pdb=" N   GLU A  30 " --> pdb=" O   ARG A 283 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   TYR A 285 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   TYR A  32 " --> pdb=" O   TYR A 285 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40
    Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 83
    Processing sheet with id=AA4, first strand: chain 'A' and resid 139 through 144
      removed outlier: 6.009A  pdb=" N   GLY A 144 " --> pdb=" O   ASP A 148 " (cutoff:3.500A)
      removed outlier: 5.109A  pdb=" N   ASP A 148 " --> pdb=" O   GLY A 144 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 244
      removed outlier: 6.663A  pdb=" N   ILE A 250 " --> pdb=" O   LYS A 242 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 256 through 258
    Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 274
    Processing sheet with id=AA8, first strand: chain 'B' and resid 81 through 83
    Processing sheet with id=AA9, first strand: chain 'B' and resid 139 through 142
    Processing sheet with id=AB1, first strand: chain 'B' and resid 239 through 244
      removed outlier: 6.863A  pdb=" N   ILE B 250 " --> pdb=" O   LYS B 242 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 256 through 258
    Processing sheet with id=AB3, first strand: chain 'B' and resid 271 through 274
    Processing sheet with id=AB4, first strand: chain 'B' and resid 281 through 282
    Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 40
      removed outlier: 3.601A  pdb=" N   VAL C  39 " --> pdb=" O   PHE C  73 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 81 through 83
      removed outlier: 3.525A  pdb=" N   GLN C 322 " --> pdb=" O   TYR C 304 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 139 through 142
    Processing sheet with id=AB8, first strand: chain 'C' and resid 239 through 244
      removed outlier: 6.865A  pdb=" N   ILE C 250 " --> pdb=" O   LYS C 242 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 256 through 258
    Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 274
    Processing sheet with id=AC2, first strand: chain 'C' and resid 281 through 282
    Processing sheet with id=AC3, first strand: chain 'D' and resid 32 through 33
      removed outlier: 6.948A  pdb=" N   TYR D  32 " --> pdb=" O   TYR D 285 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC3
    Processing sheet with id=AC4, first strand: chain 'D' and resid 39 through 40
    Processing sheet with id=AC5, first strand: chain 'D' and resid 62 through 63
    Processing sheet with id=AC6, first strand: chain 'D' and resid 81 through 83
      removed outlier: 3.581A  pdb=" N   HIS D  82 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   THR D 319 " --> pdb=" O   HIS D  82 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   TRP D 308 " --> pdb=" O   PHE D 318 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'D' and resid 141 through 142
    Processing sheet with id=AC8, first strand: chain 'D' and resid 239 through 245
      removed outlier: 6.962A  pdb=" N   ILE D 250 " --> pdb=" O   LYS D 242 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   MET D 244 " --> pdb=" O   VAL D 248 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   VAL D 248 " --> pdb=" O   MET D 244 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'D' and resid 256 through 258
    Processing sheet with id=AD1, first strand: chain 'D' and resid 271 through 275
    Processing sheet with id=AD2, first strand: chain 'D' and resid 281 through 282
    Processing sheet with id=AD3, first strand: chain 'E' and resid 32 through 33
      removed outlier: 7.458A  pdb=" N   TYR E  32 " --> pdb=" O   TYR E 285 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD3
    Processing sheet with id=AD4, first strand: chain 'E' and resid 140 through 142
    Processing sheet with id=AD5, first strand: chain 'E' and resid 239 through 244
      removed outlier: 6.691A  pdb=" N   ILE E 250 " --> pdb=" O   LYS E 242 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'E' and resid 256 through 258
    Processing sheet with id=AD7, first strand: chain 'E' and resid 271 through 274
    Processing sheet with id=AD8, first strand: chain 'E' and resid 281 through 282
    Processing sheet with id=AD9, first strand: chain 'E' and resid 303 through 309
    Processing sheet with id=AE1, first strand: chain 'F' and resid 81 through 83
    Processing sheet with id=AE2, first strand: chain 'F' and resid 139 through 144
      removed outlier: 5.595A  pdb=" N   GLY F 144 " --> pdb=" O   ASP F 148 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   ASP F 148 " --> pdb=" O   GLY F 144 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'F' and resid 243 through 245
      removed outlier: 4.151A  pdb=" N   VAL F 248 " --> pdb=" O   TYR F 245 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'F' and resid 256 through 258
    Processing sheet with id=AE5, first strand: chain 'F' and resid 271 through 274
    Processing sheet with id=AE6, first strand: chain 'F' and resid 281 through 282
    Processing sheet with id=AE7, first strand: chain 'G' and resid 32 through 33
      removed outlier: 7.593A  pdb=" N   TYR G  32 " --> pdb=" O   TYR G 285 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE7
    Processing sheet with id=AE8, first strand: chain 'G' and resid 81 through 83
    Processing sheet with id=AE9, first strand: chain 'G' and resid 140 through 144
      removed outlier: 5.618A  pdb=" N   GLY G 144 " --> pdb=" O   ASP G 148 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   ASP G 148 " --> pdb=" O   GLY G 144 " (cutoff:3.500A)
    Processing sheet with id=AF1, first strand: chain 'G' and resid 239 through 245
      removed outlier: 6.817A  pdb=" N   ILE G 250 " --> pdb=" O   LYS G 242 " (cutoff:3.500A)
      removed outlier: 5.097A  pdb=" N   MET G 244 " --> pdb=" O   VAL G 248 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   VAL G 248 " --> pdb=" O   MET G 244 " (cutoff:3.500A)
    Processing sheet with id=AF2, first strand: chain 'G' and resid 256 through 258
    Processing sheet with id=AF3, first strand: chain 'G' and resid 271 through 274

    479 hydrogen bonds defined for protein.
    1272 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.74

  Time building geometry restraints manager: 2.12 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: 6190
        1.34 -     1.46: 3927
        1.46 -     1.58: 8531
        1.58 -     1.70: 0
        1.70 -     1.82: 161
  Bond restraints: 18809
  Sorted by residual:
  bond pdb=" CA  ALA G 122 "
       pdb=" C   ALA G 122 "
    ideal  model  delta    sigma   weight residual
    1.522  1.490  0.032 1.40e-02 5.10e+03 5.28e+00
  bond pdb=" CB  VAL D 126 "
       pdb=" CG2 VAL D 126 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.14e+00
  bond pdb=" CA  PRO C 314 "
       pdb=" C   PRO C 314 "
    ideal  model  delta    sigma   weight residual
    1.528  1.517  0.011 9.10e-03 1.21e+04 1.58e+00
  bond pdb=" CA  GLY D 246 "
       pdb=" C   GLY D 246 "
    ideal  model  delta    sigma   weight residual
    1.514  1.530 -0.016 1.41e-02 5.03e+03 1.26e+00
  bond pdb=" CG  LYS D 139 "
       pdb=" CD  LYS D 139 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.20e+00
  ... (remaining 18804 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.78: 25116
        2.78 -     5.56: 303
        5.56 -     8.34: 36
        8.34 -    11.12: 3
       11.12 -    13.90: 1
  Bond angle restraints: 25459
  Sorted by residual:
  angle pdb=" N   ILE A  57 "
        pdb=" CA  ILE A  57 "
        pdb=" C   ILE A  57 "
      ideal   model   delta    sigma   weight residual
     113.71  108.01    5.70 9.50e-01 1.11e+00 3.59e+01
  angle pdb=" C   PHE D 200 "
        pdb=" N   ASP D 201 "
        pdb=" CA  ASP D 201 "
      ideal   model   delta    sigma   weight residual
     122.31  136.21  -13.90 2.34e+00 1.83e-01 3.53e+01
  angle pdb=" N   LEU C 136 "
        pdb=" CA  LEU C 136 "
        pdb=" C   LEU C 136 "
      ideal   model   delta    sigma   weight residual
     114.62  108.40    6.22 1.14e+00 7.69e-01 2.98e+01
  angle pdb=" N   ILE C  57 "
        pdb=" CA  ILE C  57 "
        pdb=" C   ILE C  57 "
      ideal   model   delta    sigma   weight residual
     113.71  108.94    4.77 9.50e-01 1.11e+00 2.52e+01
  angle pdb=" N   LEU A 136 "
        pdb=" CA  LEU A 136 "
        pdb=" C   LEU A 136 "
      ideal   model   delta    sigma   weight residual
     114.62  109.64    4.98 1.14e+00 7.69e-01 1.91e+01
  ... (remaining 25454 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 10291
       17.99 -    35.98: 984
       35.98 -    53.97: 153
       53.97 -    71.96: 34
       71.96 -    89.94: 25
  Dihedral angle restraints: 11487
    sinusoidal: 4683
      harmonic: 6804
  Sorted by residual:
  dihedral pdb=" CA  VAL E 135 "
           pdb=" C   VAL E 135 "
           pdb=" N   LEU E 136 "
           pdb=" CA  LEU E 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.66   34.34     0      5.00e+00 4.00e-02 4.72e+01
  dihedral pdb=" CA  ALA A  51 "
           pdb=" C   ALA A  51 "
           pdb=" N   LEU A  52 "
           pdb=" CA  LEU A  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.08  -33.92     0      5.00e+00 4.00e-02 4.60e+01
  dihedral pdb=" CA  VAL F 135 "
           pdb=" C   VAL F 135 "
           pdb=" N   LEU F 136 "
           pdb=" CA  LEU F 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.35   31.65     0      5.00e+00 4.00e-02 4.01e+01
  ... (remaining 11484 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1998
       0.044 -    0.088: 572
       0.088 -    0.132: 189
       0.132 -    0.175: 14
       0.175 -    0.219: 6
  Chirality restraints: 2779
  Sorted by residual:
  chirality pdb=" CB  ILE F 198 "
            pdb=" CA  ILE F 198 "
            pdb=" CG1 ILE F 198 "
            pdb=" CG2 ILE F 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CB  ILE C 198 "
            pdb=" CA  ILE C 198 "
            pdb=" CG1 ILE C 198 "
            pdb=" CG2 ILE C 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  PRO A  21 "
            pdb=" N   PRO A  21 "
            pdb=" C   PRO A  21 "
            pdb=" CB  PRO A  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 2776 not shown)

  Planarity restraints: 3367
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  20 "    0.041 5.00e-02 4.00e+02   6.22e-02 6.19e+00
        pdb=" N   PRO A  21 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A  21 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A  21 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  20 "    0.038 5.00e-02 4.00e+02   5.81e-02 5.40e+00
        pdb=" N   PRO C  21 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO C  21 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C  21 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  55 "    0.038 5.00e-02 4.00e+02   5.75e-02 5.29e+00
        pdb=" N   PRO B  56 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B  56 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B  56 "    0.032 5.00e-02 4.00e+02
  ... (remaining 3364 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 293
        2.62 -     3.19: 16925
        3.19 -     3.76: 27449
        3.76 -     4.33: 37578
        4.33 -     4.90: 61252
  Nonbonded interactions: 143497
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E  53 "
            pdb=" OH  TYR F 140 "
     model   vdw
     2.051 3.040
  nonbonded pdb=" OG  SER B  55 "
            pdb=" O   ALA C 146 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" O   GLN C  43 "
            pdb=" OG1 THR D  89 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" OH  TYR B  53 "
            pdb=" OH  TYR C 140 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OE2 GLU E 127 "
            pdb=" OH  TYR E 285 "
     model   vdw
     2.196 3.040
  ... (remaining 143492 not shown)

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

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:             35.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     16.610
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
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   0.048  18809  Z= 0.157
  Angle     :  0.746  13.897  25459  Z= 0.395
  Chirality :  0.045   0.219   2779
  Planarity :  0.005   0.062   3367
  Dihedral  : 14.577  89.945   7119
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 15.33
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 12.14 %
    Favored  : 87.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.17), residues: 2331
  helix: -0.90 (0.22), residues: 558
  sheet: -1.90 (0.24), residues: 478
  loop : -2.15 (0.17), residues: 1295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG G  64 
 TYR   0.024   0.001   TYR B 245 
 PHE   0.015   0.001   PHE C  17 
 TRP   0.029   0.001   TRP F 308 
 HIS   0.015   0.004   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (18809)
  covalent geometry    : angle       0.74563 (25459)
  hydrogen bonds       : bond        0.17633 (  479)
  hydrogen bonds       : angle       7.00687 ( 1272)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 MET cc_start: 0.8565 (tpp) cc_final: 0.8185 (tpp)
REVERT: A  142 MET cc_start: 0.9088 (mtm) cc_final: 0.7672 (mtp)
REVERT: A  326 LEU cc_start: 0.9103 (tp) cc_final: 0.8762 (tp)
REVERT: B  154 MET cc_start: 0.8516 (tpp) cc_final: 0.7970 (mmt)
REVERT: B  326 LEU cc_start: 0.8390 (tt) cc_final: 0.8179 (tt)
REVERT: C   22 LEU cc_start: 0.9295 (tp) cc_final: 0.8999 (tp)
REVERT: C  227 GLU cc_start: 0.7469 (pm20) cc_final: 0.7212 (pm20)
REVERT: E  114 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8317 (tm-30)
REVERT: E  154 MET cc_start: 0.8140 (tpp) cc_final: 0.7866 (tpp)
REVERT: F  212 LYS cc_start: 0.8434 (mtpp) cc_final: 0.7861 (mtpp)
REVERT: F  308 TRP cc_start: 0.8138 (p-90) cc_final: 0.7634 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.1383
  time to fit residues: 56.4666
Evaluate side-chains
  217 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 216 optimal weight:    0.8980
   chunk 98 optimal weight:    0.7980
   chunk 194 optimal weight:    1.9990
   chunk 227 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 200 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  49 ASN
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 ASN
B  15 GLN
B  99 GLN
B 130 GLN
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 ASN
C 322 GLN
** D  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 160 ASN
E  82 HIS
** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  87 GLN
F 278 GLN
** G  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.093168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.077253 restraints weight = 52814.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.079481 restraints weight = 29344.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.081004 restraints weight = 19941.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.082012 restraints weight = 15376.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.082657 restraints weight = 12868.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051  18809  Z= 0.288
  Angle     :  0.772   8.737  25459  Z= 0.391
  Chirality :  0.049   0.242   2779
  Planarity :  0.006   0.075   3367
  Dihedral  :  5.649  32.645   2583
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 14.46 %
    Favored  : 85.46 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 11.02 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.81 (0.17), residues: 2331
  helix: -0.91 (0.21), residues: 563
  sheet: -2.15 (0.23), residues: 486
  loop : -2.21 (0.17), residues: 1282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  64 
 TYR   0.039   0.002   TYR E 245 
 PHE   0.021   0.002   PHE G  23 
 TRP   0.019   0.002   TRP G 308 
 HIS   0.007   0.002   HIS E  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00666 (18809)
  covalent geometry    : angle       0.77180 (25459)
  hydrogen bonds       : bond        0.04732 (  479)
  hydrogen bonds       : angle       6.02532 ( 1272)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 217
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.8300 (mmm) cc_final: 0.7645 (tpt)
REVERT: A  129 MET cc_start: 0.8423 (tpp) cc_final: 0.8186 (tpp)
REVERT: A  142 MET cc_start: 0.9092 (mtm) cc_final: 0.8103 (mtm)
REVERT: A  233 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8197 (pttm)
REVERT: A  244 MET cc_start: 0.8580 (mmm) cc_final: 0.8049 (mmm)
REVERT: A  326 LEU cc_start: 0.9302 (tp) cc_final: 0.8984 (tp)
REVERT: B  154 MET cc_start: 0.8758 (tpp) cc_final: 0.7988 (mmt)
REVERT: B  272 MET cc_start: 0.8697 (ppp) cc_final: 0.8117 (ppp)
REVERT: C   22 LEU cc_start: 0.9432 (tp) cc_final: 0.9135 (tp)
REVERT: C  233 LYS cc_start: 0.9191 (ptpp) cc_final: 0.8946 (ptpp)
REVERT: E  114 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8420 (tm-30)
REVERT: E  128 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7721 (tm-30)
REVERT: E  129 MET cc_start: 0.8557 (tmm) cc_final: 0.8111 (tmm)
REVERT: E  154 MET cc_start: 0.8176 (tpp) cc_final: 0.7809 (mmm)
REVERT: E  219 ASP cc_start: 0.8566 (t0) cc_final: 0.8227 (t0)
REVERT: G   71 SER cc_start: 0.8198 (t) cc_final: 0.7344 (m)
REVERT: G   72 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7564 (mt-10)
REVERT: G   92 ARG cc_start: 0.5037 (mtm180) cc_final: 0.3943 (mtt90)
REVERT: G  197 ILE cc_start: 0.8854 (mp) cc_final: 0.8574 (mm)
  outliers start: 17
  outliers final: 12
  residues processed: 229
  average time/residue: 0.1408
  time to fit residues: 49.4886
Evaluate side-chains
  203 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 191
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  310 THR
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  228 LEU
Chi-restraints excluded: chain F residue  267 LEU
Chi-restraints excluded: chain F residue  338 VAL
Chi-restraints excluded: chain G residue   70 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 187 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 150 optimal weight:    0.5980
   chunk 162 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 168 optimal weight:    0.9980
   chunk 199 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 217 optimal weight:    0.8980
   chunk 145 optimal weight:    0.5980
   chunk 177 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  15 GLN
** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 164 GLN
** G  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.086655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.071927 restraints weight = 52788.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.074048 restraints weight = 29632.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.075462 restraints weight = 20158.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.076439 restraints weight = 15534.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.077099 restraints weight = 12966.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  18809  Z= 0.241
  Angle     :  0.714   8.601  25459  Z= 0.361
  Chirality :  0.047   0.219   2779
  Planarity :  0.005   0.065   3367
  Dihedral  :  5.545  33.449   2583
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 13.56 %
    Favored  : 86.36 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.34 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.32 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.77 (0.17), residues: 2331
  helix: -0.54 (0.22), residues: 530
  sheet: -2.15 (0.23), residues: 486
  loop : -2.32 (0.17), residues: 1315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG F 109 
 TYR   0.030   0.002   TYR E 245 
 PHE   0.019   0.001   PHE C  17 
 TRP   0.017   0.002   TRP F 308 
 HIS   0.004   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 (18809)
  covalent geometry    : angle       0.71380 (25459)
  hydrogen bonds       : bond        0.04362 (  479)
  hydrogen bonds       : angle       5.87189 ( 1272)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 213
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.8265 (mmm) cc_final: 0.7811 (mmm)
REVERT: A  129 MET cc_start: 0.8496 (tpp) cc_final: 0.8150 (tpp)
REVERT: A  142 MET cc_start: 0.8987 (mtm) cc_final: 0.8589 (mtm)
REVERT: A  244 MET cc_start: 0.8170 (mmm) cc_final: 0.7892 (mmm)
REVERT: A  326 LEU cc_start: 0.9285 (tp) cc_final: 0.9019 (tp)
REVERT: B  272 MET cc_start: 0.8681 (ppp) cc_final: 0.8112 (ppp)
REVERT: C   22 LEU cc_start: 0.9431 (tp) cc_final: 0.9202 (tp)
REVERT: C  233 LYS cc_start: 0.9167 (ptpp) cc_final: 0.8951 (ptpp)
REVERT: D  229 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7952 (pm20)
REVERT: E  114 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8300 (tm-30)
REVERT: E  129 MET cc_start: 0.8503 (tmm) cc_final: 0.8040 (tmm)
REVERT: E  219 ASP cc_start: 0.8547 (t0) cc_final: 0.8286 (t0)
REVERT: E  244 MET cc_start: 0.8095 (mmt) cc_final: 0.7701 (tpt)
REVERT: F  109 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7900 (ttp80)
REVERT: F  272 MET cc_start: 0.8591 (ppp) cc_final: 0.8380 (ppp)
REVERT: G   22 LEU cc_start: 0.9137 (tp) cc_final: 0.8931 (tt)
REVERT: G   24 LEU cc_start: 0.9384 (mm) cc_final: 0.9089 (mm)
REVERT: G   72 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7688 (mt-10)
REVERT: G   82 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.6831 (m-70)
REVERT: G   92 ARG cc_start: 0.4988 (mtm180) cc_final: 0.3811 (mtt90)
REVERT: G  197 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8703 (mm)
REVERT: G  327 MET cc_start: 0.8516 (mmp) cc_final: 0.7998 (mmp)
  outliers start: 42
  outliers final: 21
  residues processed: 245
  average time/residue: 0.1387
  time to fit residues: 52.3918
Evaluate side-chains
  225 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 202
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  140 TYR
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain D residue   82 HIS
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  310 THR
Chi-restraints excluded: chain E residue  126 VAL
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  228 LEU
Chi-restraints excluded: chain F residue  326 LEU
Chi-restraints excluded: chain F residue  338 VAL
Chi-restraints excluded: chain G residue   82 HIS
Chi-restraints excluded: chain G residue  197 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 115 optimal weight:    0.0370
   chunk 81 optimal weight:    0.6980
   chunk 173 optimal weight:    0.7980
   chunk 90 optimal weight:    0.4980
   chunk 153 optimal weight:    2.9990
   chunk 129 optimal weight:    0.5980
   chunk 157 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 ASN
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 160 ASN
** G  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.087594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.072859 restraints weight = 52493.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.075008 restraints weight = 29320.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.076458 restraints weight = 19887.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.077439 restraints weight = 15251.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.078051 restraints weight = 12701.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  18809  Z= 0.183
  Angle     :  0.681   9.543  25459  Z= 0.340
  Chirality :  0.045   0.205   2779
  Planarity :  0.005   0.062   3367
  Dihedral  :  5.359  34.532   2583
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 13.08 %
    Favored  : 86.83 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 15.64 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.32 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.59 (0.17), residues: 2331
  helix: -0.35 (0.23), residues: 530
  sheet: -1.98 (0.24), residues: 462
  loop : -2.27 (0.16), residues: 1339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 109 
 TYR   0.027   0.001   TYR E 245 
 PHE   0.012   0.001   PHE G  23 
 TRP   0.014   0.001   TRP F 308 
 HIS   0.005   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (18809)
  covalent geometry    : angle       0.68112 (25459)
  hydrogen bonds       : bond        0.03953 (  479)
  hydrogen bonds       : angle       5.69624 ( 1272)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 212
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7756 (mmm)
REVERT: A  129 MET cc_start: 0.8502 (tpp) cc_final: 0.8190 (tpp)
REVERT: A  142 MET cc_start: 0.9139 (mtm) cc_final: 0.8824 (mtm)
REVERT: A  233 LYS cc_start: 0.8698 (ptmm) cc_final: 0.8371 (pttm)
REVERT: A  244 MET cc_start: 0.8152 (mmm) cc_final: 0.7877 (mmm)
REVERT: A  326 LEU cc_start: 0.9281 (tp) cc_final: 0.8968 (tp)
REVERT: B   88 MET cc_start: 0.8419 (mmm) cc_final: 0.8159 (mmm)
REVERT: B  272 MET cc_start: 0.8652 (ppp) cc_final: 0.8096 (ppp)
REVERT: C   22 LEU cc_start: 0.9472 (tp) cc_final: 0.9211 (tp)
REVERT: C  287 CYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8001 (m)
REVERT: D  229 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7771 (pm20)
REVERT: E  114 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8301 (tm-30)
REVERT: E  154 MET cc_start: 0.8268 (mmt) cc_final: 0.7779 (tpp)
REVERT: E  219 ASP cc_start: 0.8496 (t0) cc_final: 0.8272 (t0)
REVERT: E  244 MET cc_start: 0.8106 (mmt) cc_final: 0.7669 (tpt)
REVERT: E  259 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8108 (tm-30)
REVERT: E  327 MET cc_start: 0.7794 (mmm) cc_final: 0.7545 (mmm)
REVERT: F  109 ARG cc_start: 0.8211 (ttp80) cc_final: 0.7953 (ttp80)
REVERT: F  272 MET cc_start: 0.8656 (ppp) cc_final: 0.8358 (ppp)
REVERT: G   22 LEU cc_start: 0.9130 (tp) cc_final: 0.8930 (tt)
REVERT: G   24 LEU cc_start: 0.9374 (mm) cc_final: 0.8981 (mt)
REVERT: G   82 HIS cc_start: 0.8204 (OUTLIER) cc_final: 0.6824 (m-70)
REVERT: G   92 ARG cc_start: 0.4864 (mtm180) cc_final: 0.3574 (mtt90)
REVERT: G  197 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8715 (mm)
REVERT: G  327 MET cc_start: 0.8589 (mmp) cc_final: 0.8134 (mmp)
  outliers start: 47
  outliers final: 31
  residues processed: 247
  average time/residue: 0.1391
  time to fit residues: 53.2185
Evaluate side-chains
  235 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 199
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  140 TYR
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  287 CYS
Chi-restraints excluded: chain D residue   82 HIS
Chi-restraints excluded: chain D residue  116 MET
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  310 THR
Chi-restraints excluded: chain E residue  126 VAL
Chi-restraints excluded: chain E residue  259 GLU
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  228 LEU
Chi-restraints excluded: chain F residue  267 LEU
Chi-restraints excluded: chain F residue  321 ILE
Chi-restraints excluded: chain F residue  326 LEU
Chi-restraints excluded: chain G residue   70 THR
Chi-restraints excluded: chain G residue   82 HIS
Chi-restraints excluded: chain G residue  189 LEU
Chi-restraints excluded: chain G residue  197 ILE
Chi-restraints excluded: chain G residue  321 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 117 optimal weight:    0.9990
   chunk 166 optimal weight:    0.1980
   chunk 57 optimal weight:    0.8980
   chunk 194 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 204 optimal weight:    1.9990
   chunk 133 optimal weight:    0.8980
   chunk 125 optimal weight:    0.0060
   chunk 3 optimal weight:    0.1980
   overall best weight:    0.3596

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS
F 115 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.095312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.080109 restraints weight = 51610.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.082366 restraints weight = 28482.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.083877 restraints weight = 19207.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.084926 restraints weight = 14695.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.085640 restraints weight = 12171.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  18809  Z= 0.143
  Angle     :  0.649   8.688  25459  Z= 0.322
  Chirality :  0.044   0.202   2779
  Planarity :  0.004   0.062   3367
  Dihedral  :  5.135  35.049   2583
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 12.05 %
    Favored  : 87.86 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.00 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.32 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.38 (0.17), residues: 2331
  helix: -0.03 (0.24), residues: 516
  sheet: -1.87 (0.24), residues: 466
  loop : -2.17 (0.16), residues: 1349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 109 
 TYR   0.027   0.001   TYR E 245 
 PHE   0.010   0.001   PHE G  23 
 TRP   0.011   0.001   TRP F 308 
 HIS   0.003   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (18809)
  covalent geometry    : angle       0.64851 (25459)
  hydrogen bonds       : bond        0.03615 (  479)
  hydrogen bonds       : angle       5.53013 ( 1272)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 216
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7751 (mmm)
REVERT: A  129 MET cc_start: 0.8555 (tpp) cc_final: 0.8266 (tpp)
REVERT: A  142 MET cc_start: 0.9075 (mtm) cc_final: 0.8780 (mtm)
REVERT: A  233 LYS cc_start: 0.8632 (ptmm) cc_final: 0.8330 (pttm)
REVERT: A  326 LEU cc_start: 0.9222 (tp) cc_final: 0.8932 (tp)
REVERT: B  130 GLN cc_start: 0.8897 (tt0) cc_final: 0.8470 (tt0)
REVERT: B  272 MET cc_start: 0.8622 (ppp) cc_final: 0.8197 (ppp)
REVERT: C   22 LEU cc_start: 0.9464 (tp) cc_final: 0.9218 (tp)
REVERT: D   82 HIS cc_start: 0.8884 (OUTLIER) cc_final: 0.7974 (m-70)
REVERT: D  117 ARG cc_start: 0.7808 (mmp80) cc_final: 0.7601 (mmt180)
REVERT: D  128 GLU cc_start: 0.8246 (tp30) cc_final: 0.8034 (tp30)
REVERT: D  129 MET cc_start: 0.8987 (tmm) cc_final: 0.8573 (tmm)
REVERT: D  229 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7713 (pm20)
REVERT: E  114 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8229 (tm-30)
REVERT: E  129 MET cc_start: 0.8499 (tmm) cc_final: 0.8065 (tmm)
REVERT: E  154 MET cc_start: 0.8222 (mmt) cc_final: 0.7982 (mmt)
REVERT: E  259 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8076 (tm-30)
REVERT: F   23 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.7982 (m-10)
REVERT: F  244 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8060 (mmm)
REVERT: F  272 MET cc_start: 0.8606 (ppp) cc_final: 0.8251 (ppp)
REVERT: F  320 MET cc_start: 0.6707 (mtt) cc_final: 0.6418 (mtt)
REVERT: G   24 LEU cc_start: 0.9299 (mm) cc_final: 0.8915 (mt)
REVERT: G   72 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7566 (mt-10)
REVERT: G   82 HIS cc_start: 0.8241 (OUTLIER) cc_final: 0.6831 (m-70)
REVERT: G   92 ARG cc_start: 0.4787 (mtm180) cc_final: 0.4307 (mtt90)
REVERT: G  197 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8728 (mm)
REVERT: G  327 MET cc_start: 0.8626 (mmp) cc_final: 0.8139 (mmp)
  outliers start: 47
  outliers final: 33
  residues processed: 251
  average time/residue: 0.1414
  time to fit residues: 54.5148
Evaluate side-chains
  239 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 199
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  140 TYR
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain D residue   82 HIS
Chi-restraints excluded: chain D residue  116 MET
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  310 THR
Chi-restraints excluded: chain E residue   82 HIS
Chi-restraints excluded: chain E residue  126 VAL
Chi-restraints excluded: chain E residue  259 GLU
Chi-restraints excluded: chain E residue  321 ILE
Chi-restraints excluded: chain F residue   23 PHE
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  228 LEU
Chi-restraints excluded: chain F residue  244 MET
Chi-restraints excluded: chain F residue  267 LEU
Chi-restraints excluded: chain F residue  326 LEU
Chi-restraints excluded: chain G residue   70 THR
Chi-restraints excluded: chain G residue   82 HIS
Chi-restraints excluded: chain G residue  197 ILE
Chi-restraints excluded: chain G residue  321 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 17 optimal weight:    0.3980
   chunk 72 optimal weight:    0.8980
   chunk 141 optimal weight:    0.1980
   chunk 101 optimal weight:    0.9980
   chunk 138 optimal weight:    0.4980
   chunk 221 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9990
   chunk 173 optimal weight:    0.1980
   chunk 40 optimal weight:    0.4980
   chunk 132 optimal weight:    1.9990
   overall best weight:    0.3580

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 115 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.096095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.080572 restraints weight = 51223.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.082887 restraints weight = 28151.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.084456 restraints weight = 18969.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.085511 restraints weight = 14476.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.086183 restraints weight = 12011.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18809  Z= 0.143
  Angle     :  0.653   8.788  25459  Z= 0.322
  Chirality :  0.044   0.189   2779
  Planarity :  0.004   0.058   3367
  Dihedral  :  5.044  33.833   2583
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 12.27 %
    Favored  : 87.64 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 17.30 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.17), residues: 2331
  helix:  0.08 (0.24), residues: 516
  sheet: -1.82 (0.24), residues: 466
  loop : -2.13 (0.17), residues: 1349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 110 
 TYR   0.024   0.001   TYR E 245 
 PHE   0.009   0.001   PHE C 335 
 TRP   0.010   0.001   TRP F 308 
 HIS   0.011   0.002   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (18809)
  covalent geometry    : angle       0.65257 (25459)
  hydrogen bonds       : bond        0.03526 (  479)
  hydrogen bonds       : angle       5.46764 ( 1272)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 214
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7753 (mmm)
REVERT: A  129 MET cc_start: 0.8589 (tpp) cc_final: 0.8310 (tpp)
REVERT: A  233 LYS cc_start: 0.8632 (ptmm) cc_final: 0.8357 (pttm)
REVERT: A  326 LEU cc_start: 0.9209 (tp) cc_final: 0.8915 (tp)
REVERT: A  327 MET cc_start: 0.9231 (mmp) cc_final: 0.8915 (mmm)
REVERT: B  130 GLN cc_start: 0.8923 (tt0) cc_final: 0.8498 (tt0)
REVERT: B  272 MET cc_start: 0.8582 (ppp) cc_final: 0.8148 (ppp)
REVERT: B  287 CYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8073 (t)
REVERT: D  128 GLU cc_start: 0.8286 (tp30) cc_final: 0.8013 (tp30)
REVERT: D  229 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7681 (pm20)
REVERT: E  114 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8184 (tm-30)
REVERT: E  129 MET cc_start: 0.8515 (tmm) cc_final: 0.8058 (tmm)
REVERT: E  154 MET cc_start: 0.8203 (mmt) cc_final: 0.7467 (mmm)
REVERT: E  221 ARG cc_start: 0.6965 (tpt170) cc_final: 0.6742 (tpt170)
REVERT: E  259 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8087 (tm-30)
REVERT: F   23 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7839 (m-10)
REVERT: G   24 LEU cc_start: 0.9229 (mm) cc_final: 0.8989 (mt)
REVERT: G   72 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7608 (mt-10)
REVERT: G   82 HIS cc_start: 0.8286 (OUTLIER) cc_final: 0.6874 (m-70)
REVERT: G   92 ARG cc_start: 0.4746 (mtm180) cc_final: 0.4285 (mtt90)
REVERT: G  272 MET cc_start: 0.8517 (ptm) cc_final: 0.8295 (ptm)
  outliers start: 55
  outliers final: 38
  residues processed: 253
  average time/residue: 0.1326
  time to fit residues: 52.1909
Evaluate side-chains
  245 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 202
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  287 CYS
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  140 TYR
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   82 HIS
Chi-restraints excluded: chain D residue  116 MET
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  207 LEU
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain E residue   82 HIS
Chi-restraints excluded: chain E residue  259 GLU
Chi-restraints excluded: chain E residue  321 ILE
Chi-restraints excluded: chain F residue   23 PHE
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  228 LEU
Chi-restraints excluded: chain F residue  244 MET
Chi-restraints excluded: chain F residue  267 LEU
Chi-restraints excluded: chain F residue  326 LEU
Chi-restraints excluded: chain G residue   70 THR
Chi-restraints excluded: chain G residue   82 HIS
Chi-restraints excluded: chain G residue  189 LEU
Chi-restraints excluded: chain G residue  321 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 74 optimal weight:    0.4980
   chunk 172 optimal weight:    0.0980
   chunk 228 optimal weight:    0.4980
   chunk 114 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0370
   chunk 109 optimal weight:    0.9980
   chunk 142 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 157 optimal weight:    0.2980
   overall best weight:    0.2858

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS
** F   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.097024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.081422 restraints weight = 51714.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.083752 restraints weight = 28298.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.085321 restraints weight = 18997.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.086405 restraints weight = 14510.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.087066 restraints weight = 11998.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  18809  Z= 0.129
  Angle     :  0.656  11.181  25459  Z= 0.320
  Chirality :  0.044   0.268   2779
  Planarity :  0.004   0.058   3367
  Dihedral  :  4.954  34.316   2583
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.58 %
    Favored  : 88.33 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 18.61 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.17), residues: 2331
  helix:  0.16 (0.24), residues: 521
  sheet: -1.74 (0.24), residues: 466
  loop : -2.08 (0.17), residues: 1344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 110 
 TYR   0.023   0.001   TYR E 245 
 PHE   0.011   0.001   PHE F 208 
 TRP   0.015   0.001   TRP A 205 
 HIS   0.002   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (18809)
  covalent geometry    : angle       0.65558 (25459)
  hydrogen bonds       : bond        0.03404 (  479)
  hydrogen bonds       : angle       5.38522 ( 1272)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 212
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.8181 (mmm) cc_final: 0.7818 (mmm)
REVERT: A  129 MET cc_start: 0.8555 (tpp) cc_final: 0.8229 (tpp)
REVERT: A  142 MET cc_start: 0.8879 (mtm) cc_final: 0.8651 (mtm)
REVERT: A  233 LYS cc_start: 0.8635 (ptmm) cc_final: 0.8361 (pttm)
REVERT: A  326 LEU cc_start: 0.9165 (tp) cc_final: 0.8940 (tp)
REVERT: B  287 CYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8033 (t)
REVERT: D   82 HIS cc_start: 0.8723 (OUTLIER) cc_final: 0.7858 (m-70)
REVERT: D  117 ARG cc_start: 0.7768 (mmp80) cc_final: 0.7561 (mmt180)
REVERT: D  128 GLU cc_start: 0.8272 (tp30) cc_final: 0.7955 (tp30)
REVERT: D  229 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7618 (pm20)
REVERT: E  114 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8171 (tm-30)
REVERT: E  129 MET cc_start: 0.8510 (tmm) cc_final: 0.8067 (tmm)
REVERT: E  154 MET cc_start: 0.8227 (mmt) cc_final: 0.7503 (mmm)
REVERT: E  259 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8120 (tm-30)
REVERT: F   23 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7853 (m-10)
REVERT: G   24 LEU cc_start: 0.9223 (mm) cc_final: 0.8754 (mt)
REVERT: G   72 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7638 (mt-10)
REVERT: G   82 HIS cc_start: 0.8310 (OUTLIER) cc_final: 0.6957 (m-70)
REVERT: G   92 ARG cc_start: 0.4738 (mtm180) cc_final: 0.3297 (mtt180)
REVERT: G  129 MET cc_start: 0.8839 (tpp) cc_final: 0.8442 (tpp)
REVERT: G  272 MET cc_start: 0.8440 (ptm) cc_final: 0.8151 (ptm)
REVERT: G  327 MET cc_start: 0.8493 (mmp) cc_final: 0.8010 (mmp)
  outliers start: 53
  outliers final: 35
  residues processed: 251
  average time/residue: 0.1299
  time to fit residues: 51.2431
Evaluate side-chains
  241 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 201
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  287 CYS
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  140 TYR
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain D residue   49 ASN
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   82 HIS
Chi-restraints excluded: chain D residue  116 MET
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  207 LEU
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain E residue   82 HIS
Chi-restraints excluded: chain E residue  126 VAL
Chi-restraints excluded: chain E residue  259 GLU
Chi-restraints excluded: chain F residue   23 PHE
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  228 LEU
Chi-restraints excluded: chain F residue  244 MET
Chi-restraints excluded: chain F residue  267 LEU
Chi-restraints excluded: chain F residue  326 LEU
Chi-restraints excluded: chain G residue   70 THR
Chi-restraints excluded: chain G residue   82 HIS
Chi-restraints excluded: chain G residue  189 LEU
Chi-restraints excluded: chain G residue  321 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 138 optimal weight:    0.0980
   chunk 5 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0970
   chunk 30 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9980
   chunk 169 optimal weight:    0.9990
   chunk 133 optimal weight:    0.2980
   chunk 183 optimal weight:    0.0050
   chunk 203 optimal weight:    0.6980
   chunk 127 optimal weight:    0.8980
   overall best weight:    0.2192

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  15 GLN
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS
** F   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 115 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.090383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.075379 restraints weight = 52129.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.077604 restraints weight = 28967.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.079092 restraints weight = 19586.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.080115 restraints weight = 15014.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.080808 restraints weight = 12473.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  18809  Z= 0.121
  Angle     :  0.674  11.300  25459  Z= 0.326
  Chirality :  0.044   0.256   2779
  Planarity :  0.004   0.059   3367
  Dihedral  :  4.861  34.433   2583
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.54 %
    Favored  : 88.37 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.22 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.09 (0.17), residues: 2331
  helix:  0.22 (0.24), residues: 523
  sheet: -1.64 (0.25), residues: 462
  loop : -2.02 (0.17), residues: 1346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 109 
 TYR   0.023   0.001   TYR E 245 
 PHE   0.011   0.001   PHE F 208 
 TRP   0.017   0.001   TRP A 205 
 HIS   0.011   0.002   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (18809)
  covalent geometry    : angle       0.67369 (25459)
  hydrogen bonds       : bond        0.03274 (  479)
  hydrogen bonds       : angle       5.31763 ( 1272)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 212
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.9391 (tt) cc_final: 0.9181 (tp)
REVERT: A  129 MET cc_start: 0.8530 (tpp) cc_final: 0.8222 (tpp)
REVERT: A  233 LYS cc_start: 0.8499 (ptmm) cc_final: 0.8255 (pttm)
REVERT: B   88 MET cc_start: 0.8331 (mmm) cc_final: 0.8125 (mmm)
REVERT: B  287 CYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8089 (t)
REVERT: D  229 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7706 (pm20)
REVERT: D  322 GLN cc_start: 0.8436 (pt0) cc_final: 0.8011 (pt0)
REVERT: E  114 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8175 (tm-30)
REVERT: E  129 MET cc_start: 0.8516 (tmm) cc_final: 0.8081 (tmm)
REVERT: E  154 MET cc_start: 0.8222 (mmt) cc_final: 0.7506 (mmm)
REVERT: E  221 ARG cc_start: 0.7225 (tpp-160) cc_final: 0.6768 (tpt90)
REVERT: E  259 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8079 (tm-30)
REVERT: F   23 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7810 (m-10)
REVERT: G   24 LEU cc_start: 0.9221 (mm) cc_final: 0.8784 (mt)
REVERT: G   82 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.7154 (m-70)
REVERT: G   92 ARG cc_start: 0.4935 (mtm180) cc_final: 0.3475 (mtt180)
REVERT: G  272 MET cc_start: 0.8428 (ptm) cc_final: 0.8136 (ptm)
REVERT: G  327 MET cc_start: 0.8507 (mmp) cc_final: 0.8058 (mmp)
  outliers start: 46
  outliers final: 31
  residues processed: 245
  average time/residue: 0.1327
  time to fit residues: 51.0687
Evaluate side-chains
  245 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 210
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  287 CYS
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue  116 MET
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  207 LEU
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain E residue   82 HIS
Chi-restraints excluded: chain E residue  259 GLU
Chi-restraints excluded: chain E residue  321 ILE
Chi-restraints excluded: chain F residue   23 PHE
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  228 LEU
Chi-restraints excluded: chain F residue  267 LEU
Chi-restraints excluded: chain F residue  326 LEU
Chi-restraints excluded: chain G residue   70 THR
Chi-restraints excluded: chain G residue   82 HIS
Chi-restraints excluded: chain G residue  189 LEU
Chi-restraints excluded: chain G residue  321 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 111 optimal weight:    0.7980
   chunk 145 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 215 optimal weight:    0.7980
   chunk 100 optimal weight:    0.3980
   chunk 172 optimal weight:    0.0570
   chunk 103 optimal weight:    0.2980
   chunk 97 optimal weight:    0.9990
   chunk 125 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS
F   8 GLN
G 270 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.096315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.080800 restraints weight = 51603.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.083091 restraints weight = 28764.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.084630 restraints weight = 19449.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.085675 restraints weight = 14917.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.086351 restraints weight = 12397.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  18809  Z= 0.156
  Angle     :  0.692  11.539  25459  Z= 0.335
  Chirality :  0.045   0.257   2779
  Planarity :  0.004   0.058   3367
  Dihedral  :  4.976  33.758   2583
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 12.23 %
    Favored  : 87.69 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 19.06 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.11 (0.17), residues: 2331
  helix:  0.20 (0.24), residues: 524
  sheet: -1.66 (0.24), residues: 462
  loop : -2.03 (0.17), residues: 1345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 110 
 TYR   0.026   0.001   TYR B 140 
 PHE   0.010   0.001   PHE G  23 
 TRP   0.016   0.001   TRP A 205 
 HIS   0.003   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (18809)
  covalent geometry    : angle       0.69186 (25459)
  hydrogen bonds       : bond        0.03483 (  479)
  hydrogen bonds       : angle       5.39379 ( 1272)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 209
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.9404 (tt) cc_final: 0.9194 (tp)
REVERT: A  129 MET cc_start: 0.8561 (tpp) cc_final: 0.8276 (tpp)
REVERT: A  233 LYS cc_start: 0.8533 (ptmm) cc_final: 0.8185 (pttm)
REVERT: B  287 CYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8155 (t)
REVERT: C   23 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8493 (m-10)
REVERT: D   82 HIS cc_start: 0.8834 (OUTLIER) cc_final: 0.7313 (m90)
REVERT: D  229 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7763 (pm20)
REVERT: D  322 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8053 (pt0)
REVERT: E  114 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8192 (tm-30)
REVERT: E  128 GLU cc_start: 0.8203 (tp30) cc_final: 0.7935 (tp30)
REVERT: E  129 MET cc_start: 0.8510 (tmm) cc_final: 0.8041 (tmm)
REVERT: E  154 MET cc_start: 0.8271 (mmt) cc_final: 0.7562 (mmm)
REVERT: E  221 ARG cc_start: 0.7334 (tpp-160) cc_final: 0.6898 (tpt170)
REVERT: E  259 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8098 (tm-30)
REVERT: F   23 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.7911 (m-10)
REVERT: G   24 LEU cc_start: 0.9286 (mm) cc_final: 0.8909 (mt)
REVERT: G   82 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.6855 (m-70)
REVERT: G   92 ARG cc_start: 0.4827 (mtm180) cc_final: 0.4386 (mtt90)
REVERT: G  154 MET cc_start: 0.8154 (mmm) cc_final: 0.7933 (mmm)
REVERT: G  216 GLU cc_start: 0.7352 (pp20) cc_final: 0.6845 (pp20)
REVERT: G  272 MET cc_start: 0.8486 (ptm) cc_final: 0.8247 (ptm)
REVERT: G  327 MET cc_start: 0.8493 (mmp) cc_final: 0.8085 (mmp)
  outliers start: 47
  outliers final: 32
  residues processed: 245
  average time/residue: 0.1390
  time to fit residues: 52.7273
Evaluate side-chains
  241 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 202
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  287 CYS
Chi-restraints excluded: chain C residue   23 PHE
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  140 TYR
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain D residue   49 ASN
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   82 HIS
Chi-restraints excluded: chain D residue  116 MET
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  207 LEU
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  322 GLN
Chi-restraints excluded: chain E residue  259 GLU
Chi-restraints excluded: chain E residue  321 ILE
Chi-restraints excluded: chain F residue   23 PHE
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  228 LEU
Chi-restraints excluded: chain F residue  267 LEU
Chi-restraints excluded: chain G residue   70 THR
Chi-restraints excluded: chain G residue   74 THR
Chi-restraints excluded: chain G residue   82 HIS
Chi-restraints excluded: chain G residue  189 LEU
Chi-restraints excluded: chain G residue  321 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 76 optimal weight:    0.2980
   chunk 166 optimal weight:    0.4980
   chunk 66 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0980
   chunk 109 optimal weight:    0.9980
   chunk 201 optimal weight:    0.0870
   chunk 37 optimal weight:    0.9990
   chunk 77 optimal weight:    0.5980
   chunk 222 optimal weight:    0.9980
   overall best weight:    0.3158

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.097181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.081619 restraints weight = 51443.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.083931 restraints weight = 28582.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.085485 restraints weight = 19382.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.086541 restraints weight = 14873.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.087274 restraints weight = 12344.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  18809  Z= 0.138
  Angle     :  0.701  12.616  25459  Z= 0.337
  Chirality :  0.045   0.245   2779
  Planarity :  0.005   0.120   3367
  Dihedral  :  4.980  34.425   2583
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  : 11.45 %
    Favored  : 88.50 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 19.87 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.06 (0.17), residues: 2331
  helix:  0.21 (0.24), residues: 524
  sheet: -1.66 (0.25), residues: 434
  loop : -1.97 (0.16), residues: 1373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 110 
 TYR   0.023   0.001   TYR E 245 
 PHE   0.009   0.001   PHE G  23 
 TRP   0.019   0.001   TRP A 205 
 HIS   0.005   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (18809)
  covalent geometry    : angle       0.70065 (25459)
  hydrogen bonds       : bond        0.03377 (  479)
  hydrogen bonds       : angle       5.37377 ( 1272)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 210
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 MET cc_start: 0.8540 (tpp) cc_final: 0.8227 (tpp)
REVERT: A  233 LYS cc_start: 0.8511 (ptmm) cc_final: 0.8096 (pttm)
REVERT: B  136 LEU cc_start: 0.9021 (tp) cc_final: 0.8724 (pp)
REVERT: B  287 CYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8114 (t)
REVERT: B  327 MET cc_start: 0.8836 (mmp) cc_final: 0.8566 (mmp)
REVERT: C   23 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8438 (m-10)
REVERT: C  320 MET cc_start: 0.8624 (ttp) cc_final: 0.8153 (tmm)
REVERT: D  229 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7713 (pm20)
REVERT: D  322 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8039 (pt0)
REVERT: E  114 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8179 (tm-30)
REVERT: E  129 MET cc_start: 0.8494 (tmm) cc_final: 0.8044 (tmm)
REVERT: E  154 MET cc_start: 0.8243 (mmt) cc_final: 0.7547 (mmm)
REVERT: E  259 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8090 (tm-30)
REVERT: F   23 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7954 (m-10)
REVERT: G   24 LEU cc_start: 0.9282 (mm) cc_final: 0.8889 (mt)
REVERT: G   82 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.6947 (m-70)
REVERT: G   87 GLN cc_start: 0.6507 (pm20) cc_final: 0.6277 (pm20)
REVERT: G   92 ARG cc_start: 0.4887 (mtm180) cc_final: 0.4456 (mtt90)
REVERT: G  136 LEU cc_start: 0.8990 (mt) cc_final: 0.8776 (mt)
REVERT: G  216 GLU cc_start: 0.7279 (pp20) cc_final: 0.6808 (pp20)
REVERT: G  327 MET cc_start: 0.8483 (mmp) cc_final: 0.8071 (mmp)
  outliers start: 39
  outliers final: 30
  residues processed: 238
  average time/residue: 0.1285
  time to fit residues: 48.0736
Evaluate side-chains
  244 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 208
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  287 CYS
Chi-restraints excluded: chain C residue   23 PHE
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  140 TYR
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  207 LEU
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  322 GLN
Chi-restraints excluded: chain E residue   82 HIS
Chi-restraints excluded: chain E residue  259 GLU
Chi-restraints excluded: chain E residue  321 ILE
Chi-restraints excluded: chain F residue   23 PHE
Chi-restraints excluded: chain F residue  228 LEU
Chi-restraints excluded: chain F residue  267 LEU
Chi-restraints excluded: chain G residue   70 THR
Chi-restraints excluded: chain G residue   74 THR
Chi-restraints excluded: chain G residue   82 HIS
Chi-restraints excluded: chain G residue  189 LEU
Chi-restraints excluded: chain G residue  321 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 124 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 147 optimal weight:    0.1980
   chunk 190 optimal weight:    0.5980
   chunk 10 optimal weight:    0.1980
   chunk 66 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 118 optimal weight:    0.2980
   chunk 86 optimal weight:    0.3980
   overall best weight:    0.3380

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.097106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.081506 restraints weight = 51487.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.083812 restraints weight = 28652.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.085361 restraints weight = 19417.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.086421 restraints weight = 14907.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.087149 restraints weight = 12394.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  18809  Z= 0.141
  Angle     :  0.698  12.492  25459  Z= 0.334
  Chirality :  0.044   0.240   2779
  Planarity :  0.005   0.104   3367
  Dihedral  :  4.943  33.828   2583
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  : 12.14 %
    Favored  : 87.82 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 19.62 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.32 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.04 (0.17), residues: 2331
  helix:  0.21 (0.24), residues: 524
  sheet: -1.64 (0.25), residues: 434
  loop : -1.96 (0.17), residues: 1373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 110 
 TYR   0.024   0.001   TYR E 245 
 PHE   0.009   0.001   PHE G  23 
 TRP   0.019   0.001   TRP A 205 
 HIS   0.002   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (18809)
  covalent geometry    : angle       0.69754 (25459)
  hydrogen bonds       : bond        0.03393 (  479)
  hydrogen bonds       : angle       5.39670 ( 1272)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3243.03 seconds
wall clock time: 57 minutes 7.85 seconds (3427.85 seconds total)