Starting phenix.real_space_refine
on Wed Jun 11 02:26:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f32_28829/06_2025/8f32_28829.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f32_28829/06_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_28829/06_2025/8f32_28829.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f32_28829/06_2025/8f32_28829.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f32_28829/06_2025/8f32_28829.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f32_28829/06_2025/8f32_28829.cif"
  }
  resolution = 3.71
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
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): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12545
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      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: "A"
      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:
    C, B, E, D
  Time building chain proxies: 4.98, per 1000 atoms: 0.40
  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: 2.85
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 1.29
  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: 3.87

  Time building geometry restraints manager: 3.40 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: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     26.660
  Find NCS groups from input model:        0.230
  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:             0.010
  Load rotamer database and sin/cos tables:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.850
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (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
 TRP   0.014   0.002   TRP A  43 
 HIS   0.013   0.003   HIS C 169 
 PHE   0.018   0.002   PHE B 308 
 TYR   0.020   0.002   TYR D 245 
 ARG   0.003   0.000   ARG C 286 

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

*********************** 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  : 1.685 
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: 0.6574 (t0)
REVERT: C   86 ASP cc_start: 0.7052 (t70) cc_final: 0.6644 (t0)
REVERT: C  115 ASP cc_start: 0.6719 (t0) cc_final: 0.5810 (t0)
REVERT: C  117 ARG cc_start: 0.7805 (mmt180) cc_final: 0.7204 (mmt180)
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: 0.6651 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 276
  average time/residue: 0.2355
  time to fit residues: 93.1813
Evaluate side-chains
  202 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 1.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    7.9990
   chunk 113 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 38 optimal weight:    0.3980
   chunk 76 optimal weight:    9.9990
   chunk 60 optimal weight:    8.9990
   chunk 117 optimal weight:   10.0000
   chunk 45 optimal weight:   10.0000
   chunk 71 optimal weight:    5.9990
   chunk 87 optimal weight:   20.0000
   chunk 136 optimal weight:   10.0000
   overall best weight:    3.6186

-------------------------------------------------------------------------------
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 = 0.3644 r_free = 0.3644 target = 0.150044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.118662 restraints weight = 17178.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.122340 restraints weight = 10984.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.125208 restraints weight = 8153.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  12880  Z= 0.243
  Angle     :  0.632   5.706  17545  Z= 0.337
  Chirality :  0.049   0.138   1950
  Planarity :  0.005   0.045   2235
  Dihedral  :  5.301  25.146   1690
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.93 %
    Favored  : 86.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.22), residues: 1525
  helix:  0.71 (0.24), residues: 495
  sheet: -0.24 (0.23), residues: 475
  loop : -1.83 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  43 
 HIS   0.007   0.002   HIS B 169 
 PHE   0.024   0.002   PHE B  19 
 TYR   0.012   0.002   TYR B 258 
 ARG   0.003   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04003 (  575)
  hydrogen bonds       : angle       5.19516 ( 1800)
  covalent geometry    : bond        0.00575 (12880)
  covalent geometry    : angle       0.63197 (17545)

*********************** 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: 23
    poor density    : 206
  time to evaluate  : 1.437 
Fit side-chains
   revert: symmetry clash
REVERT: D   86 ASP cc_start: 0.6939 (t70) cc_final: 0.6491 (t0)
  outliers start: 23
  outliers final: 19
  residues processed: 211
  average time/residue: 0.2393
  time to fit residues: 73.4565
Evaluate side-chains
  197 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 178
  time to evaluate  : 1.449 
-------------------------------------------------------------------------------
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  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  212 LEU
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  212 LEU
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 145 optimal weight:    0.5980
   chunk 84 optimal weight:    0.3980
   chunk 63 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9990
   chunk 27 optimal weight:   10.0000
   chunk 66 optimal weight:    0.0470
   chunk 106 optimal weight:    4.9990
   chunk 5 optimal weight:    7.9990
   chunk 146 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.6080

-------------------------------------------------------------------------------
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
C 169 HIS
B 177 HIS
A  89 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.156889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.127559 restraints weight = 17099.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.131440 restraints weight = 10525.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.134148 restraints weight = 7689.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12880  Z= 0.102
  Angle     :  0.482   4.681  17545  Z= 0.256
  Chirality :  0.045   0.133   1950
  Planarity :  0.003   0.045   2235
  Dihedral  :  4.500  19.271   1690
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.05 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.22), residues: 1525
  helix:  1.54 (0.25), residues: 490
  sheet:  0.08 (0.24), residues: 465
  loop : -1.64 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  43 
 HIS   0.006   0.001   HIS B 169 
 PHE   0.020   0.001   PHE A  19 
 TYR   0.008   0.001   TYR D 245 
 ARG   0.002   0.000   ARG B 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03081 (  575)
  hydrogen bonds       : angle       4.56646 ( 1800)
  covalent geometry    : bond        0.00231 (12880)
  covalent geometry    : angle       0.48218 (17545)

*********************** 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
  263 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 233
  time to evaluate  : 1.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  264 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.7059 (mp10)
REVERT: D   86 ASP cc_start: 0.6981 (t70) cc_final: 0.6512 (t0)
REVERT: D  264 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6952 (mp10)
REVERT: C  113 ASP cc_start: 0.6803 (p0) cc_final: 0.6583 (p0)
REVERT: A  113 ASP cc_start: 0.6873 (p0) cc_final: 0.6652 (p0)
  outliers start: 30
  outliers final: 16
  residues processed: 241
  average time/residue: 0.2332
  time to fit residues: 82.4686
Evaluate side-chains
  203 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 185
  time to evaluate  : 1.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain E residue  260 THR
Chi-restraints excluded: chain E residue  264 GLN
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  260 THR
Chi-restraints excluded: chain C residue  264 GLN
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  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 74 optimal weight:    4.9990
   chunk 116 optimal weight:    9.9990
   chunk 25 optimal weight:    8.9990
   chunk 82 optimal weight:    0.8980
   chunk 129 optimal weight:    0.0470
   chunk 55 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 90 optimal weight:   10.0000
   chunk 84 optimal weight:    0.1980
   chunk 79 optimal weight:    6.9990
   chunk 45 optimal weight:   10.0000
   overall best weight:    1.4280

-------------------------------------------------------------------------------
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 = 0.3681 r_free = 0.3681 target = 0.153520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.123396 restraints weight = 17011.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.127259 restraints weight = 10752.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.129832 restraints weight = 7910.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12880  Z= 0.128
  Angle     :  0.495   4.581  17545  Z= 0.263
  Chirality :  0.045   0.128   1950
  Planarity :  0.003   0.038   2235
  Dihedral  :  4.386  17.877   1690
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 14.84 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.22), residues: 1525
  helix:  1.70 (0.25), residues: 495
  sheet:  0.18 (0.24), residues: 465
  loop : -1.64 (0.26), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  43 
 HIS   0.008   0.001   HIS B 169 
 PHE   0.023   0.001   PHE B  19 
 TYR   0.010   0.001   TYR C  24 
 ARG   0.003   0.000   ARG C 299 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03189 (  575)
  hydrogen bonds       : angle       4.47487 ( 1800)
  covalent geometry    : bond        0.00301 (12880)
  covalent geometry    : angle       0.49497 (17545)

*********************** 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
  264 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 222
  time to evaluate  : 1.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  264 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.7069 (mp10)
REVERT: D   22 LYS cc_start: 0.8525 (pttm) cc_final: 0.8166 (pttm)
REVERT: D   86 ASP cc_start: 0.6903 (t70) cc_final: 0.6461 (t0)
REVERT: D  255 ARG cc_start: 0.6572 (mtt90) cc_final: 0.6084 (mtt-85)
REVERT: D  264 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6954 (mp10)
REVERT: B  255 ARG cc_start: 0.6561 (mtt90) cc_final: 0.6126 (mtt-85)
REVERT: A  113 ASP cc_start: 0.6870 (p0) cc_final: 0.6660 (p0)
  outliers start: 42
  outliers final: 33
  residues processed: 237
  average time/residue: 0.2403
  time to fit residues: 83.9752
Evaluate side-chains
  221 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 186
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
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  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  260 THR
Chi-restraints excluded: chain E residue  264 GLN
Chi-restraints excluded: chain D residue   61 THR
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  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  168 THR
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 C residue  278 LEU
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  195 ILE
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   93 MET
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
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 64 optimal weight:    0.3980
   chunk 132 optimal weight:    9.9990
   chunk 111 optimal weight:   10.0000
   chunk 71 optimal weight:    0.0970
   chunk 104 optimal weight:    0.0010
   chunk 4 optimal weight:    9.9990
   chunk 116 optimal weight:    0.5980
   chunk 80 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 60 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   overall best weight:    1.2186

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.154898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.124870 restraints weight = 16933.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.128776 restraints weight = 10679.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.131445 restraints weight = 7838.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12880  Z= 0.119
  Angle     :  0.494   5.327  17545  Z= 0.260
  Chirality :  0.045   0.128   1950
  Planarity :  0.003   0.033   2235
  Dihedral  :  4.253  17.082   1690
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 16.07 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.23), residues: 1525
  helix:  1.93 (0.25), residues: 490
  sheet:  0.12 (0.23), residues: 490
  loop : -1.66 (0.26), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  43 
 HIS   0.009   0.001   HIS B 169 
 PHE   0.018   0.001   PHE B  19 
 TYR   0.007   0.001   TYR B 245 
 ARG   0.003   0.000   ARG C 299 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03096 (  575)
  hydrogen bonds       : angle       4.35247 ( 1800)
  covalent geometry    : bond        0.00280 (12880)
  covalent geometry    : angle       0.49425 (17545)

*********************** 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
  259 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 213
  time to evaluate  : 1.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  113 ASP cc_start: 0.6713 (p0) cc_final: 0.6503 (p0)
REVERT: E  255 ARG cc_start: 0.6427 (mtt90) cc_final: 0.6074 (mtt-85)
REVERT: D  255 ARG cc_start: 0.6780 (mtt90) cc_final: 0.6231 (mtt-85)
REVERT: A   54 LYS cc_start: 0.7377 (mmtt) cc_final: 0.7144 (tppt)
REVERT: A  255 ARG cc_start: 0.6631 (mtt90) cc_final: 0.6244 (mtt-85)
  outliers start: 46
  outliers final: 38
  residues processed: 231
  average time/residue: 0.2283
  time to fit residues: 78.0671
Evaluate side-chains
  220 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 182
  time to evaluate  : 1.433 
-------------------------------------------------------------------------------
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  168 THR
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  260 THR
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  176 ASP
Chi-restraints excluded: chain D residue  195 ILE
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  227 SER
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  121 PHE
Chi-restraints excluded: chain C residue  168 THR
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 C residue  278 LEU
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  168 THR
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  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
Chi-restraints excluded: chain A residue  266 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 34 optimal weight:    0.0770
   chunk 79 optimal weight:    5.9990
   chunk 119 optimal weight:    7.9990
   chunk 135 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 115 optimal weight:    3.9990
   chunk 28 optimal weight:   20.0000
   chunk 88 optimal weight:    8.9990
   chunk 132 optimal weight:   10.0000
   chunk 128 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   overall best weight:    4.4146

-------------------------------------------------------------------------------
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
A  89 ASN
A 151 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.147655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.116626 restraints weight = 17561.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.120332 restraints weight = 11030.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.122978 restraints weight = 8187.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067  12880  Z= 0.281
  Angle     :  0.661   9.997  17545  Z= 0.346
  Chirality :  0.050   0.152   1950
  Planarity :  0.004   0.035   2235
  Dihedral  :  5.015  27.006   1690
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 16.00 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.22), residues: 1525
  helix:  1.43 (0.25), residues: 495
  sheet: -0.11 (0.23), residues: 465
  loop : -1.78 (0.26), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 160 
 HIS   0.008   0.002   HIS B 169 
 PHE   0.024   0.002   PHE A  19 
 TYR   0.013   0.002   TYR E 258 
 ARG   0.005   0.000   ARG D 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04076 (  575)
  hydrogen bonds       : angle       4.94222 ( 1800)
  covalent geometry    : bond        0.00667 (12880)
  covalent geometry    : angle       0.66115 (17545)

*********************** 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
  279 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 211
  time to evaluate  : 1.362 
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: A   54 LYS cc_start: 0.7490 (mmtt) cc_final: 0.7206 (tppt)
  outliers start: 68
  outliers final: 54
  residues processed: 248
  average time/residue: 0.2230
  time to fit residues: 81.6005
Evaluate side-chains
  228 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 174
  time to evaluate  : 1.345 
-------------------------------------------------------------------------------
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  145 ILE
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  256 LEU
Chi-restraints excluded: chain E residue  260 THR
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  103 ASN
Chi-restraints excluded: chain D residue  145 ILE
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  256 LEU
Chi-restraints excluded: chain D residue  260 THR
Chi-restraints excluded: chain D residue  264 GLN
Chi-restraints excluded: chain D residue  279 LEU
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  212 LEU
Chi-restraints excluded: chain C residue  227 SER
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 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  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   60 ASN
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  145 ILE
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  260 THR
Chi-restraints excluded: chain A residue  264 GLN
Chi-restraints excluded: chain A residue  266 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 139 optimal weight:    4.9990
   chunk 123 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 113 optimal weight:    0.8980
   chunk 7 optimal weight:    7.9990
   chunk 146 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
E  21 ASN
E 169 HIS
E 285 HIS
D  42 GLN
D  89 ASN
D 285 HIS
C  60 ASN
C 285 HIS
B  42 GLN
B 285 HIS
A  89 ASN
A 151 ASN
A 177 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.152436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.122536 restraints weight = 17126.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.126433 restraints weight = 10596.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.128897 restraints weight = 7723.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12880  Z= 0.122
  Angle     :  0.516   6.159  17545  Z= 0.272
  Chirality :  0.045   0.139   1950
  Planarity :  0.003   0.035   2235
  Dihedral  :  4.446  18.541   1690
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.22), residues: 1525
  helix:  1.79 (0.25), residues: 490
  sheet:  0.04 (0.23), residues: 465
  loop : -1.69 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  43 
 HIS   0.010   0.002   HIS B 169 
 PHE   0.021   0.001   PHE A  19 
 TYR   0.011   0.001   TYR D 203 
 ARG   0.002   0.000   ARG C 299 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03127 (  575)
  hydrogen bonds       : angle       4.52286 ( 1800)
  covalent geometry    : bond        0.00281 (12880)
  covalent geometry    : angle       0.51580 (17545)

*********************** 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
  259 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 207
  time to evaluate  : 1.379 
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  113 ASP cc_start: 0.6824 (p0) cc_final: 0.6608 (p0)
REVERT: E  237 THR cc_start: 0.8741 (m) cc_final: 0.8535 (m)
REVERT: D  255 ARG cc_start: 0.6623 (mtt90) cc_final: 0.6115 (mtt-85)
REVERT: C  223 PHE cc_start: 0.8121 (m-80) cc_final: 0.7911 (m-80)
REVERT: A   54 LYS cc_start: 0.7360 (mmtt) cc_final: 0.7107 (tppt)
  outliers start: 52
  outliers final: 38
  residues processed: 234
  average time/residue: 0.2545
  time to fit residues: 89.1104
Evaluate side-chains
  222 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 184
  time to evaluate  : 1.547 
-------------------------------------------------------------------------------
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  118 LEU
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  230 GLU
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  118 LEU
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  168 THR
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  118 LEU
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  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 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 145 optimal weight:    0.9990
   chunk 93 optimal weight:   20.0000
   chunk 118 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0970
   chunk 82 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 113 optimal weight:    7.9990
   chunk 117 optimal weight:    9.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
E 169 HIS
C  60 ASN
A 151 ASN

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 = 0.152043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.121830 restraints weight = 17185.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.125516 restraints weight = 10746.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.128190 restraints weight = 7949.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12880  Z= 0.138
  Angle     :  0.530   8.652  17545  Z= 0.276
  Chirality :  0.045   0.131   1950
  Planarity :  0.003   0.032   2235
  Dihedral  :  4.392  19.135   1690
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 17.38 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.23), residues: 1525
  helix:  1.81 (0.25), residues: 490
  sheet:  0.10 (0.24), residues: 465
  loop : -1.66 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  43 
 HIS   0.009   0.001   HIS B 169 
 PHE   0.025   0.001   PHE B 236 
 TYR   0.010   0.001   TYR E 245 
 ARG   0.003   0.000   ARG A 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03190 (  575)
  hydrogen bonds       : angle       4.51220 ( 1800)
  covalent geometry    : bond        0.00326 (12880)
  covalent geometry    : angle       0.53038 (17545)

*********************** 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
  247 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 194
  time to evaluate  : 1.344 
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  113 ASP cc_start: 0.6870 (p0) cc_final: 0.6645 (p0)
REVERT: E  264 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7363 (mm110)
REVERT: D  255 ARG cc_start: 0.6741 (mpt90) cc_final: 0.6239 (mtt-85)
REVERT: A   54 LYS cc_start: 0.7405 (mmtt) cc_final: 0.7116 (tppt)
  outliers start: 53
  outliers final: 47
  residues processed: 226
  average time/residue: 0.2374
  time to fit residues: 78.3441
Evaluate side-chains
  230 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 182
  time to evaluate  : 1.491 
-------------------------------------------------------------------------------
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  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   61 THR
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  230 GLU
Chi-restraints excluded: chain D residue  260 THR
Chi-restraints excluded: chain D residue  264 GLN
Chi-restraints excluded: chain D residue  279 LEU
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  145 ILE
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   58 VAL
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   84 SER
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  195 ILE
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 A residue   39 ILE
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  151 ASN
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 1 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 133 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 64 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   overall best weight:    2.1986

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.149943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.119395 restraints weight = 17164.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.123199 restraints weight = 10779.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.125756 restraints weight = 7953.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.3132

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= 0.166
  Angle     :  0.553   6.431  17545  Z= 0.289
  Chirality :  0.046   0.156   1950
  Planarity :  0.003   0.034   2235
  Dihedral  :  4.466  20.523   1690
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 17.24 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.23), residues: 1525
  helix:  1.78 (0.25), residues: 490
  sheet:  0.06 (0.24), residues: 465
  loop : -1.65 (0.27), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  43 
 HIS   0.009   0.002   HIS B 169 
 PHE   0.026   0.001   PHE B  19 
 TYR   0.008   0.001   TYR C 258 
 ARG   0.002   0.000   ARG D 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03288 (  575)
  hydrogen bonds       : angle       4.56298 ( 1800)
  covalent geometry    : bond        0.00392 (12880)
  covalent geometry    : angle       0.55256 (17545)

*********************** 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
  244 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 185
  time to evaluate  : 1.678 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  113 ASP cc_start: 0.6898 (p0) cc_final: 0.6670 (p0)
REVERT: E  264 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7320 (mm110)
REVERT: D  255 ARG cc_start: 0.6656 (mpt90) cc_final: 0.6142 (mtt-85)
REVERT: C  230 GLU cc_start: 0.7385 (pm20) cc_final: 0.6487 (pt0)
REVERT: A   54 LYS cc_start: 0.7418 (mmtt) cc_final: 0.7123 (tppt)
  outliers start: 59
  outliers final: 51
  residues processed: 216
  average time/residue: 0.2648
  time to fit residues: 84.0929
Evaluate side-chains
  227 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 175
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
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  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   61 THR
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  230 GLU
Chi-restraints excluded: chain D residue  243 VAL
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 D residue  279 LEU
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  118 LEU
Chi-restraints excluded: chain C residue  145 ILE
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 C residue  266 ILE
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   84 SER
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  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 A residue   39 ILE
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 127 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 122 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 74 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 131 optimal weight:    3.9990
   overall best weight:    1.0984

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.154399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.124710 restraints weight = 17022.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.128636 restraints weight = 10605.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.131128 restraints weight = 7734.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.3156

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= 0.119
  Angle     :  0.524   8.006  17545  Z= 0.273
  Chirality :  0.045   0.188   1950
  Planarity :  0.003   0.033   2235
  Dihedral  :  4.304  17.323   1690
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 17.60 %
    Favored  : 78.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.23), residues: 1525
  helix:  1.85 (0.25), residues: 490
  sheet:  0.15 (0.24), residues: 465
  loop : -1.60 (0.27), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  43 
 HIS   0.009   0.002   HIS B 169 
 PHE   0.025   0.001   PHE B  19 
 TYR   0.007   0.001   TYR D 245 
 ARG   0.003   0.000   ARG B 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03049 (  575)
  hydrogen bonds       : angle       4.44781 ( 1800)
  covalent geometry    : bond        0.00276 (12880)
  covalent geometry    : angle       0.52362 (17545)

********************** 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
  246 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 193
  time to evaluate  : 1.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  113 ASP cc_start: 0.6770 (p0) cc_final: 0.6561 (p0)
REVERT: E  255 ARG cc_start: 0.6554 (mtt90) cc_final: 0.6074 (mtt-85)
REVERT: E  264 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7198 (mm110)
REVERT: D  117 ARG cc_start: 0.7908 (mpt180) cc_final: 0.7410 (mmt180)
REVERT: D  264 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.6857 (mp10)
REVERT: A   54 LYS cc_start: 0.7383 (mmtt) cc_final: 0.7097 (tppt)
  outliers start: 53
  outliers final: 47
  residues processed: 221
  average time/residue: 0.2792
  time to fit residues: 90.7314
Evaluate side-chains
  224 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 175
  time to evaluate  : 3.131 
-------------------------------------------------------------------------------
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  118 LEU
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  152 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  264 GLN
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  243 VAL
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 D residue  279 LEU
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  168 THR
Chi-restraints excluded: chain C residue  195 ILE
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   84 SER
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  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 A residue   39 ILE
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  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  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 128 optimal weight:   10.0000
   chunk 113 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 139 optimal weight:    0.4980
   chunk 104 optimal weight:    0.0060
   chunk 102 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0040
   chunk 40 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 87 optimal weight:    9.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    0.7012

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.155443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.125830 restraints weight = 17092.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.129634 restraints weight = 10500.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.132440 restraints weight = 7610.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.3208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12880  Z= 0.107
  Angle     :  0.513   8.559  17545  Z= 0.268
  Chirality :  0.045   0.189   1950
  Planarity :  0.003   0.034   2235
  Dihedral  :  4.187  17.269   1690
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 18.47 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.23), residues: 1525
  helix:  1.88 (0.25), residues: 490
  sheet:  0.31 (0.24), residues: 470
  loop : -1.55 (0.27), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  43 
 HIS   0.010   0.001   HIS B 169 
 PHE   0.025   0.001   PHE D  19 
 TYR   0.006   0.001   TYR E 258 
 ARG   0.004   0.000   ARG C 299 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02967 (  575)
  hydrogen bonds       : angle       4.36648 ( 1800)
  covalent geometry    : bond        0.00243 (12880)
  covalent geometry    : angle       0.51266 (17545)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3903.97 seconds
wall clock time: 70 minutes 28.44 seconds (4228.44 seconds total)