Starting phenix.real_space_refine
on Sat Aug 23 12:27:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gn5_34155/08_2025/8gn5_34155.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gn5_34155/08_2025/8gn5_34155.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gn5_34155/08_2025/8gn5_34155.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gn5_34155/08_2025/8gn5_34155.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gn5_34155/08_2025/8gn5_34155.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gn5_34155/08_2025/8gn5_34155.cif"
  }
  resolution = 4.02
  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=   0.073
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      52      5.16       5
     C    7588      2.51       5
     N    2108      2.21       5
     O    2348      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12096
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 396, 3024
          Classifications: {'peptide': 396}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 376}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 396, 3024
          Classifications: {'peptide': 396}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 376}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 396, 3024
          Classifications: {'peptide': 396}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 376}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 396, 3024
          Classifications: {'peptide': 396}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 376}
          Chain breaks: 1
  Time building chain proxies: 3.20, per 1000 atoms: 0.26
  Number of scatterers: 12096
  At special positions: 0
  Unit cell: (137.747, 103.96, 166.336, 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      52     16.00
     O    2348      8.00
     N    2108      7.00
     C    7588      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: 0.69
  Conformation dependent library (CDL) restraints added in 641.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2968

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 28 sheets defined
      22.5% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 24
      removed outlier: 4.066A  pdb=" N   LEU A  11 " --> pdb=" O   GLN A   7 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ASP A  14 " --> pdb=" O   THR A  10 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   THR A  24 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 30
      removed outlier: 3.522A  pdb=" N   ALA A  30 " --> pdb=" O   ALA A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 95
      removed outlier: 4.258A  pdb=" N   ARG A  95 " --> pdb=" O   ASP A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 127
      removed outlier: 4.797A  pdb=" N   ARG A 102 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   ARG A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ILE A 104 " --> pdb=" O   TYR A 100 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   ASN A 114 " --> pdb=" O   LYS A 110 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   VAL A 115 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLU A 116 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 157
      removed outlier: 4.152A  pdb=" N   ASP A 150 " --> pdb=" O   ASN A 146 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   MET A 155 " --> pdb=" O   ALA A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 176
      removed outlier: 4.397A  pdb=" N   LYS A 176 " --> pdb=" O   PRO A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 179
      No H-bonds generated for 'chain 'A' and resid 177 through 179'
    Processing helix  chain 'A' and resid 321 through 326
      removed outlier: 3.511A  pdb=" N   ALA A 326 " --> pdb=" O   PRO A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 419
      No H-bonds generated for 'chain 'A' and resid 417 through 419'
    Processing helix  chain 'B' and resid 8 through 22
      removed outlier: 4.516A  pdb=" N   ASP B  14 " --> pdb=" O   THR B  10 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLU B  18 " --> pdb=" O   ASP B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 91 through 95
      removed outlier: 3.600A  pdb=" N   ARG B  95 " --> pdb=" O   ASP B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 127
      removed outlier: 4.278A  pdb=" N   ARG B 102 " --> pdb=" O   THR B  98 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   ARG B 103 " --> pdb=" O   ALA B  99 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ILE B 104 " --> pdb=" O   TYR B 100 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LYS B 110 " --> pdb=" O   SER B 106 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ASN B 114 " --> pdb=" O   LYS B 110 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   VAL B 115 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLU B 116 " --> pdb=" O   ALA B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 159
      removed outlier: 4.410A  pdb=" N   ASP B 150 " --> pdb=" O   ASN B 146 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   MET B 155 " --> pdb=" O   ALA B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 176
      removed outlier: 3.563A  pdb=" N   LYS B 176 " --> pdb=" O   PRO B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 179
      No H-bonds generated for 'chain 'B' and resid 177 through 179'
    Processing helix  chain 'B' and resid 321 through 326
    Processing helix  chain 'B' and resid 417 through 419
      No H-bonds generated for 'chain 'B' and resid 417 through 419'
    Processing helix  chain 'C' and resid 7 through 23
      removed outlier: 4.080A  pdb=" N   LEU C  11 " --> pdb=" O   GLN C   7 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   GLU C  18 " --> pdb=" O   ASP C  14 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER C  21 " --> pdb=" O   ILE C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 30
    Processing helix  chain 'C' and resid 91 through 95
      removed outlier: 4.148A  pdb=" N   ARG C  95 " --> pdb=" O   ASP C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 127
      removed outlier: 4.676A  pdb=" N   ARG C 102 " --> pdb=" O   THR C  98 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ARG C 103 " --> pdb=" O   ALA C  99 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ILE C 104 " --> pdb=" O   TYR C 100 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   ASN C 114 " --> pdb=" O   LYS C 110 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   VAL C 115 " --> pdb=" O   LEU C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 146 through 159
      removed outlier: 3.805A  pdb=" N   ASP C 150 " --> pdb=" O   ASN C 146 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   MET C 155 " --> pdb=" O   ALA C 151 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ARG C 158 " --> pdb=" O   ILE C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 171 through 178
      removed outlier: 3.951A  pdb=" N   LYS C 176 " --> pdb=" O   PRO C 172 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LYS C 177 " --> pdb=" O   GLN C 173 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 323 through 328
    Processing helix  chain 'C' and resid 417 through 419
      No H-bonds generated for 'chain 'C' and resid 417 through 419'
    Processing helix  chain 'D' and resid 7 through 24
      removed outlier: 4.181A  pdb=" N   LEU D  11 " --> pdb=" O   GLN D   7 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   THR D  24 " --> pdb=" O   ILE D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 25 through 28
    Processing helix  chain 'D' and resid 90 through 94
    Processing helix  chain 'D' and resid 96 through 127
      removed outlier: 4.412A  pdb=" N   ARG D 102 " --> pdb=" O   THR D  98 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ARG D 103 " --> pdb=" O   ALA D  99 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ILE D 104 " --> pdb=" O   TYR D 100 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   ASN D 114 " --> pdb=" O   LYS D 110 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   VAL D 115 " --> pdb=" O   LEU D 111 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   VAL D 119 " --> pdb=" O   VAL D 115 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA D 124 " --> pdb=" O   ALA D 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 146 through 157
      removed outlier: 4.041A  pdb=" N   ASP D 150 " --> pdb=" O   ASN D 146 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   MET D 155 " --> pdb=" O   ALA D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 171 through 176
      removed outlier: 3.786A  pdb=" N   LYS D 176 " --> pdb=" O   PRO D 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 321 through 326
      removed outlier: 3.909A  pdb=" N   ALA D 326 " --> pdb=" O   PRO D 322 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 417 through 419
      No H-bonds generated for 'chain 'D' and resid 417 through 419'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32
      removed outlier: 6.827A  pdb=" N   LYS A  31 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   ARG A 360 " --> pdb=" O   ASN A 414 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASN A 414 " --> pdb=" O   ARG A 360 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50
    Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59
      removed outlier: 4.622A  pdb=" N   GLN A  58 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASN B  84 " --> pdb=" O   GLN A  58 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   GLY B 403 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 89
      removed outlier: 4.125A  pdb=" N   GLY A 403 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   ASN A 389 " --> pdb=" O   TRP A 410 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 132
      removed outlier: 6.352A  pdb=" N   LEU A 129 " --> pdb=" O   VAL A 423 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   LEU A 425 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ILE A 131 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASN A 351 " --> pdb=" O   GLY A 424 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 242 through 243
    Processing sheet with id=AA7, first strand: chain 'A' and resid 257 through 260
      removed outlier: 3.706A  pdb=" N   ARG A 299 " --> pdb=" O   GLU A 307 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   THR A 309 " --> pdb=" O   VAL A 297 " (cutoff:3.500A)
      removed outlier: 5.586A  pdb=" N   VAL A 297 " --> pdb=" O   THR A 309 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 279 through 281
      removed outlier: 5.382A  pdb=" N   PHE A 280 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 31 through 32
      removed outlier: 3.600A  pdb=" N   ILE B 361 " --> pdb=" O   LYS B  31 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 50
    Processing sheet with id=AB2, first strand: chain 'B' and resid 129 through 132
      removed outlier: 6.521A  pdb=" N   LEU B 129 " --> pdb=" O   VAL B 423 " (cutoff:3.500A)
      removed outlier: 7.666A  pdb=" N   LEU B 425 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   ILE B 131 " --> pdb=" O   LEU B 425 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ASN B 351 " --> pdb=" O   GLY B 424 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL B 352 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 241 through 243
    Processing sheet with id=AB4, first strand: chain 'B' and resid 257 through 260
      removed outlier: 3.795A  pdb=" N   ARG B 299 " --> pdb=" O   GLU B 307 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   THR B 309 " --> pdb=" O   VAL B 297 " (cutoff:3.500A)
      removed outlier: 5.666A  pdb=" N   VAL B 297 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 279 through 281
      removed outlier: 5.520A  pdb=" N   PHE B 280 " --> pdb=" O   LEU B 289 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 31 through 33
      removed outlier: 6.784A  pdb=" N   LYS C  31 " --> pdb=" O   ILE C 361 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 46 through 51
      removed outlier: 4.200A  pdb=" N   LEU C  73 " --> pdb=" O   VAL C  51 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 83 through 89
      removed outlier: 3.601A  pdb=" N   GLY C 403 " --> pdb=" O   LEU C  89 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   ASN C 389 " --> pdb=" O   TRP C 410 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 129 through 132
      removed outlier: 6.407A  pdb=" N   LEU C 129 " --> pdb=" O   VAL C 423 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   LEU C 425 " --> pdb=" O   LEU C 129 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ILE C 131 " --> pdb=" O   LEU C 425 " (cutoff:3.500A)
      removed outlier: 8.559A  pdb=" N   LEU C 212 " --> pdb=" O   THR C 166 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   TYR C 168 " --> pdb=" O   LEU C 212 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 242 through 243
    Processing sheet with id=AC2, first strand: chain 'C' and resid 257 through 260
      removed outlier: 3.695A  pdb=" N   ARG C 299 " --> pdb=" O   GLU C 307 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   THR C 309 " --> pdb=" O   VAL C 297 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   VAL C 297 " --> pdb=" O   THR C 309 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 279 through 281
      removed outlier: 5.102A  pdb=" N   PHE C 280 " --> pdb=" O   LEU C 289 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 31 through 33
    Processing sheet with id=AC5, first strand: chain 'D' and resid 46 through 51
      removed outlier: 4.180A  pdb=" N   LEU D  73 " --> pdb=" O   VAL D  51 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 83 through 89
      removed outlier: 3.589A  pdb=" N   GLY D 403 " --> pdb=" O   LEU D  89 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   SER D 402 " --> pdb=" O   ASP D 397 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   ASN D 389 " --> pdb=" O   TRP D 410 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LYS D 377 " --> pdb=" O   THR D 394 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'D' and resid 129 through 132
      removed outlier: 6.401A  pdb=" N   LEU D 129 " --> pdb=" O   VAL D 423 " (cutoff:3.500A)
      removed outlier: 8.027A  pdb=" N   LEU D 425 " --> pdb=" O   LEU D 129 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   ILE D 131 " --> pdb=" O   LEU D 425 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'D' and resid 242 through 243
    Processing sheet with id=AC9, first strand: chain 'D' and resid 257 through 260
      removed outlier: 3.704A  pdb=" N   ARG D 299 " --> pdb=" O   GLU D 307 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   THR D 309 " --> pdb=" O   VAL D 297 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   VAL D 297 " --> pdb=" O   THR D 309 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'D' and resid 279 through 281
      removed outlier: 5.613A  pdb=" N   PHE D 280 " --> pdb=" O   LEU D 289 " (cutoff:3.500A)

    385 hydrogen bonds defined for protein.
    1011 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.96

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3853
        1.34 -     1.46: 1717
        1.46 -     1.58: 6653
        1.58 -     1.71: 1
        1.71 -     1.83: 100
  Bond restraints: 12324
  Sorted by residual:
  bond pdb=" CA  ARG B 109 "
       pdb=" C   ARG B 109 "
    ideal  model  delta    sigma   weight residual
    1.524  1.585 -0.061 1.27e-02 6.20e+03 2.32e+01
  bond pdb=" CA  ARG A 406 "
       pdb=" C   ARG A 406 "
    ideal  model  delta    sigma   weight residual
    1.522  1.567 -0.045 1.14e-02 7.69e+03 1.59e+01
  bond pdb=" CA  ARG A 162 "
       pdb=" C   ARG A 162 "
    ideal  model  delta    sigma   weight residual
    1.531  1.580 -0.049 1.39e-02 5.18e+03 1.25e+01
  bond pdb=" CA  ARG B 162 "
       pdb=" C   ARG B 162 "
    ideal  model  delta    sigma   weight residual
    1.521  1.564 -0.043 1.23e-02 6.61e+03 1.24e+01
  bond pdb=" CA  ARG A 417 "
       pdb=" C   ARG A 417 "
    ideal  model  delta    sigma   weight residual
    1.524  1.566 -0.042 1.26e-02 6.30e+03 1.12e+01
  ... (remaining 12319 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 11621
        1.81 -     3.62: 4370
        3.62 -     5.43: 690
        5.43 -     7.23: 79
        7.23 -     9.04: 8
  Bond angle restraints: 16768
  Sorted by residual:
  angle pdb=" N   ARG B  90 "
        pdb=" CA  ARG B  90 "
        pdb=" C   ARG B  90 "
      ideal   model   delta    sigma   weight residual
     110.33  101.78    8.55 1.29e+00 6.01e-01 4.39e+01
  angle pdb=" CA  ASP A 253 "
        pdb=" CB  ASP A 253 "
        pdb=" CG  ASP A 253 "
      ideal   model   delta    sigma   weight residual
     112.60  118.99   -6.39 1.00e+00 1.00e+00 4.08e+01
  angle pdb=" CA  PHE C 256 "
        pdb=" CB  PHE C 256 "
        pdb=" CG  PHE C 256 "
      ideal   model   delta    sigma   weight residual
     113.80  119.79   -5.99 1.00e+00 1.00e+00 3.58e+01
  angle pdb=" N   ARG A  90 "
        pdb=" CA  ARG A  90 "
        pdb=" C   ARG A  90 "
      ideal   model   delta    sigma   weight residual
     110.41  103.08    7.33 1.23e+00 6.61e-01 3.55e+01
  angle pdb=" CA  ASP B 347 "
        pdb=" CB  ASP B 347 "
        pdb=" CG  ASP B 347 "
      ideal   model   delta    sigma   weight residual
     112.60  118.23   -5.63 1.00e+00 1.00e+00 3.17e+01
  ... (remaining 16763 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 6854
       17.87 -    35.75: 487
       35.75 -    53.62: 65
       53.62 -    71.49: 23
       71.49 -    89.36: 11
  Dihedral angle restraints: 7440
    sinusoidal: 2868
      harmonic: 4572
  Sorted by residual:
  dihedral pdb=" CA  ASN C  84 "
           pdb=" C   ASN C  84 "
           pdb=" N   ASP C  85 "
           pdb=" CA  ASP C  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.65   29.35     0      5.00e+00 4.00e-02 3.44e+01
  dihedral pdb=" CA  ASN B  84 "
           pdb=" C   ASN B  84 "
           pdb=" N   ASP B  85 "
           pdb=" CA  ASP B  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.01   28.99     0      5.00e+00 4.00e-02 3.36e+01
  dihedral pdb=" CA  ALA C 151 "
           pdb=" C   ALA C 151 "
           pdb=" N   GLU C 152 "
           pdb=" CA  GLU C 152 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.33   28.67     0      5.00e+00 4.00e-02 3.29e+01
  ... (remaining 7437 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1029
       0.069 -    0.138: 636
       0.138 -    0.208: 203
       0.208 -    0.277: 53
       0.277 -    0.346: 19
  Chirality restraints: 1940
  Sorted by residual:
  chirality pdb=" CA  THR C 221 "
            pdb=" N   THR C 221 "
            pdb=" C   THR C 221 "
            pdb=" CB  THR C 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.18    0.35 2.00e-01 2.50e+01 2.99e+00
  chirality pdb=" CA  THR A 260 "
            pdb=" N   THR A 260 "
            pdb=" C   THR A 260 "
            pdb=" CB  THR A 260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.19    0.34 2.00e-01 2.50e+01 2.83e+00
  chirality pdb=" CA  THR A 221 "
            pdb=" N   THR A 221 "
            pdb=" C   THR A 221 "
            pdb=" CB  THR A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.21    0.32 2.00e-01 2.50e+01 2.52e+00
  ... (remaining 1937 not shown)

  Planarity restraints: 2200
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 410 "    0.132 2.00e-02 2.50e+03   6.92e-02 1.20e+02
        pdb=" CG  TRP B 410 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 410 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 410 "   -0.046 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 410 "   -0.055 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 410 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 410 "   -0.107 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 410 "    0.075 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 410 "   -0.028 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 410 "    0.078 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 410 "    0.126 2.00e-02 2.50e+03   6.00e-02 9.01e+01
        pdb=" CG  TRP A 410 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 410 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 410 "   -0.058 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 410 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 410 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 410 "   -0.073 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 410 "    0.066 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 410 "   -0.020 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 410 "    0.058 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 410 "    0.114 2.00e-02 2.50e+03   5.66e-02 8.00e+01
        pdb=" CG  TRP C 410 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 410 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 410 "   -0.041 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 410 "   -0.038 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 410 "    0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 410 "   -0.063 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 410 "    0.076 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 410 "   -0.035 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 410 "    0.050 2.00e-02 2.50e+03
  ... (remaining 2197 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 523
        2.75 -     3.29: 12244
        3.29 -     3.83: 15994
        3.83 -     4.36: 19935
        4.36 -     4.90: 33011
  Nonbonded interactions: 81707
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B  52 "
            pdb=" NH1 ARG B 417 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" N   ARG B  90 "
            pdb=" O   ARG B  90 "
     model   vdw
     2.446 2.496
  nonbonded pdb=" N   ARG C  90 "
            pdb=" O   ARG C  90 "
     model   vdw
     2.497 2.496
  nonbonded pdb=" OE2 GLU B  15 "
            pdb=" NH1 ARG B 101 "
     model   vdw
     2.504 3.120
  nonbonded pdb=" NH2 ARG A 162 "
            pdb=" O   ASP A 356 "
     model   vdw
     2.507 3.120
  ... (remaining 81702 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'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.230
  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:          0.190
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     12.430
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
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      :  0.012   0.061  12324  Z= 0.705
  Angle     :  1.811   9.043  16768  Z= 1.214
  Chirality :  0.097   0.346   1940
  Planarity :  0.012   0.097   2200
  Dihedral  : 13.402  89.362   4472
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 1.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.29 (0.19), residues: 1568
  helix: -1.84 (0.27), residues: 250
  sheet: -0.04 (0.26), residues: 344
  loop : -0.87 (0.18), residues: 974

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 158 
 TYR   0.103   0.022   TYR A 175 
 PHE   0.101   0.014   PHE D 280 
 TRP   0.132   0.022   TRP B 410 
 HIS   0.009   0.002   HIS B 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.01151 (12324)
  covalent geometry    : angle       1.81147 (16768)
  hydrogen bonds       : bond        0.20306 (  385)
  hydrogen bonds       : angle       7.46721 ( 1011)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  680 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 680
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 THR cc_start: 0.9395 (p) cc_final: 0.9092 (t)
REVERT: A   66 LYS cc_start: 0.8323 (mtpp) cc_final: 0.7827 (mtmm)
REVERT: A   93 ASP cc_start: 0.8780 (m-30) cc_final: 0.8415 (m-30)
REVERT: A  121 ASN cc_start: 0.9135 (t0) cc_final: 0.8730 (t0)
REVERT: A  169 PHE cc_start: 0.9110 (m-80) cc_final: 0.8835 (m-10)
REVERT: A  216 LYS cc_start: 0.9274 (mmtt) cc_final: 0.8946 (mmtt)
REVERT: A  284 MET cc_start: 0.8832 (mmt) cc_final: 0.8409 (mmt)
REVERT: A  291 GLN cc_start: 0.8961 (pm20) cc_final: 0.8633 (pm20)
REVERT: A  311 LYS cc_start: 0.9423 (tttt) cc_final: 0.8892 (tttp)
REVERT: A  317 ASP cc_start: 0.8293 (t0) cc_final: 0.7451 (t0)
REVERT: A  319 SER cc_start: 0.8898 (m) cc_final: 0.8556 (p)
REVERT: A  321 SER cc_start: 0.8526 (t) cc_final: 0.8080 (t)
REVERT: A  331 ASN cc_start: 0.8957 (t0) cc_final: 0.8599 (t0)
REVERT: A  336 ASP cc_start: 0.9144 (t0) cc_final: 0.8944 (t70)
REVERT: A  349 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.8068 (tpt-90)
REVERT: A  356 ASP cc_start: 0.8799 (t0) cc_final: 0.8530 (t0)
REVERT: A  357 ASP cc_start: 0.8637 (m-30) cc_final: 0.8187 (m-30)
REVERT: A  359 ILE cc_start: 0.9279 (mt) cc_final: 0.8969 (mm)
REVERT: B   45 ASN cc_start: 0.8674 (t0) cc_final: 0.8275 (t0)
REVERT: B   48 TRP cc_start: 0.9173 (m100) cc_final: 0.8693 (m100)
REVERT: B  135 ASP cc_start: 0.7792 (m-30) cc_final: 0.7560 (m-30)
REVERT: B  180 TYR cc_start: 0.7959 (m-80) cc_final: 0.6696 (m-80)
REVERT: B  213 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7644 (mtm-85)
REVERT: B  230 VAL cc_start: 0.9173 (t) cc_final: 0.8887 (p)
REVERT: B  249 LYS cc_start: 0.8410 (mtmt) cc_final: 0.8099 (mtpp)
REVERT: B  284 MET cc_start: 0.8858 (mmm) cc_final: 0.8406 (mmt)
REVERT: C   63 LEU cc_start: 0.7966 (mt) cc_final: 0.7729 (mp)
REVERT: C  126 MET cc_start: 0.8437 (ttm) cc_final: 0.8090 (ttm)
REVERT: C  143 ASP cc_start: 0.8340 (t70) cc_final: 0.8048 (t0)
REVERT: C  145 TRP cc_start: 0.9426 (t60) cc_final: 0.9041 (t60)
REVERT: C  279 LYS cc_start: 0.7771 (mttp) cc_final: 0.7156 (mmmt)
REVERT: C  346 LYS cc_start: 0.8580 (tttt) cc_final: 0.8293 (ttmm)
REVERT: C  359 ILE cc_start: 0.9236 (mt) cc_final: 0.8910 (mm)
REVERT: C  389 ASN cc_start: 0.9165 (m-40) cc_final: 0.8481 (m110)
REVERT: D   18 GLU cc_start: 0.8118 (tt0) cc_final: 0.7590 (mm-30)
REVERT: D   42 ARG cc_start: 0.7543 (mmt180) cc_final: 0.7187 (mmt180)
REVERT: D   96 ASP cc_start: 0.8308 (t0) cc_final: 0.7903 (t0)
REVERT: D  116 GLU cc_start: 0.8181 (tt0) cc_final: 0.7980 (tt0)
REVERT: D  126 MET cc_start: 0.8074 (ttm) cc_final: 0.7691 (ttp)
REVERT: D  173 GLN cc_start: 0.7473 (tt0) cc_final: 0.7049 (tm-30)
REVERT: D  216 LYS cc_start: 0.9275 (mmtt) cc_final: 0.8624 (mmmt)
REVERT: D  243 LEU cc_start: 0.8338 (mt) cc_final: 0.8073 (mt)
REVERT: D  253 ASP cc_start: 0.7502 (t0) cc_final: 0.7103 (t0)
REVERT: D  279 LYS cc_start: 0.8322 (mttt) cc_final: 0.7809 (mmtt)
REVERT: D  292 ASP cc_start: 0.9191 (p0) cc_final: 0.8529 (p0)
REVERT: D  349 ARG cc_start: 0.8869 (ttm-80) cc_final: 0.8509 (mtp-110)
REVERT: D  362 VAL cc_start: 0.9547 (t) cc_final: 0.9152 (m)
REVERT: D  377 LYS cc_start: 0.8951 (tppt) cc_final: 0.8691 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 680
  average time/residue: 0.1040
  time to fit residues: 99.9336
Evaluate side-chains
  515 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 515
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0870
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:   30.0000
   chunk 149 optimal weight:    5.9990
   overall best weight:    3.0164

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

Flipped N/Q/H residues before XYZ refinement:
A  74 ASN
** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 287 HIS
A 370 HIS
A 389 ASN
A 428 GLN
B  74 ASN
B  84 ASN
B 369 ASN
B 389 ASN
C  43 HIS
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 251 ASN
** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 344 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.123579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.104520 restraints weight = 18645.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.108014 restraints weight = 9701.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.110319 restraints weight = 6033.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.112028 restraints weight = 4245.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.113008 restraints weight = 3226.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12324  Z= 0.146
  Angle     :  0.637   6.541  16768  Z= 0.354
  Chirality :  0.045   0.198   1940
  Planarity :  0.004   0.040   2200
  Dihedral  :  6.592  49.738   1680
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.86 (0.20), residues: 1568
  helix: -0.96 (0.29), residues: 266
  sheet:  0.23 (0.24), residues: 428
  loop : -0.82 (0.19), residues: 874

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 101 
 TYR   0.012   0.001   TYR C 100 
 PHE   0.016   0.002   PHE B 147 
 TRP   0.018   0.002   TRP D 241 
 HIS   0.004   0.001   HIS D 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (12324)
  covalent geometry    : angle       0.63723 (16768)
  hydrogen bonds       : bond        0.05344 (  385)
  hydrogen bonds       : angle       5.40791 ( 1011)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  562 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 562
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8820 (tttm) cc_final: 0.8382 (tttm)
REVERT: A   46 THR cc_start: 0.9114 (p) cc_final: 0.8897 (p)
REVERT: A   90 ARG cc_start: 0.8036 (mmm-85) cc_final: 0.7687 (mmm-85)
REVERT: A  121 ASN cc_start: 0.9007 (t0) cc_final: 0.8664 (t0)
REVERT: A  213 ARG cc_start: 0.8022 (ptt180) cc_final: 0.7460 (ptt180)
REVERT: A  216 LYS cc_start: 0.9226 (mmtt) cc_final: 0.9000 (mmtt)
REVERT: A  284 MET cc_start: 0.8940 (mmt) cc_final: 0.8523 (mmt)
REVERT: A  311 LYS cc_start: 0.9450 (tttt) cc_final: 0.8948 (tttm)
REVERT: A  317 ASP cc_start: 0.8365 (t0) cc_final: 0.7956 (t0)
REVERT: A  356 ASP cc_start: 0.8999 (t0) cc_final: 0.8016 (t0)
REVERT: A  359 ILE cc_start: 0.9281 (mt) cc_final: 0.9037 (mm)
REVERT: A  362 VAL cc_start: 0.9369 (t) cc_final: 0.9132 (m)
REVERT: B   48 TRP cc_start: 0.9158 (m100) cc_final: 0.8854 (m100)
REVERT: B   83 ASP cc_start: 0.9109 (t0) cc_final: 0.8597 (t0)
REVERT: B  135 ASP cc_start: 0.7974 (m-30) cc_final: 0.7748 (m-30)
REVERT: B  164 MET cc_start: 0.8107 (tpp) cc_final: 0.7501 (tpp)
REVERT: B  268 LYS cc_start: 0.9008 (mtpt) cc_final: 0.8636 (mtpt)
REVERT: B  289 LEU cc_start: 0.8962 (mm) cc_final: 0.8630 (mm)
REVERT: C   40 MET cc_start: 0.8480 (ttm) cc_final: 0.8116 (ttt)
REVERT: C   48 TRP cc_start: 0.9133 (m100) cc_final: 0.8886 (m100)
REVERT: C   75 VAL cc_start: 0.9030 (t) cc_final: 0.8719 (t)
REVERT: C   81 GLU cc_start: 0.7800 (mp0) cc_final: 0.7586 (mp0)
REVERT: C   97 GLU cc_start: 0.8301 (tt0) cc_final: 0.8019 (tt0)
REVERT: C  143 ASP cc_start: 0.8180 (t70) cc_final: 0.7630 (t0)
REVERT: C  145 TRP cc_start: 0.9392 (t60) cc_final: 0.9128 (t60)
REVERT: C  234 GLN cc_start: 0.8679 (mt0) cc_final: 0.8206 (mp-120)
REVERT: C  241 TRP cc_start: 0.8449 (m100) cc_final: 0.8208 (m100)
REVERT: C  279 LYS cc_start: 0.7946 (mttp) cc_final: 0.7484 (mmmt)
REVERT: C  284 MET cc_start: 0.9342 (mmp) cc_final: 0.9025 (mmt)
REVERT: C  359 ILE cc_start: 0.9309 (mt) cc_final: 0.9011 (mm)
REVERT: C  389 ASN cc_start: 0.9224 (m-40) cc_final: 0.8335 (m110)
REVERT: D   44 SER cc_start: 0.8706 (t) cc_final: 0.8403 (p)
REVERT: D   85 ASP cc_start: 0.8884 (t0) cc_final: 0.8475 (t0)
REVERT: D  118 LYS cc_start: 0.8866 (tppt) cc_final: 0.8292 (ttmm)
REVERT: D  163 ASP cc_start: 0.8555 (t0) cc_final: 0.8181 (t0)
REVERT: D  173 GLN cc_start: 0.7822 (tt0) cc_final: 0.7130 (tm-30)
REVERT: D  174 ASP cc_start: 0.8780 (m-30) cc_final: 0.8528 (m-30)
REVERT: D  216 LYS cc_start: 0.9248 (mmtt) cc_final: 0.8628 (mmmt)
REVERT: D  241 TRP cc_start: 0.7529 (m100) cc_final: 0.7093 (m100)
REVERT: D  243 LEU cc_start: 0.8236 (mt) cc_final: 0.7941 (mt)
REVERT: D  253 ASP cc_start: 0.7657 (t0) cc_final: 0.7387 (t0)
REVERT: D  279 LYS cc_start: 0.8063 (mttt) cc_final: 0.7729 (mmtt)
REVERT: D  292 ASP cc_start: 0.9113 (p0) cc_final: 0.8480 (p0)
REVERT: D  338 MET cc_start: 0.7097 (mmt) cc_final: 0.6710 (mmm)
REVERT: D  349 ARG cc_start: 0.8726 (ttm-80) cc_final: 0.8488 (mtt-85)
REVERT: D  357 ASP cc_start: 0.8621 (t70) cc_final: 0.8143 (t70)
REVERT: D  371 GLU cc_start: 0.8714 (pp20) cc_final: 0.8101 (pp20)
REVERT: D  407 ILE cc_start: 0.7998 (pt) cc_final: 0.7612 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 562
  average time/residue: 0.0950
  time to fit residues: 78.4296
Evaluate side-chains
  472 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 472
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 92 optimal weight:    1.9990
   chunk 96 optimal weight:    9.9990
   chunk 154 optimal weight:    8.9990
   chunk 149 optimal weight:    4.9990
   chunk 31 optimal weight:    8.9990
   chunk 143 optimal weight:    8.9990
   chunk 108 optimal weight:   20.0000
   chunk 85 optimal weight:    9.9990
   chunk 66 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  54 HIS
** A  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 428 GLN
B  54 HIS
B  84 ASN
B 370 HIS
C  88 GLN
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 251 ASN
** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 414 ASN
D  74 ASN
D 251 ASN
D 305 HIS
** D 414 ASN ** 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 = 0.3188 r_free = 0.3188 target = 0.118985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.099563 restraints weight = 19206.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.102950 restraints weight = 9957.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.105275 restraints weight = 6244.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.106884 restraints weight = 4415.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.108059 restraints weight = 3407.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  12324  Z= 0.241
  Angle     :  0.683   8.546  16768  Z= 0.372
  Chirality :  0.047   0.195   1940
  Planarity :  0.005   0.062   2200
  Dihedral  :  6.329  45.408   1680
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.97 (0.20), residues: 1568
  helix: -0.88 (0.30), residues: 264
  sheet:  0.20 (0.25), residues: 418
  loop : -0.96 (0.20), residues: 886

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 101 
 TYR   0.019   0.002   TYR D 100 
 PHE   0.018   0.002   PHE B 170 
 TRP   0.019   0.002   TRP C 354 
 HIS   0.004   0.001   HIS D 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 (12324)
  covalent geometry    : angle       0.68263 (16768)
  hydrogen bonds       : bond        0.06114 (  385)
  hydrogen bonds       : angle       5.55519 ( 1011)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  530 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 530
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 MET cc_start: 0.8843 (ttp) cc_final: 0.8474 (mtp)
REVERT: A  121 ASN cc_start: 0.9053 (t0) cc_final: 0.8724 (t0)
REVERT: A  216 LYS cc_start: 0.9265 (mmtt) cc_final: 0.9017 (mmtt)
REVERT: A  284 MET cc_start: 0.8843 (mmt) cc_final: 0.8521 (mmt)
REVERT: A  311 LYS cc_start: 0.9510 (tttt) cc_final: 0.8997 (tttm)
REVERT: A  317 ASP cc_start: 0.8414 (t0) cc_final: 0.8107 (t0)
REVERT: A  359 ILE cc_start: 0.9353 (mt) cc_final: 0.9138 (mm)
REVERT: A  362 VAL cc_start: 0.9388 (t) cc_final: 0.9185 (m)
REVERT: B  268 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8658 (mtpt)
REVERT: B  274 SER cc_start: 0.9170 (t) cc_final: 0.8912 (t)
REVERT: B  338 MET cc_start: 0.8681 (mmm) cc_final: 0.8048 (tpp)
REVERT: C   40 MET cc_start: 0.8539 (ttm) cc_final: 0.8046 (ttt)
REVERT: C  279 LYS cc_start: 0.7944 (mttp) cc_final: 0.7709 (mmmt)
REVERT: C  284 MET cc_start: 0.9302 (mmp) cc_final: 0.9076 (mmt)
REVERT: C  357 ASP cc_start: 0.8569 (t0) cc_final: 0.8365 (t0)
REVERT: C  359 ILE cc_start: 0.9276 (mt) cc_final: 0.8973 (mm)
REVERT: C  361 ILE cc_start: 0.9527 (mt) cc_final: 0.9289 (mm)
REVERT: C  389 ASN cc_start: 0.9244 (m-40) cc_final: 0.8813 (m110)
REVERT: C  395 GLN cc_start: 0.9476 (tp40) cc_final: 0.9249 (tp40)
REVERT: D   44 SER cc_start: 0.8616 (t) cc_final: 0.8145 (p)
REVERT: D   66 LYS cc_start: 0.7225 (mmtm) cc_final: 0.6602 (tppt)
REVERT: D   71 LEU cc_start: 0.7424 (tp) cc_final: 0.7150 (tp)
REVERT: D   74 ASN cc_start: 0.9109 (m-40) cc_final: 0.8873 (m110)
REVERT: D  118 LYS cc_start: 0.8862 (tppt) cc_final: 0.8276 (ttmm)
REVERT: D  163 ASP cc_start: 0.8685 (t0) cc_final: 0.8319 (t0)
REVERT: D  164 MET cc_start: 0.4151 (ttp) cc_final: 0.3804 (ttp)
REVERT: D  174 ASP cc_start: 0.8821 (m-30) cc_final: 0.8612 (m-30)
REVERT: D  216 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8145 (mmmt)
REVERT: D  241 TRP cc_start: 0.7927 (m100) cc_final: 0.7625 (m100)
REVERT: D  253 ASP cc_start: 0.7923 (t0) cc_final: 0.7686 (t0)
REVERT: D  279 LYS cc_start: 0.7776 (mttt) cc_final: 0.7345 (mmtt)
REVERT: D  281 LEU cc_start: 0.8281 (mp) cc_final: 0.8027 (mp)
REVERT: D  292 ASP cc_start: 0.9043 (p0) cc_final: 0.8423 (p0)
REVERT: D  320 LEU cc_start: 0.7918 (mp) cc_final: 0.7710 (mp)
REVERT: D  338 MET cc_start: 0.7261 (mmt) cc_final: 0.6859 (mmm)
REVERT: D  349 ARG cc_start: 0.8809 (ttm-80) cc_final: 0.8389 (ttm-80)
REVERT: D  357 ASP cc_start: 0.8681 (t70) cc_final: 0.8157 (t70)
REVERT: D  371 GLU cc_start: 0.8873 (pp20) cc_final: 0.8514 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 530
  average time/residue: 0.0967
  time to fit residues: 75.2813
Evaluate side-chains
  466 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 466
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 126 optimal weight:    6.9990
   chunk 128 optimal weight:    9.9990
   chunk 62 optimal weight:    8.9990
   chunk 38 optimal weight:    6.9990
   chunk 153 optimal weight:    7.9990
   chunk 79 optimal weight:    3.9990
   chunk 29 optimal weight:    7.9990
   chunk 121 optimal weight:    8.9990
   chunk 148 optimal weight:    5.9990
   chunk 81 optimal weight:    6.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  84 ASN
** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 283 GLN
B  74 ASN
B 389 ASN
C  88 GLN
C 161 ASN
C 251 ASN
C 414 ASN
** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.119611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.100209 restraints weight = 19103.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.103615 restraints weight = 9919.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.105995 restraints weight = 6229.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.107613 restraints weight = 4394.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.108820 restraints weight = 3395.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.3917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  12324  Z= 0.221
  Angle     :  0.650   8.725  16768  Z= 0.352
  Chirality :  0.045   0.190   1940
  Planarity :  0.005   0.054   2200
  Dihedral  :  6.023  46.831   1680
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.08 %
    Favored  : 96.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.04 (0.20), residues: 1568
  helix: -0.77 (0.30), residues: 260
  sheet:  0.08 (0.25), residues: 428
  loop : -1.04 (0.20), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 101 
 TYR   0.022   0.002   TYR C 100 
 PHE   0.018   0.002   PHE B  86 
 TRP   0.050   0.002   TRP C 410 
 HIS   0.004   0.001   HIS B 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 (12324)
  covalent geometry    : angle       0.65011 (16768)
  hydrogen bonds       : bond        0.05567 (  385)
  hydrogen bonds       : angle       5.43331 ( 1011)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  526 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 525
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 MET cc_start: 0.8378 (mtm) cc_final: 0.7831 (mtm)
REVERT: A   49 MET cc_start: 0.8796 (ttp) cc_final: 0.8447 (mtp)
REVERT: A  116 GLU cc_start: 0.8696 (tp30) cc_final: 0.8323 (tp30)
REVERT: A  121 ASN cc_start: 0.8983 (t0) cc_final: 0.8698 (t0)
REVERT: A  214 SER cc_start: 0.9108 (t) cc_final: 0.8390 (t)
REVERT: A  216 LYS cc_start: 0.9293 (mmtt) cc_final: 0.9047 (mmtt)
REVERT: A  311 LYS cc_start: 0.9458 (tttt) cc_final: 0.8987 (tttm)
REVERT: A  385 ASP cc_start: 0.9376 (p0) cc_final: 0.9066 (p0)
REVERT: B   15 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7976 (mm-30)
REVERT: B   73 LEU cc_start: 0.9247 (mt) cc_final: 0.9031 (mp)
REVERT: B   84 ASN cc_start: 0.8399 (m-40) cc_final: 0.8166 (m-40)
REVERT: B  268 LYS cc_start: 0.8950 (mtpt) cc_final: 0.8628 (mtpt)
REVERT: B  274 SER cc_start: 0.9168 (t) cc_final: 0.8911 (t)
REVERT: B  410 TRP cc_start: 0.9224 (t60) cc_final: 0.8981 (t60)
REVERT: C   40 MET cc_start: 0.8584 (ttm) cc_final: 0.8063 (ttt)
REVERT: C  279 LYS cc_start: 0.8012 (mttp) cc_final: 0.7590 (mmmt)
REVERT: C  327 TYR cc_start: 0.8682 (m-80) cc_final: 0.8278 (m-10)
REVERT: C  359 ILE cc_start: 0.9317 (mt) cc_final: 0.9021 (mm)
REVERT: C  389 ASN cc_start: 0.9275 (m-40) cc_final: 0.8766 (m110)
REVERT: D   42 ARG cc_start: 0.7528 (mmt180) cc_final: 0.7261 (mmt180)
REVERT: D   44 SER cc_start: 0.8464 (t) cc_final: 0.8020 (p)
REVERT: D   72 GLU cc_start: 0.8135 (tt0) cc_final: 0.7719 (tt0)
REVERT: D  116 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8263 (tm-30)
REVERT: D  118 LYS cc_start: 0.8811 (tppt) cc_final: 0.8247 (ttmm)
REVERT: D  241 TRP cc_start: 0.7997 (m100) cc_final: 0.7692 (m100)
REVERT: D  253 ASP cc_start: 0.8147 (t0) cc_final: 0.7931 (t0)
REVERT: D  279 LYS cc_start: 0.7708 (mttt) cc_final: 0.7409 (mmtt)
REVERT: D  292 ASP cc_start: 0.9062 (p0) cc_final: 0.8345 (p0)
REVERT: D  311 LYS cc_start: 0.9168 (ttmm) cc_final: 0.8956 (ttpt)
REVERT: D  320 LEU cc_start: 0.7894 (mp) cc_final: 0.7646 (mp)
REVERT: D  338 MET cc_start: 0.7450 (mmt) cc_final: 0.7106 (mmm)
REVERT: D  349 ARG cc_start: 0.8780 (ttm-80) cc_final: 0.8210 (ttt90)
REVERT: D  357 ASP cc_start: 0.8692 (t70) cc_final: 0.8151 (t70)
REVERT: D  371 GLU cc_start: 0.8863 (pp20) cc_final: 0.8376 (pp20)
REVERT: D  407 ILE cc_start: 0.8144 (pt) cc_final: 0.7678 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 526
  average time/residue: 0.0868
  time to fit residues: 68.1726
Evaluate side-chains
  478 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 477
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 78 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 112 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9990
   chunk 26 optimal weight:    7.9990
   chunk 8 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 106 optimal weight:    0.0870
   overall best weight:    4.4166

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

Flipped N/Q/H residues before XYZ refinement:
A  84 ASN
** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  43 HIS
C  88 GLN
C 251 ASN
C 364 GLN
D  74 ASN
D 324 GLN
** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.121863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.102084 restraints weight = 18813.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.105626 restraints weight = 9741.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.108067 restraints weight = 6094.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.109749 restraints weight = 4281.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.111003 restraints weight = 3293.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.4186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12324  Z= 0.168
  Angle     :  0.598   6.351  16768  Z= 0.323
  Chirality :  0.044   0.167   1940
  Planarity :  0.004   0.048   2200
  Dihedral  :  5.671  50.158   1680
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.97 (0.20), residues: 1568
  helix: -0.58 (0.31), residues: 256
  sheet:  0.14 (0.25), residues: 426
  loop : -1.04 (0.20), residues: 886

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  95 
 TYR   0.024   0.002   TYR D 100 
 PHE   0.025   0.002   PHE B 156 
 TRP   0.034   0.002   TRP C 410 
 HIS   0.003   0.001   HIS B 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (12324)
  covalent geometry    : angle       0.59782 (16768)
  hydrogen bonds       : bond        0.05174 (  385)
  hydrogen bonds       : angle       5.26042 ( 1011)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  552 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 552
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 MET cc_start: 0.8751 (ttp) cc_final: 0.8532 (mtp)
REVERT: A  121 ASN cc_start: 0.8911 (t0) cc_final: 0.8609 (t0)
REVERT: A  126 MET cc_start: 0.8954 (ttp) cc_final: 0.8746 (ttm)
REVERT: A  164 MET cc_start: 0.7048 (mpp) cc_final: 0.5838 (mpp)
REVERT: A  214 SER cc_start: 0.9014 (t) cc_final: 0.8729 (t)
REVERT: A  249 LYS cc_start: 0.8205 (mtpp) cc_final: 0.7806 (mtpt)
REVERT: A  311 LYS cc_start: 0.9488 (tttt) cc_final: 0.8987 (tttm)
REVERT: A  317 ASP cc_start: 0.8450 (t0) cc_final: 0.8244 (t0)
REVERT: A  385 ASP cc_start: 0.9384 (p0) cc_final: 0.9082 (p0)
REVERT: B   15 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8016 (mm-30)
REVERT: B   49 MET cc_start: 0.8320 (ptm) cc_final: 0.8089 (ptm)
REVERT: B  268 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8579 (mtpt)
REVERT: B  289 LEU cc_start: 0.8929 (mm) cc_final: 0.8573 (mm)
REVERT: B  320 LEU cc_start: 0.9413 (mp) cc_final: 0.9091 (mp)
REVERT: B  410 TRP cc_start: 0.9257 (t60) cc_final: 0.8994 (t60)
REVERT: C   81 GLU cc_start: 0.7893 (mp0) cc_final: 0.7651 (mp0)
REVERT: C  169 PHE cc_start: 0.9309 (m-80) cc_final: 0.9003 (m-10)
REVERT: C  279 LYS cc_start: 0.7942 (mttp) cc_final: 0.7565 (mmmt)
REVERT: C  327 TYR cc_start: 0.8696 (m-80) cc_final: 0.8317 (m-10)
REVERT: C  344 ASN cc_start: 0.8435 (t0) cc_final: 0.8135 (t0)
REVERT: C  359 ILE cc_start: 0.9316 (mt) cc_final: 0.9049 (mm)
REVERT: C  389 ASN cc_start: 0.9306 (m-40) cc_final: 0.8774 (m110)
REVERT: C  411 TYR cc_start: 0.9306 (p90) cc_final: 0.9082 (p90)
REVERT: D    5 GLU cc_start: 0.7853 (mp0) cc_final: 0.7439 (mp0)
REVERT: D   42 ARG cc_start: 0.7466 (mmt180) cc_final: 0.7106 (mmt180)
REVERT: D   44 SER cc_start: 0.8384 (t) cc_final: 0.8017 (p)
REVERT: D   66 LYS cc_start: 0.7362 (mmtm) cc_final: 0.6774 (tppt)
REVERT: D  116 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8258 (tm-30)
REVERT: D  118 LYS cc_start: 0.8805 (tppt) cc_final: 0.8229 (ttmt)
REVERT: D  177 LYS cc_start: 0.9210 (mmmm) cc_final: 0.8862 (mttp)
REVERT: D  216 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8912 (mmtt)
REVERT: D  241 TRP cc_start: 0.7913 (m100) cc_final: 0.7553 (m100)
REVERT: D  253 ASP cc_start: 0.8227 (t0) cc_final: 0.8016 (t0)
REVERT: D  279 LYS cc_start: 0.7638 (mttt) cc_final: 0.7380 (mmtt)
REVERT: D  292 ASP cc_start: 0.9013 (p0) cc_final: 0.8265 (p0)
REVERT: D  311 LYS cc_start: 0.9182 (ttmm) cc_final: 0.8958 (ttpt)
REVERT: D  320 LEU cc_start: 0.7997 (mp) cc_final: 0.7734 (mp)
REVERT: D  338 MET cc_start: 0.7427 (mmt) cc_final: 0.7083 (mmm)
REVERT: D  349 ARG cc_start: 0.8757 (ttm-80) cc_final: 0.8151 (ttt90)
REVERT: D  357 ASP cc_start: 0.8714 (t70) cc_final: 0.8179 (t70)
REVERT: D  371 GLU cc_start: 0.8852 (pp20) cc_final: 0.8379 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 552
  average time/residue: 0.0953
  time to fit residues: 78.2292
Evaluate side-chains
  484 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 484
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 100 optimal weight:    5.9990
   chunk 115 optimal weight:    9.9990
   chunk 138 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 122 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 87 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 149 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  84 ASN
A 113 ASN
A 251 ASN
** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
B 389 ASN
C  84 ASN
C  88 GLN
C 161 ASN
C 251 ASN
D 369 ASN
** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 428 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.121366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.102180 restraints weight = 19113.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.105531 restraints weight = 9911.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.107920 restraints weight = 6218.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.109606 restraints weight = 4369.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.110713 restraints weight = 3349.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.4324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12324  Z= 0.174
  Angle     :  0.612   9.631  16768  Z= 0.327
  Chirality :  0.044   0.162   1940
  Planarity :  0.004   0.053   2200
  Dihedral  :  5.630  51.770   1680
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.38 %
    Favored  : 98.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.93 (0.20), residues: 1568
  helix: -0.35 (0.31), residues: 268
  sheet:  0.17 (0.25), residues: 424
  loop : -1.09 (0.20), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  95 
 TYR   0.016   0.002   TYR C 100 
 PHE   0.014   0.002   PHE C 147 
 TRP   0.039   0.003   TRP A 354 
 HIS   0.003   0.001   HIS B 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (12324)
  covalent geometry    : angle       0.61156 (16768)
  hydrogen bonds       : bond        0.05149 (  385)
  hydrogen bonds       : angle       5.27042 ( 1011)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  538 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 535
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASN cc_start: 0.8874 (t0) cc_final: 0.8600 (t0)
REVERT: A  126 MET cc_start: 0.8919 (ttp) cc_final: 0.8626 (ttm)
REVERT: A  155 MET cc_start: 0.8523 (ttp) cc_final: 0.8316 (ttp)
REVERT: A  214 SER cc_start: 0.8992 (t) cc_final: 0.8686 (t)
REVERT: A  311 LYS cc_start: 0.9503 (tttt) cc_final: 0.9120 (tttm)
REVERT: A  317 ASP cc_start: 0.8455 (t0) cc_final: 0.8254 (t0)
REVERT: A  385 ASP cc_start: 0.9402 (p0) cc_final: 0.9170 (p0)
REVERT: B   15 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7845 (mm-30)
REVERT: B   26 MET cc_start: 0.8616 (mmm) cc_final: 0.8105 (mmm)
REVERT: B   49 MET cc_start: 0.8208 (ptm) cc_final: 0.7973 (ptm)
REVERT: B  268 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8579 (mtpt)
REVERT: B  376 MET cc_start: 0.7603 (ttm) cc_final: 0.7395 (ttm)
REVERT: C   81 GLU cc_start: 0.7896 (mp0) cc_final: 0.7673 (mp0)
REVERT: C  159 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7907 (mt-10)
REVERT: C  279 LYS cc_start: 0.7989 (mttp) cc_final: 0.7676 (mmtt)
REVERT: C  327 TYR cc_start: 0.8693 (m-80) cc_final: 0.8289 (m-10)
REVERT: C  344 ASN cc_start: 0.8327 (t0) cc_final: 0.7968 (t0)
REVERT: C  359 ILE cc_start: 0.9317 (mt) cc_final: 0.9037 (mm)
REVERT: C  389 ASN cc_start: 0.9344 (m-40) cc_final: 0.8775 (m110)
REVERT: D    5 GLU cc_start: 0.7856 (mp0) cc_final: 0.7380 (mp0)
REVERT: D   42 ARG cc_start: 0.7552 (mmt180) cc_final: 0.7088 (mmt180)
REVERT: D   44 SER cc_start: 0.8405 (t) cc_final: 0.8019 (p)
REVERT: D   66 LYS cc_start: 0.7378 (mmtm) cc_final: 0.6773 (tppt)
REVERT: D  116 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8169 (tm-30)
REVERT: D  118 LYS cc_start: 0.8838 (tppt) cc_final: 0.8270 (ttmm)
REVERT: D  177 LYS cc_start: 0.9192 (mmmm) cc_final: 0.8912 (mtpp)
REVERT: D  241 TRP cc_start: 0.7872 (m100) cc_final: 0.7483 (m100)
REVERT: D  253 ASP cc_start: 0.8299 (t0) cc_final: 0.8077 (t0)
REVERT: D  279 LYS cc_start: 0.7632 (mttt) cc_final: 0.7330 (mmtt)
REVERT: D  292 ASP cc_start: 0.9002 (p0) cc_final: 0.8251 (p0)
REVERT: D  311 LYS cc_start: 0.9174 (ttmm) cc_final: 0.8962 (ttpt)
REVERT: D  349 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8460 (ttm-80)
REVERT: D  357 ASP cc_start: 0.8701 (t70) cc_final: 0.8116 (t70)
REVERT: D  370 HIS cc_start: 0.8558 (m90) cc_final: 0.8222 (m90)
REVERT: D  371 GLU cc_start: 0.8872 (pp20) cc_final: 0.8421 (pp20)
  outliers start: 3
  outliers final: 2
  residues processed: 536
  average time/residue: 0.0928
  time to fit residues: 74.7752
Evaluate side-chains
  471 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 469
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 118 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0060
   chunk 97 optimal weight:    1.9990
   chunk 101 optimal weight:    9.9990
   chunk 54 optimal weight:    9.9990
   chunk 48 optimal weight:    8.9990
   chunk 74 optimal weight:    5.9990
   chunk 17 optimal weight:    9.9990
   chunk 113 optimal weight:    5.9990
   overall best weight:    3.4004

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

Flipped N/Q/H residues before XYZ refinement:
A  84 ASN
B  74 ASN
B 389 ASN
C  84 ASN
C  88 GLN
C 251 ASN
** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.122689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.103164 restraints weight = 18973.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.106664 restraints weight = 9868.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.109093 restraints weight = 6183.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.110691 restraints weight = 4364.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.111981 restraints weight = 3371.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.4477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12324  Z= 0.141
  Angle     :  0.578   7.399  16768  Z= 0.310
  Chirality :  0.043   0.161   1940
  Planarity :  0.004   0.055   2200
  Dihedral  :  5.357  54.295   1680
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.31 %
    Favored  : 98.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.84 (0.20), residues: 1568
  helix: -0.19 (0.31), residues: 268
  sheet:  0.30 (0.26), residues: 416
  loop : -1.11 (0.20), residues: 884

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  95 
 TYR   0.019   0.002   TYR D 100 
 PHE   0.019   0.002   PHE C 169 
 TRP   0.037   0.002   TRP A 410 
 HIS   0.003   0.001   HIS D 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (12324)
  covalent geometry    : angle       0.57831 (16768)
  hydrogen bonds       : bond        0.04712 (  385)
  hydrogen bonds       : angle       5.10783 ( 1011)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  544 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 543
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8635 (mm-30)
REVERT: A  121 ASN cc_start: 0.8861 (t0) cc_final: 0.8591 (t0)
REVERT: A  214 SER cc_start: 0.9020 (t) cc_final: 0.8754 (t)
REVERT: A  311 LYS cc_start: 0.9522 (tttt) cc_final: 0.9051 (tttm)
REVERT: A  385 ASP cc_start: 0.9458 (p0) cc_final: 0.9103 (p0)
REVERT: B   15 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7761 (mm-30)
REVERT: B   26 MET cc_start: 0.8550 (mmm) cc_final: 0.8242 (mmm)
REVERT: B  118 LYS cc_start: 0.9273 (tppp) cc_final: 0.8920 (ttpt)
REVERT: B  268 LYS cc_start: 0.8855 (mtpt) cc_final: 0.8572 (mtpt)
REVERT: B  376 MET cc_start: 0.7689 (ttm) cc_final: 0.7474 (ttm)
REVERT: C   71 LEU cc_start: 0.8575 (tp) cc_final: 0.8196 (tt)
REVERT: C   81 GLU cc_start: 0.7833 (mp0) cc_final: 0.7598 (mp0)
REVERT: C   84 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8254 (m-40)
REVERT: C  159 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7823 (mt-10)
REVERT: C  221 THR cc_start: 0.9030 (m) cc_final: 0.8712 (p)
REVERT: C  279 LYS cc_start: 0.8003 (mttp) cc_final: 0.7742 (mmtt)
REVERT: C  327 TYR cc_start: 0.8719 (m-80) cc_final: 0.8296 (m-10)
REVERT: C  344 ASN cc_start: 0.8415 (t0) cc_final: 0.8006 (t0)
REVERT: C  359 ILE cc_start: 0.9325 (mt) cc_final: 0.9060 (mm)
REVERT: C  389 ASN cc_start: 0.9359 (m-40) cc_final: 0.8827 (m110)
REVERT: D    5 GLU cc_start: 0.7844 (mp0) cc_final: 0.7381 (mp0)
REVERT: D   42 ARG cc_start: 0.7328 (mmt180) cc_final: 0.6905 (mmt180)
REVERT: D   44 SER cc_start: 0.8235 (t) cc_final: 0.7969 (p)
REVERT: D   66 LYS cc_start: 0.7426 (mmtm) cc_final: 0.6851 (tppt)
REVERT: D  116 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8183 (tm-30)
REVERT: D  118 LYS cc_start: 0.8901 (tppt) cc_final: 0.8317 (ttmm)
REVERT: D  173 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8348 (tm-30)
REVERT: D  174 ASP cc_start: 0.8734 (m-30) cc_final: 0.8409 (m-30)
REVERT: D  177 LYS cc_start: 0.9224 (mmmm) cc_final: 0.8969 (mttp)
REVERT: D  216 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8555 (mmtt)
REVERT: D  241 TRP cc_start: 0.7914 (m100) cc_final: 0.7600 (m100)
REVERT: D  279 LYS cc_start: 0.7646 (mttt) cc_final: 0.7384 (mmtt)
REVERT: D  292 ASP cc_start: 0.9086 (p0) cc_final: 0.8427 (p0)
REVERT: D  320 LEU cc_start: 0.8144 (mp) cc_final: 0.7894 (mp)
REVERT: D  338 MET cc_start: 0.7656 (mmt) cc_final: 0.7440 (mmm)
REVERT: D  349 ARG cc_start: 0.8714 (ttm-80) cc_final: 0.8166 (ttt90)
REVERT: D  354 TRP cc_start: 0.9540 (p90) cc_final: 0.9219 (p90)
REVERT: D  370 HIS cc_start: 0.8507 (m90) cc_final: 0.8152 (m90)
REVERT: D  371 GLU cc_start: 0.8895 (pp20) cc_final: 0.8387 (pp20)
  outliers start: 1
  outliers final: 0
  residues processed: 543
  average time/residue: 0.0809
  time to fit residues: 66.2382
Evaluate side-chains
  485 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 484
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 152 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   chunk 125 optimal weight:    6.9990
   chunk 137 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 108 optimal weight:    0.6980
   chunk 36 optimal weight:    8.9990
   chunk 52 optimal weight:   30.0000
   chunk 26 optimal weight:    7.9990
   overall best weight:    4.9388

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

Flipped N/Q/H residues before XYZ refinement:
A  28 GLN
A  84 ASN
** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
C  88 GLN
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 251 ASN
C 395 GLN
D   7 GLN
** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.121176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.101916 restraints weight = 19020.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.105310 restraints weight = 9937.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.107682 restraints weight = 6252.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.109300 restraints weight = 4429.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.110488 restraints weight = 3410.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.4591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  12324  Z= 0.188
  Angle     :  0.633   9.694  16768  Z= 0.335
  Chirality :  0.044   0.217   1940
  Planarity :  0.004   0.057   2200
  Dihedral  :  5.554  53.230   1680
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.00 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.89 (0.20), residues: 1568
  helix: -0.20 (0.31), residues: 266
  sheet:  0.28 (0.25), residues: 414
  loop : -1.16 (0.20), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  95 
 TYR   0.022   0.002   TYR B 100 
 PHE   0.032   0.002   PHE B 156 
 TRP   0.047   0.002   TRP A 410 
 HIS   0.003   0.001   HIS D  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 (12324)
  covalent geometry    : angle       0.63292 (16768)
  hydrogen bonds       : bond        0.05222 (  385)
  hydrogen bonds       : angle       5.26283 ( 1011)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  535 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 534
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8572 (mm-30)
REVERT: A   28 GLN cc_start: 0.9237 (tt0) cc_final: 0.8953 (tt0)
REVERT: A   31 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8572 (mtpp)
REVERT: A  121 ASN cc_start: 0.8882 (t0) cc_final: 0.7250 (t0)
REVERT: A  125 GLU cc_start: 0.7781 (mt-10) cc_final: 0.6768 (mt-10)
REVERT: A  214 SER cc_start: 0.8998 (t) cc_final: 0.8710 (t)
REVERT: A  311 LYS cc_start: 0.9541 (tttt) cc_final: 0.9040 (tttm)
REVERT: A  385 ASP cc_start: 0.9476 (p0) cc_final: 0.9115 (p0)
REVERT: A  395 GLN cc_start: 0.9050 (tp-100) cc_final: 0.8788 (tp40)
REVERT: B   26 MET cc_start: 0.8575 (mmm) cc_final: 0.8074 (mmm)
REVERT: B  164 MET cc_start: 0.7948 (mmm) cc_final: 0.7257 (tpp)
REVERT: B  268 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8574 (mtpt)
REVERT: B  410 TRP cc_start: 0.9291 (t60) cc_final: 0.9052 (t60)
REVERT: C   40 MET cc_start: 0.7669 (ttm) cc_final: 0.7443 (ttt)
REVERT: C  143 ASP cc_start: 0.8037 (t0) cc_final: 0.7816 (t0)
REVERT: C  152 GLU cc_start: 0.8751 (tp30) cc_final: 0.8349 (tp30)
REVERT: C  159 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7861 (mt-10)
REVERT: C  279 LYS cc_start: 0.7994 (mttp) cc_final: 0.7759 (mmtt)
REVERT: C  327 TYR cc_start: 0.8701 (m-80) cc_final: 0.8386 (m-10)
REVERT: C  344 ASN cc_start: 0.8569 (t0) cc_final: 0.8164 (t0)
REVERT: C  359 ILE cc_start: 0.9381 (mt) cc_final: 0.9086 (mm)
REVERT: C  389 ASN cc_start: 0.9335 (m-40) cc_final: 0.8743 (m110)
REVERT: D    5 GLU cc_start: 0.7939 (mp0) cc_final: 0.7456 (mp0)
REVERT: D   15 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8329 (mm-30)
REVERT: D   18 GLU cc_start: 0.8398 (tt0) cc_final: 0.8039 (mm-30)
REVERT: D   42 ARG cc_start: 0.7513 (mmt180) cc_final: 0.7002 (mmt180)
REVERT: D   44 SER cc_start: 0.8403 (t) cc_final: 0.8047 (p)
REVERT: D   66 LYS cc_start: 0.7442 (mmtm) cc_final: 0.6855 (tppt)
REVERT: D  116 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8210 (tm-30)
REVERT: D  118 LYS cc_start: 0.8948 (tppt) cc_final: 0.8329 (ttmm)
REVERT: D  177 LYS cc_start: 0.9233 (mmmm) cc_final: 0.8924 (mttp)
REVERT: D  216 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8561 (mmtt)
REVERT: D  241 TRP cc_start: 0.7963 (m100) cc_final: 0.7640 (m100)
REVERT: D  279 LYS cc_start: 0.7733 (mttt) cc_final: 0.7403 (mmmt)
REVERT: D  292 ASP cc_start: 0.9106 (p0) cc_final: 0.8444 (p0)
REVERT: D  320 LEU cc_start: 0.8113 (mp) cc_final: 0.7838 (mp)
REVERT: D  338 MET cc_start: 0.7748 (mmt) cc_final: 0.7446 (mmm)
REVERT: D  349 ARG cc_start: 0.8740 (ttm-80) cc_final: 0.8199 (ttt90)
REVERT: D  357 ASP cc_start: 0.8712 (t70) cc_final: 0.8170 (t70)
REVERT: D  370 HIS cc_start: 0.8490 (m90) cc_final: 0.8142 (m90)
REVERT: D  371 GLU cc_start: 0.8910 (pp20) cc_final: 0.8322 (pp20)
  outliers start: 1
  outliers final: 1
  residues processed: 534
  average time/residue: 0.0851
  time to fit residues: 68.4684
Evaluate side-chains
  475 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 474
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 63 optimal weight:    7.9990
   chunk 41 optimal weight:    4.9990
   chunk 123 optimal weight:    6.9990
   chunk 146 optimal weight:    8.9990
   chunk 78 optimal weight:   10.0000
   chunk 103 optimal weight:   20.0000
   chunk 73 optimal weight:    4.9990
   chunk 58 optimal weight:   10.0000
   chunk 84 optimal weight:    5.9990
   chunk 87 optimal weight:    9.9990
   chunk 131 optimal weight:    5.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  84 ASN
A 242 GLN
** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
** B  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 ASN
C  88 GLN
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 251 ASN
D  84 ASN
D 369 ASN
** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.120167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.100924 restraints weight = 19059.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.104289 restraints weight = 9970.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.106631 restraints weight = 6282.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.108183 restraints weight = 4464.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.109356 restraints weight = 3460.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.4631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12324  Z= 0.215
  Angle     :  0.665  11.260  16768  Z= 0.350
  Chirality :  0.045   0.185   1940
  Planarity :  0.005   0.058   2200
  Dihedral  :  5.720  54.140   1680
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.54 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.02 (0.20), residues: 1568
  helix: -0.33 (0.31), residues: 254
  sheet:  0.19 (0.25), residues: 414
  loop : -1.22 (0.20), residues: 900

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  95 
 TYR   0.023   0.002   TYR D 100 
 PHE   0.025   0.002   PHE C 169 
 TRP   0.052   0.003   TRP A 410 
 HIS   0.004   0.001   HIS B 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 (12324)
  covalent geometry    : angle       0.66458 (16768)
  hydrogen bonds       : bond        0.05522 (  385)
  hydrogen bonds       : angle       5.38006 ( 1011)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  526 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 525
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 GLN cc_start: 0.9247 (tt0) cc_final: 0.8983 (tt0)
REVERT: A  121 ASN cc_start: 0.8882 (t0) cc_final: 0.7324 (t0)
REVERT: A  125 GLU cc_start: 0.7949 (mt-10) cc_final: 0.6964 (mt-10)
REVERT: A  214 SER cc_start: 0.8962 (t) cc_final: 0.8656 (t)
REVERT: A  229 THR cc_start: 0.8535 (p) cc_final: 0.8306 (p)
REVERT: A  311 LYS cc_start: 0.9458 (tttt) cc_final: 0.9086 (tttm)
REVERT: A  317 ASP cc_start: 0.8510 (t0) cc_final: 0.8303 (t0)
REVERT: A  356 ASP cc_start: 0.8901 (t0) cc_final: 0.8659 (t0)
REVERT: A  385 ASP cc_start: 0.9488 (p0) cc_final: 0.9139 (p0)
REVERT: A  395 GLN cc_start: 0.9040 (tp-100) cc_final: 0.8778 (tp40)
REVERT: B   26 MET cc_start: 0.8597 (mmm) cc_final: 0.7865 (mmt)
REVERT: B  164 MET cc_start: 0.8042 (mmm) cc_final: 0.7302 (tpp)
REVERT: B  241 TRP cc_start: 0.8333 (p-90) cc_final: 0.7972 (p-90)
REVERT: B  268 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8592 (mtpt)
REVERT: B  274 SER cc_start: 0.9201 (t) cc_final: 0.8969 (t)
REVERT: B  376 MET cc_start: 0.7802 (ttm) cc_final: 0.7574 (ttm)
REVERT: B  410 TRP cc_start: 0.9296 (t60) cc_final: 0.9075 (t60)
REVERT: B  425 LEU cc_start: 0.9176 (mp) cc_final: 0.8936 (mp)
REVERT: C   40 MET cc_start: 0.7761 (ttm) cc_final: 0.7474 (ttt)
REVERT: C   81 GLU cc_start: 0.7953 (mp0) cc_final: 0.7709 (mp0)
REVERT: C  143 ASP cc_start: 0.8332 (t0) cc_final: 0.8044 (t0)
REVERT: C  152 GLU cc_start: 0.8919 (tp30) cc_final: 0.8446 (tp30)
REVERT: C  159 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7802 (mt-10)
REVERT: C  279 LYS cc_start: 0.7965 (mttp) cc_final: 0.7670 (mmtt)
REVERT: C  344 ASN cc_start: 0.8576 (t0) cc_final: 0.8071 (t0)
REVERT: C  359 ILE cc_start: 0.9336 (mt) cc_final: 0.9023 (mm)
REVERT: C  389 ASN cc_start: 0.9309 (m-40) cc_final: 0.9099 (m-40)
REVERT: C  395 GLN cc_start: 0.9476 (tp-100) cc_final: 0.9054 (tp-100)
REVERT: D   15 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8186 (mm-30)
REVERT: D   18 GLU cc_start: 0.8396 (tt0) cc_final: 0.8036 (mm-30)
REVERT: D   42 ARG cc_start: 0.7470 (mmt180) cc_final: 0.6892 (mmt180)
REVERT: D   44 SER cc_start: 0.8380 (t) cc_final: 0.7979 (p)
REVERT: D   66 LYS cc_start: 0.7455 (mmtm) cc_final: 0.6819 (tppt)
REVERT: D  116 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8232 (tm-30)
REVERT: D  118 LYS cc_start: 0.8907 (tppt) cc_final: 0.8317 (ttmm)
REVERT: D  177 LYS cc_start: 0.9276 (mmmm) cc_final: 0.9001 (mttp)
REVERT: D  216 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8559 (mmtt)
REVERT: D  241 TRP cc_start: 0.7922 (m100) cc_final: 0.7675 (m100)
REVERT: D  279 LYS cc_start: 0.7669 (mttt) cc_final: 0.7333 (mmmt)
REVERT: D  292 ASP cc_start: 0.8980 (p0) cc_final: 0.8301 (p0)
REVERT: D  320 LEU cc_start: 0.8149 (mp) cc_final: 0.7917 (mp)
REVERT: D  321 SER cc_start: 0.8410 (t) cc_final: 0.8202 (t)
REVERT: D  338 MET cc_start: 0.7707 (mmt) cc_final: 0.7188 (mmm)
REVERT: D  349 ARG cc_start: 0.8704 (ttm-80) cc_final: 0.8325 (ttt90)
REVERT: D  357 ASP cc_start: 0.8760 (t70) cc_final: 0.8188 (t70)
REVERT: D  370 HIS cc_start: 0.8589 (m90) cc_final: 0.8227 (m90)
REVERT: D  371 GLU cc_start: 0.8989 (pp20) cc_final: 0.8426 (pp20)
  outliers start: 1
  outliers final: 0
  residues processed: 525
  average time/residue: 0.0879
  time to fit residues: 69.5758
Evaluate side-chains
  477 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 477
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 105 optimal weight:    6.9990
   chunk 97 optimal weight:    8.9990
   chunk 102 optimal weight:    6.9990
   chunk 69 optimal weight:   10.0000
   chunk 60 optimal weight:    6.9990
   chunk 75 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 143 optimal weight:    6.9990
   chunk 113 optimal weight:    0.9980
   chunk 47 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   overall best weight:    4.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  84 ASN
A 242 GLN
** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
C  88 GLN
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 369 ASN
D 395 GLN
** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.120599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.101219 restraints weight = 19116.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.104674 restraints weight = 9920.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.106993 restraints weight = 6215.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.108668 restraints weight = 4383.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.109770 restraints weight = 3379.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.4727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12324  Z= 0.191
  Angle     :  0.645  10.659  16768  Z= 0.342
  Chirality :  0.045   0.206   1940
  Planarity :  0.005   0.058   2200
  Dihedral  :  5.712  62.376   1680
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.31 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.98 (0.20), residues: 1568
  helix: -0.19 (0.31), residues: 262
  sheet:  0.29 (0.26), residues: 406
  loop : -1.26 (0.20), residues: 900

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  95 
 TYR   0.024   0.002   TYR D 100 
 PHE   0.023   0.002   PHE C 169 
 TRP   0.045   0.003   TRP A 410 
 HIS   0.003   0.001   HIS D  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 (12324)
  covalent geometry    : angle       0.64520 (16768)
  hydrogen bonds       : bond        0.05378 (  385)
  hydrogen bonds       : angle       5.35213 ( 1011)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  525 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 524
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 SER cc_start: 0.8774 (m) cc_final: 0.8276 (t)
REVERT: A  121 ASN cc_start: 0.8861 (t0) cc_final: 0.7262 (t0)
REVERT: A  125 GLU cc_start: 0.7974 (mt-10) cc_final: 0.6941 (mt-10)
REVERT: A  143 ASP cc_start: 0.7921 (t70) cc_final: 0.7270 (t70)
REVERT: A  214 SER cc_start: 0.8937 (t) cc_final: 0.8611 (t)
REVERT: A  229 THR cc_start: 0.8522 (p) cc_final: 0.8289 (p)
REVERT: A  249 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7642 (mtpt)
REVERT: A  311 LYS cc_start: 0.9472 (tttt) cc_final: 0.9088 (tttm)
REVERT: A  356 ASP cc_start: 0.8887 (t0) cc_final: 0.8604 (t0)
REVERT: A  385 ASP cc_start: 0.9516 (p0) cc_final: 0.9172 (p0)
REVERT: A  395 GLN cc_start: 0.9054 (tp-100) cc_final: 0.8794 (tp40)
REVERT: B   26 MET cc_start: 0.8577 (mmm) cc_final: 0.7823 (mmt)
REVERT: B   81 GLU cc_start: 0.6974 (mp0) cc_final: 0.6756 (mp0)
REVERT: B  164 MET cc_start: 0.8030 (mmm) cc_final: 0.7308 (tpp)
REVERT: B  241 TRP cc_start: 0.8401 (p-90) cc_final: 0.7995 (p-90)
REVERT: B  274 SER cc_start: 0.9216 (t) cc_final: 0.8976 (t)
REVERT: B  376 MET cc_start: 0.7869 (ttm) cc_final: 0.7643 (ttm)
REVERT: B  410 TRP cc_start: 0.9284 (t60) cc_final: 0.9075 (t60)
REVERT: C   40 MET cc_start: 0.7769 (ttm) cc_final: 0.7471 (ttt)
REVERT: C   81 GLU cc_start: 0.7933 (mp0) cc_final: 0.7688 (mp0)
REVERT: C  143 ASP cc_start: 0.8334 (t0) cc_final: 0.8052 (t0)
REVERT: C  152 GLU cc_start: 0.8920 (tp30) cc_final: 0.8462 (tp30)
REVERT: C  159 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7842 (mt-10)
REVERT: C  279 LYS cc_start: 0.7930 (mttp) cc_final: 0.7651 (mmtt)
REVERT: C  344 ASN cc_start: 0.8702 (t0) cc_final: 0.8291 (t0)
REVERT: C  359 ILE cc_start: 0.9349 (mt) cc_final: 0.9039 (mm)
REVERT: C  363 SER cc_start: 0.8616 (t) cc_final: 0.8245 (t)
REVERT: C  389 ASN cc_start: 0.9323 (m-40) cc_final: 0.8203 (m110)
REVERT: C  395 GLN cc_start: 0.9498 (tp-100) cc_final: 0.9129 (tp-100)
REVERT: D   15 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8161 (mm-30)
REVERT: D   18 GLU cc_start: 0.8410 (tt0) cc_final: 0.8049 (mm-30)
REVERT: D   23 ILE cc_start: 0.9002 (tt) cc_final: 0.8786 (tt)
REVERT: D   42 ARG cc_start: 0.7450 (mmt180) cc_final: 0.6888 (mmt180)
REVERT: D   44 SER cc_start: 0.8335 (t) cc_final: 0.7976 (p)
REVERT: D   66 LYS cc_start: 0.7457 (mmtm) cc_final: 0.6810 (tppt)
REVERT: D  118 LYS cc_start: 0.8908 (tppt) cc_final: 0.8261 (ttmm)
REVERT: D  163 ASP cc_start: 0.8837 (t0) cc_final: 0.8452 (t0)
REVERT: D  173 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8307 (tm-30)
REVERT: D  174 ASP cc_start: 0.8801 (m-30) cc_final: 0.8468 (m-30)
REVERT: D  177 LYS cc_start: 0.9268 (mmmm) cc_final: 0.8968 (mttp)
REVERT: D  279 LYS cc_start: 0.7665 (mttt) cc_final: 0.7342 (mmmt)
REVERT: D  292 ASP cc_start: 0.8985 (p0) cc_final: 0.8307 (p0)
REVERT: D  320 LEU cc_start: 0.8149 (mp) cc_final: 0.7892 (mp)
REVERT: D  338 MET cc_start: 0.7641 (mmt) cc_final: 0.7046 (mmm)
REVERT: D  349 ARG cc_start: 0.8689 (ttm-80) cc_final: 0.8269 (ttt90)
REVERT: D  357 ASP cc_start: 0.8737 (t70) cc_final: 0.8154 (t70)
REVERT: D  370 HIS cc_start: 0.8586 (m90) cc_final: 0.8225 (m90)
REVERT: D  371 GLU cc_start: 0.9043 (pp20) cc_final: 0.8399 (pp20)
  outliers start: 1
  outliers final: 1
  residues processed: 524
  average time/residue: 0.0849
  time to fit residues: 67.3308
Evaluate side-chains
  486 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 485
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 73 optimal weight:    2.9990
   chunk 30 optimal weight:    9.9990
   chunk 112 optimal weight:    3.9990
   chunk 110 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 146 optimal weight:    9.9990
   chunk 63 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0060
   overall best weight:    3.4004

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

Flipped N/Q/H residues before XYZ refinement:
A  84 ASN
A 242 GLN
** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
** B  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 364 GLN
** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 369 ASN
** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 428 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.122820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.103550 restraints weight = 18729.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.107018 restraints weight = 9723.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.109343 restraints weight = 6091.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.110914 restraints weight = 4305.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.112125 restraints weight = 3321.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.4837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12324  Z= 0.146
  Angle     :  0.611  10.540  16768  Z= 0.323
  Chirality :  0.044   0.209   1940
  Planarity :  0.004   0.055   2200
  Dihedral  :  5.474  62.671   1680
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.89 (0.21), residues: 1568
  helix:  0.00 (0.31), residues: 264
  sheet:  0.36 (0.26), residues: 406
  loop : -1.26 (0.20), residues: 898

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  95 
 TYR   0.021   0.002   TYR D 100 
 PHE   0.016   0.002   PHE C  86 
 TRP   0.041   0.002   TRP C 410 
 HIS   0.005   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (12324)
  covalent geometry    : angle       0.61106 (16768)
  hydrogen bonds       : bond        0.04891 (  385)
  hydrogen bonds       : angle       5.23772 ( 1011)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2079.99 seconds
wall clock time: 36 minutes 29.56 seconds (2189.56 seconds total)