Starting phenix.real_space_refine
on Thu Sep 18 01:54:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ngi_49385/09_2025/9ngi_49385_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ngi_49385/09_2025/9ngi_49385.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ngi_49385/09_2025/9ngi_49385.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ngi_49385/09_2025/9ngi_49385.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ngi_49385/09_2025/9ngi_49385_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ngi_49385/09_2025/9ngi_49385_neut.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     Na      9      4.78       5
     C    8305      2.51       5
     N    2115      2.21       5
     O    2275      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12729
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2540
          Classifications: {'peptide': 310}
          Link IDs: {'PTRANS': 13, 'TRANS': 296}
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 13
          Unusual residues: {' NA': 9, '3CN': 1}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 2.00, per 1000 atoms: 0.16
  Number of scatterers: 12729
  At special positions: 0
  Unit cell: (92.008, 92.008, 123.256, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      25     16.00
     Na      9     11.00
     O    2275      8.00
     N    2115      7.00
     C    8305      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Conformation dependent library (CDL) restraints added in 524.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2930

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 20 sheets defined
      37.4% alpha, 40.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 70
    Processing helix  chain 'A' and resid 118 through 121
    Processing helix  chain 'A' and resid 176 through 179
    Processing helix  chain 'A' and resid 201 through 208
    Processing helix  chain 'A' and resid 208 through 222
    Processing helix  chain 'A' and resid 223 through 225
      No H-bonds generated for 'chain 'A' and resid 223 through 225'
    Processing helix  chain 'A' and resid 227 through 245
      removed outlier: 3.912A  pdb=" N   THR A 234 " --> pdb=" O   GLU A 230 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   SER A 235 " --> pdb=" O   ARG A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 253
      removed outlier: 3.695A  pdb=" N   ILE A 252 " --> pdb=" O   TYR A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 287
    Processing helix  chain 'A' and resid 302 through 320
      removed outlier: 3.978A  pdb=" N   LEU A 306 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 70
    Processing helix  chain 'B' and resid 118 through 121
    Processing helix  chain 'B' and resid 176 through 179
    Processing helix  chain 'B' and resid 201 through 208
    Processing helix  chain 'B' and resid 208 through 222
    Processing helix  chain 'B' and resid 223 through 225
      No H-bonds generated for 'chain 'B' and resid 223 through 225'
    Processing helix  chain 'B' and resid 227 through 245
      removed outlier: 3.912A  pdb=" N   THR B 234 " --> pdb=" O   GLU B 230 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   SER B 235 " --> pdb=" O   ARG B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 253
      removed outlier: 3.694A  pdb=" N   ILE B 252 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 287
    Processing helix  chain 'B' and resid 302 through 320
      removed outlier: 3.978A  pdb=" N   LEU B 306 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 70
    Processing helix  chain 'C' and resid 118 through 121
    Processing helix  chain 'C' and resid 176 through 179
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 208 through 222
    Processing helix  chain 'C' and resid 223 through 225
      No H-bonds generated for 'chain 'C' and resid 223 through 225'
    Processing helix  chain 'C' and resid 227 through 245
      removed outlier: 3.912A  pdb=" N   THR C 234 " --> pdb=" O   GLU C 230 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   SER C 235 " --> pdb=" O   ARG C 231 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 253
      removed outlier: 3.695A  pdb=" N   ILE C 252 " --> pdb=" O   TYR C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 287
    Processing helix  chain 'C' and resid 302 through 320
      removed outlier: 3.978A  pdb=" N   LEU C 306 " --> pdb=" O   LEU C 302 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 70
    Processing helix  chain 'D' and resid 118 through 121
    Processing helix  chain 'D' and resid 176 through 179
    Processing helix  chain 'D' and resid 201 through 208
    Processing helix  chain 'D' and resid 208 through 222
    Processing helix  chain 'D' and resid 223 through 225
      No H-bonds generated for 'chain 'D' and resid 223 through 225'
    Processing helix  chain 'D' and resid 227 through 245
      removed outlier: 3.912A  pdb=" N   THR D 234 " --> pdb=" O   GLU D 230 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   SER D 235 " --> pdb=" O   ARG D 231 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 247 through 253
      removed outlier: 3.695A  pdb=" N   ILE D 252 " --> pdb=" O   TYR D 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 260 through 287
    Processing helix  chain 'D' and resid 302 through 320
      removed outlier: 3.978A  pdb=" N   LEU D 306 " --> pdb=" O   LEU D 302 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 70
    Processing helix  chain 'E' and resid 118 through 121
    Processing helix  chain 'E' and resid 176 through 179
    Processing helix  chain 'E' and resid 201 through 208
    Processing helix  chain 'E' and resid 208 through 222
    Processing helix  chain 'E' and resid 223 through 225
      No H-bonds generated for 'chain 'E' and resid 223 through 225'
    Processing helix  chain 'E' and resid 227 through 245
      removed outlier: 3.912A  pdb=" N   THR E 234 " --> pdb=" O   GLU E 230 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   SER E 235 " --> pdb=" O   ARG E 231 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 247 through 253
      removed outlier: 3.696A  pdb=" N   ILE E 252 " --> pdb=" O   TYR E 248 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 260 through 287
    Processing helix  chain 'E' and resid 302 through 320
      removed outlier: 3.978A  pdb=" N   LEU E 306 " --> pdb=" O   LEU E 302 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58
      removed outlier: 4.775A  pdb=" N   SER A 109 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58
      removed outlier: 3.809A  pdb=" N   GLY A  37 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   THR A  32 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   GLY A  25 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   LYS A  34 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   ILE A  23 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ASP A  36 " --> pdb=" O   ASN A  21 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   THR A  44 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   ASP A  13 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   VAL A  14 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ILE A 145 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   VAL A  16 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   VAL A 147 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ILE A  18 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.937A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.937A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 58
      removed outlier: 4.775A  pdb=" N   SER B 109 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 58
      removed outlier: 3.810A  pdb=" N   GLY B  37 " --> pdb=" O   PHE B 106 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   THR B  32 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   GLY B  25 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   LYS B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   ILE B  23 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ASP B  36 " --> pdb=" O   ASN B  21 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   THR B  44 " --> pdb=" O   ASP B  13 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   ASP B  13 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   VAL B  14 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   ILE B 145 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   VAL B  16 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   VAL B 147 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ILE B  18 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.937A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.937A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 58
      removed outlier: 4.775A  pdb=" N   SER C 109 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 56 through 58
      removed outlier: 3.810A  pdb=" N   GLY C  37 " --> pdb=" O   PHE C 106 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   THR C  32 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   GLY C  25 " --> pdb=" O   THR C  32 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   LYS C  34 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   ILE C  23 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ASP C  36 " --> pdb=" O   ASN C  21 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   THR C  44 " --> pdb=" O   ASP C  13 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   ASP C  13 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   VAL C  14 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   ILE C 145 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   VAL C  16 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   VAL C 147 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ILE C  18 " --> pdb=" O   VAL C 147 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.937A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.937A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 56 through 58
      removed outlier: 4.775A  pdb=" N   SER D 109 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 56 through 58
      removed outlier: 3.808A  pdb=" N   GLY D  37 " --> pdb=" O   PHE D 106 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   THR D  32 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   GLY D  25 " --> pdb=" O   THR D  32 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   LYS D  34 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   ILE D  23 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ASP D  36 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   THR D  44 " --> pdb=" O   ASP D  13 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   ASP D  13 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   VAL D  14 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   ILE D 145 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   VAL D  16 " --> pdb=" O   ILE D 145 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   VAL D 147 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ILE D  18 " --> pdb=" O   VAL D 147 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.937A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.937A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 56 through 58
      removed outlier: 4.775A  pdb=" N   SER E 109 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 56 through 58
      removed outlier: 3.809A  pdb=" N   GLY E  37 " --> pdb=" O   PHE E 106 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   THR E  32 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   GLY E  25 " --> pdb=" O   THR E  32 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   LYS E  34 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   ILE E  23 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ASP E  36 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   THR E  44 " --> pdb=" O   ASP E  13 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   ASP E  13 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   VAL E  14 " --> pdb=" O   SER E 143 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ILE E 145 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   VAL E  16 " --> pdb=" O   ILE E 145 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   VAL E 147 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ILE E  18 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.936A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.936A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)

    710 hydrogen bonds defined for protein.
    2040 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.34

  Time building geometry restraints manager: 1.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4006
        1.34 -     1.46: 2999
        1.46 -     1.58: 6010
        1.58 -     1.69: 5
        1.69 -     1.81: 45
  Bond restraints: 13065
  Sorted by residual:
  bond pdb=" CA  THR D 149 "
       pdb=" CB  THR D 149 "
    ideal  model  delta    sigma   weight residual
    1.531  1.625 -0.095 3.28e-02 9.30e+02 8.31e+00
  bond pdb=" CA  THR E 149 "
       pdb=" CB  THR E 149 "
    ideal  model  delta    sigma   weight residual
    1.531  1.625 -0.094 3.28e-02 9.30e+02 8.27e+00
  bond pdb=" CA  THR A 149 "
       pdb=" CB  THR A 149 "
    ideal  model  delta    sigma   weight residual
    1.531  1.625 -0.094 3.28e-02 9.30e+02 8.25e+00
  bond pdb=" CA  THR B 149 "
       pdb=" CB  THR B 149 "
    ideal  model  delta    sigma   weight residual
    1.531  1.625 -0.094 3.28e-02 9.30e+02 8.19e+00
  bond pdb=" CA  THR C 149 "
       pdb=" CB  THR C 149 "
    ideal  model  delta    sigma   weight residual
    1.531  1.624 -0.094 3.28e-02 9.30e+02 8.17e+00
  ... (remaining 13060 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 16837
        1.79 -     3.57: 782
        3.57 -     5.36: 106
        5.36 -     7.14: 30
        7.14 -     8.93: 25
  Bond angle restraints: 17780
  Sorted by residual:
  angle pdb=" CA  PRO D  85 "
        pdb=" N   PRO D  85 "
        pdb=" CD  PRO D  85 "
      ideal   model   delta    sigma   weight residual
     112.00  106.56    5.44 1.40e+00 5.10e-01 1.51e+01
  angle pdb=" CA  PRO E  85 "
        pdb=" N   PRO E  85 "
        pdb=" CD  PRO E  85 "
      ideal   model   delta    sigma   weight residual
     112.00  106.57    5.43 1.40e+00 5.10e-01 1.50e+01
  angle pdb=" C   ASN E  60 "
        pdb=" N   THR E  61 "
        pdb=" CA  THR E  61 "
      ideal   model   delta    sigma   weight residual
     121.54  128.93   -7.39 1.91e+00 2.74e-01 1.50e+01
  angle pdb=" CA  PRO B  85 "
        pdb=" N   PRO B  85 "
        pdb=" CD  PRO B  85 "
      ideal   model   delta    sigma   weight residual
     112.00  106.58    5.42 1.40e+00 5.10e-01 1.50e+01
  angle pdb=" C   ASN A  60 "
        pdb=" N   THR A  61 "
        pdb=" CA  THR A  61 "
      ideal   model   delta    sigma   weight residual
     121.54  128.93   -7.39 1.91e+00 2.74e-01 1.50e+01
  ... (remaining 17775 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.43: 6729
       16.43 -    32.85: 711
       32.85 -    49.28: 125
       49.28 -    65.70: 15
       65.70 -    82.13: 25
  Dihedral angle restraints: 7605
    sinusoidal: 3060
      harmonic: 4545
  Sorted by residual:
  dihedral pdb=" CA  PRO E 201 "
           pdb=" C   PRO E 201 "
           pdb=" N   SER E 202 "
           pdb=" CA  SER E 202 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.16  -19.84     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CA  PRO A 201 "
           pdb=" C   PRO A 201 "
           pdb=" N   SER A 202 "
           pdb=" CA  SER A 202 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.16  -19.84     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  PRO C 201 "
           pdb=" C   PRO C 201 "
           pdb=" N   SER C 202 "
           pdb=" CA  SER C 202 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.16  -19.84     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 7602 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1035
       0.037 -    0.075: 581
       0.075 -    0.112: 228
       0.112 -    0.149: 71
       0.149 -    0.187: 40
  Chirality restraints: 1955
  Sorted by residual:
  chirality pdb=" CB  ILE D  18 "
            pdb=" CA  ILE D  18 "
            pdb=" CG1 ILE D  18 "
            pdb=" CG2 ILE D  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.70e-01
  chirality pdb=" CB  ILE E  18 "
            pdb=" CA  ILE E  18 "
            pdb=" CG1 ILE E  18 "
            pdb=" CG2 ILE E  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.67e-01
  chirality pdb=" CA  PHE B 304 "
            pdb=" N   PHE B 304 "
            pdb=" C   PHE B 304 "
            pdb=" CB  PHE B 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.46e-01
  ... (remaining 1952 not shown)

  Planarity restraints: 2265
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E  84 "    0.093 5.00e-02 4.00e+02   1.39e-01 3.08e+01
        pdb=" N   PRO E  85 "   -0.240 5.00e-02 4.00e+02
        pdb=" CA  PRO E  85 "    0.075 5.00e-02 4.00e+02
        pdb=" CD  PRO E  85 "    0.072 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  84 "    0.093 5.00e-02 4.00e+02   1.39e-01 3.08e+01
        pdb=" N   PRO C  85 "   -0.240 5.00e-02 4.00e+02
        pdb=" CA  PRO C  85 "    0.075 5.00e-02 4.00e+02
        pdb=" CD  PRO C  85 "    0.072 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  84 "    0.093 5.00e-02 4.00e+02   1.39e-01 3.08e+01
        pdb=" N   PRO A  85 "   -0.240 5.00e-02 4.00e+02
        pdb=" CA  PRO A  85 "    0.075 5.00e-02 4.00e+02
        pdb=" CD  PRO A  85 "    0.072 5.00e-02 4.00e+02
  ... (remaining 2262 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 3056
        2.80 -     3.32: 11939
        3.32 -     3.85: 21026
        3.85 -     4.37: 23424
        4.37 -     4.90: 40635
  Nonbonded interactions: 100080
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 122 "
            pdb=" N   ARG A 123 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" OD1 ASP E 122 "
            pdb=" N   ARG E 123 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" OD1 ASP D 122 "
            pdb=" N   ARG D 123 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OD1 ASP B 122 "
            pdb=" N   ARG B 123 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OD1 ASP C 122 "
            pdb=" N   ARG C 123 "
     model   vdw
     2.270 3.120
  ... (remaining 100075 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 11 through 401)
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.670
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     11.630
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
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      :  0.006   0.095  13065  Z= 0.239
  Angle     :  0.917   8.931  17780  Z= 0.501
  Chirality :  0.057   0.187   1955
  Planarity :  0.010   0.139   2265
  Dihedral  : 14.494  82.126   4675
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.25 (0.20), residues: 1540
  helix: -0.30 (0.21), residues: 515
  sheet:  0.17 (0.24), residues: 475
  loop : -2.17 (0.23), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C 163 
 TYR   0.023   0.002   TYR D 248 
 PHE   0.028   0.002   PHE E  78 
 TRP   0.063   0.004   TRP E 220 
 HIS   0.004   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 (13065)
  covalent geometry    : angle       0.91683 (17780)
  hydrogen bonds       : bond        0.19528 (  620)
  hydrogen bonds       : angle       8.37200 ( 2040)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  434 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 434
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8431 (pm20)
REVERT: A  115 ASP cc_start: 0.7529 (t70) cc_final: 0.6654 (m-30)
REVERT: A  131 GLU cc_start: 0.8781 (mt-10) cc_final: 0.7746 (mt-10)
REVERT: A  247 PHE cc_start: 0.7977 (m-10) cc_final: 0.7521 (m-10)
REVERT: B   19 PHE cc_start: 0.7868 (t80) cc_final: 0.7253 (t80)
REVERT: B   64 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8471 (pm20)
REVERT: B  102 TYR cc_start: 0.8276 (t80) cc_final: 0.7884 (t80)
REVERT: B  107 LEU cc_start: 0.7434 (tt) cc_final: 0.7205 (tt)
REVERT: B  115 ASP cc_start: 0.7616 (t70) cc_final: 0.6813 (m-30)
REVERT: B  131 GLU cc_start: 0.8703 (mt-10) cc_final: 0.7647 (mt-10)
REVERT: B  192 THR cc_start: 0.8444 (m) cc_final: 0.8144 (m)
REVERT: B  223 PHE cc_start: 0.8634 (m-10) cc_final: 0.8074 (m-10)
REVERT: B  247 PHE cc_start: 0.7971 (m-10) cc_final: 0.7455 (m-10)
REVERT: C   64 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8485 (pm20)
REVERT: C  115 ASP cc_start: 0.7517 (t70) cc_final: 0.6679 (m-30)
REVERT: C  131 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8043 (mt-10)
REVERT: C  150 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7545 (tm-30)
REVERT: C  159 GLU cc_start: 0.8508 (pm20) cc_final: 0.7628 (tt0)
REVERT: C  192 THR cc_start: 0.8364 (m) cc_final: 0.7737 (p)
REVERT: C  223 PHE cc_start: 0.8615 (m-10) cc_final: 0.8279 (m-10)
REVERT: C  247 PHE cc_start: 0.7907 (m-10) cc_final: 0.7559 (m-10)
REVERT: C  266 ILE cc_start: 0.8624 (tp) cc_final: 0.7777 (tp)
REVERT: D   64 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8416 (pm20)
REVERT: D  102 TYR cc_start: 0.8198 (t80) cc_final: 0.7770 (t80)
REVERT: D  115 ASP cc_start: 0.7511 (t70) cc_final: 0.6715 (m-30)
REVERT: D  131 GLU cc_start: 0.8639 (mt-10) cc_final: 0.7565 (mt-10)
REVERT: D  150 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7527 (tm-30)
REVERT: D  199 ARG cc_start: 0.8342 (ttm-80) cc_final: 0.7469 (ttm-80)
REVERT: D  223 PHE cc_start: 0.8692 (m-10) cc_final: 0.8414 (m-10)
REVERT: D  247 PHE cc_start: 0.8022 (m-10) cc_final: 0.7607 (m-10)
REVERT: D  266 ILE cc_start: 0.8535 (tp) cc_final: 0.8330 (tp)
REVERT: E  115 ASP cc_start: 0.7574 (t70) cc_final: 0.6709 (m-30)
REVERT: E  131 GLU cc_start: 0.8769 (mt-10) cc_final: 0.7688 (mt-10)
REVERT: E  192 THR cc_start: 0.8445 (m) cc_final: 0.8057 (m)
REVERT: E  199 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7512 (ttm-80)
REVERT: E  214 LEU cc_start: 0.8555 (mp) cc_final: 0.8309 (mp)
REVERT: E  252 ILE cc_start: 0.8897 (mp) cc_final: 0.8671 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 434
  average time/residue: 0.1064
  time to fit residues: 68.0079
Evaluate side-chains
  346 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 346
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    6.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 139 GLN
B 139 GLN
C 139 GLN
D 139 GLN
E 139 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.123847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.094776 restraints weight = 30613.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.097885 restraints weight = 19016.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.099826 restraints weight = 13538.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.100808 restraints weight = 10684.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.100813 restraints weight = 9298.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13065  Z= 0.246
  Angle     :  0.665   7.075  17780  Z= 0.353
  Chirality :  0.048   0.151   1955
  Planarity :  0.006   0.084   2265
  Dihedral  :  5.636  22.415   1715
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.21), residues: 1540
  helix:  0.85 (0.22), residues: 530
  sheet:  0.11 (0.25), residues: 450
  loop : -2.28 (0.22), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  91 
 TYR   0.018   0.002   TYR D 204 
 PHE   0.013   0.002   PHE B 247 
 TRP   0.020   0.002   TRP E 220 
 HIS   0.004   0.001   HIS C 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 (13065)
  covalent geometry    : angle       0.66499 (17780)
  hydrogen bonds       : bond        0.04333 (  620)
  hydrogen bonds       : angle       5.77137 ( 2040)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  362 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 362
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A   93 MET cc_start: 0.9030 (tpp) cc_final: 0.8639 (tpp)
REVERT: A  102 TYR cc_start: 0.8196 (t80) cc_final: 0.7831 (t80)
REVERT: A  107 LEU cc_start: 0.8108 (tt) cc_final: 0.7743 (tt)
REVERT: A  140 LEU cc_start: 0.9228 (tt) cc_final: 0.9018 (tt)
REVERT: A  191 ILE cc_start: 0.8770 (mt) cc_final: 0.8551 (mt)
REVERT: A  198 VAL cc_start: 0.8946 (p) cc_final: 0.8740 (m)
REVERT: A  265 MET cc_start: 0.8906 (ttt) cc_final: 0.8705 (ttt)
REVERT: B   19 PHE cc_start: 0.7940 (t80) cc_final: 0.7599 (t80)
REVERT: B   93 MET cc_start: 0.8997 (tpp) cc_final: 0.8603 (tpp)
REVERT: B  102 TYR cc_start: 0.8317 (t80) cc_final: 0.7941 (t80)
REVERT: B  107 LEU cc_start: 0.7921 (tt) cc_final: 0.7613 (tt)
REVERT: B  131 GLU cc_start: 0.8871 (mt-10) cc_final: 0.7729 (mt-10)
REVERT: B  198 VAL cc_start: 0.8986 (p) cc_final: 0.8675 (m)
REVERT: B  199 ARG cc_start: 0.8376 (ttm-80) cc_final: 0.7967 (ttm-80)
REVERT: B  301 ARG cc_start: 0.7519 (ptp90) cc_final: 0.7142 (ptp-110)
REVERT: C   64 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8489 (pm20)
REVERT: C  102 TYR cc_start: 0.8217 (t80) cc_final: 0.7915 (t80)
REVERT: C  131 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8004 (mt-10)
REVERT: C  148 TYR cc_start: 0.7953 (m-80) cc_final: 0.7747 (m-80)
REVERT: C  156 GLU cc_start: 0.8508 (pp20) cc_final: 0.8293 (pp20)
REVERT: C  199 ARG cc_start: 0.8543 (ttm-80) cc_final: 0.8102 (ttm-80)
REVERT: C  212 LEU cc_start: 0.9207 (tp) cc_final: 0.8935 (tp)
REVERT: C  265 MET cc_start: 0.8791 (ttt) cc_final: 0.8590 (ttt)
REVERT: C  266 ILE cc_start: 0.8634 (tp) cc_final: 0.7922 (tp)
REVERT: D   77 GLU cc_start: 0.7635 (pm20) cc_final: 0.7284 (pm20)
REVERT: D  102 TYR cc_start: 0.8235 (t80) cc_final: 0.7860 (t80)
REVERT: D  131 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8022 (mt-10)
REVERT: D  198 VAL cc_start: 0.9033 (p) cc_final: 0.8825 (m)
REVERT: D  199 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8079 (ttm-80)
REVERT: D  212 LEU cc_start: 0.9103 (tp) cc_final: 0.8780 (tp)
REVERT: D  223 PHE cc_start: 0.8686 (m-80) cc_final: 0.8201 (m-10)
REVERT: E   77 GLU cc_start: 0.7661 (pm20) cc_final: 0.6937 (pm20)
REVERT: E   93 MET cc_start: 0.9082 (tpp) cc_final: 0.8659 (tpp)
REVERT: E  102 TYR cc_start: 0.8215 (t80) cc_final: 0.7790 (t80)
REVERT: E  131 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7100 (mt-10)
REVERT: E  199 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8237 (ttm-80)
REVERT: E  203 TYR cc_start: 0.8413 (t80) cc_final: 0.7999 (t80)
REVERT: E  301 ARG cc_start: 0.7242 (mtt180) cc_final: 0.7037 (ptp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 362
  average time/residue: 0.0955
  time to fit residues: 52.4199
Evaluate side-chains
  290 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 93 optimal weight:    0.0170
   chunk 124 optimal weight:    0.0970
   chunk 91 optimal weight:   20.0000
   chunk 116 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 76 optimal weight:    8.9990
   chunk 12 optimal weight:    0.8980
   chunk 113 optimal weight:    7.9990
   chunk 83 optimal weight:    8.9990
   chunk 90 optimal weight:    0.2980
   chunk 152 optimal weight:    5.9990
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
A 139 GLN
B  69 ASN
B 139 GLN
B 285 HIS
C 139 GLN
D  69 ASN
D 139 GLN
E 139 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.131413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.101506 restraints weight = 30036.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.104917 restraints weight = 18026.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.107289 restraints weight = 12597.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.108707 restraints weight = 9698.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.109362 restraints weight = 8139.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  13065  Z= 0.106
  Angle     :  0.556   6.032  17780  Z= 0.294
  Chirality :  0.047   0.157   1955
  Planarity :  0.005   0.058   2265
  Dihedral  :  4.908  19.841   1715
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.38 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.22), residues: 1540
  helix:  1.25 (0.23), residues: 505
  sheet:  0.56 (0.23), residues: 520
  loop : -1.73 (0.26), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 199 
 TYR   0.026   0.001   TYR E 148 
 PHE   0.010   0.001   PHE A 119 
 TRP   0.009   0.001   TRP C 206 
 HIS   0.005   0.001   HIS D 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (13065)
  covalent geometry    : angle       0.55629 (17780)
  hydrogen bonds       : bond        0.03535 (  620)
  hydrogen bonds       : angle       4.96479 ( 2040)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  404 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 403
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8497 (pm20)
REVERT: A  102 TYR cc_start: 0.8168 (t80) cc_final: 0.7923 (t80)
REVERT: A  107 LEU cc_start: 0.7587 (tt) cc_final: 0.7068 (tt)
REVERT: A  115 ASP cc_start: 0.7747 (t70) cc_final: 0.6637 (m-30)
REVERT: A  198 VAL cc_start: 0.8921 (p) cc_final: 0.8668 (m)
REVERT: A  212 LEU cc_start: 0.9083 (tp) cc_final: 0.8862 (tp)
REVERT: A  265 MET cc_start: 0.8838 (ttt) cc_final: 0.8556 (ttt)
REVERT: B   64 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8504 (pm20)
REVERT: B   79 ILE cc_start: 0.9205 (mm) cc_final: 0.8826 (mm)
REVERT: B  102 TYR cc_start: 0.8187 (t80) cc_final: 0.7877 (t80)
REVERT: B  115 ASP cc_start: 0.7613 (t70) cc_final: 0.6572 (m-30)
REVERT: B  198 VAL cc_start: 0.8993 (p) cc_final: 0.8713 (m)
REVERT: B  223 PHE cc_start: 0.8652 (m-10) cc_final: 0.8324 (m-10)
REVERT: C   64 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8435 (pm20)
REVERT: C   93 MET cc_start: 0.8880 (tpp) cc_final: 0.8597 (tpp)
REVERT: C  107 LEU cc_start: 0.7711 (tp) cc_final: 0.7488 (tp)
REVERT: C  115 ASP cc_start: 0.7532 (t70) cc_final: 0.6624 (m-30)
REVERT: C  131 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7217 (mt-10)
REVERT: C  212 LEU cc_start: 0.9095 (tp) cc_final: 0.8724 (tp)
REVERT: C  223 PHE cc_start: 0.8744 (m-10) cc_final: 0.8464 (m-10)
REVERT: C  265 MET cc_start: 0.8734 (ttt) cc_final: 0.8464 (ttt)
REVERT: C  266 ILE cc_start: 0.8545 (tp) cc_final: 0.7712 (tp)
REVERT: D   64 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8394 (pm20)
REVERT: D  102 TYR cc_start: 0.8163 (t80) cc_final: 0.7866 (t80)
REVERT: D  115 ASP cc_start: 0.7552 (t70) cc_final: 0.6671 (m-30)
REVERT: D  198 VAL cc_start: 0.8923 (p) cc_final: 0.8679 (m)
REVERT: D  212 LEU cc_start: 0.9039 (tp) cc_final: 0.8750 (tp)
REVERT: D  265 MET cc_start: 0.8722 (ttt) cc_final: 0.8480 (ttt)
REVERT: E  102 TYR cc_start: 0.8150 (t80) cc_final: 0.7894 (t80)
REVERT: E  107 LEU cc_start: 0.7543 (tt) cc_final: 0.7003 (tt)
REVERT: E  131 GLU cc_start: 0.8644 (mt-10) cc_final: 0.6906 (mt-10)
REVERT: E  203 TYR cc_start: 0.8519 (t80) cc_final: 0.8299 (t80)
REVERT: E  212 LEU cc_start: 0.8958 (tp) cc_final: 0.8726 (tp)
REVERT: E  265 MET cc_start: 0.8732 (ttt) cc_final: 0.8463 (ttt)
  outliers start: 1
  outliers final: 0
  residues processed: 403
  average time/residue: 0.0891
  time to fit residues: 54.6748
Evaluate side-chains
  328 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 328
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 126 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 81 optimal weight:    0.5980
   chunk 92 optimal weight:   10.0000
   chunk 147 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 58 optimal weight:   20.0000
   chunk 28 optimal weight:    9.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 139 GLN
B 139 GLN
B 285 HIS
C 139 GLN
D 139 GLN
D 285 HIS
E 139 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.125257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.096037 restraints weight = 30545.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.099394 restraints weight = 18226.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.101706 restraints weight = 12694.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.103352 restraints weight = 9773.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.104323 restraints weight = 8062.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13065  Z= 0.170
  Angle     :  0.590   5.750  17780  Z= 0.312
  Chirality :  0.047   0.182   1955
  Planarity :  0.005   0.056   2265
  Dihedral  :  5.044  22.256   1715
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  5.70 %
    Favored  : 94.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.22), residues: 1540
  helix:  1.44 (0.23), residues: 505
  sheet:  0.13 (0.25), residues: 450
  loop : -1.89 (0.24), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 199 
 TYR   0.017   0.002   TYR A 203 
 PHE   0.015   0.001   PHE B 228 
 TRP   0.013   0.001   TRP C 206 
 HIS   0.003   0.001   HIS D 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (13065)
  covalent geometry    : angle       0.59006 (17780)
  hydrogen bonds       : bond        0.03625 (  620)
  hydrogen bonds       : angle       5.11849 ( 2040)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 379
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 VAL cc_start: 0.9077 (t) cc_final: 0.8863 (t)
REVERT: A   64 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8545 (pm20)
REVERT: A   77 GLU cc_start: 0.7670 (pp20) cc_final: 0.7415 (pp20)
REVERT: A  102 TYR cc_start: 0.8346 (t80) cc_final: 0.8069 (t80)
REVERT: A  107 LEU cc_start: 0.7921 (tt) cc_final: 0.7682 (tp)
REVERT: A  198 VAL cc_start: 0.8924 (p) cc_final: 0.8674 (m)
REVERT: A  212 LEU cc_start: 0.9106 (tp) cc_final: 0.8789 (tp)
REVERT: A  265 MET cc_start: 0.8864 (ttt) cc_final: 0.8543 (ttt)
REVERT: B   39 ILE cc_start: 0.9133 (tp) cc_final: 0.8667 (pt)
REVERT: B   64 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8557 (pm20)
REVERT: B  102 TYR cc_start: 0.8400 (t80) cc_final: 0.8127 (t80)
REVERT: B  107 LEU cc_start: 0.7773 (tt) cc_final: 0.7374 (tt)
REVERT: B  198 VAL cc_start: 0.8970 (p) cc_final: 0.8634 (m)
REVERT: B  212 LEU cc_start: 0.9057 (tp) cc_final: 0.8805 (tp)
REVERT: C   19 PHE cc_start: 0.8207 (t80) cc_final: 0.7980 (t80)
REVERT: C   39 ILE cc_start: 0.9097 (tp) cc_final: 0.8679 (pt)
REVERT: C   64 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8521 (pm20)
REVERT: C   79 ILE cc_start: 0.9232 (mm) cc_final: 0.9031 (mm)
REVERT: C   93 MET cc_start: 0.8874 (tpp) cc_final: 0.8572 (tpp)
REVERT: C  102 TYR cc_start: 0.8667 (t80) cc_final: 0.8218 (t80)
REVERT: C  107 LEU cc_start: 0.7811 (tp) cc_final: 0.7587 (tp)
REVERT: C  212 LEU cc_start: 0.9046 (tp) cc_final: 0.8628 (tp)
REVERT: C  265 MET cc_start: 0.8763 (ttt) cc_final: 0.8457 (ttt)
REVERT: C  266 ILE cc_start: 0.8573 (tp) cc_final: 0.7824 (tp)
REVERT: D   39 ILE cc_start: 0.9114 (tp) cc_final: 0.8625 (pt)
REVERT: D   64 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8507 (pm20)
REVERT: D  102 TYR cc_start: 0.8323 (t80) cc_final: 0.8074 (t80)
REVERT: D  140 LEU cc_start: 0.9183 (tt) cc_final: 0.8971 (tt)
REVERT: D  198 VAL cc_start: 0.8937 (p) cc_final: 0.8638 (m)
REVERT: D  212 LEU cc_start: 0.9044 (tp) cc_final: 0.8717 (tp)
REVERT: D  265 MET cc_start: 0.8766 (ttt) cc_final: 0.8517 (ttt)
REVERT: D  285 HIS cc_start: 0.7590 (OUTLIER) cc_final: 0.7390 (t70)
REVERT: E   64 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8686 (pm20)
REVERT: E  102 TYR cc_start: 0.8318 (t80) cc_final: 0.8058 (t80)
REVERT: E  131 GLU cc_start: 0.8242 (mt-10) cc_final: 0.6982 (mt-10)
REVERT: E  140 LEU cc_start: 0.9114 (tt) cc_final: 0.8886 (tt)
REVERT: E  203 TYR cc_start: 0.8643 (t80) cc_final: 0.8438 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 379
  average time/residue: 0.0920
  time to fit residues: 53.3632
Evaluate side-chains
  309 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 308
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 113 optimal weight:    6.9990
   chunk 80 optimal weight:    9.9990
   chunk 97 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 70 optimal weight:    0.6980
   chunk 152 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 37 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9990
   chunk 131 optimal weight:    8.9990
   chunk 94 optimal weight:    0.0070
   overall best weight:    2.5404

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 139 GLN
** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 GLN
C 139 GLN
** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 139 GLN
E 139 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.125644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.096964 restraints weight = 30751.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.100052 restraints weight = 18289.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.102790 restraints weight = 12894.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.104284 restraints weight = 9806.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.105601 restraints weight = 8063.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13065  Z= 0.155
  Angle     :  0.578   5.661  17780  Z= 0.304
  Chirality :  0.047   0.141   1955
  Planarity :  0.004   0.053   2265
  Dihedral  :  5.011  22.196   1715
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.22), residues: 1540
  helix:  1.11 (0.23), residues: 540
  sheet:  0.07 (0.25), residues: 450
  loop : -1.85 (0.25), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  91 
 TYR   0.018   0.002   TYR D 203 
 PHE   0.008   0.001   PHE D  19 
 TRP   0.013   0.001   TRP C 206 
 HIS   0.004   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (13065)
  covalent geometry    : angle       0.57802 (17780)
  hydrogen bonds       : bond        0.03444 (  620)
  hydrogen bonds       : angle       4.98741 ( 2040)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  379 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 379
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A   39 ILE cc_start: 0.9024 (tp) cc_final: 0.8605 (pt)
REVERT: A   64 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8691 (pm20)
REVERT: A   77 GLU cc_start: 0.7772 (pp20) cc_final: 0.7418 (pp20)
REVERT: A  102 TYR cc_start: 0.8327 (t80) cc_final: 0.8014 (t80)
REVERT: A  107 LEU cc_start: 0.7891 (tt) cc_final: 0.7596 (tt)
REVERT: A  161 TRP cc_start: 0.7046 (m-10) cc_final: 0.6688 (m-10)
REVERT: A  198 VAL cc_start: 0.8910 (p) cc_final: 0.8645 (m)
REVERT: A  212 LEU cc_start: 0.9068 (tp) cc_final: 0.8717 (tp)
REVERT: A  265 MET cc_start: 0.8804 (ttt) cc_final: 0.8439 (ttt)
REVERT: B   39 ILE cc_start: 0.9128 (tp) cc_final: 0.8669 (pt)
REVERT: B   64 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8660 (pm20)
REVERT: B  102 TYR cc_start: 0.8374 (t80) cc_final: 0.8147 (t80)
REVERT: B  107 LEU cc_start: 0.7856 (tt) cc_final: 0.7550 (tp)
REVERT: B  131 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8348 (mt-10)
REVERT: B  198 VAL cc_start: 0.8968 (p) cc_final: 0.8627 (m)
REVERT: B  265 MET cc_start: 0.8918 (ttt) cc_final: 0.8690 (ttt)
REVERT: C   39 ILE cc_start: 0.9089 (tp) cc_final: 0.8629 (pt)
REVERT: C   64 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8617 (pm20)
REVERT: C   77 GLU cc_start: 0.7739 (pp20) cc_final: 0.7458 (pp20)
REVERT: C   93 MET cc_start: 0.8933 (tpp) cc_final: 0.8598 (tpp)
REVERT: C  102 TYR cc_start: 0.8612 (t80) cc_final: 0.8141 (t80)
REVERT: C  107 LEU cc_start: 0.7926 (tp) cc_final: 0.7661 (tp)
REVERT: C  212 LEU cc_start: 0.9025 (tp) cc_final: 0.8547 (tp)
REVERT: C  223 PHE cc_start: 0.8653 (m-10) cc_final: 0.8169 (m-10)
REVERT: C  265 MET cc_start: 0.8732 (ttt) cc_final: 0.8445 (ttt)
REVERT: C  266 ILE cc_start: 0.8585 (tp) cc_final: 0.7876 (tp)
REVERT: D   39 ILE cc_start: 0.9104 (tp) cc_final: 0.8626 (pt)
REVERT: D   64 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8621 (pm20)
REVERT: D   77 GLU cc_start: 0.7527 (pm20) cc_final: 0.7033 (pm20)
REVERT: D  102 TYR cc_start: 0.8334 (t80) cc_final: 0.8049 (t80)
REVERT: D  140 LEU cc_start: 0.9171 (tt) cc_final: 0.8960 (tt)
REVERT: D  198 VAL cc_start: 0.8924 (p) cc_final: 0.8655 (m)
REVERT: D  212 LEU cc_start: 0.9015 (tp) cc_final: 0.8658 (tp)
REVERT: D  265 MET cc_start: 0.8714 (ttt) cc_final: 0.8449 (ttt)
REVERT: D  301 ARG cc_start: 0.6566 (ptp90) cc_final: 0.5744 (ttm170)
REVERT: E   34 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8403 (mptt)
REVERT: E   64 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8664 (pm20)
REVERT: E  102 TYR cc_start: 0.8284 (t80) cc_final: 0.7962 (t80)
REVERT: E  107 LEU cc_start: 0.7925 (tt) cc_final: 0.7327 (tt)
REVERT: E  131 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7032 (mt-10)
REVERT: E  140 LEU cc_start: 0.9077 (tt) cc_final: 0.8843 (tt)
REVERT: E  203 TYR cc_start: 0.8461 (t80) cc_final: 0.8256 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 379
  average time/residue: 0.1024
  time to fit residues: 59.0419
Evaluate side-chains
  310 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 310
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 109 optimal weight:   10.0000
   chunk 87 optimal weight:    8.9990
   chunk 20 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0970
   chunk 63 optimal weight:    0.0070
   chunk 88 optimal weight:    0.9980
   chunk 68 optimal weight:    9.9990
   chunk 7 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0070
   chunk 93 optimal weight:    9.9990
   overall best weight:    0.3614

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 139 GLN
B 139 GLN
C  69 ASN
C 139 GLN
D 139 GLN
E  69 ASN
E 139 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.131465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.102483 restraints weight = 29800.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.105327 restraints weight = 17736.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.108461 restraints weight = 12676.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.110049 restraints weight = 9563.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.111361 restraints weight = 7804.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.3330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  13065  Z= 0.105
  Angle     :  0.551   5.638  17780  Z= 0.289
  Chirality :  0.047   0.172   1955
  Planarity :  0.004   0.047   2265
  Dihedral  :  4.685  21.456   1715
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.22), residues: 1540
  helix:  1.28 (0.23), residues: 535
  sheet:  0.40 (0.25), residues: 470
  loop : -1.69 (0.25), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  91 
 TYR   0.019   0.001   TYR C 203 
 PHE   0.014   0.001   PHE A 228 
 TRP   0.021   0.001   TRP B 220 
 HIS   0.003   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (13065)
  covalent geometry    : angle       0.55094 (17780)
  hydrogen bonds       : bond        0.03114 (  620)
  hydrogen bonds       : angle       4.71026 ( 2040)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  399 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 399
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8703 (pm20)
REVERT: A  102 TYR cc_start: 0.8271 (t80) cc_final: 0.7936 (t80)
REVERT: A  114 MET cc_start: 0.7258 (ttm) cc_final: 0.6935 (ttp)
REVERT: A  161 TRP cc_start: 0.7120 (m-10) cc_final: 0.6777 (m-10)
REVERT: A  198 VAL cc_start: 0.8860 (p) cc_final: 0.8604 (m)
REVERT: A  199 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7783 (ttm-80)
REVERT: A  212 LEU cc_start: 0.9029 (tp) cc_final: 0.8662 (tp)
REVERT: A  239 MET cc_start: 0.9001 (ttp) cc_final: 0.8664 (ttt)
REVERT: A  265 MET cc_start: 0.8761 (ttt) cc_final: 0.8385 (ttt)
REVERT: B   64 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8638 (pm20)
REVERT: B  114 MET cc_start: 0.8141 (ttm) cc_final: 0.7076 (ttp)
REVERT: B  131 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8082 (mt-10)
REVERT: B  148 TYR cc_start: 0.7858 (m-80) cc_final: 0.7643 (m-80)
REVERT: B  198 VAL cc_start: 0.8911 (p) cc_final: 0.8602 (m)
REVERT: B  199 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7891 (ttm-80)
REVERT: B  221 SER cc_start: 0.8519 (m) cc_final: 0.8252 (p)
REVERT: C   34 LYS cc_start: 0.8558 (mttp) cc_final: 0.8289 (mptt)
REVERT: C   64 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8568 (pm20)
REVERT: C   77 GLU cc_start: 0.7743 (pp20) cc_final: 0.7451 (pp20)
REVERT: C   93 MET cc_start: 0.8886 (tpp) cc_final: 0.8523 (tpp)
REVERT: C  102 TYR cc_start: 0.8597 (t80) cc_final: 0.8100 (t80)
REVERT: C  131 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8254 (mt-10)
REVERT: C  212 LEU cc_start: 0.9047 (tp) cc_final: 0.8556 (tp)
REVERT: C  221 SER cc_start: 0.8653 (m) cc_final: 0.8345 (p)
REVERT: C  223 PHE cc_start: 0.8292 (m-10) cc_final: 0.8063 (m-10)
REVERT: C  265 MET cc_start: 0.8670 (ttt) cc_final: 0.8398 (ttt)
REVERT: C  266 ILE cc_start: 0.8484 (tp) cc_final: 0.8213 (mt)
REVERT: D   39 ILE cc_start: 0.9116 (tp) cc_final: 0.8636 (pt)
REVERT: D   64 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8568 (pm20)
REVERT: D  102 TYR cc_start: 0.8260 (t80) cc_final: 0.8058 (t80)
REVERT: D  114 MET cc_start: 0.7947 (ttm) cc_final: 0.7704 (ttp)
REVERT: D  115 ASP cc_start: 0.7783 (t70) cc_final: 0.6734 (m-30)
REVERT: D  122 ASP cc_start: 0.7313 (t70) cc_final: 0.7017 (t70)
REVERT: D  140 LEU cc_start: 0.9057 (tt) cc_final: 0.8840 (tt)
REVERT: D  198 VAL cc_start: 0.8851 (p) cc_final: 0.8625 (m)
REVERT: D  212 LEU cc_start: 0.8961 (tp) cc_final: 0.8619 (tp)
REVERT: D  265 MET cc_start: 0.8638 (ttt) cc_final: 0.8365 (ttt)
REVERT: E  102 TYR cc_start: 0.8203 (t80) cc_final: 0.7863 (t80)
REVERT: E  107 LEU cc_start: 0.7567 (tt) cc_final: 0.7204 (tt)
REVERT: E  114 MET cc_start: 0.7459 (mtm) cc_final: 0.7081 (ttm)
REVERT: E  115 ASP cc_start: 0.7984 (t0) cc_final: 0.6810 (m-30)
REVERT: E  140 LEU cc_start: 0.8994 (tt) cc_final: 0.8788 (tt)
REVERT: E  199 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7057 (ttp-170)
REVERT: E  212 LEU cc_start: 0.8901 (tp) cc_final: 0.8663 (tp)
REVERT: E  221 SER cc_start: 0.8606 (m) cc_final: 0.8267 (p)
REVERT: E  265 MET cc_start: 0.8738 (ttt) cc_final: 0.8492 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 399
  average time/residue: 0.0983
  time to fit residues: 60.0870
Evaluate side-chains
  318 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 318
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 131 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 68 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 126 optimal weight:    7.9990
   chunk 47 optimal weight:    9.9990
   chunk 110 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 139 GLN
A 285 HIS
** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 GLN
B 285 HIS
** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 139 GLN
** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 139 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.122595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.094591 restraints weight = 31130.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.097880 restraints weight = 19039.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.099750 restraints weight = 13278.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.101494 restraints weight = 10409.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.102370 restraints weight = 8582.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  13065  Z= 0.246
  Angle     :  0.663   7.707  17780  Z= 0.354
  Chirality :  0.049   0.190   1955
  Planarity :  0.005   0.054   2265
  Dihedral  :  5.361  22.507   1715
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.22), residues: 1540
  helix:  1.24 (0.23), residues: 535
  sheet: -0.24 (0.25), residues: 450
  loop : -1.92 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  91 
 TYR   0.021   0.002   TYR E 204 
 PHE   0.016   0.002   PHE C 228 
 TRP   0.019   0.002   TRP C 206 
 HIS   0.004   0.001   HIS D 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00544 (13065)
  covalent geometry    : angle       0.66349 (17780)
  hydrogen bonds       : bond        0.03778 (  620)
  hydrogen bonds       : angle       5.27697 ( 2040)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  373 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 373
  time to evaluate  : 0.502 
Fit side-chains
REVERT: A   39 ILE cc_start: 0.9017 (tp) cc_final: 0.8553 (pt)
REVERT: A   64 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8697 (pm20)
REVERT: A   77 GLU cc_start: 0.7726 (pp20) cc_final: 0.7508 (pp20)
REVERT: A  102 TYR cc_start: 0.8324 (t80) cc_final: 0.7951 (t80)
REVERT: A  107 LEU cc_start: 0.8047 (tt) cc_final: 0.7648 (tp)
REVERT: A  161 TRP cc_start: 0.7118 (m-10) cc_final: 0.6843 (m-10)
REVERT: A  198 VAL cc_start: 0.8948 (p) cc_final: 0.8677 (m)
REVERT: A  203 TYR cc_start: 0.8510 (t80) cc_final: 0.8220 (t80)
REVERT: A  212 LEU cc_start: 0.9167 (tp) cc_final: 0.8845 (tp)
REVERT: A  265 MET cc_start: 0.8748 (ttt) cc_final: 0.8389 (ttt)
REVERT: A  301 ARG cc_start: 0.7017 (ptp90) cc_final: 0.6573 (ttp-170)
REVERT: B   39 ILE cc_start: 0.9121 (tp) cc_final: 0.8728 (pt)
REVERT: B   64 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8627 (pm20)
REVERT: B  131 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8226 (mt-10)
REVERT: B  198 VAL cc_start: 0.8987 (p) cc_final: 0.8650 (m)
REVERT: B  212 LEU cc_start: 0.9202 (tp) cc_final: 0.8970 (tp)
REVERT: B  301 ARG cc_start: 0.7007 (ptp90) cc_final: 0.6005 (ttm170)
REVERT: C   39 ILE cc_start: 0.9068 (tp) cc_final: 0.8498 (pt)
REVERT: C   64 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8681 (pm20)
REVERT: C   93 MET cc_start: 0.9035 (tpp) cc_final: 0.8707 (tpp)
REVERT: C  102 TYR cc_start: 0.8592 (t80) cc_final: 0.8076 (t80)
REVERT: C  148 TYR cc_start: 0.8003 (m-80) cc_final: 0.7799 (m-80)
REVERT: C  199 ARG cc_start: 0.6753 (ttp-170) cc_final: 0.6380 (ttp-170)
REVERT: C  212 LEU cc_start: 0.9184 (tp) cc_final: 0.8725 (tp)
REVERT: C  223 PHE cc_start: 0.8356 (m-10) cc_final: 0.8073 (m-10)
REVERT: C  265 MET cc_start: 0.8660 (ttt) cc_final: 0.8408 (ttt)
REVERT: C  266 ILE cc_start: 0.8626 (tp) cc_final: 0.7885 (tp)
REVERT: D   39 ILE cc_start: 0.9137 (tp) cc_final: 0.8679 (pt)
REVERT: D   64 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8643 (pm20)
REVERT: D  102 TYR cc_start: 0.8365 (t80) cc_final: 0.8053 (t80)
REVERT: D  131 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8350 (mt-10)
REVERT: D  140 LEU cc_start: 0.9137 (tt) cc_final: 0.8914 (tt)
REVERT: D  150 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7285 (tm-30)
REVERT: D  198 VAL cc_start: 0.8981 (p) cc_final: 0.8740 (m)
REVERT: D  199 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.8072 (ttp-170)
REVERT: D  203 TYR cc_start: 0.8543 (t80) cc_final: 0.8240 (t80)
REVERT: D  212 LEU cc_start: 0.8997 (tp) cc_final: 0.8636 (tp)
REVERT: D  265 MET cc_start: 0.8713 (ttt) cc_final: 0.8465 (ttt)
REVERT: D  266 ILE cc_start: 0.8666 (tp) cc_final: 0.8398 (tp)
REVERT: E   39 ILE cc_start: 0.9070 (tp) cc_final: 0.8640 (pt)
REVERT: E   64 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8692 (pm20)
REVERT: E  102 TYR cc_start: 0.8324 (t80) cc_final: 0.7997 (t80)
REVERT: E  131 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7116 (mt-10)
REVERT: E  140 LEU cc_start: 0.9071 (tt) cc_final: 0.8816 (tt)
REVERT: E  203 TYR cc_start: 0.8415 (t80) cc_final: 0.8029 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 373
  average time/residue: 0.1015
  time to fit residues: 57.9967
Evaluate side-chains
  317 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 317
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 122 optimal weight:    9.9990
   chunk 136 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 154 optimal weight:    5.9990
   chunk 106 optimal weight:    3.9990
   chunk 137 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0070
   chunk 101 optimal weight:    6.9990
   chunk 104 optimal weight:    0.9980
   chunk 142 optimal weight:    1.9990
   overall best weight:    1.8004

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 124 GLN
A 139 GLN
** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 GLN
C 139 GLN
** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 139 GLN
E 139 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.126401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.097610 restraints weight = 30372.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.100687 restraints weight = 17986.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.103423 restraints weight = 12654.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.104867 restraints weight = 9636.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.106200 restraints weight = 7993.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13065  Z= 0.138
  Angle     :  0.592   6.276  17780  Z= 0.315
  Chirality :  0.048   0.176   1955
  Planarity :  0.004   0.049   2265
  Dihedral  :  5.205  21.307   1715
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.22), residues: 1540
  helix:  1.36 (0.23), residues: 540
  sheet: -0.28 (0.25), residues: 450
  loop : -1.82 (0.25), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  91 
 TYR   0.020   0.001   TYR C 203 
 PHE   0.010   0.001   PHE C  19 
 TRP   0.040   0.002   TRP D 220 
 HIS   0.003   0.001   HIS A 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (13065)
  covalent geometry    : angle       0.59239 (17780)
  hydrogen bonds       : bond        0.03396 (  620)
  hydrogen bonds       : angle       5.01619 ( 2040)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  375 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 375
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 ILE cc_start: 0.9060 (tp) cc_final: 0.8594 (pt)
REVERT: A   64 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8691 (pm20)
REVERT: A  102 TYR cc_start: 0.8293 (t80) cc_final: 0.7856 (t80)
REVERT: A  107 LEU cc_start: 0.7889 (tt) cc_final: 0.7222 (tt)
REVERT: A  161 TRP cc_start: 0.7134 (m-10) cc_final: 0.6858 (m-10)
REVERT: A  198 VAL cc_start: 0.8897 (p) cc_final: 0.8653 (m)
REVERT: A  212 LEU cc_start: 0.9168 (tp) cc_final: 0.8816 (tp)
REVERT: A  265 MET cc_start: 0.8736 (ttt) cc_final: 0.8364 (ttt)
REVERT: A  301 ARG cc_start: 0.6897 (ptp90) cc_final: 0.6565 (ttp-170)
REVERT: B   39 ILE cc_start: 0.9133 (tp) cc_final: 0.8738 (pt)
REVERT: B   64 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8665 (pm20)
REVERT: B   77 GLU cc_start: 0.7745 (pp20) cc_final: 0.7485 (pp20)
REVERT: B  191 ILE cc_start: 0.8788 (mt) cc_final: 0.8583 (mt)
REVERT: B  198 VAL cc_start: 0.8905 (p) cc_final: 0.8577 (m)
REVERT: B  212 LEU cc_start: 0.9160 (tp) cc_final: 0.8932 (tp)
REVERT: B  265 MET cc_start: 0.8749 (ttt) cc_final: 0.8514 (ttt)
REVERT: C   39 ILE cc_start: 0.9071 (tp) cc_final: 0.8592 (pt)
REVERT: C   64 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8612 (pm20)
REVERT: C  102 TYR cc_start: 0.8594 (t80) cc_final: 0.8129 (t80)
REVERT: C  107 LEU cc_start: 0.7832 (tp) cc_final: 0.7579 (tp)
REVERT: C  131 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8294 (mt-10)
REVERT: C  191 ILE cc_start: 0.8792 (mt) cc_final: 0.8559 (mt)
REVERT: C  212 LEU cc_start: 0.9079 (tp) cc_final: 0.8567 (tp)
REVERT: C  265 MET cc_start: 0.8711 (ttt) cc_final: 0.8401 (ttt)
REVERT: C  266 ILE cc_start: 0.8575 (tp) cc_final: 0.7670 (tp)
REVERT: C  301 ARG cc_start: 0.7148 (ptp90) cc_final: 0.6528 (ttp-170)
REVERT: D   39 ILE cc_start: 0.9158 (tp) cc_final: 0.8719 (pt)
REVERT: D   64 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8611 (pm20)
REVERT: D  102 TYR cc_start: 0.8402 (t80) cc_final: 0.8051 (t80)
REVERT: D  115 ASP cc_start: 0.7443 (t70) cc_final: 0.6645 (m-30)
REVERT: D  131 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8266 (mt-10)
REVERT: D  140 LEU cc_start: 0.9159 (tt) cc_final: 0.8922 (tt)
REVERT: D  198 VAL cc_start: 0.8962 (p) cc_final: 0.8696 (m)
REVERT: D  199 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.7954 (ttp-170)
REVERT: D  212 LEU cc_start: 0.9140 (tp) cc_final: 0.8869 (tp)
REVERT: D  265 MET cc_start: 0.8647 (ttt) cc_final: 0.8404 (ttt)
REVERT: D  301 ARG cc_start: 0.6581 (ptp90) cc_final: 0.5649 (ttm170)
REVERT: E  102 TYR cc_start: 0.8365 (t80) cc_final: 0.8094 (t80)
REVERT: E  131 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7090 (mt-10)
REVERT: E  140 LEU cc_start: 0.9104 (tt) cc_final: 0.8837 (tt)
REVERT: E  212 LEU cc_start: 0.9104 (tp) cc_final: 0.8874 (tp)
REVERT: E  265 MET cc_start: 0.8813 (ttt) cc_final: 0.8550 (ttt)
REVERT: E  301 ARG cc_start: 0.6731 (ptp90) cc_final: 0.6294 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 375
  average time/residue: 0.1021
  time to fit residues: 58.4448
Evaluate side-chains
  308 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 308
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 136 optimal weight:    9.9990
   chunk 68 optimal weight:    8.9990
   chunk 73 optimal weight:    2.9990
   chunk 58 optimal weight:    9.9990
   chunk 147 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9980
   chunk 91 optimal weight:   20.0000
   chunk 69 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 14 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 139 GLN
A 285 HIS
** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 GLN
C 139 GLN
** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 139 GLN
E 139 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.126406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.098552 restraints weight = 30135.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.101524 restraints weight = 18269.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.104081 restraints weight = 13003.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.105539 restraints weight = 9943.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.106851 restraints weight = 8264.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.3629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13065  Z= 0.119
  Angle     :  0.576   6.460  17780  Z= 0.303
  Chirality :  0.048   0.170   1955
  Planarity :  0.004   0.048   2265
  Dihedral  :  4.948  19.824   1715
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.01 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.22), residues: 1540
  helix:  1.36 (0.23), residues: 540
  sheet: -0.29 (0.25), residues: 450
  loop : -1.83 (0.24), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 199 
 TYR   0.018   0.001   TYR C 203 
 PHE   0.011   0.001   PHE C  19 
 TRP   0.015   0.001   TRP B 206 
 HIS   0.003   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (13065)
  covalent geometry    : angle       0.57640 (17780)
  hydrogen bonds       : bond        0.03202 (  620)
  hydrogen bonds       : angle       4.88773 ( 2040)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  389 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 388
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8725 (pm20)
REVERT: A  102 TYR cc_start: 0.8235 (t80) cc_final: 0.7834 (t80)
REVERT: A  107 LEU cc_start: 0.7760 (tt) cc_final: 0.7069 (tt)
REVERT: A  162 ILE cc_start: 0.6572 (tt) cc_final: 0.6270 (tt)
REVERT: A  198 VAL cc_start: 0.8904 (p) cc_final: 0.8581 (m)
REVERT: A  199 ARG cc_start: 0.8285 (ttm-80) cc_final: 0.8031 (ttm-80)
REVERT: A  210 LEU cc_start: 0.9006 (tp) cc_final: 0.8780 (tt)
REVERT: A  212 LEU cc_start: 0.9116 (tp) cc_final: 0.8842 (tp)
REVERT: A  214 LEU cc_start: 0.8421 (mp) cc_final: 0.8183 (mp)
REVERT: A  265 MET cc_start: 0.8644 (ttt) cc_final: 0.8434 (ttt)
REVERT: A  301 ARG cc_start: 0.6852 (ptp90) cc_final: 0.6559 (ttp-170)
REVERT: B   64 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8644 (pm20)
REVERT: B  191 ILE cc_start: 0.8749 (mt) cc_final: 0.8536 (mt)
REVERT: B  198 VAL cc_start: 0.8919 (p) cc_final: 0.8544 (m)
REVERT: B  212 LEU cc_start: 0.9102 (tp) cc_final: 0.8858 (tp)
REVERT: B  265 MET cc_start: 0.8730 (ttt) cc_final: 0.8515 (ttt)
REVERT: C   64 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8614 (pm20)
REVERT: C  102 TYR cc_start: 0.8571 (t80) cc_final: 0.8200 (t80)
REVERT: C  115 ASP cc_start: 0.7693 (t70) cc_final: 0.6661 (m-30)
REVERT: C  131 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8071 (mt-10)
REVERT: C  150 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7896 (tm-30)
REVERT: C  191 ILE cc_start: 0.8831 (mt) cc_final: 0.8624 (mt)
REVERT: C  212 LEU cc_start: 0.9019 (tp) cc_final: 0.8533 (tp)
REVERT: C  265 MET cc_start: 0.8610 (ttt) cc_final: 0.8304 (ttt)
REVERT: C  266 ILE cc_start: 0.8580 (tp) cc_final: 0.7811 (tp)
REVERT: C  301 ARG cc_start: 0.7045 (ptp90) cc_final: 0.6461 (ttp-170)
REVERT: D   64 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8607 (pm20)
REVERT: D  102 TYR cc_start: 0.8338 (t80) cc_final: 0.8060 (t80)
REVERT: D  115 ASP cc_start: 0.7365 (t70) cc_final: 0.6739 (m-30)
REVERT: D  140 LEU cc_start: 0.9140 (tt) cc_final: 0.8918 (tt)
REVERT: D  161 TRP cc_start: 0.7134 (m-10) cc_final: 0.6875 (m-10)
REVERT: D  198 VAL cc_start: 0.8922 (p) cc_final: 0.8634 (m)
REVERT: D  199 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7887 (ttp-170)
REVERT: D  212 LEU cc_start: 0.9068 (tp) cc_final: 0.8771 (tp)
REVERT: D  265 MET cc_start: 0.8627 (ttt) cc_final: 0.8351 (ttt)
REVERT: D  301 ARG cc_start: 0.6111 (ptp90) cc_final: 0.5433 (ttm170)
REVERT: E  102 TYR cc_start: 0.8226 (t80) cc_final: 0.7992 (t80)
REVERT: E  107 LEU cc_start: 0.7868 (tt) cc_final: 0.7236 (tt)
REVERT: E  131 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7071 (mt-10)
REVERT: E  140 LEU cc_start: 0.9034 (tt) cc_final: 0.8787 (tt)
REVERT: E  212 LEU cc_start: 0.9013 (tp) cc_final: 0.8734 (tp)
REVERT: E  265 MET cc_start: 0.8777 (ttt) cc_final: 0.8476 (ttt)
REVERT: E  301 ARG cc_start: 0.6521 (ptp90) cc_final: 0.6286 (ttp-170)
  outliers start: 1
  outliers final: 0
  residues processed: 388
  average time/residue: 0.1027
  time to fit residues: 60.9870
Evaluate side-chains
  301 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 301
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 143 optimal weight:    2.9990
   chunk 93 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0060
   chunk 152 optimal weight:    0.0370
   chunk 100 optimal weight:    0.5980
   chunk 147 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.4874

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 124 GLN
A 139 GLN
** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 GLN
C 139 GLN
** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 139 GLN
E 139 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.129655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.101674 restraints weight = 30262.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.104911 restraints weight = 18289.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.107125 restraints weight = 12846.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.108602 restraints weight = 9933.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.109101 restraints weight = 8265.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  13065  Z= 0.113
  Angle     :  0.583   6.761  17780  Z= 0.307
  Chirality :  0.048   0.205   1955
  Planarity :  0.004   0.048   2265
  Dihedral  :  4.767  18.865   1715
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.22), residues: 1540
  helix:  1.25 (0.22), residues: 540
  sheet: -0.14 (0.24), residues: 485
  loop : -1.56 (0.26), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  91 
 TYR   0.019   0.001   TYR C 203 
 PHE   0.021   0.001   PHE C 274 
 TRP   0.016   0.002   TRP A 220 
 HIS   0.003   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (13065)
  covalent geometry    : angle       0.58260 (17780)
  hydrogen bonds       : bond        0.03180 (  620)
  hydrogen bonds       : angle       4.73239 ( 2040)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  402 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 402
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8775 (pm20)
REVERT: A  102 TYR cc_start: 0.8216 (t80) cc_final: 0.7660 (t80)
REVERT: A  199 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.7997 (ttm-80)
REVERT: A  210 LEU cc_start: 0.8965 (tp) cc_final: 0.8741 (tt)
REVERT: A  212 LEU cc_start: 0.9054 (tp) cc_final: 0.8778 (tp)
REVERT: A  214 LEU cc_start: 0.8378 (mp) cc_final: 0.8110 (mp)
REVERT: A  301 ARG cc_start: 0.6687 (ptp90) cc_final: 0.6482 (ttp-170)
REVERT: B   64 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8596 (pm20)
REVERT: B  161 TRP cc_start: 0.7235 (m-10) cc_final: 0.6958 (m-10)
REVERT: B  198 VAL cc_start: 0.8792 (p) cc_final: 0.8440 (m)
REVERT: B  212 LEU cc_start: 0.9085 (tp) cc_final: 0.8844 (tp)
REVERT: B  265 MET cc_start: 0.8716 (ttt) cc_final: 0.8511 (ttt)
REVERT: C   34 LYS cc_start: 0.8526 (mttp) cc_final: 0.8230 (mptt)
REVERT: C   39 ILE cc_start: 0.9117 (tp) cc_final: 0.8704 (pt)
REVERT: C   64 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8571 (pm20)
REVERT: C   77 GLU cc_start: 0.7798 (pp20) cc_final: 0.7417 (pp20)
REVERT: C  102 TYR cc_start: 0.8438 (t80) cc_final: 0.8212 (t80)
REVERT: C  115 ASP cc_start: 0.7768 (t70) cc_final: 0.7176 (m-30)
REVERT: C  131 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8094 (mt-10)
REVERT: C  212 LEU cc_start: 0.9015 (tp) cc_final: 0.8542 (tp)
REVERT: C  221 SER cc_start: 0.8633 (m) cc_final: 0.8294 (p)
REVERT: C  265 MET cc_start: 0.8535 (ttt) cc_final: 0.8293 (ttt)
REVERT: C  294 ASP cc_start: 0.7687 (m-30) cc_final: 0.7146 (m-30)
REVERT: D   34 LYS cc_start: 0.8416 (mptt) cc_final: 0.8212 (mptt)
REVERT: D   39 ILE cc_start: 0.9075 (tp) cc_final: 0.8688 (pt)
REVERT: D   64 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8553 (pm20)
REVERT: D  102 TYR cc_start: 0.8213 (t80) cc_final: 0.7981 (t80)
REVERT: D  107 LEU cc_start: 0.7748 (tp) cc_final: 0.6227 (mp)
REVERT: D  115 ASP cc_start: 0.7193 (t70) cc_final: 0.6648 (m-30)
REVERT: D  161 TRP cc_start: 0.7169 (m-10) cc_final: 0.6912 (m-10)
REVERT: D  198 VAL cc_start: 0.8885 (p) cc_final: 0.8593 (m)
REVERT: D  212 LEU cc_start: 0.8935 (tp) cc_final: 0.8657 (tp)
REVERT: D  265 MET cc_start: 0.8534 (ttt) cc_final: 0.8272 (ttt)
REVERT: D  294 ASP cc_start: 0.7758 (m-30) cc_final: 0.7489 (m-30)
REVERT: D  301 ARG cc_start: 0.5949 (ptp90) cc_final: 0.5384 (ttm170)
REVERT: E  107 LEU cc_start: 0.7776 (tt) cc_final: 0.7140 (tt)
REVERT: E  115 ASP cc_start: 0.7782 (t70) cc_final: 0.6687 (m-30)
REVERT: E  131 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7145 (mt-10)
REVERT: E  140 LEU cc_start: 0.8980 (tt) cc_final: 0.8775 (tt)
REVERT: E  212 LEU cc_start: 0.8989 (tp) cc_final: 0.8728 (tp)
REVERT: E  265 MET cc_start: 0.8743 (ttt) cc_final: 0.8434 (ttt)
REVERT: E  301 ARG cc_start: 0.6483 (ptp90) cc_final: 0.6270 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 402
  average time/residue: 0.0988
  time to fit residues: 61.1594
Evaluate side-chains
  321 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 321
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 111 optimal weight:    0.8980
   chunk 142 optimal weight:    7.9990
   chunk 141 optimal weight:   20.0000
   chunk 49 optimal weight:    3.9990
   chunk 80 optimal weight:   10.0000
   chunk 131 optimal weight:    9.9990
   chunk 13 optimal weight:    0.3980
   chunk 78 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 139 GLN
** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 GLN
C 139 GLN
** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 139 GLN
** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 139 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.128945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.100521 restraints weight = 30449.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.103821 restraints weight = 18451.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.106058 restraints weight = 12948.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.107434 restraints weight = 10028.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.108069 restraints weight = 8442.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13065  Z= 0.122
  Angle     :  0.589   6.887  17780  Z= 0.306
  Chirality :  0.047   0.169   1955
  Planarity :  0.004   0.050   2265
  Dihedral  :  4.765  17.918   1715
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.22), residues: 1540
  helix:  1.23 (0.23), residues: 540
  sheet: -0.05 (0.25), residues: 460
  loop : -1.52 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 199 
 TYR   0.016   0.001   TYR A 203 
 PHE   0.017   0.001   PHE B 274 
 TRP   0.017   0.002   TRP D 206 
 HIS   0.003   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (13065)
  covalent geometry    : angle       0.58898 (17780)
  hydrogen bonds       : bond        0.03073 (  620)
  hydrogen bonds       : angle       4.70387 ( 2040)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2585.33 seconds
wall clock time: 45 minutes 19.16 seconds (2719.16 seconds total)