Starting phenix.real_space_refine
on Thu Feb  5 08:05:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m4a_63620/02_2026/9m4a_63620.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m4a_63620/02_2026/9m4a_63620.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m4a_63620/02_2026/9m4a_63620.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m4a_63620/02_2026/9m4a_63620.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m4a_63620/02_2026/9m4a_63620.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m4a_63620/02_2026/9m4a_63620.cif"
  }
  resolution = 3.46
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    9947      2.51       5
     N    2702      2.21       5
     O    3115      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15813
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "G"
      Number of atoms: 2259
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2259
          Classifications: {'peptide': 280}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270}
          Chain breaks: 1
  Restraints were copied for chains:
    A, B, C, D, E, F
  Time building chain proxies: 2.12, per 1000 atoms: 0.13
  Number of scatterers: 15813
  At special positions: 0
  Unit cell: (110.4, 111.32, 95.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      49     16.00
     O    3115      8.00
     N    2702      7.00
     C    9947      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: 1.19
  Conformation dependent library (CDL) restraints added in 564.1 milliseconds
  

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3668

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 43 sheets defined
      6.4% alpha, 49.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'G' and resid 1 through 6
    Processing helix  chain 'G' and resid 205 through 209
    Processing helix  chain 'G' and resid 217 through 223
      removed outlier: 4.145A  pdb=" N   SER G 221 " --> pdb=" O   SER G 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1 through 6
    Processing helix  chain 'A' and resid 205 through 209
    Processing helix  chain 'A' and resid 217 through 223
      removed outlier: 4.145A  pdb=" N   SER A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1 through 6
    Processing helix  chain 'B' and resid 205 through 209
    Processing helix  chain 'B' and resid 217 through 223
      removed outlier: 4.145A  pdb=" N   SER B 221 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1 through 6
    Processing helix  chain 'C' and resid 205 through 209
    Processing helix  chain 'C' and resid 217 through 223
      removed outlier: 4.144A  pdb=" N   SER C 221 " --> pdb=" O   SER C 217 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1 through 6
    Processing helix  chain 'D' and resid 205 through 209
    Processing helix  chain 'D' and resid 217 through 223
      removed outlier: 4.146A  pdb=" N   SER D 221 " --> pdb=" O   SER D 217 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1 through 6
    Processing helix  chain 'E' and resid 205 through 209
    Processing helix  chain 'E' and resid 217 through 223
      removed outlier: 4.145A  pdb=" N   SER E 221 " --> pdb=" O   SER E 217 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1 through 6
    Processing helix  chain 'F' and resid 205 through 209
    Processing helix  chain 'F' and resid 217 through 223
      removed outlier: 4.145A  pdb=" N   SER F 221 " --> pdb=" O   SER F 217 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'G' and resid 21 through 22
    Processing sheet with id=AA2, first strand: chain 'G' and resid 21 through 22
    Processing sheet with id=AA3, first strand: chain 'G' and resid 26 through 29
      removed outlier: 3.585A  pdb=" N   ASP G  29 " --> pdb=" O   MET G  34 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 75 through 76
      removed outlier: 6.314A  pdb=" N   ASP G 254 " --> pdb=" O   PRO G  81 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   TYR G 256 " --> pdb=" O   ALA G  79 " (cutoff:3.500A)
      removed outlier: 5.624A  pdb=" N   ALA G  79 " --> pdb=" O   TYR G 256 " (cutoff:3.500A)
      removed outlier: 8.628A  pdb=" N   SER G  82 " --> pdb=" O   PHE G 171 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE G 171 " --> pdb=" O   SER G  82 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   GLY G 166 " --> pdb=" O   GLU G 158 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'G' and resid 75 through 76
      removed outlier: 6.774A  pdb=" N   THR G 243 " --> pdb=" O   TYR G 282 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   TYR G 282 " --> pdb=" O   THR G 243 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE G 245 " --> pdb=" O   GLU G 280 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLU G 280 " --> pdb=" O   ILE G 245 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   VAL G 247 " --> pdb=" O   SER G 278 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   SER G 278 " --> pdb=" O   VAL G 247 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   TYR G 249 " --> pdb=" O   ASP G 276 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ASP G 276 " --> pdb=" O   TYR G 249 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ARG G 251 " --> pdb=" O   TRP G 274 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   TRP G 274 " --> pdb=" O   ARG G 251 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ARG G 253 " --> pdb=" O   ASP G 272 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ASP G 272 " --> pdb=" O   ARG G 253 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 111 through 120
    Processing sheet with id=AA7, first strand: chain 'G' and resid 174 through 176
      removed outlier: 4.779A  pdb=" N   GLY G 180 " --> pdb=" O   ASN G 176 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 21 through 22
    Processing sheet with id=AA9, first strand: chain 'A' and resid 21 through 22
    Processing sheet with id=AB1, first strand: chain 'A' and resid 26 through 29
      removed outlier: 3.584A  pdb=" N   ASP A  29 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 75 through 76
      removed outlier: 6.315A  pdb=" N   ASP A 254 " --> pdb=" O   PRO A  81 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   TYR A 256 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
      removed outlier: 5.624A  pdb=" N   ALA A  79 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 8.628A  pdb=" N   SER A  82 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE A 171 " --> pdb=" O   SER A  82 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   GLY A 166 " --> pdb=" O   GLU A 158 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 75 through 76
      removed outlier: 6.775A  pdb=" N   THR A 243 " --> pdb=" O   TYR A 282 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   TYR A 282 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE A 245 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLU A 280 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   VAL A 247 " --> pdb=" O   SER A 278 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   SER A 278 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   TYR A 249 " --> pdb=" O   ASP A 276 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ASP A 276 " --> pdb=" O   TYR A 249 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ARG A 251 " --> pdb=" O   TRP A 274 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   TRP A 274 " --> pdb=" O   ARG A 251 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ARG A 253 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ASP A 272 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 174 through 176
      removed outlier: 4.778A  pdb=" N   GLY A 180 " --> pdb=" O   ASN A 176 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 21 through 22
    Processing sheet with id=AB6, first strand: chain 'B' and resid 21 through 22
    Processing sheet with id=AB7, first strand: chain 'B' and resid 26 through 29
      removed outlier: 3.586A  pdb=" N   ASP B  29 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 75 through 76
      removed outlier: 6.314A  pdb=" N   ASP B 254 " --> pdb=" O   PRO B  81 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   TYR B 256 " --> pdb=" O   ALA B  79 " (cutoff:3.500A)
      removed outlier: 5.624A  pdb=" N   ALA B  79 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
      removed outlier: 8.628A  pdb=" N   SER B  82 " --> pdb=" O   PHE B 171 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE B 171 " --> pdb=" O   SER B  82 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   GLY B 166 " --> pdb=" O   GLU B 158 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 75 through 76
      removed outlier: 6.772A  pdb=" N   THR B 243 " --> pdb=" O   TYR B 282 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   TYR B 282 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ILE B 245 " --> pdb=" O   GLU B 280 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLU B 280 " --> pdb=" O   ILE B 245 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   VAL B 247 " --> pdb=" O   SER B 278 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   SER B 278 " --> pdb=" O   VAL B 247 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   TYR B 249 " --> pdb=" O   ASP B 276 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ASP B 276 " --> pdb=" O   TYR B 249 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ARG B 251 " --> pdb=" O   TRP B 274 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   TRP B 274 " --> pdb=" O   ARG B 251 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ARG B 253 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ASP B 272 " --> pdb=" O   ARG B 253 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 174 through 176
      removed outlier: 4.778A  pdb=" N   GLY B 180 " --> pdb=" O   ASN B 176 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 21 through 22
    Processing sheet with id=AC3, first strand: chain 'C' and resid 21 through 22
    Processing sheet with id=AC4, first strand: chain 'C' and resid 26 through 29
      removed outlier: 3.585A  pdb=" N   ASP C  29 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 75 through 76
      removed outlier: 6.314A  pdb=" N   ASP C 254 " --> pdb=" O   PRO C  81 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   TYR C 256 " --> pdb=" O   ALA C  79 " (cutoff:3.500A)
      removed outlier: 5.624A  pdb=" N   ALA C  79 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
      removed outlier: 8.628A  pdb=" N   SER C  82 " --> pdb=" O   PHE C 171 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE C 171 " --> pdb=" O   SER C  82 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   GLY C 166 " --> pdb=" O   GLU C 158 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 75 through 76
      removed outlier: 6.774A  pdb=" N   THR C 243 " --> pdb=" O   TYR C 282 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   TYR C 282 " --> pdb=" O   THR C 243 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE C 245 " --> pdb=" O   GLU C 280 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLU C 280 " --> pdb=" O   ILE C 245 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   VAL C 247 " --> pdb=" O   SER C 278 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   SER C 278 " --> pdb=" O   VAL C 247 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   TYR C 249 " --> pdb=" O   ASP C 276 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ASP C 276 " --> pdb=" O   TYR C 249 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ARG C 251 " --> pdb=" O   TRP C 274 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   TRP C 274 " --> pdb=" O   ARG C 251 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ARG C 253 " --> pdb=" O   ASP C 272 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ASP C 272 " --> pdb=" O   ARG C 253 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'C' and resid 174 through 176
      removed outlier: 4.780A  pdb=" N   GLY C 180 " --> pdb=" O   ASN C 176 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'D' and resid 21 through 22
    Processing sheet with id=AC9, first strand: chain 'D' and resid 21 through 22
    Processing sheet with id=AD1, first strand: chain 'D' and resid 26 through 29
      removed outlier: 3.584A  pdb=" N   ASP D  29 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'D' and resid 75 through 76
      removed outlier: 6.314A  pdb=" N   ASP D 254 " --> pdb=" O   PRO D  81 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   TYR D 256 " --> pdb=" O   ALA D  79 " (cutoff:3.500A)
      removed outlier: 5.623A  pdb=" N   ALA D  79 " --> pdb=" O   TYR D 256 " (cutoff:3.500A)
      removed outlier: 8.628A  pdb=" N   SER D  82 " --> pdb=" O   PHE D 171 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE D 171 " --> pdb=" O   SER D  82 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   GLY D 166 " --> pdb=" O   GLU D 158 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'D' and resid 75 through 76
      removed outlier: 6.773A  pdb=" N   THR D 243 " --> pdb=" O   TYR D 282 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   TYR D 282 " --> pdb=" O   THR D 243 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE D 245 " --> pdb=" O   GLU D 280 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLU D 280 " --> pdb=" O   ILE D 245 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   VAL D 247 " --> pdb=" O   SER D 278 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   SER D 278 " --> pdb=" O   VAL D 247 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   TYR D 249 " --> pdb=" O   ASP D 276 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ASP D 276 " --> pdb=" O   TYR D 249 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ARG D 251 " --> pdb=" O   TRP D 274 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   TRP D 274 " --> pdb=" O   ARG D 251 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ARG D 253 " --> pdb=" O   ASP D 272 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ASP D 272 " --> pdb=" O   ARG D 253 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'D' and resid 174 through 176
      removed outlier: 4.778A  pdb=" N   GLY D 180 " --> pdb=" O   ASN D 176 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'E' and resid 21 through 22
    Processing sheet with id=AD6, first strand: chain 'E' and resid 21 through 22
    Processing sheet with id=AD7, first strand: chain 'E' and resid 26 through 29
      removed outlier: 3.585A  pdb=" N   ASP E  29 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'E' and resid 75 through 76
      removed outlier: 6.314A  pdb=" N   ASP E 254 " --> pdb=" O   PRO E  81 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   TYR E 256 " --> pdb=" O   ALA E  79 " (cutoff:3.500A)
      removed outlier: 5.624A  pdb=" N   ALA E  79 " --> pdb=" O   TYR E 256 " (cutoff:3.500A)
      removed outlier: 8.629A  pdb=" N   SER E  82 " --> pdb=" O   PHE E 171 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE E 171 " --> pdb=" O   SER E  82 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   GLY E 166 " --> pdb=" O   GLU E 158 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'E' and resid 75 through 76
      removed outlier: 6.774A  pdb=" N   THR E 243 " --> pdb=" O   TYR E 282 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   TYR E 282 " --> pdb=" O   THR E 243 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ILE E 245 " --> pdb=" O   GLU E 280 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   GLU E 280 " --> pdb=" O   ILE E 245 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   VAL E 247 " --> pdb=" O   SER E 278 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   SER E 278 " --> pdb=" O   VAL E 247 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   TYR E 249 " --> pdb=" O   ASP E 276 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ASP E 276 " --> pdb=" O   TYR E 249 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ARG E 251 " --> pdb=" O   TRP E 274 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   TRP E 274 " --> pdb=" O   ARG E 251 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ARG E 253 " --> pdb=" O   ASP E 272 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ASP E 272 " --> pdb=" O   ARG E 253 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'E' and resid 174 through 176
      removed outlier: 4.778A  pdb=" N   GLY E 180 " --> pdb=" O   ASN E 176 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'F' and resid 21 through 22
    Processing sheet with id=AE3, first strand: chain 'F' and resid 21 through 22
    Processing sheet with id=AE4, first strand: chain 'F' and resid 26 through 29
      removed outlier: 3.586A  pdb=" N   ASP F  29 " --> pdb=" O   MET F  34 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'F' and resid 75 through 76
      removed outlier: 6.314A  pdb=" N   ASP F 254 " --> pdb=" O   PRO F  81 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   TYR F 256 " --> pdb=" O   ALA F  79 " (cutoff:3.500A)
      removed outlier: 5.624A  pdb=" N   ALA F  79 " --> pdb=" O   TYR F 256 " (cutoff:3.500A)
      removed outlier: 8.628A  pdb=" N   SER F  82 " --> pdb=" O   PHE F 171 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE F 171 " --> pdb=" O   SER F  82 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   GLY F 166 " --> pdb=" O   GLU F 158 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'F' and resid 75 through 76
      removed outlier: 6.773A  pdb=" N   THR F 243 " --> pdb=" O   TYR F 282 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   TYR F 282 " --> pdb=" O   THR F 243 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ILE F 245 " --> pdb=" O   GLU F 280 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   GLU F 280 " --> pdb=" O   ILE F 245 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   VAL F 247 " --> pdb=" O   SER F 278 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   SER F 278 " --> pdb=" O   VAL F 247 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   TYR F 249 " --> pdb=" O   ASP F 276 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ASP F 276 " --> pdb=" O   TYR F 249 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ARG F 251 " --> pdb=" O   TRP F 274 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   TRP F 274 " --> pdb=" O   ARG F 251 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ARG F 253 " --> pdb=" O   ASP F 272 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ASP F 272 " --> pdb=" O   ARG F 253 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'F' and resid 174 through 176
      removed outlier: 4.779A  pdb=" N   GLY F 180 " --> pdb=" O   ASN F 176 " (cutoff:3.500A)

    588 hydrogen bonds defined for protein.
    1449 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: 2.62

  Time building geometry restraints manager: 1.65 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: 5117
        1.34 -     1.46: 3015
        1.46 -     1.57: 7940
        1.57 -     1.69: 0
        1.69 -     1.81: 98
  Bond restraints: 16170
  Sorted by residual:
  bond pdb=" N   ALA F   1 "
       pdb=" CA  ALA F   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.00e+00
  bond pdb=" N   ALA E   1 "
       pdb=" CA  ALA E   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.80e+00
  bond pdb=" N   ALA C   1 "
       pdb=" CA  ALA C   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.79e+00
  bond pdb=" N   ALA D   1 "
       pdb=" CA  ALA D   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.77e+00
  bond pdb=" N   ALA A   1 "
       pdb=" CA  ALA A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.75e+00
  ... (remaining 16165 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.88: 20743
        0.88 -     1.76: 926
        1.76 -     2.64: 136
        2.64 -     3.52: 42
        3.52 -     4.40: 35
  Bond angle restraints: 21882
  Sorted by residual:
  angle pdb=" N   SER A 262 "
        pdb=" CA  SER A 262 "
        pdb=" CB  SER A 262 "
      ideal   model   delta    sigma   weight residual
     114.17  110.69    3.48 1.14e+00 7.69e-01 9.33e+00
  angle pdb=" N   SER B 262 "
        pdb=" CA  SER B 262 "
        pdb=" CB  SER B 262 "
      ideal   model   delta    sigma   weight residual
     114.17  110.69    3.48 1.14e+00 7.69e-01 9.30e+00
  angle pdb=" N   SER F 262 "
        pdb=" CA  SER F 262 "
        pdb=" CB  SER F 262 "
      ideal   model   delta    sigma   weight residual
     114.17  110.71    3.46 1.14e+00 7.69e-01 9.19e+00
  angle pdb=" N   SER G 262 "
        pdb=" CA  SER G 262 "
        pdb=" CB  SER G 262 "
      ideal   model   delta    sigma   weight residual
     114.17  110.73    3.44 1.14e+00 7.69e-01 9.12e+00
  angle pdb=" N   SER E 262 "
        pdb=" CA  SER E 262 "
        pdb=" CB  SER E 262 "
      ideal   model   delta    sigma   weight residual
     114.17  110.75    3.42 1.14e+00 7.69e-01 9.01e+00
  ... (remaining 21877 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.78: 8638
       10.78 -    21.56: 756
       21.56 -    32.34: 133
       32.34 -    43.13: 56
       43.13 -    53.91: 42
  Dihedral angle restraints: 9625
    sinusoidal: 3913
      harmonic: 5712
  Sorted by residual:
  dihedral pdb=" CA  ILE D 248 "
           pdb=" C   ILE D 248 "
           pdb=" N   TYR D 249 "
           pdb=" CA  TYR D 249 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.18   15.82     0      5.00e+00 4.00e-02 1.00e+01
  dihedral pdb=" CA  ILE B 248 "
           pdb=" C   ILE B 248 "
           pdb=" N   TYR B 249 "
           pdb=" CA  TYR B 249 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.19   15.81     0      5.00e+00 4.00e-02 1.00e+01
  dihedral pdb=" CA  ILE E 248 "
           pdb=" C   ILE E 248 "
           pdb=" N   TYR E 249 "
           pdb=" CA  TYR E 249 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.20   15.80     0      5.00e+00 4.00e-02 9.99e+00
  ... (remaining 9622 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1255
       0.026 -    0.052: 735
       0.052 -    0.079: 127
       0.079 -    0.105: 107
       0.105 -    0.131: 107
  Chirality restraints: 2331
  Sorted by residual:
  chirality pdb=" CA  ILE F  61 "
            pdb=" N   ILE F  61 "
            pdb=" C   ILE F  61 "
            pdb=" CB  ILE F  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.28e-01
  chirality pdb=" CA  ILE F 142 "
            pdb=" N   ILE F 142 "
            pdb=" C   ILE F 142 "
            pdb=" CB  ILE F 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-01
  chirality pdb=" CA  ILE C  55 "
            pdb=" N   ILE C  55 "
            pdb=" C   ILE C  55 "
            pdb=" CB  ILE C  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.20e-01
  ... (remaining 2328 not shown)

  Planarity restraints: 2814
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D 180 "   -0.018 5.00e-02 4.00e+02   2.70e-02 1.16e+00
        pdb=" N   PRO D 181 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO D 181 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO D 181 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY F 180 "   -0.018 5.00e-02 4.00e+02   2.68e-02 1.15e+00
        pdb=" N   PRO F 181 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO F 181 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO F 181 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 180 "    0.018 5.00e-02 4.00e+02   2.68e-02 1.15e+00
        pdb=" N   PRO B 181 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO B 181 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 181 "    0.015 5.00e-02 4.00e+02
  ... (remaining 2811 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 268
        2.65 -     3.22: 14925
        3.22 -     3.78: 21495
        3.78 -     4.34: 32510
        4.34 -     4.90: 57145
  Nonbonded interactions: 126343
  Sorted by model distance:
  nonbonded pdb=" O   THR E 261 "
            pdb=" OG  SER E 262 "
     model   vdw
     2.092 3.040
  nonbonded pdb=" O   THR C 261 "
            pdb=" OG  SER C 262 "
     model   vdw
     2.092 3.040
  nonbonded pdb=" O   THR A 261 "
            pdb=" OG  SER A 262 "
     model   vdw
     2.092 3.040
  nonbonded pdb=" O   THR F 261 "
            pdb=" OG  SER F 262 "
     model   vdw
     2.092 3.040
  nonbonded pdb=" O   THR G 261 "
            pdb=" OG  SER G 262 "
     model   vdw
     2.092 3.040
  ... (remaining 126338 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'G'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     13.410
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  16170  Z= 0.157
  Angle     :  0.465   4.403  21882  Z= 0.262
  Chirality :  0.042   0.131   2331
  Planarity :  0.003   0.027   2814
  Dihedral  :  9.573  53.907   5957
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  3.20 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole: -1.37 (0.20), residues: 1932
  helix: -1.05 (0.78), residues: 42
  sheet: -0.74 (0.17), residues: 1001
  loop : -0.95 (0.21), residues: 889

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  56 
 TYR   0.008   0.001   TYR F 249 
 PHE   0.006   0.001   PHE B 224 
 TRP   0.004   0.001   TRP D  80 
 HIS   0.002   0.001   HIS F  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (16170)
  covalent geometry    : angle       0.46495 (21882)
  hydrogen bonds       : bond        0.28553 (  532)
  hydrogen bonds       : angle      12.83139 ( 1449)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  440 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 433
  time to evaluate  : 0.506 
Fit side-chains
REVERT: G   46 LYS cc_start: 0.8114 (pttp) cc_final: 0.7813 (tppt)
REVERT: A   46 LYS cc_start: 0.8280 (pttp) cc_final: 0.7953 (tppt)
REVERT: A  209 ASN cc_start: 0.7699 (t0) cc_final: 0.7498 (t0)
REVERT: B   29 ASP cc_start: 0.7878 (t0) cc_final: 0.7584 (t70)
REVERT: C   46 LYS cc_start: 0.8231 (pttp) cc_final: 0.7796 (tppt)
REVERT: E   29 ASP cc_start: 0.7643 (t0) cc_final: 0.7395 (t70)
REVERT: E   46 LYS cc_start: 0.8356 (pttp) cc_final: 0.7949 (tppt)
REVERT: F   46 LYS cc_start: 0.8225 (pttp) cc_final: 0.7751 (tppt)
  outliers start: 7
  outliers final: 1
  residues processed: 440
  average time/residue: 0.1483
  time to fit residues: 90.0620
Evaluate side-chains
  244 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 243
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  100 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 194 optimal weight:    6.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    0.6980
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
G 269 ASN
** A   6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
B 269 ASN
C   6 ASN
C 269 ASN
D 269 ASN
E 269 ASN
F 269 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.158108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.133190 restraints weight = 17949.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 1.99
r_work: 0.3345 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  16170  Z= 0.205
  Angle     :  0.647   7.596  21882  Z= 0.352
  Chirality :  0.049   0.164   2331
  Planarity :  0.004   0.030   2814
  Dihedral  :  4.490  56.688   2123
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 10.69 %
    Favored  : 87.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole: -1.38 (0.18), residues: 1932
  helix:  None (None), residues: 0
  sheet: -0.92 (0.15), residues: 931
  loop : -0.79 (0.19), residues: 1001

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 184 
 TYR   0.021   0.002   TYR C 191 
 PHE   0.026   0.002   PHE C 196 
 TRP   0.009   0.001   TRP G 167 
 HIS   0.007   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 (16170)
  covalent geometry    : angle       0.64671 (21882)
  hydrogen bonds       : bond        0.04450 (  532)
  hydrogen bonds       : angle       7.15094 ( 1449)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 313
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
REVERT: G   46 LYS cc_start: 0.8637 (pttp) cc_final: 0.7863 (tppt)
REVERT: G  227 ASP cc_start: 0.8007 (t0) cc_final: 0.7807 (t0)
REVERT: A   30 LYS cc_start: 0.7970 (ptpp) cc_final: 0.7533 (ptpp)
REVERT: A   46 LYS cc_start: 0.8849 (pttp) cc_final: 0.7964 (tppt)
REVERT: A   75 LYS cc_start: 0.7524 (mttp) cc_final: 0.7211 (tppt)
REVERT: A  209 ASN cc_start: 0.8655 (t0) cc_final: 0.8147 (t0)
REVERT: A  227 ASP cc_start: 0.8037 (t0) cc_final: 0.7836 (t0)
REVERT: B   30 LYS cc_start: 0.8051 (ptpp) cc_final: 0.7592 (ptpp)
REVERT: B   75 LYS cc_start: 0.7451 (mttm) cc_final: 0.7184 (mmtt)
REVERT: B  227 ASP cc_start: 0.8096 (t0) cc_final: 0.7850 (t0)
REVERT: C  227 ASP cc_start: 0.8024 (t0) cc_final: 0.7813 (t0)
REVERT: E   46 LYS cc_start: 0.8758 (pttp) cc_final: 0.7902 (tppt)
REVERT: E  227 ASP cc_start: 0.7947 (t0) cc_final: 0.7735 (t0)
REVERT: F    6 ASN cc_start: 0.7466 (m-40) cc_final: 0.6848 (p0)
REVERT: F   46 LYS cc_start: 0.8564 (pttp) cc_final: 0.8069 (tppt)
REVERT: F   75 LYS cc_start: 0.7535 (mttm) cc_final: 0.7271 (mmtt)
  outliers start: 33
  outliers final: 18
  residues processed: 325
  average time/residue: 0.1200
  time to fit residues: 57.6706
Evaluate side-chains
  249 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 231
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  145 THR
Chi-restraints excluded: chain A residue   93 ASN
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  145 THR
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  197 MET
Chi-restraints excluded: chain D residue  145 THR
Chi-restraints excluded: chain D residue  291 MET
Chi-restraints excluded: chain E residue  145 THR
Chi-restraints excluded: chain F residue  145 THR
Chi-restraints excluded: chain F residue  175 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 78 optimal weight:    0.0010
   chunk 158 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 170 optimal weight:    6.9990
   chunk 174 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 136 optimal weight:    5.9990
   chunk 172 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    1.5592

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

Flipped N/Q/H residues before XYZ refinement:
C   6 ASN
E 293 ASN
F 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.155627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.130332 restraints weight = 18284.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 2.02
r_work: 0.3300 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.4284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  16170  Z= 0.171
  Angle     :  0.568   8.050  21882  Z= 0.305
  Chirality :  0.046   0.160   2331
  Planarity :  0.003   0.029   2814
  Dihedral  :  4.295  56.602   2123
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 11.14 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole: -1.03 (0.18), residues: 1932
  helix: -1.10 (0.70), residues: 42
  sheet: -0.41 (0.15), residues: 1043
  loop : -0.86 (0.21), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 277 
 TYR   0.017   0.002   TYR C 191 
 PHE   0.025   0.002   PHE B 196 
 TRP   0.009   0.001   TRP D 167 
 HIS   0.006   0.002   HIS G  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (16170)
  covalent geometry    : angle       0.56834 (21882)
  hydrogen bonds       : bond        0.03963 (  532)
  hydrogen bonds       : angle       6.54698 ( 1449)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  352 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 296
  time to evaluate  : 0.601 
Fit side-chains
REVERT: G   46 LYS cc_start: 0.8815 (pttp) cc_final: 0.7971 (tppt)
REVERT: G  179 TRP cc_start: 0.7090 (t60) cc_final: 0.6838 (t-100)
REVERT: G  227 ASP cc_start: 0.8020 (t0) cc_final: 0.7815 (t0)
REVERT: A   30 LYS cc_start: 0.8306 (ptpp) cc_final: 0.7842 (ptpp)
REVERT: A   46 LYS cc_start: 0.8805 (pttp) cc_final: 0.7842 (tppt)
REVERT: A   75 LYS cc_start: 0.7625 (mttp) cc_final: 0.7393 (tppt)
REVERT: A  209 ASN cc_start: 0.8675 (t0) cc_final: 0.8359 (t0)
REVERT: A  227 ASP cc_start: 0.8152 (t0) cc_final: 0.7918 (t0)
REVERT: B   70 GLU cc_start: 0.8099 (pp20) cc_final: 0.7766 (pp20)
REVERT: B   75 LYS cc_start: 0.7575 (mttm) cc_final: 0.7190 (ttmm)
REVERT: B  227 ASP cc_start: 0.8114 (t0) cc_final: 0.7851 (t0)
REVERT: C   30 LYS cc_start: 0.8306 (ptpp) cc_final: 0.7975 (ptpp)
REVERT: C  174 MET cc_start: 0.8382 (ptm) cc_final: 0.8158 (ptm)
REVERT: C  227 ASP cc_start: 0.8062 (t0) cc_final: 0.7825 (t0)
REVERT: D   45 ASP cc_start: 0.7418 (t70) cc_final: 0.7052 (t0)
REVERT: D  204 MET cc_start: 0.8176 (pmm) cc_final: 0.7811 (pmm)
REVERT: E   46 LYS cc_start: 0.8775 (pttp) cc_final: 0.7886 (tppt)
REVERT: E  227 ASP cc_start: 0.8042 (t0) cc_final: 0.7807 (t0)
REVERT: E  277 ARG cc_start: 0.8622 (mtp-110) cc_final: 0.8413 (mtp-110)
REVERT: E  279 SER cc_start: 0.8980 (t) cc_final: 0.8769 (p)
REVERT: F   46 LYS cc_start: 0.8704 (pttp) cc_final: 0.7963 (tppt)
REVERT: F   75 LYS cc_start: 0.7538 (mttm) cc_final: 0.7254 (mmtt)
REVERT: F  227 ASP cc_start: 0.8007 (t0) cc_final: 0.7754 (t0)
  outliers start: 56
  outliers final: 26
  residues processed: 330
  average time/residue: 0.1285
  time to fit residues: 62.0748
Evaluate side-chains
  270 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 244
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  113 MET
Chi-restraints excluded: chain G residue  145 THR
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  118 TYR
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  113 MET
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain C residue  145 THR
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  197 MET
Chi-restraints excluded: chain C residue  291 MET
Chi-restraints excluded: chain D residue  145 THR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  291 MET
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  118 TYR
Chi-restraints excluded: chain E residue  145 THR
Chi-restraints excluded: chain E residue  291 MET
Chi-restraints excluded: chain E residue  293 ASN
Chi-restraints excluded: chain F residue  145 THR
Chi-restraints excluded: chain F residue  175 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   chunk 165 optimal weight:    2.9990
   chunk 156 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 154 optimal weight:    4.9990
   chunk 147 optimal weight:    0.0470
   chunk 180 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 166 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   overall best weight:    1.3282

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

Flipped N/Q/H residues before XYZ refinement:
A   6 ASN
E   6 ASN
E 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.155698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.130476 restraints weight = 18087.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.03
r_work: 0.3325 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.4564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  16170  Z= 0.154
  Angle     :  0.546   6.616  21882  Z= 0.295
  Chirality :  0.046   0.144   2331
  Planarity :  0.003   0.045   2814
  Dihedral  :  4.185  52.797   2123
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 12.00 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole: -1.01 (0.19), residues: 1932
  helix:  None (None), residues: 0
  sheet: -0.48 (0.15), residues: 1050
  loop : -0.76 (0.22), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 104 
 TYR   0.014   0.001   TYR C 191 
 PHE   0.022   0.002   PHE B 196 
 TRP   0.006   0.001   TRP D 167 
 HIS   0.005   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (16170)
  covalent geometry    : angle       0.54635 (21882)
  hydrogen bonds       : bond        0.03503 (  532)
  hydrogen bonds       : angle       6.19630 ( 1449)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 278
  time to evaluate  : 0.645 
Fit side-chains
REVERT: G   46 LYS cc_start: 0.8813 (pttp) cc_final: 0.8017 (tppt)
REVERT: G   70 GLU cc_start: 0.8131 (pp20) cc_final: 0.7841 (pp20)
REVERT: G   75 LYS cc_start: 0.7868 (tppt) cc_final: 0.7601 (mptt)
REVERT: G  174 MET cc_start: 0.8271 (ptm) cc_final: 0.8065 (ptt)
REVERT: G  179 TRP cc_start: 0.7089 (t60) cc_final: 0.6884 (t-100)
REVERT: A   30 LYS cc_start: 0.8317 (ptpp) cc_final: 0.7929 (ptpp)
REVERT: A   75 LYS cc_start: 0.7816 (mttp) cc_final: 0.7582 (tppt)
REVERT: A  191 TYR cc_start: 0.8751 (m-80) cc_final: 0.8506 (m-80)
REVERT: A  209 ASN cc_start: 0.8715 (t0) cc_final: 0.8398 (t0)
REVERT: B   70 GLU cc_start: 0.8211 (pp20) cc_final: 0.7949 (pp20)
REVERT: B   75 LYS cc_start: 0.7787 (mttm) cc_final: 0.7539 (mmtt)
REVERT: B  118 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6807 (p90)
REVERT: B  227 ASP cc_start: 0.8045 (t0) cc_final: 0.7805 (t0)
REVERT: C   30 LYS cc_start: 0.8411 (ptpp) cc_final: 0.8049 (ptpp)
REVERT: C   70 GLU cc_start: 0.8131 (pp20) cc_final: 0.7843 (pp20)
REVERT: C   75 LYS cc_start: 0.7915 (tppt) cc_final: 0.7713 (tppt)
REVERT: C  174 MET cc_start: 0.8375 (ptm) cc_final: 0.8157 (ptm)
REVERT: C  227 ASP cc_start: 0.7988 (t0) cc_final: 0.7762 (t0)
REVERT: D   70 GLU cc_start: 0.8203 (pp20) cc_final: 0.7934 (pp20)
REVERT: D  179 TRP cc_start: 0.7102 (t60) cc_final: 0.6821 (t-100)
REVERT: D  191 TYR cc_start: 0.8870 (m-80) cc_final: 0.8527 (m-80)
REVERT: E   46 LYS cc_start: 0.8764 (pttp) cc_final: 0.7862 (tppt)
REVERT: E   70 GLU cc_start: 0.8077 (pp20) cc_final: 0.7797 (pp20)
REVERT: E  191 TYR cc_start: 0.8798 (m-80) cc_final: 0.8526 (m-80)
REVERT: E  227 ASP cc_start: 0.8011 (t0) cc_final: 0.7802 (t0)
REVERT: E  277 ARG cc_start: 0.8648 (mtp-110) cc_final: 0.8446 (mtp-110)
REVERT: F   46 LYS cc_start: 0.8699 (pttp) cc_final: 0.7925 (tppt)
REVERT: F   70 GLU cc_start: 0.8250 (pp20) cc_final: 0.7827 (pp20)
REVERT: F   75 LYS cc_start: 0.7705 (mttm) cc_final: 0.7356 (mmtt)
REVERT: F  191 TYR cc_start: 0.8734 (m-80) cc_final: 0.8334 (m-80)
REVERT: F  227 ASP cc_start: 0.7900 (t0) cc_final: 0.7688 (t0)
  outliers start: 47
  outliers final: 34
  residues processed: 302
  average time/residue: 0.1265
  time to fit residues: 56.5861
Evaluate side-chains
  287 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 252
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   90 LEU
Chi-restraints excluded: chain G residue  113 MET
Chi-restraints excluded: chain G residue  145 THR
Chi-restraints excluded: chain G residue  243 THR
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  118 TYR
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  113 MET
Chi-restraints excluded: chain B residue  118 TYR
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain C residue  113 MET
Chi-restraints excluded: chain C residue  145 THR
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  197 MET
Chi-restraints excluded: chain C residue  291 MET
Chi-restraints excluded: chain D residue  145 THR
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain D residue  291 MET
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  145 THR
Chi-restraints excluded: chain E residue  197 MET
Chi-restraints excluded: chain E residue  230 THR
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain F residue   57 THR
Chi-restraints excluded: chain F residue  113 MET
Chi-restraints excluded: chain F residue  145 THR
Chi-restraints excluded: chain F residue  175 VAL
Chi-restraints excluded: chain F residue  231 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 185 optimal weight:    0.0980
   chunk 95 optimal weight:    2.9990
   chunk 40 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 123 optimal weight:    4.9990
   chunk 168 optimal weight:    0.5980
   chunk 178 optimal weight:    0.9980
   chunk 113 optimal weight:    6.9990
   chunk 136 optimal weight:    6.9990
   chunk 83 optimal weight:    0.6980
   chunk 103 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 201 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.161747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.138703 restraints weight = 17649.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.05
r_work: 0.3385 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.4774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020  16170  Z= 0.131
  Angle     :  0.514   6.155  21882  Z= 0.277
  Chirality :  0.045   0.139   2331
  Planarity :  0.003   0.026   2814
  Dihedral  :  4.046  50.096   2123
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 12.97 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole: -0.90 (0.19), residues: 1932
  helix:  None (None), residues: 0
  sheet: -0.35 (0.15), residues: 1071
  loop : -0.77 (0.22), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 184 
 TYR   0.012   0.001   TYR C 191 
 PHE   0.020   0.001   PHE B 196 
 TRP   0.005   0.001   TRP D 167 
 HIS   0.004   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (16170)
  covalent geometry    : angle       0.51374 (21882)
  hydrogen bonds       : bond        0.03235 (  532)
  hydrogen bonds       : angle       5.93065 ( 1449)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 272
  time to evaluate  : 0.611 
Fit side-chains
REVERT: G   75 LYS cc_start: 0.7978 (tppt) cc_final: 0.7735 (mptt)
REVERT: A   30 LYS cc_start: 0.8332 (ptpp) cc_final: 0.7957 (ptpp)
REVERT: A  209 ASN cc_start: 0.8547 (t0) cc_final: 0.8266 (t0)
REVERT: B  118 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.6456 (p90)
REVERT: C   30 LYS cc_start: 0.8406 (ptpp) cc_final: 0.8023 (ptpp)
REVERT: C   70 GLU cc_start: 0.8086 (pp20) cc_final: 0.7875 (pp20)
REVERT: C  118 TYR cc_start: 0.6756 (OUTLIER) cc_final: 0.6357 (p90)
REVERT: D  191 TYR cc_start: 0.8768 (m-80) cc_final: 0.8526 (m-80)
REVERT: E   46 LYS cc_start: 0.8709 (pttp) cc_final: 0.7891 (tppt)
REVERT: E   75 LYS cc_start: 0.7989 (tppt) cc_final: 0.7678 (mptt)
REVERT: F   75 LYS cc_start: 0.7774 (mttm) cc_final: 0.7477 (mmtt)
REVERT: F  191 TYR cc_start: 0.8749 (m-80) cc_final: 0.8464 (m-80)
  outliers start: 59
  outliers final: 42
  residues processed: 307
  average time/residue: 0.1216
  time to fit residues: 56.2088
Evaluate side-chains
  300 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 256
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   90 LEU
Chi-restraints excluded: chain G residue  113 MET
Chi-restraints excluded: chain G residue  145 THR
Chi-restraints excluded: chain G residue  231 VAL
Chi-restraints excluded: chain G residue  243 THR
Chi-restraints excluded: chain G residue  277 ARG
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  118 TYR
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue  113 MET
Chi-restraints excluded: chain B residue  118 TYR
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain C residue  113 MET
Chi-restraints excluded: chain C residue  118 TYR
Chi-restraints excluded: chain C residue  145 THR
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  197 MET
Chi-restraints excluded: chain C residue  291 MET
Chi-restraints excluded: chain D residue  145 THR
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  291 MET
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  145 THR
Chi-restraints excluded: chain E residue  230 THR
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain E residue  243 THR
Chi-restraints excluded: chain E residue  291 MET
Chi-restraints excluded: chain F residue  113 MET
Chi-restraints excluded: chain F residue  145 THR
Chi-restraints excluded: chain F residue  175 VAL
Chi-restraints excluded: chain F residue  197 MET
Chi-restraints excluded: chain F residue  231 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 157 optimal weight:    7.9990
   chunk 35 optimal weight:    9.9990
   chunk 182 optimal weight:    0.5980
   chunk 174 optimal weight:    3.9990
   chunk 176 optimal weight:    0.5980
   chunk 185 optimal weight:    0.6980
   chunk 166 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0370
   chunk 85 optimal weight:    0.5980
   chunk 143 optimal weight:    5.9990
   overall best weight:    0.5058

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.164707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.142073 restraints weight = 17481.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 1.98
r_work: 0.3416 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.4979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  16170  Z= 0.097
  Angle     :  0.486   5.107  21882  Z= 0.263
  Chirality :  0.044   0.139   2331
  Planarity :  0.003   0.036   2814
  Dihedral  :  3.701  16.515   2121
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 13.49 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole: -0.79 (0.19), residues: 1932
  helix:  None (None), residues: 0
  sheet: -0.20 (0.15), residues: 1050
  loop : -0.80 (0.22), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 184 
 TYR   0.010   0.001   TYR C 191 
 PHE   0.020   0.001   PHE E 196 
 TRP   0.006   0.001   TRP F 179 
 HIS   0.003   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 (16170)
  covalent geometry    : angle       0.48579 (21882)
  hydrogen bonds       : bond        0.02865 (  532)
  hydrogen bonds       : angle       5.54955 ( 1449)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 261
  time to evaluate  : 0.623 
Fit side-chains
REVERT: G   75 LYS cc_start: 0.7984 (tppt) cc_final: 0.7697 (mptt)
REVERT: A   30 LYS cc_start: 0.8285 (ptpp) cc_final: 0.7864 (ptpp)
REVERT: A  204 MET cc_start: 0.8151 (pmm) cc_final: 0.7825 (pmm)
REVERT: A  209 ASN cc_start: 0.8516 (t0) cc_final: 0.8209 (t0)
REVERT: B  118 TYR cc_start: 0.6866 (OUTLIER) cc_final: 0.6256 (p90)
REVERT: C   30 LYS cc_start: 0.8326 (ptpp) cc_final: 0.8019 (ptpp)
REVERT: C   75 LYS cc_start: 0.7974 (tppt) cc_final: 0.7653 (mptt)
REVERT: C  118 TYR cc_start: 0.6713 (OUTLIER) cc_final: 0.6111 (p90)
REVERT: D   70 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7870 (tm-30)
REVERT: D  191 TYR cc_start: 0.8724 (m-80) cc_final: 0.8499 (m-80)
REVERT: E   46 LYS cc_start: 0.8675 (pttp) cc_final: 0.7890 (tppt)
REVERT: E   75 LYS cc_start: 0.7854 (tppt) cc_final: 0.7550 (mptt)
REVERT: E  115 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8800 (p)
REVERT: F   75 LYS cc_start: 0.7684 (mttm) cc_final: 0.7421 (mmtt)
REVERT: F  191 TYR cc_start: 0.8699 (m-80) cc_final: 0.8431 (m-80)
  outliers start: 57
  outliers final: 39
  residues processed: 293
  average time/residue: 0.1240
  time to fit residues: 54.8912
Evaluate side-chains
  286 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 243
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   90 LEU
Chi-restraints excluded: chain G residue  145 THR
Chi-restraints excluded: chain G residue  175 VAL
Chi-restraints excluded: chain G residue  231 VAL
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  118 TYR
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue  113 MET
Chi-restraints excluded: chain B residue  118 TYR
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain C residue  113 MET
Chi-restraints excluded: chain C residue  118 TYR
Chi-restraints excluded: chain C residue  145 THR
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   70 GLU
Chi-restraints excluded: chain D residue  113 MET
Chi-restraints excluded: chain D residue  145 THR
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  291 MET
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  113 MET
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  145 THR
Chi-restraints excluded: chain E residue  175 VAL
Chi-restraints excluded: chain E residue  197 MET
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain E residue  291 MET
Chi-restraints excluded: chain F residue  113 MET
Chi-restraints excluded: chain F residue  145 THR
Chi-restraints excluded: chain F residue  175 VAL
Chi-restraints excluded: chain F residue  197 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 156 optimal weight:    4.9990
   chunk 124 optimal weight:    0.8980
   chunk 60 optimal weight:    6.9990
   chunk 110 optimal weight:    3.9990
   chunk 160 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0970
   chunk 125 optimal weight:    6.9990
   chunk 188 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 177 optimal weight:    0.0570
   overall best weight:    1.6100

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

Flipped N/Q/H residues before XYZ refinement:
G   6 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.158218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.135875 restraints weight = 17612.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 1.89
r_work: 0.3367 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.5121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025  16170  Z= 0.172
  Angle     :  0.556   7.597  21882  Z= 0.301
  Chirality :  0.046   0.147   2331
  Planarity :  0.003   0.038   2814
  Dihedral  :  4.034  14.636   2121
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 14.23 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole: -0.95 (0.19), residues: 1932
  helix:  None (None), residues: 0
  sheet: -0.33 (0.15), residues: 1071
  loop : -0.88 (0.22), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 184 
 TYR   0.014   0.002   TYR E  65 
 PHE   0.021   0.002   PHE E 196 
 TRP   0.007   0.001   TRP F 179 
 HIS   0.006   0.002   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (16170)
  covalent geometry    : angle       0.55558 (21882)
  hydrogen bonds       : bond        0.03395 (  532)
  hydrogen bonds       : angle       5.86763 ( 1449)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 267
  time to evaluate  : 0.611 
Fit side-chains
REVERT: G   31 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8069 (pt0)
REVERT: G   46 LYS cc_start: 0.8765 (pttp) cc_final: 0.8004 (tppt)
REVERT: G  227 ASP cc_start: 0.7869 (t0) cc_final: 0.7639 (t0)
REVERT: A   30 LYS cc_start: 0.8482 (ptpp) cc_final: 0.7967 (ptpp)
REVERT: A  209 ASN cc_start: 0.8689 (t0) cc_final: 0.8445 (t0)
REVERT: A  279 SER cc_start: 0.9011 (t) cc_final: 0.8721 (p)
REVERT: B  118 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6408 (p90)
REVERT: B  227 ASP cc_start: 0.8030 (t0) cc_final: 0.7776 (t0)
REVERT: C   30 LYS cc_start: 0.8589 (ptpp) cc_final: 0.8293 (ptpp)
REVERT: C   75 LYS cc_start: 0.7961 (tppt) cc_final: 0.7623 (mptt)
REVERT: C  118 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.6212 (p90)
REVERT: C  227 ASP cc_start: 0.8039 (t0) cc_final: 0.7793 (t0)
REVERT: D  191 TYR cc_start: 0.8919 (m-80) cc_final: 0.8703 (m-80)
REVERT: E   46 LYS cc_start: 0.8789 (pttp) cc_final: 0.7982 (tppt)
REVERT: E  115 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8819 (p)
REVERT: E  191 TYR cc_start: 0.8583 (m-80) cc_final: 0.8380 (m-80)
REVERT: E  227 ASP cc_start: 0.8026 (t0) cc_final: 0.7748 (t0)
REVERT: F  191 TYR cc_start: 0.8813 (m-80) cc_final: 0.8600 (m-80)
REVERT: F  227 ASP cc_start: 0.8044 (t0) cc_final: 0.7814 (t0)
  outliers start: 58
  outliers final: 46
  residues processed: 303
  average time/residue: 0.1293
  time to fit residues: 57.8443
Evaluate side-chains
  297 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 248
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   90 LEU
Chi-restraints excluded: chain G residue  113 MET
Chi-restraints excluded: chain G residue  145 THR
Chi-restraints excluded: chain G residue  175 VAL
Chi-restraints excluded: chain G residue  231 VAL
Chi-restraints excluded: chain G residue  277 ARG
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  118 TYR
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue  113 MET
Chi-restraints excluded: chain B residue  118 TYR
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain C residue  113 MET
Chi-restraints excluded: chain C residue  118 TYR
Chi-restraints excluded: chain C residue  145 THR
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  197 MET
Chi-restraints excluded: chain D residue   70 GLU
Chi-restraints excluded: chain D residue  113 MET
Chi-restraints excluded: chain D residue  145 THR
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  291 MET
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  113 MET
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  145 THR
Chi-restraints excluded: chain E residue  175 VAL
Chi-restraints excluded: chain E residue  197 MET
Chi-restraints excluded: chain E residue  230 THR
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain F residue  113 MET
Chi-restraints excluded: chain F residue  145 THR
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  175 VAL
Chi-restraints excluded: chain F residue  197 MET
Chi-restraints excluded: chain F residue  231 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 160 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 153 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 188 optimal weight:    0.7980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 201 ASN
F   6 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.160136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.137677 restraints weight = 17822.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 1.91
r_work: 0.3388 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.5211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  16170  Z= 0.133
  Angle     :  0.526   6.416  21882  Z= 0.284
  Chirality :  0.045   0.139   2331
  Planarity :  0.003   0.060   2814
  Dihedral  :  3.939  14.648   2121
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 13.94 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole: -0.97 (0.19), residues: 1932
  helix:  None (None), residues: 0
  sheet: -0.36 (0.15), residues: 1071
  loop : -0.88 (0.22), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 281 
 TYR   0.014   0.001   TYR A 191 
 PHE   0.020   0.002   PHE D 196 
 TRP   0.008   0.001   TRP F 179 
 HIS   0.004   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (16170)
  covalent geometry    : angle       0.52581 (21882)
  hydrogen bonds       : bond        0.03113 (  532)
  hydrogen bonds       : angle       5.67647 ( 1449)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 255
  time to evaluate  : 0.620 
Fit side-chains
REVERT: G   31 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8086 (pt0)
REVERT: G   75 LYS cc_start: 0.8022 (tppt) cc_final: 0.7759 (mptt)
REVERT: G  227 ASP cc_start: 0.7887 (t0) cc_final: 0.7646 (t0)
REVERT: A   30 LYS cc_start: 0.8465 (ptpp) cc_final: 0.7973 (ptpp)
REVERT: A  204 MET cc_start: 0.8239 (pmm) cc_final: 0.7828 (pmm)
REVERT: A  209 ASN cc_start: 0.8696 (t0) cc_final: 0.8412 (t0)
REVERT: A  227 ASP cc_start: 0.8050 (t0) cc_final: 0.7832 (t0)
REVERT: B  118 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6365 (p90)
REVERT: B  227 ASP cc_start: 0.8058 (t0) cc_final: 0.7801 (t0)
REVERT: C   30 LYS cc_start: 0.8628 (ptpp) cc_final: 0.8270 (ptpp)
REVERT: C   31 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8104 (pt0)
REVERT: C   75 LYS cc_start: 0.7902 (tppt) cc_final: 0.7578 (mptt)
REVERT: C  118 TYR cc_start: 0.6914 (OUTLIER) cc_final: 0.6168 (p90)
REVERT: C  227 ASP cc_start: 0.8001 (t0) cc_final: 0.7734 (t0)
REVERT: D  191 TYR cc_start: 0.8900 (m-80) cc_final: 0.8670 (m-80)
REVERT: E   46 LYS cc_start: 0.8772 (pttp) cc_final: 0.7984 (tppt)
REVERT: E   75 LYS cc_start: 0.7955 (tppt) cc_final: 0.7699 (mptt)
REVERT: E  118 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.6432 (p90)
REVERT: E  179 TRP cc_start: 0.7334 (t60) cc_final: 0.7066 (t-100)
REVERT: E  227 ASP cc_start: 0.8012 (t0) cc_final: 0.7753 (t0)
REVERT: F  191 TYR cc_start: 0.8788 (m-80) cc_final: 0.8584 (m-80)
REVERT: F  227 ASP cc_start: 0.8066 (t0) cc_final: 0.7851 (t0)
  outliers start: 64
  outliers final: 55
  residues processed: 297
  average time/residue: 0.1121
  time to fit residues: 50.8071
Evaluate side-chains
  307 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 249
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   90 LEU
Chi-restraints excluded: chain G residue  113 MET
Chi-restraints excluded: chain G residue  145 THR
Chi-restraints excluded: chain G residue  175 VAL
Chi-restraints excluded: chain G residue  231 VAL
Chi-restraints excluded: chain G residue  243 THR
Chi-restraints excluded: chain G residue  277 ARG
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  118 TYR
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  113 MET
Chi-restraints excluded: chain B residue  118 TYR
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  197 MET
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain C residue  113 MET
Chi-restraints excluded: chain C residue  118 TYR
Chi-restraints excluded: chain C residue  145 THR
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  197 MET
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain D residue   70 GLU
Chi-restraints excluded: chain D residue  113 MET
Chi-restraints excluded: chain D residue  145 THR
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  291 MET
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  113 MET
Chi-restraints excluded: chain E residue  118 TYR
Chi-restraints excluded: chain E residue  145 THR
Chi-restraints excluded: chain E residue  175 VAL
Chi-restraints excluded: chain E residue  197 MET
Chi-restraints excluded: chain E residue  230 THR
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain E residue  243 THR
Chi-restraints excluded: chain F residue  113 MET
Chi-restraints excluded: chain F residue  145 THR
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  175 VAL
Chi-restraints excluded: chain F residue  197 MET
Chi-restraints excluded: chain F residue  231 VAL
Chi-restraints excluded: chain F residue  243 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 99 optimal weight:    5.9990
   chunk 148 optimal weight:    0.5980
   chunk 137 optimal weight:    0.0870
   chunk 160 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 64 optimal weight:    0.2980
   chunk 105 optimal weight:    0.9980
   chunk 175 optimal weight:    9.9990
   chunk 44 optimal weight:    1.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 201 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.165060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.141897 restraints weight = 17996.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 2.04
r_work: 0.3428 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3267 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.5343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  16170  Z= 0.103
  Angle     :  0.504   8.122  21882  Z= 0.271
  Chirality :  0.044   0.138   2331
  Planarity :  0.003   0.047   2814
  Dihedral  :  3.779  15.212   2121
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 14.80 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole: -0.87 (0.19), residues: 1932
  helix:  None (None), residues: 0
  sheet: -0.27 (0.15), residues: 1071
  loop : -0.86 (0.22), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 281 
 TYR   0.012   0.001   TYR A 191 
 PHE   0.020   0.001   PHE B 196 
 TRP   0.008   0.001   TRP F 179 
 HIS   0.003   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (16170)
  covalent geometry    : angle       0.50436 (21882)
  hydrogen bonds       : bond        0.02817 (  532)
  hydrogen bonds       : angle       5.38433 ( 1449)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 251
  time to evaluate  : 0.567 
Fit side-chains
REVERT: G   31 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8039 (pt0)
REVERT: G   75 LYS cc_start: 0.7972 (tppt) cc_final: 0.7702 (mptt)
REVERT: G  227 ASP cc_start: 0.7835 (t0) cc_final: 0.7621 (t0)
REVERT: A   30 LYS cc_start: 0.8437 (ptpp) cc_final: 0.7931 (ptpp)
REVERT: A  204 MET cc_start: 0.8256 (pmm) cc_final: 0.7837 (pmm)
REVERT: A  279 SER cc_start: 0.8989 (t) cc_final: 0.8716 (p)
REVERT: B  118 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6387 (p90)
REVERT: B  227 ASP cc_start: 0.7968 (t0) cc_final: 0.7737 (t0)
REVERT: C   30 LYS cc_start: 0.8549 (ptpp) cc_final: 0.8234 (ptpp)
REVERT: C   31 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7922 (mt-10)
REVERT: C   75 LYS cc_start: 0.7831 (tppt) cc_final: 0.7507 (mptt)
REVERT: C  118 TYR cc_start: 0.6828 (OUTLIER) cc_final: 0.5927 (p90)
REVERT: C  227 ASP cc_start: 0.8023 (t0) cc_final: 0.7776 (t0)
REVERT: C  287 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7894 (mm-30)
REVERT: D  191 TYR cc_start: 0.8822 (m-80) cc_final: 0.8543 (m-80)
REVERT: D  287 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7779 (mm-30)
REVERT: E   75 LYS cc_start: 0.7910 (tppt) cc_final: 0.7679 (mptt)
REVERT: E  118 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.6129 (p90)
REVERT: E  179 TRP cc_start: 0.7321 (t60) cc_final: 0.7030 (t-100)
REVERT: F  191 TYR cc_start: 0.8739 (m-80) cc_final: 0.8508 (m-80)
REVERT: F  227 ASP cc_start: 0.7997 (t0) cc_final: 0.7790 (t0)
  outliers start: 60
  outliers final: 49
  residues processed: 292
  average time/residue: 0.1107
  time to fit residues: 49.8358
Evaluate side-chains
  284 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 232
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   90 LEU
Chi-restraints excluded: chain G residue  113 MET
Chi-restraints excluded: chain G residue  145 THR
Chi-restraints excluded: chain G residue  175 VAL
Chi-restraints excluded: chain G residue  231 VAL
Chi-restraints excluded: chain G residue  243 THR
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  118 TYR
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  113 MET
Chi-restraints excluded: chain B residue  118 TYR
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain C residue  113 MET
Chi-restraints excluded: chain C residue  118 TYR
Chi-restraints excluded: chain C residue  145 THR
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain D residue  113 MET
Chi-restraints excluded: chain D residue  145 THR
Chi-restraints excluded: chain D residue  146 LEU
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  243 THR
Chi-restraints excluded: chain D residue  291 MET
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  113 MET
Chi-restraints excluded: chain E residue  118 TYR
Chi-restraints excluded: chain E residue  145 THR
Chi-restraints excluded: chain E residue  175 VAL
Chi-restraints excluded: chain E residue  230 THR
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain E residue  243 THR
Chi-restraints excluded: chain F residue  113 MET
Chi-restraints excluded: chain F residue  145 THR
Chi-restraints excluded: chain F residue  175 VAL
Chi-restraints excluded: chain F residue  197 MET
Chi-restraints excluded: chain F residue  231 VAL
Chi-restraints excluded: chain F residue  243 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 40 optimal weight:   10.0000
   chunk 187 optimal weight:    4.9990
   chunk 83 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 85 optimal weight:   10.0000
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
C 209 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.160039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.137465 restraints weight = 18098.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.86
r_work: 0.3362 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.5381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  16170  Z= 0.168
  Angle     :  0.562   8.147  21882  Z= 0.303
  Chirality :  0.046   0.147   2331
  Planarity :  0.003   0.044   2814
  Dihedral  :  4.048  14.895   2121
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 15.54 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole: -1.04 (0.19), residues: 1932
  helix:  None (None), residues: 0
  sheet: -0.41 (0.15), residues: 1071
  loop : -0.91 (0.22), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 281 
 TYR   0.015   0.001   TYR A 191 
 PHE   0.021   0.002   PHE B 196 
 TRP   0.017   0.001   TRP A 265 
 HIS   0.005   0.002   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (16170)
  covalent geometry    : angle       0.56227 (21882)
  hydrogen bonds       : bond        0.03235 (  532)
  hydrogen bonds       : angle       5.68704 ( 1449)

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

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

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3864 Ramachandran restraints generated.
    1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 251
  time to evaluate  : 0.741 
Fit side-chains
REVERT: G   75 LYS cc_start: 0.8044 (tppt) cc_final: 0.7784 (mptt)
REVERT: G  227 ASP cc_start: 0.7899 (t0) cc_final: 0.7688 (t0)
REVERT: G  287 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7845 (mm-30)
REVERT: A   30 LYS cc_start: 0.8474 (ptpp) cc_final: 0.7959 (ptpp)
REVERT: A   31 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7976 (mt-10)
REVERT: A   75 LYS cc_start: 0.8043 (tppt) cc_final: 0.7520 (mmtt)
REVERT: A  279 SER cc_start: 0.9018 (t) cc_final: 0.8749 (p)
REVERT: B   31 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7984 (pt0)
REVERT: B  118 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.6388 (p90)
REVERT: B  227 ASP cc_start: 0.8067 (t0) cc_final: 0.7803 (t0)
REVERT: C   30 LYS cc_start: 0.8664 (ptpp) cc_final: 0.8303 (ptpp)
REVERT: C   31 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8139 (pt0)
REVERT: C   75 LYS cc_start: 0.7857 (tppt) cc_final: 0.7504 (mptt)
REVERT: C  118 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.6014 (p90)
REVERT: C  227 ASP cc_start: 0.8114 (t0) cc_final: 0.7843 (t0)
REVERT: C  287 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7953 (mm-30)
REVERT: D  191 TYR cc_start: 0.8912 (m-80) cc_final: 0.8703 (m-80)
REVERT: D  277 ARG cc_start: 0.8648 (mtp-110) cc_final: 0.8438 (mtp-110)
REVERT: D  287 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7824 (mm-30)
REVERT: E   46 LYS cc_start: 0.8704 (pttp) cc_final: 0.7924 (tppt)
REVERT: E   75 LYS cc_start: 0.8052 (tppt) cc_final: 0.7791 (mptt)
REVERT: E  118 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.6250 (p90)
REVERT: E  179 TRP cc_start: 0.7342 (t60) cc_final: 0.7081 (t-100)
REVERT: E  227 ASP cc_start: 0.8056 (t0) cc_final: 0.7799 (t0)
REVERT: E  287 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7893 (mm-30)
REVERT: F   75 LYS cc_start: 0.8244 (tppt) cc_final: 0.8026 (tppt)
  outliers start: 59
  outliers final: 54
  residues processed: 291
  average time/residue: 0.1320
  time to fit residues: 57.0533
Evaluate side-chains
  300 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 243
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   90 LEU
Chi-restraints excluded: chain G residue  113 MET
Chi-restraints excluded: chain G residue  118 TYR
Chi-restraints excluded: chain G residue  145 THR
Chi-restraints excluded: chain G residue  175 VAL
Chi-restraints excluded: chain G residue  231 VAL
Chi-restraints excluded: chain G residue  243 THR
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  118 TYR
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  113 MET
Chi-restraints excluded: chain B residue  118 TYR
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain C residue  113 MET
Chi-restraints excluded: chain C residue  118 TYR
Chi-restraints excluded: chain C residue  145 THR
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  197 MET
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain D residue   70 GLU
Chi-restraints excluded: chain D residue  113 MET
Chi-restraints excluded: chain D residue  145 THR
Chi-restraints excluded: chain D residue  146 LEU
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  243 THR
Chi-restraints excluded: chain D residue  291 MET
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  113 MET
Chi-restraints excluded: chain E residue  118 TYR
Chi-restraints excluded: chain E residue  145 THR
Chi-restraints excluded: chain E residue  175 VAL
Chi-restraints excluded: chain E residue  197 MET
Chi-restraints excluded: chain E residue  230 THR
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain E residue  243 THR
Chi-restraints excluded: chain F residue  113 MET
Chi-restraints excluded: chain F residue  145 THR
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  175 VAL
Chi-restraints excluded: chain F residue  197 MET
Chi-restraints excluded: chain F residue  231 VAL
Chi-restraints excluded: chain F residue  243 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 144 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 132 optimal weight:    0.9990
   chunk 117 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 95 optimal weight:    9.9990
   chunk 46 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0870
   overall best weight:    1.1564

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

Flipped N/Q/H residues before XYZ refinement:
A 201 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.161091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.138587 restraints weight = 18064.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 1.88
r_work: 0.3377 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.5461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  16170  Z= 0.140
  Angle     :  0.543   7.982  21882  Z= 0.292
  Chirality :  0.045   0.137   2331
  Planarity :  0.003   0.038   2814
  Dihedral  :  3.980  15.596   2121
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 15.43 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole: -1.05 (0.19), residues: 1932
  helix:  None (None), residues: 0
  sheet: -0.42 (0.15), residues: 1071
  loop : -0.91 (0.22), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 281 
 TYR   0.015   0.001   TYR F 191 
 PHE   0.022   0.002   PHE B 196 
 TRP   0.014   0.001   TRP A 265 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (16170)
  covalent geometry    : angle       0.54303 (21882)
  hydrogen bonds       : bond        0.03081 (  532)
  hydrogen bonds       : angle       5.58630 ( 1449)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3338.47 seconds
wall clock time: 58 minutes 17.19 seconds (3497.19 seconds total)