Starting phenix.real_space_refine
on Sat Aug 23 13:16:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f32_28829/08_2025/8f32_28829.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f32_28829/08_2025/8f32_28829.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f32_28829/08_2025/8f32_28829.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f32_28829/08_2025/8f32_28829.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f32_28829/08_2025/8f32_28829.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f32_28829/08_2025/8f32_28829.cif"
  }
  resolution = 3.71
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
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      30      5.16       5
     C    8180      2.51       5
     N    2085      2.21       5
     O    2250      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12545
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "E"
      Number of atoms: 2505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
    Chain: "E"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'3CN': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    D, C, B, A
  Time building chain proxies: 1.62, per 1000 atoms: 0.13
  Number of scatterers: 12545
  At special positions: 0
  Unit cell: (88.41, 88.41, 122.932, 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      30     16.00
     O    2250      8.00
     N    2085      7.00
     C    8180      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: 1.06
  Conformation dependent library (CDL) restraints added in 589.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2910

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 15 sheets defined
      31.9% alpha, 34.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'E' and resid 62 through 70
      removed outlier: 3.633A  pdb=" N   TRP E  66 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 201 through 208
    Processing helix  chain 'E' and resid 209 through 222
    Processing helix  chain 'E' and resid 223 through 225
      No H-bonds generated for 'chain 'E' and resid 223 through 225'
    Processing helix  chain 'E' and resid 227 through 248
      removed outlier: 3.626A  pdb=" N   ARG E 231 " --> pdb=" O   SER E 227 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 260 through 286
    Processing helix  chain 'E' and resid 303 through 317
    Processing helix  chain 'D' and resid 62 through 70
      removed outlier: 3.633A  pdb=" N   TRP D  66 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 201 through 208
    Processing helix  chain 'D' and resid 209 through 222
    Processing helix  chain 'D' and resid 223 through 225
      No H-bonds generated for 'chain 'D' and resid 223 through 225'
    Processing helix  chain 'D' and resid 227 through 248
      removed outlier: 3.626A  pdb=" N   ARG D 231 " --> pdb=" O   SER D 227 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 260 through 286
    Processing helix  chain 'D' and resid 303 through 317
    Processing helix  chain 'C' and resid 62 through 70
      removed outlier: 3.633A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 209 through 222
    Processing helix  chain 'C' and resid 223 through 225
      No H-bonds generated for 'chain 'C' and resid 223 through 225'
    Processing helix  chain 'C' and resid 227 through 248
      removed outlier: 3.626A  pdb=" N   ARG C 231 " --> pdb=" O   SER C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 286
    Processing helix  chain 'C' and resid 303 through 317
    Processing helix  chain 'B' and resid 62 through 70
      removed outlier: 3.634A  pdb=" N   TRP B  66 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 208
    Processing helix  chain 'B' and resid 209 through 222
    Processing helix  chain 'B' and resid 223 through 225
      No H-bonds generated for 'chain 'B' and resid 223 through 225'
    Processing helix  chain 'B' and resid 227 through 248
      removed outlier: 3.626A  pdb=" N   ARG B 231 " --> pdb=" O   SER B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 286
    Processing helix  chain 'B' and resid 303 through 317
    Processing helix  chain 'A' and resid 62 through 70
      removed outlier: 3.634A  pdb=" N   TRP A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 208
    Processing helix  chain 'A' and resid 209 through 222
    Processing helix  chain 'A' and resid 223 through 225
      No H-bonds generated for 'chain 'A' and resid 223 through 225'
    Processing helix  chain 'A' and resid 227 through 248
      removed outlier: 3.627A  pdb=" N   ARG A 231 " --> pdb=" O   SER A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 286
    Processing helix  chain 'A' and resid 303 through 317
    Processing sheet with id=AA1, first strand: chain 'E' and resid 56 through 58
      removed outlier: 4.717A  pdb=" N   SER E 109 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 56 through 58
      removed outlier: 6.085A  pdb=" N   THR E  32 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   GLY E  25 " --> pdb=" O   THR E  32 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   LYS E  34 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   ILE E  23 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ASP E  36 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   THR E  44 " --> pdb=" O   ASP E  13 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   ASP E  13 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   VAL E  12 " --> pdb=" O   ARG E 141 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   SER E 143 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   VAL E  14 " --> pdb=" O   SER E 143 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ILE E 145 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   VAL E  16 " --> pdb=" O   ILE E 145 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   VAL E 147 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ILE E  18 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.569A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   ASP E 196 " --> pdb=" O   LYS E 165 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   LYS E 165 " --> pdb=" O   ASP E 196 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   VAL E 198 " --> pdb=" O   ARG E 163 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ARG E 163 " --> pdb=" O   VAL E 198 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 56 through 58
      removed outlier: 4.717A  pdb=" N   SER D 109 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 56 through 58
      removed outlier: 6.085A  pdb=" N   THR D  32 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   GLY D  25 " --> pdb=" O   THR D  32 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   LYS D  34 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   ILE D  23 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ASP D  36 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   THR D  44 " --> pdb=" O   ASP D  13 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   ASP D  13 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   VAL D  12 " --> pdb=" O   ARG D 141 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   SER D 143 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   VAL D  14 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ILE D 145 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   VAL D  16 " --> pdb=" O   ILE D 145 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   VAL D 147 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ILE D  18 " --> pdb=" O   VAL D 147 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.569A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   ASP D 196 " --> pdb=" O   LYS D 165 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   LYS D 165 " --> pdb=" O   ASP D 196 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   VAL D 198 " --> pdb=" O   ARG D 163 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ARG D 163 " --> pdb=" O   VAL D 198 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58
      removed outlier: 4.718A  pdb=" N   SER C 109 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 56 through 58
      removed outlier: 6.085A  pdb=" N   THR C  32 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   GLY C  25 " --> pdb=" O   THR C  32 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   LYS C  34 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   ILE C  23 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ASP C  36 " --> pdb=" O   ASN C  21 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   THR C  44 " --> pdb=" O   ASP C  13 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   ASP C  13 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   VAL C  12 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   SER C 143 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   VAL C  14 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ILE C 145 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   VAL C  16 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   VAL C 147 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ILE C  18 " --> pdb=" O   VAL C 147 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.569A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   ASP C 196 " --> pdb=" O   LYS C 165 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   LYS C 165 " --> pdb=" O   ASP C 196 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   VAL C 198 " --> pdb=" O   ARG C 163 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ARG C 163 " --> pdb=" O   VAL C 198 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 56 through 58
      removed outlier: 4.716A  pdb=" N   SER B 109 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 56 through 58
      removed outlier: 6.085A  pdb=" N   THR B  32 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   GLY B  25 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   LYS B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   ILE B  23 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ASP B  36 " --> pdb=" O   ASN B  21 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   THR B  44 " --> pdb=" O   ASP B  13 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   ASP B  13 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   VAL B  12 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   SER B 143 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   VAL B  14 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ILE B 145 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   VAL B  16 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   VAL B 147 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   ILE B  18 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.570A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   ASP B 196 " --> pdb=" O   LYS B 165 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   LYS B 165 " --> pdb=" O   ASP B 196 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   VAL B 198 " --> pdb=" O   ARG B 163 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ARG B 163 " --> pdb=" O   VAL B 198 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 56 through 58
      removed outlier: 4.717A  pdb=" N   SER A 109 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 56 through 58
      removed outlier: 6.085A  pdb=" N   THR A  32 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   GLY A  25 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   LYS A  34 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   ILE A  23 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ASP A  36 " --> pdb=" O   ASN A  21 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   THR A  44 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   ASP A  13 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   VAL A  12 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   SER A 143 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   VAL A  14 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ILE A 145 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   VAL A  16 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   VAL A 147 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ILE A  18 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.569A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   ASP A 196 " --> pdb=" O   LYS A 165 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   LYS A 165 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   VAL A 198 " --> pdb=" O   ARG A 163 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ARG A 163 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)

    615 hydrogen bonds defined for protein.
    1800 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.85

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3475
        1.33 -     1.45: 2400
        1.45 -     1.57: 6955
        1.57 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 12880
  Sorted by residual:
  bond pdb=" CB  GLU B 150 "
       pdb=" CG  GLU B 150 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 3.00e-02 1.11e+03 2.40e+00
  bond pdb=" CB  GLU C 150 "
       pdb=" CG  GLU C 150 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 3.00e-02 1.11e+03 2.39e+00
  bond pdb=" CB  GLU E 150 "
       pdb=" CG  GLU E 150 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 3.00e-02 1.11e+03 2.38e+00
  bond pdb=" CB  GLU D 150 "
       pdb=" CG  GLU D 150 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 3.00e-02 1.11e+03 2.37e+00
  bond pdb=" CB  GLU A 150 "
       pdb=" CG  GLU A 150 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 3.00e-02 1.11e+03 2.37e+00
  ... (remaining 12875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 16589
        1.59 -     3.17: 759
        3.17 -     4.76: 112
        4.76 -     6.34: 65
        6.34 -     7.93: 20
  Bond angle restraints: 17545
  Sorted by residual:
  angle pdb=" N   ILE C 157 "
        pdb=" CA  ILE C 157 "
        pdb=" C   ILE C 157 "
      ideal   model   delta    sigma   weight residual
     113.71  106.87    6.84 9.50e-01 1.11e+00 5.19e+01
  angle pdb=" N   ILE D 157 "
        pdb=" CA  ILE D 157 "
        pdb=" C   ILE D 157 "
      ideal   model   delta    sigma   weight residual
     113.71  106.87    6.84 9.50e-01 1.11e+00 5.18e+01
  angle pdb=" N   ILE B 157 "
        pdb=" CA  ILE B 157 "
        pdb=" C   ILE B 157 "
      ideal   model   delta    sigma   weight residual
     113.71  106.88    6.83 9.50e-01 1.11e+00 5.18e+01
  angle pdb=" N   ILE E 157 "
        pdb=" CA  ILE E 157 "
        pdb=" C   ILE E 157 "
      ideal   model   delta    sigma   weight residual
     113.71  106.88    6.83 9.50e-01 1.11e+00 5.17e+01
  angle pdb=" N   ILE A 157 "
        pdb=" CA  ILE A 157 "
        pdb=" C   ILE A 157 "
      ideal   model   delta    sigma   weight residual
     113.71  106.89    6.82 9.50e-01 1.11e+00 5.16e+01
  ... (remaining 17540 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.33: 6455
       14.33 -    28.66: 855
       28.66 -    42.99: 185
       42.99 -    57.32: 20
       57.32 -    71.65: 15
  Dihedral angle restraints: 7530
    sinusoidal: 3025
      harmonic: 4505
  Sorted by residual:
  dihedral pdb=" CA  SER D 227 "
           pdb=" C   SER D 227 "
           pdb=" N   PHE D 228 "
           pdb=" CA  PHE D 228 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.17  -25.83     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CA  SER A 227 "
           pdb=" C   SER A 227 "
           pdb=" N   PHE A 228 "
           pdb=" CA  PHE A 228 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.17  -25.83     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CA  SER B 227 "
           pdb=" C   SER B 227 "
           pdb=" N   PHE B 228 "
           pdb=" CA  PHE B 228 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.19  -25.81     0      5.00e+00 4.00e-02 2.67e+01
  ... (remaining 7527 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1184
       0.043 -    0.086: 515
       0.086 -    0.130: 206
       0.130 -    0.173: 40
       0.173 -    0.216: 5
  Chirality restraints: 1950
  Sorted by residual:
  chirality pdb=" CB  ILE B  39 "
            pdb=" CA  ILE B  39 "
            pdb=" CG1 ILE B  39 "
            pdb=" CG2 ILE B  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CB  ILE D  39 "
            pdb=" CA  ILE D  39 "
            pdb=" CG1 ILE D  39 "
            pdb=" CG2 ILE D  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CB  ILE C  39 "
            pdb=" CA  ILE C  39 "
            pdb=" CG1 ILE C  39 "
            pdb=" CG2 ILE C  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 1947 not shown)

  Planarity restraints: 2235
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 119 "   -0.033 5.00e-02 4.00e+02   4.98e-02 3.96e+00
        pdb=" N   PRO D 120 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO D 120 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D 120 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE E 119 "    0.033 5.00e-02 4.00e+02   4.97e-02 3.95e+00
        pdb=" N   PRO E 120 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO E 120 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO E 120 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 119 "    0.033 5.00e-02 4.00e+02   4.95e-02 3.93e+00
        pdb=" N   PRO A 120 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 120 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 120 "    0.028 5.00e-02 4.00e+02
  ... (remaining 2232 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 960
        2.74 -     3.28: 12129
        3.28 -     3.82: 20409
        3.82 -     4.36: 24824
        4.36 -     4.90: 43288
  Nonbonded interactions: 101610
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 227 "
            pdb=" OE2 GLU D 230 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OG  SER C 227 "
            pdb=" OE2 GLU C 230 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OG  SER E 227 "
            pdb=" OE2 GLU E 230 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OG  SER A 227 "
            pdb=" OE2 GLU A 230 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OG  SER B 227 "
            pdb=" OE2 GLU B 230 "
     model   vdw
     2.202 3.040
  ... (remaining 101605 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'E'
  selection = chain 'D'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'A'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.600
  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:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.570
  Find NCS groups from input model:        0.090
  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:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
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      :  0.005   0.049  12880  Z= 0.218
  Angle     :  0.837   7.926  17545  Z= 0.467
  Chirality :  0.056   0.216   1950
  Planarity :  0.006   0.050   2235
  Dihedral  : 13.435  71.655   4620
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.60 (0.21), residues: 1525
  helix: -0.87 (0.22), residues: 525
  sheet: -0.04 (0.23), residues: 490
  loop : -2.13 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 286 
 TYR   0.020   0.002   TYR D 245 
 PHE   0.018   0.002   PHE B 308 
 TRP   0.014   0.002   TRP A  43 
 HIS   0.013   0.003   HIS C 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 (12880)
  covalent geometry    : angle       0.83680 (17545)
  hydrogen bonds       : bond        0.09083 (  575)
  hydrogen bonds       : angle       6.43199 ( 1800)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 276
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
REVERT: E  187 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6593 (tm-30)
REVERT: D   86 ASP cc_start: 0.6982 (t70) cc_final: 0.6575 (t0)
REVERT: C   86 ASP cc_start: 0.7052 (t70) cc_final: 0.6643 (t0)
REVERT: C  187 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6710 (tm-30)
REVERT: B   86 ASP cc_start: 0.6869 (t70) cc_final: 0.6406 (t0)
REVERT: B  187 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6652 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 276
  average time/residue: 0.1051
  time to fit residues: 41.8681
Evaluate side-chains
  201 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    5.9990
   overall best weight:    3.3186

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

Flipped N/Q/H residues before XYZ refinement:
E  42 GLN
E 146 GLN
E 177 HIS
D  21 ASN
D 146 GLN
D 169 HIS
C  60 ASN
C 146 GLN
C 177 HIS
B  21 ASN
B  62 GLN
B 139 GLN
B 146 GLN
A  21 ASN
A  42 GLN
A 139 GLN
A 146 GLN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.150871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.119461 restraints weight = 17282.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.123257 restraints weight = 11086.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.125868 restraints weight = 8304.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.127554 restraints weight = 6826.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.128570 restraints weight = 5968.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  12880  Z= 0.225
  Angle     :  0.612   5.299  17545  Z= 0.327
  Chirality :  0.049   0.137   1950
  Planarity :  0.005   0.045   2235
  Dihedral  :  5.229  24.244   1690
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 11.71 %
    Favored  : 86.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.22), residues: 1525
  helix:  0.74 (0.24), residues: 495
  sheet: -0.11 (0.23), residues: 465
  loop : -1.84 (0.25), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 190 
 TYR   0.012   0.002   TYR B 258 
 PHE   0.023   0.002   PHE B  19 
 TRP   0.010   0.001   TRP B  43 
 HIS   0.007   0.001   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 (12880)
  covalent geometry    : angle       0.61161 (17545)
  hydrogen bonds       : bond        0.03885 (  575)
  hydrogen bonds       : angle       5.15409 ( 1800)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 208
  time to evaluate  : 0.509 
Fit side-chains
REVERT: D   86 ASP cc_start: 0.6989 (t70) cc_final: 0.6551 (t0)
  outliers start: 21
  outliers final: 17
  residues processed: 211
  average time/residue: 0.1082
  time to fit residues: 33.3176
Evaluate side-chains
  192 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 175
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  158 ASP
Chi-restraints excluded: chain E residue  168 THR
Chi-restraints excluded: chain E residue  260 THR
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  260 THR
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  168 THR
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  266 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 99 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0770
   chunk 147 optimal weight:    8.9990
   chunk 130 optimal weight:    4.9990
   chunk 101 optimal weight:    2.9990
   chunk 105 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 54 optimal weight:    7.9990
   overall best weight:    2.2144

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

Flipped N/Q/H residues before XYZ refinement:
D  89 ASN
D 177 HIS
C  60 ASN
B 177 HIS
A  89 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.151020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.120391 restraints weight = 17454.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.124249 restraints weight = 11027.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.126713 restraints weight = 8128.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.128630 restraints weight = 6661.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.129674 restraints weight = 5782.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12880  Z= 0.166
  Angle     :  0.535   4.836  17545  Z= 0.285
  Chirality :  0.047   0.130   1950
  Planarity :  0.004   0.046   2235
  Dihedral  :  4.821  21.485   1690
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.25 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.22), residues: 1525
  helix:  1.36 (0.25), residues: 495
  sheet:  0.07 (0.23), residues: 455
  loop : -1.73 (0.25), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 190 
 TYR   0.008   0.001   TYR B 258 
 PHE   0.021   0.001   PHE A  19 
 TRP   0.009   0.001   TRP D  43 
 HIS   0.008   0.001   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (12880)
  covalent geometry    : angle       0.53515 (17545)
  hydrogen bonds       : bond        0.03455 (  575)
  hydrogen bonds       : angle       4.82427 ( 1800)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 212
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  187 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6436 (tm-30)
REVERT: D   86 ASP cc_start: 0.6888 (t70) cc_final: 0.6416 (t0)
REVERT: D  264 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6973 (mp10)
REVERT: C  187 GLU cc_start: 0.6743 (tm-30) cc_final: 0.6539 (tm-30)
REVERT: B  187 GLU cc_start: 0.6747 (tm-30) cc_final: 0.6460 (tm-30)
  outliers start: 38
  outliers final: 28
  residues processed: 220
  average time/residue: 0.0953
  time to fit residues: 31.0804
Evaluate side-chains
  205 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 176
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue  168 THR
Chi-restraints excluded: chain E residue  260 THR
Chi-restraints excluded: chain E residue  264 GLN
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  176 ASP
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  260 THR
Chi-restraints excluded: chain D residue  264 GLN
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  168 THR
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  264 GLN
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  176 ASP
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  264 GLN
Chi-restraints excluded: chain A residue  266 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 104 optimal weight:    8.9990
   chunk 143 optimal weight:    2.9990
   chunk 96 optimal weight:    7.9990
   chunk 147 optimal weight:    9.9990
   chunk 117 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 144 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 63 optimal weight:   20.0000
   chunk 133 optimal weight:    3.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
C  60 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.146284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.114897 restraints weight = 17500.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.118694 restraints weight = 11190.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.121225 restraints weight = 8358.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.122811 restraints weight = 6897.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.123962 restraints weight = 6068.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068  12880  Z= 0.269
  Angle     :  0.632   6.112  17545  Z= 0.336
  Chirality :  0.050   0.141   1950
  Planarity :  0.004   0.042   2235
  Dihedral  :  5.178  27.062   1690
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 13.82 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.22), residues: 1525
  helix:  1.30 (0.25), residues: 495
  sheet: -0.24 (0.23), residues: 465
  loop : -1.83 (0.26), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 190 
 TYR   0.012   0.002   TYR C 245 
 PHE   0.017   0.002   PHE A  19 
 TRP   0.008   0.001   TRP B 160 
 HIS   0.008   0.002   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00638 (12880)
  covalent geometry    : angle       0.63230 (17545)
  hydrogen bonds       : bond        0.04052 (  575)
  hydrogen bonds       : angle       5.08805 ( 1800)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 219
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  187 GLU cc_start: 0.6625 (tm-30) cc_final: 0.6345 (tm-30)
REVERT: B  187 GLU cc_start: 0.6649 (tm-30) cc_final: 0.6382 (tm-30)
  outliers start: 63
  outliers final: 48
  residues processed: 246
  average time/residue: 0.1012
  time to fit residues: 37.1014
Evaluate side-chains
  218 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 170
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  168 THR
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  243 VAL
Chi-restraints excluded: chain E residue  256 LEU
Chi-restraints excluded: chain E residue  260 THR
Chi-restraints excluded: chain E residue  264 GLN
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  103 ASN
Chi-restraints excluded: chain D residue  176 ASP
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  227 SER
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  260 THR
Chi-restraints excluded: chain D residue  264 GLN
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  168 THR
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  264 GLN
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  176 ASP
Chi-restraints excluded: chain B residue  195 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  264 GLN
Chi-restraints excluded: chain A residue  266 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9990
   chunk 135 optimal weight:    5.9990
   chunk 130 optimal weight:    0.9990
   chunk 90 optimal weight:    8.9990
   chunk 139 optimal weight:    0.9980
   chunk 138 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0670
   overall best weight:    1.0124

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

Flipped N/Q/H residues before XYZ refinement:
D  42 GLN
C  21 ASN
C  60 ASN
B  42 GLN
A 177 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.152788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.122887 restraints weight = 17290.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.126813 restraints weight = 10737.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.129204 restraints weight = 7827.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.131093 restraints weight = 6409.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.132165 restraints weight = 5538.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12880  Z= 0.115
  Angle     :  0.496   4.646  17545  Z= 0.263
  Chirality :  0.045   0.132   1950
  Planarity :  0.003   0.037   2235
  Dihedral  :  4.473  18.087   1690
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 15.78 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.22), residues: 1525
  helix:  1.78 (0.25), residues: 490
  sheet: -0.09 (0.23), residues: 465
  loop : -1.72 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 190 
 TYR   0.010   0.001   TYR C 245 
 PHE   0.014   0.001   PHE C 308 
 TRP   0.031   0.001   TRP C 220 
 HIS   0.008   0.002   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (12880)
  covalent geometry    : angle       0.49581 (17545)
  hydrogen bonds       : bond        0.03163 (  575)
  hydrogen bonds       : angle       4.58253 ( 1800)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 217
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 ARG cc_start: 0.6625 (mtt90) cc_final: 0.6249 (mtt-85)
  outliers start: 53
  outliers final: 30
  residues processed: 245
  average time/residue: 0.0996
  time to fit residues: 36.3540
Evaluate side-chains
  209 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 179
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  260 THR
Chi-restraints excluded: chain E residue  264 GLN
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  260 THR
Chi-restraints excluded: chain D residue  264 GLN
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  264 GLN
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  195 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  264 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 54 optimal weight:    8.9990
   chunk 85 optimal weight:    0.9990
   chunk 32 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 120 optimal weight:    9.9990
   chunk 42 optimal weight:   10.0000
   chunk 121 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
C  60 ASN
A  60 ASN
A  89 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.145961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.114829 restraints weight = 17357.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.118549 restraints weight = 11010.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.121048 restraints weight = 8188.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.122612 restraints weight = 6733.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.123615 restraints weight = 5915.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.065  12880  Z= 0.276
  Angle     :  0.638   9.416  17545  Z= 0.334
  Chirality :  0.049   0.145   1950
  Planarity :  0.004   0.035   2235
  Dihedral  :  5.032  26.551   1690
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 15.71 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.22), residues: 1525
  helix:  1.51 (0.25), residues: 490
  sheet: -0.38 (0.23), residues: 475
  loop : -1.82 (0.27), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 190 
 TYR   0.012   0.002   TYR C  38 
 PHE   0.023   0.002   PHE B  19 
 TRP   0.025   0.001   TRP C 220 
 HIS   0.008   0.001   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00654 (12880)
  covalent geometry    : angle       0.63806 (17545)
  hydrogen bonds       : bond        0.03925 (  575)
  hydrogen bonds       : angle       4.98500 ( 1800)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 185
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  191 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8910 (mp)
REVERT: B  230 GLU cc_start: 0.6886 (pm20) cc_final: 0.6266 (pt0)
  outliers start: 63
  outliers final: 54
  residues processed: 219
  average time/residue: 0.0985
  time to fit residues: 31.6897
Evaluate side-chains
  226 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 171
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  168 THR
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  256 LEU
Chi-restraints excluded: chain E residue  260 THR
Chi-restraints excluded: chain E residue  264 GLN
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  260 THR
Chi-restraints excluded: chain D residue  264 GLN
Chi-restraints excluded: chain D residue  266 ILE
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  168 THR
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  230 GLU
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  264 GLN
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  195 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  264 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 117 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 120 optimal weight:   10.0000
   chunk 78 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
C  60 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.148342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.117769 restraints weight = 17141.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.121589 restraints weight = 10744.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.124137 restraints weight = 7904.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.125836 restraints weight = 6427.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.126881 restraints weight = 5648.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12880  Z= 0.165
  Angle     :  0.546   7.040  17545  Z= 0.286
  Chirality :  0.047   0.145   1950
  Planarity :  0.003   0.037   2235
  Dihedral  :  4.711  22.201   1690
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 16.07 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.22), residues: 1525
  helix:  1.65 (0.25), residues: 490
  sheet: -0.29 (0.23), residues: 465
  loop : -1.77 (0.27), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 190 
 TYR   0.008   0.001   TYR E 245 
 PHE   0.020   0.001   PHE B  19 
 TRP   0.019   0.001   TRP C 220 
 HIS   0.008   0.002   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (12880)
  covalent geometry    : angle       0.54559 (17545)
  hydrogen bonds       : bond        0.03370 (  575)
  hydrogen bonds       : angle       4.77498 ( 1800)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 189
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  113 ASP cc_start: 0.6951 (p0) cc_final: 0.6749 (p0)
REVERT: D   22 LYS cc_start: 0.8444 (pttm) cc_final: 0.8104 (pttm)
REVERT: C  191 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8926 (mp)
  outliers start: 60
  outliers final: 49
  residues processed: 221
  average time/residue: 0.0857
  time to fit residues: 28.4429
Evaluate side-chains
  218 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 168
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  168 THR
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  243 VAL
Chi-restraints excluded: chain E residue  260 THR
Chi-restraints excluded: chain E residue  264 GLN
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  103 ASN
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  260 THR
Chi-restraints excluded: chain D residue  264 GLN
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  168 THR
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  230 GLU
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  264 GLN
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  195 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  264 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 63 optimal weight:   20.0000
   chunk 57 optimal weight:    9.9990
   chunk 82 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 139 optimal weight:    0.9980
   chunk 107 optimal weight:    0.0970
   chunk 14 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9990
   chunk 96 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
C  21 ASN
C  60 ASN
A 169 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.152793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.122945 restraints weight = 17036.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.126679 restraints weight = 10432.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.129519 restraints weight = 7563.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.131110 restraints weight = 6129.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.132396 restraints weight = 5340.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.3170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12880  Z= 0.114
  Angle     :  0.512   7.340  17545  Z= 0.267
  Chirality :  0.045   0.175   1950
  Planarity :  0.003   0.036   2235
  Dihedral  :  4.409  20.610   1690
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 16.65 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.23), residues: 1525
  helix:  1.75 (0.25), residues: 490
  sheet: -0.13 (0.23), residues: 465
  loop : -1.64 (0.27), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 255 
 TYR   0.007   0.001   TYR D 258 
 PHE   0.018   0.001   PHE B  19 
 TRP   0.017   0.001   TRP C 220 
 HIS   0.008   0.001   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (12880)
  covalent geometry    : angle       0.51240 (17545)
  hydrogen bonds       : bond        0.03055 (  575)
  hydrogen bonds       : angle       4.56721 ( 1800)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 206
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  255 ARG cc_start: 0.6475 (mtt90) cc_final: 0.6012 (mtt-85)
REVERT: B  230 GLU cc_start: 0.6942 (pm20) cc_final: 0.6329 (pt0)
REVERT: A   54 LYS cc_start: 0.7383 (mmtt) cc_final: 0.7145 (tppt)
  outliers start: 62
  outliers final: 48
  residues processed: 240
  average time/residue: 0.0925
  time to fit residues: 33.1254
Evaluate side-chains
  233 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 185
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  260 THR
Chi-restraints excluded: chain E residue  264 GLN
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  260 THR
Chi-restraints excluded: chain D residue  264 GLN
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  168 THR
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  264 GLN
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  195 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  264 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 120 optimal weight:   10.0000
   chunk 122 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 136 optimal weight:    9.9990
   chunk 52 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 69 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 63 optimal weight:   10.0000
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
D  60 ASN
D  89 ASN
C  60 ASN
A  60 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.149948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.118879 restraints weight = 17292.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.122716 restraints weight = 10917.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.125278 restraints weight = 8068.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.126988 restraints weight = 6605.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.127895 restraints weight = 5782.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.3254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12880  Z= 0.186
  Angle     :  0.575   6.908  17545  Z= 0.300
  Chirality :  0.047   0.186   1950
  Planarity :  0.004   0.035   2235
  Dihedral  :  4.659  21.564   1690
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 16.73 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.23), residues: 1525
  helix:  1.70 (0.25), residues: 490
  sheet: -0.17 (0.23), residues: 465
  loop : -1.70 (0.27), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 255 
 TYR   0.009   0.001   TYR D 245 
 PHE   0.023   0.002   PHE B 236 
 TRP   0.014   0.001   TRP C 220 
 HIS   0.009   0.001   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (12880)
  covalent geometry    : angle       0.57462 (17545)
  hydrogen bonds       : bond        0.03423 (  575)
  hydrogen bonds       : angle       4.70666 ( 1800)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 176
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  255 ARG cc_start: 0.6513 (mtt90) cc_final: 0.6087 (mtt-85)
REVERT: A   54 LYS cc_start: 0.7464 (mmtt) cc_final: 0.7188 (tppt)
  outliers start: 59
  outliers final: 55
  residues processed: 210
  average time/residue: 0.0948
  time to fit residues: 29.5131
Evaluate side-chains
  220 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 165
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  168 THR
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  243 VAL
Chi-restraints excluded: chain E residue  260 THR
Chi-restraints excluded: chain E residue  264 GLN
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue  103 ASN
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  260 THR
Chi-restraints excluded: chain D residue  264 GLN
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  168 THR
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  264 GLN
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  195 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  264 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 119 optimal weight:   20.0000
   chunk 9 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 112 optimal weight:    8.9990
   chunk 12 optimal weight:    0.1980
   chunk 51 optimal weight:    0.5980
   chunk 1 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
C  60 ASN
A  60 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.151123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.120668 restraints weight = 17215.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.124776 restraints weight = 10444.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.127565 restraints weight = 7500.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.129180 restraints weight = 5984.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.130662 restraints weight = 5170.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.3245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12880  Z= 0.124
  Angle     :  0.539   6.910  17545  Z= 0.281
  Chirality :  0.046   0.180   1950
  Planarity :  0.003   0.031   2235
  Dihedral  :  4.484  19.298   1690
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 17.38 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.23), residues: 1525
  helix:  1.74 (0.25), residues: 490
  sheet: -0.07 (0.23), residues: 465
  loop : -1.63 (0.27), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 255 
 TYR   0.007   0.001   TYR D 203 
 PHE   0.018   0.001   PHE A  19 
 TRP   0.014   0.001   TRP C 220 
 HIS   0.009   0.002   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (12880)
  covalent geometry    : angle       0.53906 (17545)
  hydrogen bonds       : bond        0.03117 (  575)
  hydrogen bonds       : angle       4.56082 ( 1800)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 185
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  255 ARG cc_start: 0.6568 (mtt90) cc_final: 0.6089 (mtt-85)
REVERT: D  264 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6886 (mp10)
REVERT: A   54 LYS cc_start: 0.7472 (mmtt) cc_final: 0.7175 (tppt)
  outliers start: 51
  outliers final: 46
  residues processed: 212
  average time/residue: 0.1070
  time to fit residues: 33.2857
Evaluate side-chains
  224 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 177
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  168 THR
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  260 THR
Chi-restraints excluded: chain E residue  264 GLN
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  260 THR
Chi-restraints excluded: chain D residue  264 GLN
Chi-restraints excluded: chain D residue  266 ILE
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  168 THR
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  264 GLN
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  195 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  264 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 45 optimal weight:    9.9990
   chunk 63 optimal weight:   20.0000
   chunk 75 optimal weight:   10.0000
   chunk 141 optimal weight:    9.9990
   chunk 96 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 55 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
C  60 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.149180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.118709 restraints weight = 17214.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.122536 restraints weight = 10885.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.125115 restraints weight = 8034.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.126829 restraints weight = 6538.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.127820 restraints weight = 5683.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12880  Z= 0.156
  Angle     :  0.556   7.548  17545  Z= 0.289
  Chirality :  0.046   0.177   1950
  Planarity :  0.003   0.034   2235
  Dihedral  :  4.520  19.531   1690
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 17.75 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.23), residues: 1525
  helix:  1.72 (0.25), residues: 490
  sheet: -0.11 (0.23), residues: 475
  loop : -1.65 (0.27), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 255 
 TYR   0.010   0.001   TYR C 245 
 PHE   0.023   0.001   PHE E 236 
 TRP   0.013   0.001   TRP C 220 
 HIS   0.009   0.001   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (12880)
  covalent geometry    : angle       0.55640 (17545)
  hydrogen bonds       : bond        0.03237 (  575)
  hydrogen bonds       : angle       4.60345 ( 1800)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1750.95 seconds
wall clock time: 30 minutes 56.39 seconds (1856.39 seconds total)