Starting phenix.real_space_refine
on Wed Jul 30 05:35:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gn5_34155/07_2025/8gn5_34155.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gn5_34155/07_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_34155/07_2025/8gn5_34155.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gn5_34155/07_2025/8gn5_34155.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gn5_34155/07_2025/8gn5_34155.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gn5_34155/07_2025/8gn5_34155.cif"
  }
  resolution = 4.02
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.71, per 1000 atoms: 0.64
  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: 2.80
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 1.60
  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: 3.72

  Time building geometry restraints manager: 3.32 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: 0.03
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:             0.180
  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:          0.470
  Check model and map are aligned:         0.110
  Set scattering table:                    0.100
  Process input model:                     30.330
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.760
-------------------------------------------------------------------------------
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 : 1.08
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (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
 TRP   0.132   0.022   TRP B 410 
 HIS   0.009   0.002   HIS B 287 
 PHE   0.101   0.014   PHE D 280 
 TYR   0.103   0.022   TYR A 175 
 ARG   0.007   0.001   ARG C 158 

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

*********************** 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  : 1.206 
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: 0.2433
  time to fit residues: 230.8688
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  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    4.9990
   chunk 118 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 40 optimal weight:    8.9990
   chunk 79 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 122 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   chunk 91 optimal weight:   30.0000
   chunk 141 optimal weight:    8.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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
** 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: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.122740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.103741 restraints weight = 18570.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.107181 restraints weight = 9708.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.109458 restraints weight = 6067.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12324  Z= 0.166
  Angle     :  0.655   6.759  16768  Z= 0.364
  Chirality :  0.045   0.199   1940
  Planarity :  0.004   0.039   2200
  Dihedral  :  6.676  49.110   1680
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.20), residues: 1568
  helix: -0.98 (0.29), residues: 264
  sheet:  0.20 (0.24), residues: 428
  loop : -0.87 (0.19), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 241 
 HIS   0.005   0.001   HIS D 287 
 PHE   0.016   0.002   PHE B 147 
 TYR   0.012   0.002   TYR A 411 
 ARG   0.005   0.001   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05486 (  385)
  hydrogen bonds       : angle       5.46823 ( 1011)
  covalent geometry    : bond        0.00377 (12324)
  covalent geometry    : angle       0.65477 (16768)

*********************** 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
  564 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 564
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8857 (tttm) cc_final: 0.8429 (tttm)
REVERT: A   46 THR cc_start: 0.9174 (p) cc_final: 0.8967 (p)
REVERT: A   90 ARG cc_start: 0.8125 (mmm-85) cc_final: 0.7735 (mmm-85)
REVERT: A  121 ASN cc_start: 0.9022 (t0) cc_final: 0.8679 (t0)
REVERT: A  213 ARG cc_start: 0.8030 (ptt180) cc_final: 0.7503 (ptt180)
REVERT: A  216 LYS cc_start: 0.9227 (mmtt) cc_final: 0.9006 (mmtt)
REVERT: A  284 MET cc_start: 0.8927 (mmt) cc_final: 0.8437 (mmt)
REVERT: A  311 LYS cc_start: 0.9465 (tttt) cc_final: 0.8967 (tttm)
REVERT: A  317 ASP cc_start: 0.8409 (t0) cc_final: 0.7998 (t0)
REVERT: A  356 ASP cc_start: 0.8960 (t0) cc_final: 0.7970 (t0)
REVERT: A  359 ILE cc_start: 0.9289 (mt) cc_final: 0.9046 (mm)
REVERT: A  362 VAL cc_start: 0.9422 (t) cc_final: 0.9195 (m)
REVERT: A  385 ASP cc_start: 0.9186 (p0) cc_final: 0.8954 (p0)
REVERT: A  407 ILE cc_start: 0.8321 (pt) cc_final: 0.8112 (mt)
REVERT: B   48 TRP cc_start: 0.9173 (m100) cc_final: 0.8884 (m100)
REVERT: B   83 ASP cc_start: 0.9176 (t0) cc_final: 0.8684 (t0)
REVERT: B  164 MET cc_start: 0.8164 (tpp) cc_final: 0.7581 (tpp)
REVERT: B  249 LYS cc_start: 0.8531 (mtmt) cc_final: 0.8267 (mtpt)
REVERT: B  268 LYS cc_start: 0.8960 (mtpt) cc_final: 0.8593 (mtpt)
REVERT: B  289 LEU cc_start: 0.9007 (mm) cc_final: 0.8653 (mm)
REVERT: C   40 MET cc_start: 0.8548 (ttm) cc_final: 0.8202 (ttt)
REVERT: C   63 LEU cc_start: 0.8144 (mt) cc_final: 0.7943 (mp)
REVERT: C   75 VAL cc_start: 0.9065 (t) cc_final: 0.8785 (t)
REVERT: C   97 GLU cc_start: 0.8356 (tt0) cc_final: 0.8081 (tt0)
REVERT: C  143 ASP cc_start: 0.8140 (t70) cc_final: 0.7564 (t0)
REVERT: C  145 TRP cc_start: 0.9421 (t60) cc_final: 0.9195 (t60)
REVERT: C  234 GLN cc_start: 0.8676 (mt0) cc_final: 0.8183 (mp-120)
REVERT: C  241 TRP cc_start: 0.8502 (m100) cc_final: 0.8267 (m100)
REVERT: C  284 MET cc_start: 0.9348 (mmp) cc_final: 0.9061 (mmt)
REVERT: C  359 ILE cc_start: 0.9341 (mt) cc_final: 0.9047 (mm)
REVERT: C  389 ASN cc_start: 0.9260 (m-40) cc_final: 0.8440 (m110)
REVERT: D   44 SER cc_start: 0.8770 (t) cc_final: 0.8430 (p)
REVERT: D   85 ASP cc_start: 0.8904 (t0) cc_final: 0.8623 (t0)
REVERT: D  118 LYS cc_start: 0.8906 (tppt) cc_final: 0.8319 (ttmt)
REVERT: D  163 ASP cc_start: 0.8587 (t0) cc_final: 0.8205 (t0)
REVERT: D  173 GLN cc_start: 0.7861 (tt0) cc_final: 0.7173 (tm-30)
REVERT: D  174 ASP cc_start: 0.8775 (m-30) cc_final: 0.8527 (m-30)
REVERT: D  216 LYS cc_start: 0.9265 (mmtt) cc_final: 0.8674 (mmmt)
REVERT: D  241 TRP cc_start: 0.7693 (m100) cc_final: 0.7296 (m100)
REVERT: D  243 LEU cc_start: 0.8267 (mt) cc_final: 0.7963 (mt)
REVERT: D  253 ASP cc_start: 0.7684 (t0) cc_final: 0.7459 (t0)
REVERT: D  279 LYS cc_start: 0.8104 (mttt) cc_final: 0.7742 (mmmt)
REVERT: D  292 ASP cc_start: 0.9123 (p0) cc_final: 0.8486 (p0)
REVERT: D  338 MET cc_start: 0.7075 (mmt) cc_final: 0.6691 (mmm)
REVERT: D  349 ARG cc_start: 0.8759 (ttm-80) cc_final: 0.8495 (mtt-85)
REVERT: D  357 ASP cc_start: 0.8641 (t70) cc_final: 0.8214 (t70)
REVERT: D  371 GLU cc_start: 0.8784 (pp20) cc_final: 0.8174 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 564
  average time/residue: 0.2140
  time to fit residues: 174.1518
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  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 136 optimal weight:   30.0000
   chunk 74 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 8 optimal weight:    9.9990
   chunk 135 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 31 optimal weight:    7.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  54 HIS
** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 428 GLN
B  54 HIS
B 370 HIS
B 389 ASN
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 305 HIS
D 364 GLN
** 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 = 0.3225 r_free = 0.3225 target = 0.121877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.102605 restraints weight = 18947.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.106014 restraints weight = 9829.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.108304 restraints weight = 6141.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.3572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  12324  Z= 0.156
  Angle     :  0.601   7.634  16768  Z= 0.327
  Chirality :  0.044   0.186   1940
  Planarity :  0.005   0.061   2200
  Dihedral  :  5.893  49.481   1680
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.20), residues: 1568
  helix: -0.60 (0.30), residues: 266
  sheet:  0.29 (0.25), residues: 418
  loop : -0.86 (0.20), residues: 884

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C  48 
 HIS   0.004   0.001   HIS D 305 
 PHE   0.016   0.002   PHE B 170 
 TYR   0.021   0.002   TYR D 100 
 ARG   0.008   0.001   ARG C 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05195 (  385)
  hydrogen bonds       : angle       5.22507 ( 1011)
  covalent geometry    : bond        0.00358 (12324)
  covalent geometry    : angle       0.60130 (16768)

*********************** 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
  541 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 541
  time to evaluate  : 1.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASN cc_start: 0.8998 (t0) cc_final: 0.8663 (t0)
REVERT: A  213 ARG cc_start: 0.7854 (ptt180) cc_final: 0.7519 (ptt180)
REVERT: A  216 LYS cc_start: 0.9275 (mmtt) cc_final: 0.9055 (mmtt)
REVERT: A  284 MET cc_start: 0.8832 (mmt) cc_final: 0.8368 (mmt)
REVERT: A  311 LYS cc_start: 0.9488 (tttt) cc_final: 0.8999 (tttm)
REVERT: A  317 ASP cc_start: 0.8413 (t0) cc_final: 0.8068 (t0)
REVERT: A  385 ASP cc_start: 0.9242 (p0) cc_final: 0.9000 (p0)
REVERT: B   48 TRP cc_start: 0.9163 (m100) cc_final: 0.8857 (m100)
REVERT: B  249 LYS cc_start: 0.8503 (mtmt) cc_final: 0.8229 (mtpp)
REVERT: B  268 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8646 (mtpt)
REVERT: B  289 LEU cc_start: 0.9077 (mm) cc_final: 0.8576 (mm)
REVERT: B  338 MET cc_start: 0.8613 (mmm) cc_final: 0.7871 (tpp)
REVERT: B  349 ARG cc_start: 0.8821 (ttm-80) cc_final: 0.8574 (ttt-90)
REVERT: C   40 MET cc_start: 0.8297 (ttm) cc_final: 0.7755 (ttt)
REVERT: C   71 LEU cc_start: 0.8576 (tp) cc_final: 0.8236 (tt)
REVERT: C   97 GLU cc_start: 0.8371 (tt0) cc_final: 0.8164 (tt0)
REVERT: C  159 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7848 (mt-10)
REVERT: C  357 ASP cc_start: 0.8614 (t0) cc_final: 0.8395 (t0)
REVERT: C  359 ILE cc_start: 0.9258 (mt) cc_final: 0.8956 (mm)
REVERT: C  376 MET cc_start: 0.7247 (ttm) cc_final: 0.7013 (ttm)
REVERT: C  389 ASN cc_start: 0.9294 (m-40) cc_final: 0.8850 (m110)
REVERT: D   44 SER cc_start: 0.8647 (t) cc_final: 0.8299 (p)
REVERT: D   66 LYS cc_start: 0.7146 (mmtm) cc_final: 0.6507 (tppt)
REVERT: D   71 LEU cc_start: 0.7316 (tp) cc_final: 0.7076 (tp)
REVERT: D   85 ASP cc_start: 0.8720 (t0) cc_final: 0.8501 (t0)
REVERT: D   96 ASP cc_start: 0.8330 (t0) cc_final: 0.7557 (m-30)
REVERT: D  118 LYS cc_start: 0.8868 (tppt) cc_final: 0.8274 (ttmm)
REVERT: D  216 LYS cc_start: 0.9135 (mmtt) cc_final: 0.8203 (mmmt)
REVERT: D  241 TRP cc_start: 0.7819 (m100) cc_final: 0.7558 (m100)
REVERT: D  279 LYS cc_start: 0.7899 (mttt) cc_final: 0.7471 (mmmt)
REVERT: D  292 ASP cc_start: 0.9027 (p0) cc_final: 0.8413 (p0)
REVERT: D  338 MET cc_start: 0.7172 (mmt) cc_final: 0.6724 (mmm)
REVERT: D  349 ARG cc_start: 0.8766 (ttm-80) cc_final: 0.8383 (ttm-80)
REVERT: D  357 ASP cc_start: 0.8619 (t70) cc_final: 0.8101 (t70)
REVERT: D  371 GLU cc_start: 0.8868 (pp20) cc_final: 0.8522 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 541
  average time/residue: 0.2073
  time to fit residues: 164.3233
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  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 99 optimal weight:    8.9990
   chunk 135 optimal weight:   10.0000
   chunk 62 optimal weight:    8.9990
   chunk 29 optimal weight:    7.9990
   chunk 143 optimal weight:    9.9990
   chunk 55 optimal weight:    6.9990
   chunk 86 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 141 optimal weight:    7.9990
   chunk 112 optimal weight:    3.9990
   chunk 13 optimal weight:   20.0000
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  74 ASN
** A  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 283 GLN
B  74 ASN
B  84 ASN
C  74 ASN
C  88 GLN
C 161 ASN
C 344 ASN
C 414 ASN
D  74 ASN
D 251 ASN
D 364 GLN
** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.119171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.100615 restraints weight = 18883.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.103725 restraints weight = 10196.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.105951 restraints weight = 6513.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.3838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  12324  Z= 0.251
  Angle     :  0.685   8.849  16768  Z= 0.370
  Chirality :  0.046   0.183   1940
  Planarity :  0.005   0.057   2200
  Dihedral  :  6.068  43.876   1680
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.20), residues: 1568
  helix: -0.72 (0.30), residues: 260
  sheet:  0.09 (0.25), residues: 428
  loop : -0.98 (0.20), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP C 410 
 HIS   0.004   0.001   HIS D  43 
 PHE   0.019   0.002   PHE B  86 
 TYR   0.021   0.002   TYR C 100 
 ARG   0.011   0.001   ARG B 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06007 (  385)
  hydrogen bonds       : angle       5.53718 ( 1011)
  covalent geometry    : bond        0.00586 (12324)
  covalent geometry    : angle       0.68532 (16768)

*********************** 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
  516 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 516
  time to evaluate  : 1.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8995 (tttm) cc_final: 0.8708 (tttm)
REVERT: A  121 ASN cc_start: 0.9013 (t0) cc_final: 0.8722 (t0)
REVERT: A  311 LYS cc_start: 0.9496 (tttt) cc_final: 0.8982 (tttm)
REVERT: A  385 ASP cc_start: 0.9352 (p0) cc_final: 0.9130 (p0)
REVERT: B   15 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8053 (mm-30)
REVERT: B   73 LEU cc_start: 0.9267 (mt) cc_final: 0.9023 (mt)
REVERT: B  268 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8651 (mtpt)
REVERT: B  349 ARG cc_start: 0.8927 (ttm-80) cc_final: 0.8666 (ttt-90)
REVERT: B  410 TRP cc_start: 0.9267 (t60) cc_final: 0.8971 (t60)
REVERT: C  327 TYR cc_start: 0.8717 (m-80) cc_final: 0.8302 (m-10)
REVERT: C  359 ILE cc_start: 0.9406 (mt) cc_final: 0.9110 (mm)
REVERT: C  395 GLN cc_start: 0.9484 (tp40) cc_final: 0.9232 (tp40)
REVERT: D   40 MET cc_start: 0.8855 (mtm) cc_final: 0.8605 (mtm)
REVERT: D   42 ARG cc_start: 0.7551 (mmt180) cc_final: 0.7289 (mmt180)
REVERT: D   44 SER cc_start: 0.8549 (t) cc_final: 0.8054 (p)
REVERT: D   96 ASP cc_start: 0.8508 (t0) cc_final: 0.8002 (m-30)
REVERT: D  116 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8239 (tm-30)
REVERT: D  118 LYS cc_start: 0.8895 (tppt) cc_final: 0.8339 (ttmt)
REVERT: D  253 ASP cc_start: 0.8149 (t0) cc_final: 0.7906 (t0)
REVERT: D  279 LYS cc_start: 0.7733 (mttt) cc_final: 0.7423 (mmtt)
REVERT: D  292 ASP cc_start: 0.9080 (p0) cc_final: 0.8382 (p0)
REVERT: D  338 MET cc_start: 0.7452 (mmt) cc_final: 0.7068 (mmm)
REVERT: D  349 ARG cc_start: 0.8786 (ttm-80) cc_final: 0.8193 (ttt90)
REVERT: D  357 ASP cc_start: 0.8688 (t70) cc_final: 0.8134 (t70)
REVERT: D  370 HIS cc_start: 0.8769 (m-70) cc_final: 0.8382 (m90)
REVERT: D  371 GLU cc_start: 0.8919 (pp20) cc_final: 0.8476 (pp20)
REVERT: D  407 ILE cc_start: 0.8214 (pt) cc_final: 0.7718 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 516
  average time/residue: 0.2084
  time to fit residues: 157.7600
Evaluate side-chains
  479 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 479
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 48 optimal weight:    8.9990
   chunk 89 optimal weight:    5.9990
   chunk 130 optimal weight:   20.0000
   chunk 75 optimal weight:   10.0000
   chunk 87 optimal weight:    8.9990
   chunk 14 optimal weight:    7.9990
   chunk 47 optimal weight:    5.9990
   chunk 139 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 97 optimal weight:    0.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
A 251 ASN
** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
B 364 GLN
C  84 ASN
C  88 GLN
D 324 GLN
** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 428 GLN

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 = 0.119795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.100414 restraints weight = 18976.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.103830 restraints weight = 9774.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.106196 restraints weight = 6110.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.4144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  12324  Z= 0.217
  Angle     :  0.638   7.429  16768  Z= 0.344
  Chirality :  0.045   0.197   1940
  Planarity :  0.005   0.050   2200
  Dihedral  :  5.845  48.142   1680
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.92 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.20), residues: 1568
  helix: -0.68 (0.30), residues: 266
  sheet:  0.09 (0.25), residues: 422
  loop : -1.03 (0.20), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.003   TRP A 410 
 HIS   0.004   0.001   HIS B 370 
 PHE   0.031   0.002   PHE B 156 
 TYR   0.019   0.002   TYR C 100 
 ARG   0.007   0.001   ARG B 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05546 (  385)
  hydrogen bonds       : angle       5.40538 ( 1011)
  covalent geometry    : bond        0.00508 (12324)
  covalent geometry    : angle       0.63781 (16768)

*********************** 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
  542 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 541
  time to evaluate  : 1.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.9016 (tttm) cc_final: 0.8690 (tttm)
REVERT: A  121 ASN cc_start: 0.8961 (t0) cc_final: 0.8694 (t0)
REVERT: A  126 MET cc_start: 0.8977 (ttp) cc_final: 0.8752 (ttm)
REVERT: A  164 MET cc_start: 0.6904 (mpp) cc_final: 0.5681 (mpp)
REVERT: A  311 LYS cc_start: 0.9497 (tttt) cc_final: 0.9120 (tttm)
REVERT: A  317 ASP cc_start: 0.8513 (t0) cc_final: 0.8295 (t0)
REVERT: B   15 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8112 (mm-30)
REVERT: B   49 MET cc_start: 0.8215 (ptm) cc_final: 0.7958 (ptm)
REVERT: B   84 ASN cc_start: 0.8522 (m-40) cc_final: 0.8312 (m-40)
REVERT: B  162 ARG cc_start: 0.8945 (tpp80) cc_final: 0.8653 (mmt90)
REVERT: B  164 MET cc_start: 0.7995 (mmm) cc_final: 0.7189 (tpp)
REVERT: B  268 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8640 (mtpt)
REVERT: B  274 SER cc_start: 0.9171 (t) cc_final: 0.8913 (t)
REVERT: B  338 MET cc_start: 0.8516 (mmm) cc_final: 0.8241 (tpp)
REVERT: B  349 ARG cc_start: 0.9048 (ttm-80) cc_final: 0.8826 (ttt-90)
REVERT: B  363 SER cc_start: 0.8378 (t) cc_final: 0.7989 (t)
REVERT: C   26 MET cc_start: 0.8720 (mmm) cc_final: 0.8033 (mmm)
REVERT: C   63 LEU cc_start: 0.8126 (mt) cc_final: 0.7908 (mp)
REVERT: C  169 PHE cc_start: 0.9299 (m-80) cc_final: 0.8754 (m-10)
REVERT: C  327 TYR cc_start: 0.8734 (m-80) cc_final: 0.8355 (m-10)
REVERT: C  359 ILE cc_start: 0.9301 (mt) cc_final: 0.9008 (mm)
REVERT: D   40 MET cc_start: 0.8933 (mtm) cc_final: 0.8713 (mtm)
REVERT: D   42 ARG cc_start: 0.7575 (mmt180) cc_final: 0.7153 (mmt180)
REVERT: D   44 SER cc_start: 0.8470 (t) cc_final: 0.8071 (p)
REVERT: D   66 LYS cc_start: 0.7376 (mmtm) cc_final: 0.6745 (tppt)
REVERT: D  116 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8314 (tm-30)
REVERT: D  118 LYS cc_start: 0.8725 (tppt) cc_final: 0.8109 (ttmt)
REVERT: D  241 TRP cc_start: 0.7978 (m100) cc_final: 0.7734 (m100)
REVERT: D  253 ASP cc_start: 0.8364 (t0) cc_final: 0.8135 (t0)
REVERT: D  279 LYS cc_start: 0.7613 (mttt) cc_final: 0.7365 (mmtt)
REVERT: D  292 ASP cc_start: 0.8949 (p0) cc_final: 0.8213 (p0)
REVERT: D  338 MET cc_start: 0.7477 (mmt) cc_final: 0.7086 (mmm)
REVERT: D  349 ARG cc_start: 0.8779 (ttm-80) cc_final: 0.8175 (ttt90)
REVERT: D  357 ASP cc_start: 0.8733 (t70) cc_final: 0.8154 (t70)
REVERT: D  370 HIS cc_start: 0.8796 (m-70) cc_final: 0.8376 (m90)
REVERT: D  371 GLU cc_start: 0.8982 (pp20) cc_final: 0.8418 (pp20)
REVERT: D  407 ILE cc_start: 0.8087 (pt) cc_final: 0.7634 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 541
  average time/residue: 0.2138
  time to fit residues: 169.1233
Evaluate side-chains
  480 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 480
  time to evaluate  : 1.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 121 optimal weight:   40.0000
   chunk 136 optimal weight:   40.0000
   chunk 126 optimal weight:    0.3980
   chunk 142 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 39 optimal weight:   10.0000
   chunk 71 optimal weight:    8.9990
   chunk 117 optimal weight:    6.9990
   overall best weight:    2.8788

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

Flipped N/Q/H residues before XYZ refinement:
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 ASN
C  88 GLN
C 161 ASN
D  74 ASN
D 324 GLN
** 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 = 0.122733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.103201 restraints weight = 18928.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.106683 restraints weight = 9853.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.109065 restraints weight = 6177.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.4375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12324  Z= 0.129
  Angle     :  0.575   9.544  16768  Z= 0.308
  Chirality :  0.043   0.209   1940
  Planarity :  0.004   0.050   2200
  Dihedral  :  5.423  53.965   1680
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.62 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.20), residues: 1568
  helix: -0.21 (0.31), residues: 268
  sheet:  0.33 (0.25), residues: 408
  loop : -1.09 (0.20), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 410 
 HIS   0.003   0.001   HIS D 287 
 PHE   0.015   0.001   PHE C 147 
 TYR   0.016   0.002   TYR B 175 
 ARG   0.007   0.000   ARG C  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04643 (  385)
  hydrogen bonds       : angle       5.09310 ( 1011)
  covalent geometry    : bond        0.00293 (12324)
  covalent geometry    : angle       0.57504 (16768)

*********************** 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
  548 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 546
  time to evaluate  : 1.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8947 (tttm) cc_final: 0.8719 (tttm)
REVERT: A   46 THR cc_start: 0.9143 (p) cc_final: 0.8918 (t)
REVERT: A   49 MET cc_start: 0.8253 (mtp) cc_final: 0.7961 (mtp)
REVERT: A  121 ASN cc_start: 0.8905 (t0) cc_final: 0.8652 (t0)
REVERT: A  311 LYS cc_start: 0.9525 (tttt) cc_final: 0.9149 (tttm)
REVERT: A  317 ASP cc_start: 0.8455 (t0) cc_final: 0.8215 (t0)
REVERT: A  385 ASP cc_start: 0.9353 (p0) cc_final: 0.9035 (p0)
REVERT: B   15 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7854 (mm-30)
REVERT: B   49 MET cc_start: 0.8142 (ptm) cc_final: 0.7797 (ptm)
REVERT: B  162 ARG cc_start: 0.8834 (tpp80) cc_final: 0.8524 (mmt90)
REVERT: B  164 MET cc_start: 0.7864 (mmm) cc_final: 0.7091 (tpp)
REVERT: B  268 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8622 (mtpt)
REVERT: B  289 LEU cc_start: 0.8818 (mm) cc_final: 0.8541 (mm)
REVERT: B  317 ASP cc_start: 0.8933 (t0) cc_final: 0.8462 (t0)
REVERT: B  320 LEU cc_start: 0.9360 (mp) cc_final: 0.8933 (mp)
REVERT: B  338 MET cc_start: 0.8315 (mmm) cc_final: 0.7912 (mtp)
REVERT: B  349 ARG cc_start: 0.9101 (ttm-80) cc_final: 0.8728 (ttt-90)
REVERT: C   26 MET cc_start: 0.8511 (mmm) cc_final: 0.7951 (mmm)
REVERT: C   71 LEU cc_start: 0.8505 (tp) cc_final: 0.8064 (tt)
REVERT: C  145 TRP cc_start: 0.9241 (t60) cc_final: 0.8996 (t60)
REVERT: C  169 PHE cc_start: 0.9232 (m-80) cc_final: 0.8558 (m-10)
REVERT: C  234 GLN cc_start: 0.8855 (mt0) cc_final: 0.8398 (mp10)
REVERT: C  327 TYR cc_start: 0.8681 (m-80) cc_final: 0.8138 (m-10)
REVERT: C  359 ILE cc_start: 0.9267 (mt) cc_final: 0.9006 (mm)
REVERT: D    5 GLU cc_start: 0.7728 (mp0) cc_final: 0.7285 (mp0)
REVERT: D   42 ARG cc_start: 0.7559 (mmt180) cc_final: 0.7056 (mmt180)
REVERT: D   44 SER cc_start: 0.8349 (t) cc_final: 0.8029 (p)
REVERT: D   66 LYS cc_start: 0.7346 (mmtm) cc_final: 0.6743 (tppt)
REVERT: D   84 ASN cc_start: 0.7854 (p0) cc_final: 0.7534 (p0)
REVERT: D  116 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8276 (tm-30)
REVERT: D  118 LYS cc_start: 0.8758 (tppt) cc_final: 0.8243 (ttmt)
REVERT: D  177 LYS cc_start: 0.9207 (mmmm) cc_final: 0.8876 (mttp)
REVERT: D  241 TRP cc_start: 0.7959 (m100) cc_final: 0.7710 (m100)
REVERT: D  279 LYS cc_start: 0.7562 (mttt) cc_final: 0.7285 (mmtt)
REVERT: D  281 LEU cc_start: 0.8051 (mp) cc_final: 0.7798 (mp)
REVERT: D  292 ASP cc_start: 0.8901 (p0) cc_final: 0.8166 (p0)
REVERT: D  324 GLN cc_start: 0.8820 (mt0) cc_final: 0.8090 (mp10)
REVERT: D  338 MET cc_start: 0.7707 (mmt) cc_final: 0.7396 (mmm)
REVERT: D  349 ARG cc_start: 0.8709 (ttm-80) cc_final: 0.8413 (ttm-80)
REVERT: D  357 ASP cc_start: 0.8767 (t70) cc_final: 0.8179 (t70)
REVERT: D  370 HIS cc_start: 0.8745 (m-70) cc_final: 0.8299 (m90)
REVERT: D  371 GLU cc_start: 0.8935 (pp20) cc_final: 0.8386 (pp20)
REVERT: D  407 ILE cc_start: 0.7993 (pt) cc_final: 0.7613 (mt)
  outliers start: 2
  outliers final: 1
  residues processed: 547
  average time/residue: 0.2023
  time to fit residues: 163.6629
Evaluate side-chains
  484 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 483
  time to evaluate  : 1.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 34 optimal weight:    9.9990
   chunk 122 optimal weight:    0.0370
   chunk 79 optimal weight:    1.9990
   chunk 126 optimal weight:    7.9990
   chunk 149 optimal weight:    4.9990
   chunk 13 optimal weight:   20.0000
   chunk 10 optimal weight:    6.9990
   chunk 128 optimal weight:   10.0000
   overall best weight:    3.2066

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

Flipped N/Q/H residues before XYZ refinement:
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  88 GLN
C 395 GLN
** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 428 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.123297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.103725 restraints weight = 18825.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.107185 restraints weight = 9745.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.109617 restraints weight = 6099.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.4504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12324  Z= 0.135
  Angle     :  0.574   7.352  16768  Z= 0.306
  Chirality :  0.043   0.215   1940
  Planarity :  0.004   0.056   2200
  Dihedral  :  5.301  54.776   1680
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.20), residues: 1568
  helix: -0.09 (0.31), residues: 272
  sheet:  0.31 (0.26), residues: 410
  loop : -1.06 (0.20), residues: 886

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 410 
 HIS   0.003   0.001   HIS D 287 
 PHE   0.028   0.002   PHE B 156 
 TYR   0.020   0.002   TYR D 100 
 ARG   0.008   0.000   ARG C  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04653 (  385)
  hydrogen bonds       : angle       5.05250 ( 1011)
  covalent geometry    : bond        0.00313 (12324)
  covalent geometry    : angle       0.57397 (16768)

*********************** 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
  550 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 550
  time to evaluate  : 1.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.9002 (tttm) cc_final: 0.8704 (tttm)
REVERT: A   49 MET cc_start: 0.8281 (mtp) cc_final: 0.8007 (mtp)
REVERT: A  121 ASN cc_start: 0.8902 (t0) cc_final: 0.7532 (t0)
REVERT: A  125 GLU cc_start: 0.7740 (mt-10) cc_final: 0.6798 (mt-10)
REVERT: A  311 LYS cc_start: 0.9526 (tttt) cc_final: 0.9137 (tttm)
REVERT: A  317 ASP cc_start: 0.8467 (t0) cc_final: 0.8197 (t0)
REVERT: A  385 ASP cc_start: 0.9393 (p0) cc_final: 0.9189 (p0)
REVERT: B   15 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7818 (mm-30)
REVERT: B  118 LYS cc_start: 0.9257 (tppp) cc_final: 0.8923 (ttpt)
REVERT: B  162 ARG cc_start: 0.8795 (tpp80) cc_final: 0.8589 (mmt90)
REVERT: B  164 MET cc_start: 0.7868 (mmm) cc_final: 0.7372 (tpp)
REVERT: B  268 LYS cc_start: 0.8919 (mtpt) cc_final: 0.8616 (mtpt)
REVERT: B  289 LEU cc_start: 0.8862 (mm) cc_final: 0.8549 (mm)
REVERT: B  317 ASP cc_start: 0.8947 (t0) cc_final: 0.8441 (t0)
REVERT: B  320 LEU cc_start: 0.9367 (mp) cc_final: 0.8924 (mp)
REVERT: B  338 MET cc_start: 0.8245 (mmm) cc_final: 0.7909 (mtp)
REVERT: B  349 ARG cc_start: 0.9120 (ttm-80) cc_final: 0.8837 (ttt-90)
REVERT: C   26 MET cc_start: 0.8546 (mmm) cc_final: 0.8033 (mmm)
REVERT: C   71 LEU cc_start: 0.8549 (tp) cc_final: 0.8156 (tt)
REVERT: C  159 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7928 (mt-10)
REVERT: C  169 PHE cc_start: 0.9215 (m-80) cc_final: 0.8569 (m-10)
REVERT: C  279 LYS cc_start: 0.8218 (mmtt) cc_final: 0.8003 (mmtt)
REVERT: C  327 TYR cc_start: 0.8702 (m-80) cc_final: 0.8324 (m-10)
REVERT: C  359 ILE cc_start: 0.9293 (mt) cc_final: 0.8999 (mm)
REVERT: D    5 GLU cc_start: 0.7884 (mp0) cc_final: 0.7382 (mp0)
REVERT: D   42 ARG cc_start: 0.7591 (mmt180) cc_final: 0.7069 (mmt180)
REVERT: D   44 SER cc_start: 0.8312 (t) cc_final: 0.7938 (p)
REVERT: D   66 LYS cc_start: 0.7384 (mmtm) cc_final: 0.6756 (tppt)
REVERT: D  116 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8228 (tm-30)
REVERT: D  118 LYS cc_start: 0.8779 (tppt) cc_final: 0.8217 (ttmt)
REVERT: D  173 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8328 (tm-30)
REVERT: D  174 ASP cc_start: 0.8801 (m-30) cc_final: 0.8431 (m-30)
REVERT: D  177 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8923 (mtpp)
REVERT: D  241 TRP cc_start: 0.7986 (m100) cc_final: 0.7712 (m100)
REVERT: D  279 LYS cc_start: 0.7551 (mttt) cc_final: 0.7251 (mmtt)
REVERT: D  281 LEU cc_start: 0.8050 (mp) cc_final: 0.7789 (mp)
REVERT: D  292 ASP cc_start: 0.8953 (p0) cc_final: 0.8282 (p0)
REVERT: D  338 MET cc_start: 0.7652 (mmt) cc_final: 0.7261 (mmm)
REVERT: D  349 ARG cc_start: 0.8629 (ttm-80) cc_final: 0.8009 (ttt90)
REVERT: D  357 ASP cc_start: 0.8726 (t70) cc_final: 0.8130 (t70)
REVERT: D  370 HIS cc_start: 0.8759 (m-70) cc_final: 0.8255 (m90)
REVERT: D  371 GLU cc_start: 0.9012 (pp20) cc_final: 0.8417 (pp20)
REVERT: D  407 ILE cc_start: 0.8031 (pt) cc_final: 0.7636 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 550
  average time/residue: 0.2284
  time to fit residues: 187.2396
Evaluate side-chains
  485 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 485
  time to evaluate  : 1.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 73 optimal weight:    0.0470
   chunk 66 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 70 optimal weight:   10.0000
   chunk 155 optimal weight:    8.9990
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 77 optimal weight:    8.9990
   chunk 107 optimal weight:    7.9990
   chunk 3 optimal weight:    8.9990
   chunk 84 optimal weight:    8.9990
   overall best weight:    3.6086

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

Flipped N/Q/H residues before XYZ refinement:
A 234 GLN
** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
C  84 ASN
C  88 GLN
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 395 GLN
D 113 ASN
D 324 GLN
D 395 GLN
** 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 = 0.3247 r_free = 0.3247 target = 0.123103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.103532 restraints weight = 19068.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.107012 restraints weight = 9896.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.109372 restraints weight = 6193.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.4582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12324  Z= 0.147
  Angle     :  0.590  11.249  16768  Z= 0.313
  Chirality :  0.043   0.224   1940
  Planarity :  0.004   0.055   2200
  Dihedral  :  5.285  54.944   1680
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.21), residues: 1568
  helix:  0.01 (0.31), residues: 266
  sheet:  0.23 (0.26), residues: 414
  loop : -1.01 (0.20), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP D 354 
 HIS   0.003   0.001   HIS D 287 
 PHE   0.021   0.001   PHE B  86 
 TYR   0.023   0.002   TYR B 100 
 ARG   0.008   0.000   ARG C  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04780 (  385)
  hydrogen bonds       : angle       5.06785 ( 1011)
  covalent geometry    : bond        0.00341 (12324)
  covalent geometry    : angle       0.59030 (16768)

*********************** 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
  543 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 543
  time to evaluate  : 1.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 MET cc_start: 0.8310 (mtp) cc_final: 0.8040 (mtp)
REVERT: A  121 ASN cc_start: 0.8892 (t0) cc_final: 0.7545 (t0)
REVERT: A  125 GLU cc_start: 0.7858 (mt-10) cc_final: 0.6926 (mt-10)
REVERT: A  311 LYS cc_start: 0.9522 (tttt) cc_final: 0.9027 (tttm)
REVERT: A  317 ASP cc_start: 0.8489 (t0) cc_final: 0.8218 (t0)
REVERT: A  349 ARG cc_start: 0.8346 (ttt180) cc_final: 0.8138 (tpp-160)
REVERT: B   15 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7242 (mm-30)
REVERT: B  118 LYS cc_start: 0.9188 (tppp) cc_final: 0.8848 (ttpt)
REVERT: B  162 ARG cc_start: 0.8852 (tpp80) cc_final: 0.8631 (mmt90)
REVERT: B  164 MET cc_start: 0.7881 (mmm) cc_final: 0.7413 (tpp)
REVERT: B  268 LYS cc_start: 0.8941 (mtpt) cc_final: 0.8643 (mtpt)
REVERT: B  317 ASP cc_start: 0.8953 (t0) cc_final: 0.8392 (t0)
REVERT: B  320 LEU cc_start: 0.9359 (mp) cc_final: 0.8889 (mp)
REVERT: B  338 MET cc_start: 0.8235 (mmm) cc_final: 0.7916 (mtp)
REVERT: B  349 ARG cc_start: 0.9118 (ttm-80) cc_final: 0.8865 (ttt-90)
REVERT: B  376 MET cc_start: 0.7726 (ttm) cc_final: 0.7491 (ttm)
REVERT: C   26 MET cc_start: 0.8567 (mmm) cc_final: 0.8041 (mmm)
REVERT: C  159 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7789 (mt-10)
REVERT: C  169 PHE cc_start: 0.9176 (m-80) cc_final: 0.8551 (m-10)
REVERT: C  234 GLN cc_start: 0.8879 (mt0) cc_final: 0.8397 (mp10)
REVERT: C  279 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7875 (mmtt)
REVERT: C  292 ASP cc_start: 0.8950 (m-30) cc_final: 0.8645 (m-30)
REVERT: C  359 ILE cc_start: 0.9276 (mt) cc_final: 0.8970 (mm)
REVERT: D    5 GLU cc_start: 0.7835 (mp0) cc_final: 0.7335 (mp0)
REVERT: D   42 ARG cc_start: 0.7492 (mmt180) cc_final: 0.6887 (mmt180)
REVERT: D   44 SER cc_start: 0.8379 (t) cc_final: 0.8031 (p)
REVERT: D   66 LYS cc_start: 0.7400 (mmtm) cc_final: 0.6760 (tppt)
REVERT: D  116 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8247 (tm-30)
REVERT: D  118 LYS cc_start: 0.8764 (tppt) cc_final: 0.8216 (ttmm)
REVERT: D  177 LYS cc_start: 0.9206 (mmmm) cc_final: 0.8936 (mttp)
REVERT: D  216 LYS cc_start: 0.8760 (mmmt) cc_final: 0.8254 (mmtt)
REVERT: D  241 TRP cc_start: 0.7996 (m100) cc_final: 0.7719 (m100)
REVERT: D  242 GLN cc_start: 0.7566 (tm-30) cc_final: 0.7143 (tm-30)
REVERT: D  279 LYS cc_start: 0.7528 (mttt) cc_final: 0.7208 (mmtt)
REVERT: D  281 LEU cc_start: 0.8056 (mp) cc_final: 0.7783 (mp)
REVERT: D  292 ASP cc_start: 0.8928 (p0) cc_final: 0.8255 (p0)
REVERT: D  324 GLN cc_start: 0.8760 (mt0) cc_final: 0.8184 (mp10)
REVERT: D  349 ARG cc_start: 0.8611 (ttm-80) cc_final: 0.8009 (ttt90)
REVERT: D  370 HIS cc_start: 0.8784 (m-70) cc_final: 0.8258 (m90)
REVERT: D  371 GLU cc_start: 0.8971 (pp20) cc_final: 0.8404 (pp20)
REVERT: D  385 ASP cc_start: 0.8078 (t0) cc_final: 0.7619 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 543
  average time/residue: 0.2293
  time to fit residues: 183.8945
Evaluate side-chains
  488 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 488
  time to evaluate  : 1.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 125 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 106 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 149 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 147 optimal weight:    0.6980
   chunk 107 optimal weight:    5.9990
   chunk 59 optimal weight:    0.2980
   chunk 48 optimal weight:    3.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
A  28 GLN
A 242 GLN
B  74 ASN
C  88 GLN
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 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 = 0.3274 r_free = 0.3274 target = 0.125053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.105551 restraints weight = 18641.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.109172 restraints weight = 9519.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.111583 restraints weight = 5876.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.4737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12324  Z= 0.123
  Angle     :  0.591  11.641  16768  Z= 0.309
  Chirality :  0.043   0.232   1940
  Planarity :  0.004   0.055   2200
  Dihedral  :  5.139  56.700   1680
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.46 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.21), residues: 1568
  helix:  0.16 (0.31), residues: 268
  sheet:  0.24 (0.26), residues: 414
  loop : -0.97 (0.20), residues: 886

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 410 
 HIS   0.004   0.001   HIS D 287 
 PHE   0.019   0.001   PHE B  86 
 TYR   0.029   0.002   TYR D 100 
 ARG   0.009   0.000   ARG C  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04463 (  385)
  hydrogen bonds       : angle       4.99340 ( 1011)
  covalent geometry    : bond        0.00284 (12324)
  covalent geometry    : angle       0.59070 (16768)

*********************** 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
  541 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 540
  time to evaluate  : 1.837 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.9033 (tttm) cc_final: 0.8573 (ttpp)
REVERT: A   39 SER cc_start: 0.8877 (m) cc_final: 0.8345 (t)
REVERT: A  121 ASN cc_start: 0.8843 (t0) cc_final: 0.7432 (t0)
REVERT: A  125 GLU cc_start: 0.7852 (mt-10) cc_final: 0.6871 (mt-10)
REVERT: A  155 MET cc_start: 0.8838 (ttp) cc_final: 0.8568 (ttp)
REVERT: A  311 LYS cc_start: 0.9517 (tttt) cc_final: 0.9031 (tttm)
REVERT: A  317 ASP cc_start: 0.8454 (t0) cc_final: 0.8215 (t0)
REVERT: A  385 ASP cc_start: 0.9410 (p0) cc_final: 0.9154 (p0)
REVERT: B  162 ARG cc_start: 0.8802 (tpp80) cc_final: 0.8592 (mmt90)
REVERT: B  164 MET cc_start: 0.7871 (mmm) cc_final: 0.7356 (tpp)
REVERT: B  241 TRP cc_start: 0.8446 (p-90) cc_final: 0.8176 (p-90)
REVERT: B  268 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8619 (mtpt)
REVERT: B  291 GLN cc_start: 0.7946 (pm20) cc_final: 0.7655 (pm20)
REVERT: B  317 ASP cc_start: 0.8913 (t0) cc_final: 0.8309 (t0)
REVERT: B  320 LEU cc_start: 0.9357 (mp) cc_final: 0.8862 (mp)
REVERT: B  349 ARG cc_start: 0.9112 (ttm-80) cc_final: 0.8856 (ttt-90)
REVERT: B  376 MET cc_start: 0.7739 (ttm) cc_final: 0.7531 (ttm)
REVERT: C   26 MET cc_start: 0.8554 (mmm) cc_final: 0.8069 (mmm)
REVERT: C  143 ASP cc_start: 0.8381 (t0) cc_final: 0.8124 (t0)
REVERT: C  159 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7673 (mt-10)
REVERT: C  169 PHE cc_start: 0.9140 (m-80) cc_final: 0.8518 (m-10)
REVERT: C  234 GLN cc_start: 0.8843 (mt0) cc_final: 0.8371 (mp10)
REVERT: C  279 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7920 (mmtt)
REVERT: C  292 ASP cc_start: 0.8934 (m-30) cc_final: 0.8578 (m-30)
REVERT: C  359 ILE cc_start: 0.9259 (mt) cc_final: 0.8969 (mm)
REVERT: C  395 GLN cc_start: 0.9514 (tp-100) cc_final: 0.9311 (tp-100)
REVERT: D    5 GLU cc_start: 0.7770 (mp0) cc_final: 0.7262 (mp0)
REVERT: D   15 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8197 (mm-30)
REVERT: D   42 ARG cc_start: 0.7428 (mmt180) cc_final: 0.6888 (mmt180)
REVERT: D   44 SER cc_start: 0.8447 (t) cc_final: 0.8095 (p)
REVERT: D   66 LYS cc_start: 0.7407 (mmtm) cc_final: 0.6775 (tppt)
REVERT: D  116 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8106 (tm-30)
REVERT: D  118 LYS cc_start: 0.8805 (tppt) cc_final: 0.8228 (ttmm)
REVERT: D  177 LYS cc_start: 0.9258 (mmmm) cc_final: 0.9036 (mttp)
REVERT: D  216 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8294 (mmtt)
REVERT: D  241 TRP cc_start: 0.7996 (m100) cc_final: 0.7685 (m100)
REVERT: D  242 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7226 (tm-30)
REVERT: D  279 LYS cc_start: 0.7535 (mttt) cc_final: 0.7249 (mmtt)
REVERT: D  292 ASP cc_start: 0.8960 (p0) cc_final: 0.8287 (p0)
REVERT: D  349 ARG cc_start: 0.8602 (ttm-80) cc_final: 0.7899 (ttt90)
REVERT: D  370 HIS cc_start: 0.8758 (m-70) cc_final: 0.8313 (m90)
REVERT: D  371 GLU cc_start: 0.8962 (pp20) cc_final: 0.8416 (pp20)
REVERT: D  385 ASP cc_start: 0.8003 (t0) cc_final: 0.7557 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 540
  average time/residue: 0.2761
  time to fit residues: 217.9507
Evaluate side-chains
  494 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 493
  time to evaluate  : 1.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 134 optimal weight:    9.9990
   chunk 76 optimal weight:    9.9990
   chunk 13 optimal weight:   20.0000
   chunk 62 optimal weight:    0.9980
   chunk 140 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0470
   chunk 2 optimal weight:   10.0000
   overall best weight:    4.8084

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 ASN
A 234 GLN
** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 ASN
** B  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  74 ASN
C  88 GLN
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 ASN
** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 428 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.121953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.102278 restraints weight = 18879.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.105702 restraints weight = 9857.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.108120 restraints weight = 6192.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.4713

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= 0.185
  Angle     :  0.644  11.583  16768  Z= 0.338
  Chirality :  0.045   0.234   1940
  Planarity :  0.005   0.059   2200
  Dihedral  :  5.412  54.041   1680
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.46 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.21), residues: 1568
  helix:  0.11 (0.31), residues: 266
  sheet:  0.32 (0.26), residues: 406
  loop : -1.07 (0.20), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 410 
 HIS   0.005   0.001   HIS B 287 
 PHE   0.020   0.002   PHE B  86 
 TYR   0.032   0.002   TYR D 100 
 ARG   0.009   0.001   ARG C  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05188 (  385)
  hydrogen bonds       : angle       5.15069 ( 1011)
  covalent geometry    : bond        0.00433 (12324)
  covalent geometry    : angle       0.64414 (16768)

********************** 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
  537 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 536
  time to evaluate  : 1.289 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.9060 (tttm) cc_final: 0.8628 (ttpp)
REVERT: A   39 SER cc_start: 0.8814 (m) cc_final: 0.8334 (t)
REVERT: A  121 ASN cc_start: 0.8887 (t0) cc_final: 0.7359 (t0)
REVERT: A  125 GLU cc_start: 0.7915 (mt-10) cc_final: 0.6938 (mt-10)
REVERT: A  229 THR cc_start: 0.8433 (p) cc_final: 0.8192 (p)
REVERT: A  311 LYS cc_start: 0.9536 (tttt) cc_final: 0.9064 (tttm)
REVERT: A  317 ASP cc_start: 0.8483 (t0) cc_final: 0.8271 (t0)
REVERT: A  385 ASP cc_start: 0.9502 (p0) cc_final: 0.9208 (p0)
REVERT: B   26 MET cc_start: 0.8786 (mmm) cc_final: 0.8434 (mmt)
REVERT: B  164 MET cc_start: 0.7990 (mmm) cc_final: 0.7443 (tpp)
REVERT: B  241 TRP cc_start: 0.8509 (p-90) cc_final: 0.8263 (p-90)
REVERT: B  268 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8589 (mtpt)
REVERT: B  289 LEU cc_start: 0.8926 (mm) cc_final: 0.8644 (mm)
REVERT: B  317 ASP cc_start: 0.8921 (t0) cc_final: 0.8321 (t0)
REVERT: B  320 LEU cc_start: 0.9375 (mp) cc_final: 0.8898 (mp)
REVERT: B  349 ARG cc_start: 0.9125 (ttm-80) cc_final: 0.8916 (ttt180)
REVERT: B  376 MET cc_start: 0.7786 (ttm) cc_final: 0.7555 (ttm)
REVERT: C   26 MET cc_start: 0.8618 (mmm) cc_final: 0.8068 (mmm)
REVERT: C   81 GLU cc_start: 0.7887 (mp0) cc_final: 0.7666 (mp0)
REVERT: C  143 ASP cc_start: 0.8351 (t0) cc_final: 0.8089 (t0)
REVERT: C  159 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7852 (mt-10)
REVERT: C  169 PHE cc_start: 0.9166 (m-80) cc_final: 0.8576 (m-10)
REVERT: C  279 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7892 (mmtp)
REVERT: C  292 ASP cc_start: 0.9008 (m-30) cc_final: 0.8717 (m-30)
REVERT: C  344 ASN cc_start: 0.8445 (t0) cc_final: 0.8120 (t0)
REVERT: C  359 ILE cc_start: 0.9340 (mt) cc_final: 0.9042 (mm)
REVERT: C  395 GLN cc_start: 0.9532 (tp-100) cc_final: 0.9140 (tp-100)
REVERT: D   15 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8173 (mm-30)
REVERT: D   42 ARG cc_start: 0.7442 (mmt180) cc_final: 0.6917 (mmt180)
REVERT: D   44 SER cc_start: 0.8446 (t) cc_final: 0.8095 (p)
REVERT: D   66 LYS cc_start: 0.7425 (mmtm) cc_final: 0.6801 (tppt)
REVERT: D  116 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8230 (tm-30)
REVERT: D  118 LYS cc_start: 0.8892 (tppt) cc_final: 0.8371 (ttmm)
REVERT: D  173 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8259 (tm-30)
REVERT: D  174 ASP cc_start: 0.8767 (m-30) cc_final: 0.8423 (m-30)
REVERT: D  177 LYS cc_start: 0.9275 (mmmm) cc_final: 0.8999 (mttp)
REVERT: D  216 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8318 (mmtt)
REVERT: D  241 TRP cc_start: 0.8106 (m100) cc_final: 0.7814 (m100)
REVERT: D  242 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7282 (tm-30)
REVERT: D  279 LYS cc_start: 0.7700 (mttt) cc_final: 0.7380 (mmmt)
REVERT: D  292 ASP cc_start: 0.9000 (p0) cc_final: 0.8318 (p0)
REVERT: D  349 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.8155 (ttt90)
REVERT: D  370 HIS cc_start: 0.8689 (m-70) cc_final: 0.8276 (m90)
REVERT: D  371 GLU cc_start: 0.9022 (pp20) cc_final: 0.8425 (pp20)
REVERT: D  385 ASP cc_start: 0.8018 (t0) cc_final: 0.7571 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 536
  average time/residue: 0.2173
  time to fit residues: 171.2917
Evaluate side-chains
  493 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 492
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 141 optimal weight:    6.9990
   chunk 142 optimal weight:   20.0000
   chunk 2 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 13 optimal weight:   20.0000
   chunk 132 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 107 optimal weight:    4.9990
   chunk 143 optimal weight:    8.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 242 GLN
A 395 GLN
B  74 ASN
C  88 GLN
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 ASN
D 324 GLN
** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 395 GLN
D 428 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.123482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.103978 restraints weight = 18758.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.107528 restraints weight = 9685.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.109965 restraints weight = 6029.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.4844

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= 0.143
  Angle     :  0.611  11.223  16768  Z= 0.319
  Chirality :  0.044   0.234   1940
  Planarity :  0.004   0.057   2200
  Dihedral  :  5.301  62.365   1680
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.38 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.21), residues: 1568
  helix:  0.15 (0.31), residues: 254
  sheet:  0.24 (0.26), residues: 414
  loop : -1.01 (0.20), residues: 900

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 410 
 HIS   0.003   0.001   HIS D 287 
 PHE   0.019   0.001   PHE B  86 
 TYR   0.021   0.002   TYR B 100 
 ARG   0.009   0.000   ARG C  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04745 (  385)
  hydrogen bonds       : angle       5.03850 ( 1011)
  covalent geometry    : bond        0.00333 (12324)
  covalent geometry    : angle       0.61093 (16768)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4659.01 seconds
wall clock time: 83 minutes 30.16 seconds (5010.16 seconds total)