Starting phenix.real_space_refine
on Fri May  9 21:17:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gzt_51734/05_2025/9gzt_51734.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gzt_51734/05_2025/9gzt_51734.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gzt_51734/05_2025/9gzt_51734.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gzt_51734/05_2025/9gzt_51734.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gzt_51734/05_2025/9gzt_51734.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gzt_51734/05_2025/9gzt_51734.cif"
  }
  resolution = 2.9
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    2436      2.51       5
     N     696      2.21       5
     O     792      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3924
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 142
          Classifications: {'peptide': 19}
          Link IDs: {'TRANS': 18}
  Restraints were copied for chains:
    B, E, F, I, J, M, N, Q, R, U, V, D, G, H, K, L, O, P, S, T, W, X
  Time building chain proxies: 2.37, per 1000 atoms: 0.60
  Number of scatterers: 3924
  At special positions: 0
  Unit cell: (122.925, 74.5, 47.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     792      8.00
     N     696      7.00
     C    2436      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=12, symmetry=0
  Number of additional bonds: simple=12, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.13
  Conformation dependent library (CDL) restraints added in 472.2 milliseconds
  

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  984

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 59.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 22
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 33
      removed outlier: 6.520A  pdb=" N   LEU A  27 " --> pdb=" O   SER E  28 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   THR E  30 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   SER A  29 " --> pdb=" O   THR E  30 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   VAL E  32 " --> pdb=" O   SER A  29 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ASN A  31 " --> pdb=" O   VAL E  32 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   LEU E  27 " --> pdb=" O   SER I  28 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   THR I  30 " --> pdb=" O   LEU E  27 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   SER E  29 " --> pdb=" O   THR I  30 " (cutoff:3.500A)
      removed outlier: 8.062A  pdb=" N   VAL I  32 " --> pdb=" O   SER E  29 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   ASN E  31 " --> pdb=" O   VAL I  32 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   LEU I  27 " --> pdb=" O   SER M  28 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   THR M  30 " --> pdb=" O   LEU I  27 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   SER I  29 " --> pdb=" O   THR M  30 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   VAL M  32 " --> pdb=" O   SER I  29 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ASN I  31 " --> pdb=" O   VAL M  32 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   LEU M  27 " --> pdb=" O   SER Q  28 " (cutoff:3.500A)
      removed outlier: 8.050A  pdb=" N   THR Q  30 " --> pdb=" O   LEU M  27 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   SER M  29 " --> pdb=" O   THR Q  30 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   VAL Q  32 " --> pdb=" O   SER M  29 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ASN M  31 " --> pdb=" O   VAL Q  32 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   LEU Q  27 " --> pdb=" O   SER U  28 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   THR U  30 " --> pdb=" O   LEU Q  27 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   SER Q  29 " --> pdb=" O   THR U  30 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   VAL U  32 " --> pdb=" O   SER Q  29 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ASN Q  31 " --> pdb=" O   VAL U  32 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 14 through 22
    Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 33
      removed outlier: 6.516A  pdb=" N   LEU B  27 " --> pdb=" O   SER F  28 " (cutoff:3.500A)
      removed outlier: 8.031A  pdb=" N   THR F  30 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   SER B  29 " --> pdb=" O   THR F  30 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   VAL F  32 " --> pdb=" O   SER B  29 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ASN B  31 " --> pdb=" O   VAL F  32 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   LEU F  27 " --> pdb=" O   SER J  28 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   THR J  30 " --> pdb=" O   LEU F  27 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   SER F  29 " --> pdb=" O   THR J  30 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   VAL J  32 " --> pdb=" O   SER F  29 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ASN F  31 " --> pdb=" O   VAL J  32 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   LEU J  27 " --> pdb=" O   SER N  28 " (cutoff:3.500A)
      removed outlier: 8.035A  pdb=" N   THR N  30 " --> pdb=" O   LEU J  27 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   SER J  29 " --> pdb=" O   THR N  30 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   VAL N  32 " --> pdb=" O   SER J  29 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ASN J  31 " --> pdb=" O   VAL N  32 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   LEU N  27 " --> pdb=" O   SER R  28 " (cutoff:3.500A)
      removed outlier: 8.031A  pdb=" N   THR R  30 " --> pdb=" O   LEU N  27 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   SER N  29 " --> pdb=" O   THR R  30 " (cutoff:3.500A)
      removed outlier: 8.035A  pdb=" N   VAL R  32 " --> pdb=" O   SER N  29 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   ASN N  31 " --> pdb=" O   VAL R  32 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   LEU R  27 " --> pdb=" O   SER V  28 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   THR V  30 " --> pdb=" O   LEU R  27 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   SER R  29 " --> pdb=" O   THR V  30 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   VAL V  32 " --> pdb=" O   SER R  29 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ASN R  31 " --> pdb=" O   VAL V  32 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 15 through 20
      removed outlier: 6.439A  pdb=" N   PHE C  15 " --> pdb=" O   LEU G  16 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   HIS G  18 " --> pdb=" O   PHE C  15 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   VAL C  17 " --> pdb=" O   HIS G  18 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   SER G  20 " --> pdb=" O   VAL C  17 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   SER C  19 " --> pdb=" O   SER G  20 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   PHE G  15 " --> pdb=" O   LEU K  16 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   HIS K  18 " --> pdb=" O   PHE G  15 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   VAL G  17 " --> pdb=" O   HIS K  18 " (cutoff:3.500A)
      removed outlier: 7.705A  pdb=" N   SER K  20 " --> pdb=" O   VAL G  17 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   SER G  19 " --> pdb=" O   SER K  20 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   PHE K  15 " --> pdb=" O   LEU O  16 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   HIS O  18 " --> pdb=" O   PHE K  15 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   VAL K  17 " --> pdb=" O   HIS O  18 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   SER O  20 " --> pdb=" O   VAL K  17 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   SER K  19 " --> pdb=" O   SER O  20 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   PHE S  15 " --> pdb=" O   LEU W  16 " (cutoff:3.500A)
      removed outlier: 7.717A  pdb=" N   HIS W  18 " --> pdb=" O   PHE S  15 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   VAL S  17 " --> pdb=" O   HIS W  18 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   SER W  20 " --> pdb=" O   VAL S  17 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   SER S  19 " --> pdb=" O   SER W  20 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 25 through 31
      removed outlier: 6.296A  pdb=" N   ILE K  26 " --> pdb=" O   LEU O  27 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   SER O  29 " --> pdb=" O   ILE K  26 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   SER K  28 " --> pdb=" O   SER O  29 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   ASN O  31 " --> pdb=" O   SER K  28 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   THR K  30 " --> pdb=" O   ASN O  31 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   ILE O  26 " --> pdb=" O   LEU S  27 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   SER S  29 " --> pdb=" O   ILE O  26 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   SER O  28 " --> pdb=" O   SER S  29 " (cutoff:3.500A)
      removed outlier: 7.914A  pdb=" N   ASN S  31 " --> pdb=" O   SER O  28 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   THR O  30 " --> pdb=" O   ASN S  31 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 15 through 20
      removed outlier: 6.663A  pdb=" N   PHE D  15 " --> pdb=" O   LEU H  16 " (cutoff:3.500A)
      removed outlier: 8.012A  pdb=" N   HIS H  18 " --> pdb=" O   PHE D  15 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   VAL D  17 " --> pdb=" O   HIS H  18 " (cutoff:3.500A)
      removed outlier: 8.064A  pdb=" N   SER H  20 " --> pdb=" O   VAL D  17 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   SER D  19 " --> pdb=" O   SER H  20 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   PHE H  15 " --> pdb=" O   LEU L  16 " (cutoff:3.500A)
      removed outlier: 7.828A  pdb=" N   HIS L  18 " --> pdb=" O   PHE H  15 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   VAL H  17 " --> pdb=" O   HIS L  18 " (cutoff:3.500A)
      removed outlier: 7.909A  pdb=" N   SER L  20 " --> pdb=" O   VAL H  17 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   SER H  19 " --> pdb=" O   SER L  20 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   PHE L  15 " --> pdb=" O   LEU P  16 " (cutoff:3.500A)
      removed outlier: 7.867A  pdb=" N   HIS P  18 " --> pdb=" O   PHE L  15 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   VAL L  17 " --> pdb=" O   HIS P  18 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   SER P  20 " --> pdb=" O   VAL L  17 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   SER L  19 " --> pdb=" O   SER P  20 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   PHE P  15 " --> pdb=" O   LEU T  16 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   HIS T  18 " --> pdb=" O   PHE P  15 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   VAL P  17 " --> pdb=" O   HIS T  18 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   SER T  20 " --> pdb=" O   VAL P  17 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   SER P  19 " --> pdb=" O   SER T  20 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   PHE T  15 " --> pdb=" O   LEU X  16 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   HIS X  18 " --> pdb=" O   PHE T  15 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   VAL T  17 " --> pdb=" O   HIS X  18 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   SER X  20 " --> pdb=" O   VAL T  17 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   SER T  19 " --> pdb=" O   SER X  20 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'D' and resid 25 through 31
      removed outlier: 6.408A  pdb=" N   ILE P  26 " --> pdb=" O   LEU T  27 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   SER T  29 " --> pdb=" O   ILE P  26 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   SER P  28 " --> pdb=" O   SER T  29 " (cutoff:3.500A)
      removed outlier: 8.141A  pdb=" N   ASN T  31 " --> pdb=" O   SER P  28 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   THR P  30 " --> pdb=" O   ASN T  31 " (cutoff:3.500A)

    127 hydrogen bonds defined for protein.
    381 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.02

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 636
        1.29 -     1.35: 660
        1.35 -     1.41: 501
        1.41 -     1.48: 627
        1.48 -     1.54: 1548
  Bond restraints: 3972
  Sorted by residual:
  bond pdb=" CG1 ILE Q  26 "
       pdb=" CD1 ILE Q  26 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 1.02e+00
  bond pdb=" CG1 ILE R  26 "
       pdb=" CD1 ILE R  26 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 1.01e+00
  bond pdb=" CG1 ILE E  26 "
       pdb=" CD1 ILE E  26 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 1.00e+00
  bond pdb=" CG1 ILE A  26 "
       pdb=" CD1 ILE A  26 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 1.00e+00
  bond pdb=" CG1 ILE M  26 "
       pdb=" CD1 ILE M  26 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 9.94e-01
  ... (remaining 3967 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.86: 4421
        0.86 -     1.71: 618
        1.71 -     2.57: 217
        2.57 -     3.42: 84
        3.42 -     4.28: 48
  Bond angle restraints: 5388
  Sorted by residual:
  angle pdb=" N   VAL Q  17 "
        pdb=" CA  VAL Q  17 "
        pdb=" C   VAL Q  17 "
      ideal   model   delta    sigma   weight residual
     108.17  112.05   -3.88 1.46e+00 4.69e-01 7.05e+00
  angle pdb=" N   VAL B  17 "
        pdb=" CA  VAL B  17 "
        pdb=" C   VAL B  17 "
      ideal   model   delta    sigma   weight residual
     108.17  112.02   -3.85 1.46e+00 4.69e-01 6.97e+00
  angle pdb=" N   VAL E  17 "
        pdb=" CA  VAL E  17 "
        pdb=" C   VAL E  17 "
      ideal   model   delta    sigma   weight residual
     108.17  112.02   -3.85 1.46e+00 4.69e-01 6.95e+00
  angle pdb=" N   VAL F  17 "
        pdb=" CA  VAL F  17 "
        pdb=" C   VAL F  17 "
      ideal   model   delta    sigma   weight residual
     108.17  112.01   -3.84 1.46e+00 4.69e-01 6.92e+00
  angle pdb=" N   VAL M  17 "
        pdb=" CA  VAL M  17 "
        pdb=" C   VAL M  17 "
      ideal   model   delta    sigma   weight residual
     108.17  112.00   -3.83 1.46e+00 4.69e-01 6.89e+00
  ... (remaining 5383 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     6.61: 1716
        6.61 -    13.22: 276
       13.22 -    19.82: 108
       19.82 -    26.43: 36
       26.43 -    33.04: 84
  Dihedral angle restraints: 2220
    sinusoidal: 720
      harmonic: 1500
  Sorted by residual:
  dihedral pdb=" CA  LEU W  16 "
           pdb=" CB  LEU W  16 "
           pdb=" CG  LEU W  16 "
           pdb=" CD1 LEU W  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  147.04   32.96     3      1.50e+01 4.44e-03 5.47e+00
  dihedral pdb=" CA  LEU C  16 "
           pdb=" CB  LEU C  16 "
           pdb=" CG  LEU C  16 "
           pdb=" CD1 LEU C  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  147.05   32.95     3      1.50e+01 4.44e-03 5.47e+00
  dihedral pdb=" CA  LEU K  16 "
           pdb=" CB  LEU K  16 "
           pdb=" CG  LEU K  16 "
           pdb=" CD1 LEU K  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  147.06   32.94     3      1.50e+01 4.44e-03 5.47e+00
  ... (remaining 2217 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 400
       0.033 -    0.066: 115
       0.066 -    0.100: 76
       0.100 -    0.133: 41
       0.133 -    0.166: 16
  Chirality restraints: 648
  Sorted by residual:
  chirality pdb=" CB  VAL P  32 "
            pdb=" CA  VAL P  32 "
            pdb=" CG1 VAL P  32 "
            pdb=" CG2 VAL P  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 6.88e-01
  chirality pdb=" CB  VAL D  32 "
            pdb=" CA  VAL D  32 "
            pdb=" CG1 VAL D  32 "
            pdb=" CG2 VAL D  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 6.85e-01
  chirality pdb=" CB  VAL H  32 "
            pdb=" CA  VAL H  32 "
            pdb=" CG1 VAL H  32 "
            pdb=" CG2 VAL H  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.16 2.00e-01 2.50e+01 6.77e-01
  ... (remaining 645 not shown)

  Planarity restraints: 696
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H  23 "    0.008 2.00e-02 2.50e+03   6.58e-03 7.57e-01
        pdb=" CG  PHE H  23 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD1 PHE H  23 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE H  23 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE H  23 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE H  23 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE H  23 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE N  15 "   -0.009 2.00e-02 2.50e+03   6.58e-03 7.57e-01
        pdb=" CG  PHE N  15 "    0.014 2.00e-02 2.50e+03
        pdb=" CD1 PHE N  15 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE N  15 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE N  15 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE N  15 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE N  15 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  15 "   -0.009 2.00e-02 2.50e+03   6.55e-03 7.51e-01
        pdb=" CG  PHE A  15 "    0.015 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  15 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  15 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  15 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 693 not shown)

  Histogram of nonbonded interaction distances:
        2.60 -     3.06: 2559
        3.06 -     3.52: 3563
        3.52 -     3.98: 5880
        3.98 -     4.44: 6857
        4.44 -     4.90: 12809
  Nonbonded interactions: 31668
  Sorted by model distance:
  nonbonded pdb=" O   ASN T  22 "
            pdb=" N   PHE X  23 "
     model   vdw
     2.597 3.120
  nonbonded pdb=" N   NH2 Q  38 "
            pdb=" O   TYR U  37 "
     model   vdw
     2.661 3.120
  nonbonded pdb=" N   VAL D  32 "
            pdb=" O   VAL D  32 "
     model   vdw
     2.665 2.496
  nonbonded pdb=" N   VAL L  32 "
            pdb=" O   VAL L  32 "
     model   vdw
     2.666 2.496
  nonbonded pdb=" N   VAL H  32 "
            pdb=" O   VAL H  32 "
     model   vdw
     2.666 2.496
  ... (remaining 31663 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'U'
  selection = chain 'V'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'S'
  selection = chain 'T'
  selection = chain 'W'
  selection = chain 'X'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             10.000
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.240
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
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      :  0.007   0.104   3984  Z= 0.604
  Angle     :  0.841   4.281   5388  Z= 0.507
  Chirality :  0.054   0.166    648
  Planarity :  0.002   0.007    696
  Dihedral  : 10.897  33.041   1236
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.16 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.15 (0.24), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.18), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS Q  18 
 PHE   0.015   0.003   PHE H  23 
 TYR   0.013   0.003   TYR U  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16256 (  127)
  hydrogen bonds       : angle       7.63613 (  381)
  covalent geometry    : bond        0.00489 ( 3972)
  covalent geometry    : angle       0.84091 ( 5388)
  Misc. bond           : bond        0.10345 (   12)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.454 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1426
  time to fit residues: 9.4989
Evaluate side-chains
  26 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 28 optimal weight:    8.9990
   chunk 10 optimal weight:   20.0000
   chunk 17 optimal weight:    9.9990
   chunk 21 optimal weight:    5.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
D  21 ASN
E  18 HIS
F  18 HIS
H  21 ASN
I  18 HIS
I  35 ASN
J  18 HIS
K  21 ASN
L  21 ASN
M  18 HIS
N  18 HIS
O  21 ASN
Q  18 HIS
R  18 HIS
R  31 ASN
S  21 ASN
T  21 ASN
W  21 ASN
X  21 ASN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.107889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.081457 restraints weight = 5710.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.56
r_work: 0.3347 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3984  Z= 0.173
  Angle     :  0.560   6.157   5388  Z= 0.302
  Chirality :  0.044   0.124    648
  Planarity :  0.002   0.006    696
  Dihedral  :  5.456  19.099    516
  Min Nonbonded Distance : 2.655

Molprobity Statistics.
  All-atom Clashscore : 1.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  :  8.99 %
    Favored  : 87.06 %
  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: -3.53 (0.24), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.18), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J  18 
 PHE   0.010   0.002   PHE R  15 
 TYR   0.002   0.001   TYR U  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03283 (  127)
  hydrogen bonds       : angle       4.88021 (  381)
  covalent geometry    : bond        0.00389 ( 3972)
  covalent geometry    : angle       0.55972 ( 5388)
  Misc. bond           : bond        0.00139 (   12)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 15
  time to evaluate  : 0.465 
Fit side-chains
  outliers start: 18
  outliers final: 7
  residues processed: 28
  average time/residue: 0.0733
  time to fit residues: 3.7298
Evaluate side-chains
  21 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 14
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   32 VAL
Chi-restraints excluded: chain G residue   32 VAL
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain N residue   29 SER
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain P residue   30 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 21 optimal weight:    8.9990
   chunk 33 optimal weight:    0.4980
   chunk 11 optimal weight:   20.0000
   chunk 20 optimal weight:    5.9990
   chunk 22 optimal weight:   20.0000
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 9 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   overall best weight:    4.2988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.105651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.078679 restraints weight = 5745.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.63
r_work: 0.3300 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3984  Z= 0.210
  Angle     :  0.534   4.890   5388  Z= 0.298
  Chirality :  0.044   0.125    648
  Planarity :  0.002   0.006    696
  Dihedral  :  5.581  19.684    516
  Min Nonbonded Distance : 2.663

Molprobity Statistics.
  All-atom Clashscore : 0.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  :  9.21 %
    Favored  : 86.62 %
  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: -3.59 (0.24), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.73 (0.18), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS J  18 
 PHE   0.009   0.002   PHE M  15 
 TYR   0.004   0.001   TYR M  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03595 (  127)
  hydrogen bonds       : angle       4.53260 (  381)
  covalent geometry    : bond        0.00466 ( 3972)
  covalent geometry    : angle       0.53442 ( 5388)
  Misc. bond           : bond        0.00152 (   12)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 13
  time to evaluate  : 0.465 
Fit side-chains
REVERT: P   30 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.7782 (p)
  outliers start: 19
  outliers final: 18
  residues processed: 25
  average time/residue: 0.0603
  time to fit residues: 2.9715
Evaluate side-chains
  32 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 13
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 VAL
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   32 VAL
Chi-restraints excluded: chain G residue   30 THR
Chi-restraints excluded: chain G residue   32 VAL
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain K residue   30 THR
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain N residue   29 SER
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain P residue   30 THR
Chi-restraints excluded: chain P residue   32 VAL
Chi-restraints excluded: chain S residue   30 THR
Chi-restraints excluded: chain W residue   30 THR
Chi-restraints excluded: chain X residue   19 SER
Chi-restraints excluded: chain X residue   30 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 23 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 5 optimal weight:    8.9990
   chunk 18 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    4.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.104829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.078470 restraints weight = 5797.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 2.57
r_work: 0.3304 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3984  Z= 0.226
  Angle     :  0.522   3.711   5388  Z= 0.296
  Chirality :  0.044   0.126    648
  Planarity :  0.002   0.005    696
  Dihedral  :  5.641  19.998    516
  Min Nonbonded Distance : 2.664

Molprobity Statistics.
  All-atom Clashscore : 0.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 12.28 %
    Favored  : 82.46 %
  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: -3.62 (0.24), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.18), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS J  18 
 PHE   0.009   0.002   PHE M  15 
 TYR   0.004   0.001   TYR M  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03692 (  127)
  hydrogen bonds       : angle       4.38726 (  381)
  covalent geometry    : bond        0.00497 ( 3972)
  covalent geometry    : angle       0.52236 ( 5388)
  Misc. bond           : bond        0.00143 (   12)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 14
  time to evaluate  : 0.456 
Fit side-chains
REVERT: K   30 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7536 (p)
REVERT: P   30 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.7808 (p)
  outliers start: 24
  outliers final: 21
  residues processed: 31
  average time/residue: 0.0552
  time to fit residues: 3.3168
Evaluate side-chains
  37 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 14
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 VAL
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   32 VAL
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain G residue   30 THR
Chi-restraints excluded: chain G residue   32 VAL
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain K residue   30 THR
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain N residue   29 SER
Chi-restraints excluded: chain N residue   34 SER
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain P residue   30 THR
Chi-restraints excluded: chain P residue   32 VAL
Chi-restraints excluded: chain Q residue   34 SER
Chi-restraints excluded: chain S residue   30 THR
Chi-restraints excluded: chain V residue   34 SER
Chi-restraints excluded: chain W residue   30 THR
Chi-restraints excluded: chain X residue   30 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 17 optimal weight:   20.0000
   chunk 1 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 26 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   overall best weight:    5.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.104086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.078906 restraints weight = 6176.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 2.50
r_work: 0.3314 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
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      :  0.006   0.038   3984  Z= 0.267
  Angle     :  0.532   3.499   5388  Z= 0.306
  Chirality :  0.044   0.126    648
  Planarity :  0.002   0.006    696
  Dihedral  :  5.777  20.239    516
  Min Nonbonded Distance : 2.655

Molprobity Statistics.
  All-atom Clashscore : 0.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  : 14.47 %
    Favored  : 79.17 %
  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: -3.60 (0.24), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.73 (0.18), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E  18 
 PHE   0.011   0.002   PHE M  15 
 TYR   0.008   0.002   TYR N  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03934 (  127)
  hydrogen bonds       : angle       4.39538 (  381)
  covalent geometry    : bond        0.00585 ( 3972)
  covalent geometry    : angle       0.53240 ( 5388)
  Misc. bond           : bond        0.00182 (   12)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 23
  time to evaluate  : 0.468 
Fit side-chains
REVERT: K   30 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7631 (p)
REVERT: P   30 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.7921 (p)
  outliers start: 29
  outliers final: 25
  residues processed: 45
  average time/residue: 0.0589
  time to fit residues: 4.7758
Evaluate side-chains
  49 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 22
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 VAL
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain G residue   30 THR
Chi-restraints excluded: chain G residue   32 VAL
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain K residue   30 THR
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue   34 SER
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain P residue   30 THR
Chi-restraints excluded: chain P residue   32 VAL
Chi-restraints excluded: chain Q residue   34 SER
Chi-restraints excluded: chain R residue   34 SER
Chi-restraints excluded: chain S residue   30 THR
Chi-restraints excluded: chain T residue   30 THR
Chi-restraints excluded: chain U residue   34 SER
Chi-restraints excluded: chain V residue   34 SER
Chi-restraints excluded: chain W residue   30 THR
Chi-restraints excluded: chain X residue   30 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 3 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:   20.0000
   chunk 28 optimal weight:   20.0000
   chunk 5 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 33 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    4.7188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.108760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.082360 restraints weight = 6761.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.64
r_work: 0.3299 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3984  Z= 0.235
  Angle     :  0.505   3.071   5388  Z= 0.293
  Chirality :  0.043   0.129    648
  Planarity :  0.002   0.005    696
  Dihedral  :  5.631  19.982    516
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 0.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 17.54 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.64 (0.25), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.76 (0.19), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J  18 
 PHE   0.009   0.002   PHE M  15 
 TYR   0.009   0.002   TYR N  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03719 (  127)
  hydrogen bonds       : angle       4.34200 (  381)
  covalent geometry    : bond        0.00508 ( 3972)
  covalent geometry    : angle       0.50543 ( 5388)
  Misc. bond           : bond        0.00157 (   12)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 16
  time to evaluate  : 0.420 
Fit side-chains
REVERT: K   30 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7629 (p)
REVERT: M   34 SER cc_start: 0.8999 (OUTLIER) cc_final: 0.8498 (t)
REVERT: P   30 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.7892 (p)
REVERT: U   34 SER cc_start: 0.9089 (OUTLIER) cc_final: 0.8593 (t)
  outliers start: 28
  outliers final: 22
  residues processed: 38
  average time/residue: 0.0570
  time to fit residues: 3.9505
Evaluate side-chains
  42 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 16
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 VAL
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain G residue   30 THR
Chi-restraints excluded: chain G residue   32 VAL
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain I residue   29 SER
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain K residue   30 THR
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue   34 SER
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain P residue   30 THR
Chi-restraints excluded: chain P residue   32 VAL
Chi-restraints excluded: chain Q residue   34 SER
Chi-restraints excluded: chain R residue   34 SER
Chi-restraints excluded: chain S residue   30 THR
Chi-restraints excluded: chain T residue   30 THR
Chi-restraints excluded: chain U residue   34 SER
Chi-restraints excluded: chain V residue   34 SER
Chi-restraints excluded: chain X residue   30 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 18 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 20 optimal weight:    9.9990
   overall best weight:    6.9588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.107822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.081256 restraints weight = 6559.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 2.60
r_work: 0.3275 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.046   3984  Z= 0.350
  Angle     :  0.571   3.385   5388  Z= 0.332
  Chirality :  0.044   0.128    648
  Planarity :  0.002   0.006    696
  Dihedral  :  5.958  20.686    516
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 0.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 18.20 %
    Favored  : 75.88 %
  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: -3.75 (0.25), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.85 (0.19), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E  18 
 PHE   0.013   0.003   PHE S  23 
 TYR   0.011   0.003   TYR M  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04441 (  127)
  hydrogen bonds       : angle       4.55629 (  381)
  covalent geometry    : bond        0.00755 ( 3972)
  covalent geometry    : angle       0.57073 ( 5388)
  Misc. bond           : bond        0.00213 (   12)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 21
  time to evaluate  : 0.499 
Fit side-chains
REVERT: K   30 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7637 (p)
REVERT: M   34 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8536 (t)
REVERT: P   30 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.7886 (p)
REVERT: W   30 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8476 (m)
  outliers start: 27
  outliers final: 23
  residues processed: 43
  average time/residue: 0.0595
  time to fit residues: 4.6033
Evaluate side-chains
  47 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 20
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 VAL
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain G residue   30 THR
Chi-restraints excluded: chain G residue   32 VAL
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain I residue   29 SER
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain K residue   30 THR
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue   34 SER
Chi-restraints excluded: chain P residue   30 THR
Chi-restraints excluded: chain P residue   32 VAL
Chi-restraints excluded: chain Q residue   34 SER
Chi-restraints excluded: chain R residue   34 SER
Chi-restraints excluded: chain S residue   30 THR
Chi-restraints excluded: chain T residue   30 THR
Chi-restraints excluded: chain U residue   34 SER
Chi-restraints excluded: chain V residue   34 SER
Chi-restraints excluded: chain W residue   30 THR
Chi-restraints excluded: chain X residue   30 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 4 optimal weight:    9.9990
   chunk 35 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 32 optimal weight:    4.9990
   chunk 17 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   overall best weight:    5.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.108489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.082001 restraints weight = 6341.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 2.60
r_work: 0.3288 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   3984  Z= 0.264
  Angle     :  0.515   3.236   5388  Z= 0.300
  Chirality :  0.043   0.129    648
  Planarity :  0.002   0.006    696
  Dihedral  :  5.742  20.049    516
  Min Nonbonded Distance : 2.662

Molprobity Statistics.
  All-atom Clashscore : 0.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 19.30 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.72 (0.26), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.20), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS M  18 
 PHE   0.010   0.002   PHE M  15 
 TYR   0.009   0.002   TYR N  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03908 (  127)
  hydrogen bonds       : angle       4.43678 (  381)
  covalent geometry    : bond        0.00566 ( 3972)
  covalent geometry    : angle       0.51474 ( 5388)
  Misc. bond           : bond        0.00162 (   12)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 17
  time to evaluate  : 0.439 
Fit side-chains
REVERT: E   34 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8637 (t)
REVERT: I   29 SER cc_start: 0.9212 (OUTLIER) cc_final: 0.8904 (m)
REVERT: K   30 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7625 (p)
REVERT: M   34 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8534 (t)
REVERT: P   30 THR cc_start: 0.8398 (t) cc_final: 0.7897 (p)
REVERT: U   34 SER cc_start: 0.9116 (OUTLIER) cc_final: 0.8641 (t)
  outliers start: 25
  outliers final: 20
  residues processed: 38
  average time/residue: 0.0577
  time to fit residues: 4.0555
Evaluate side-chains
  42 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 17
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 VAL
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain G residue   30 THR
Chi-restraints excluded: chain G residue   32 VAL
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain I residue   29 SER
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain J residue   29 SER
Chi-restraints excluded: chain K residue   30 THR
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue   34 SER
Chi-restraints excluded: chain P residue   32 VAL
Chi-restraints excluded: chain Q residue   34 SER
Chi-restraints excluded: chain R residue   34 SER
Chi-restraints excluded: chain T residue   30 THR
Chi-restraints excluded: chain U residue   34 SER
Chi-restraints excluded: chain V residue   34 SER
Chi-restraints excluded: chain X residue   30 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 5 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    9.9990
   chunk 20 optimal weight:    5.9990
   chunk 23 optimal weight:   20.0000
   chunk 4 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    5.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.104168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.078335 restraints weight = 6153.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 2.58
r_work: 0.3286 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.3268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   3984  Z= 0.284
  Angle     :  0.528   3.297   5388  Z= 0.308
  Chirality :  0.043   0.129    648
  Planarity :  0.002   0.006    696
  Dihedral  :  5.845  20.251    516
  Min Nonbonded Distance : 2.661

Molprobity Statistics.
  All-atom Clashscore : 0.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 19.74 %
    Favored  : 74.78 %
  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: -3.75 (0.26), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.85 (0.20), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  18 
 PHE   0.010   0.002   PHE M  15 
 TYR   0.010   0.002   TYR N  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04047 (  127)
  hydrogen bonds       : angle       4.51420 (  381)
  covalent geometry    : bond        0.00610 ( 3972)
  covalent geometry    : angle       0.52843 ( 5388)
  Misc. bond           : bond        0.00173 (   12)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 16
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A   29 SER cc_start: 0.9266 (t) cc_final: 0.9012 (m)
REVERT: E   34 SER cc_start: 0.9191 (OUTLIER) cc_final: 0.8685 (t)
REVERT: I   29 SER cc_start: 0.9225 (OUTLIER) cc_final: 0.8910 (m)
REVERT: J   29 SER cc_start: 0.9268 (OUTLIER) cc_final: 0.9010 (m)
REVERT: K   30 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7631 (p)
REVERT: M   34 SER cc_start: 0.9050 (OUTLIER) cc_final: 0.8565 (t)
REVERT: P   30 THR cc_start: 0.8409 (t) cc_final: 0.7908 (p)
REVERT: U   34 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8665 (t)
REVERT: V   34 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8688 (t)
  outliers start: 25
  outliers final: 17
  residues processed: 37
  average time/residue: 0.0576
  time to fit residues: 3.9498
Evaluate side-chains
  39 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 15
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 VAL
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain G residue   30 THR
Chi-restraints excluded: chain G residue   32 VAL
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain I residue   29 SER
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain J residue   29 SER
Chi-restraints excluded: chain K residue   30 THR
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue   34 SER
Chi-restraints excluded: chain P residue   32 VAL
Chi-restraints excluded: chain Q residue   34 SER
Chi-restraints excluded: chain R residue   34 SER
Chi-restraints excluded: chain T residue   30 THR
Chi-restraints excluded: chain U residue   34 SER
Chi-restraints excluded: chain V residue   34 SER
Chi-restraints excluded: chain X residue   30 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 11 optimal weight:   20.0000
   chunk 10 optimal weight:   20.0000
   chunk 3 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 22 optimal weight:   20.0000
   chunk 35 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    3.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.109838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.083130 restraints weight = 6201.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 2.62
r_work: 0.3301 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start:          0.3242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3984  Z= 0.204
  Angle     :  0.479   2.969   5388  Z= 0.279
  Chirality :  0.043   0.129    648
  Planarity :  0.002   0.005    696
  Dihedral  :  5.616  19.770    516
  Min Nonbonded Distance : 2.661

Molprobity Statistics.
  All-atom Clashscore : 0.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 20.83 %
    Favored  : 74.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.72 (0.26), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.20), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS M  18 
 PHE   0.008   0.002   PHE M  15 
 TYR   0.007   0.002   TYR N  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03478 (  127)
  hydrogen bonds       : angle       4.33028 (  381)
  covalent geometry    : bond        0.00438 ( 3972)
  covalent geometry    : angle       0.47868 ( 5388)
  Misc. bond           : bond        0.00125 (   12)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 15
  time to evaluate  : 0.450 
Fit side-chains
REVERT: E   34 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8638 (t)
REVERT: I   29 SER cc_start: 0.9225 (OUTLIER) cc_final: 0.8887 (m)
REVERT: K   30 THR cc_start: 0.8072 (OUTLIER) cc_final: 0.7605 (p)
REVERT: M   34 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8573 (t)
REVERT: P   30 THR cc_start: 0.8388 (t) cc_final: 0.7888 (p)
REVERT: U   34 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8653 (t)
REVERT: V   34 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8682 (t)
  outliers start: 21
  outliers final: 15
  residues processed: 32
  average time/residue: 0.0574
  time to fit residues: 3.5253
Evaluate side-chains
  36 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 15
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   32 VAL
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain G residue   30 THR
Chi-restraints excluded: chain G residue   32 VAL
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain I residue   29 SER
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain J residue   29 SER
Chi-restraints excluded: chain K residue   30 THR
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain P residue   32 VAL
Chi-restraints excluded: chain Q residue   34 SER
Chi-restraints excluded: chain R residue   34 SER
Chi-restraints excluded: chain T residue   30 THR
Chi-restraints excluded: chain U residue   34 SER
Chi-restraints excluded: chain V residue   34 SER
Chi-restraints excluded: chain X residue   30 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 23 optimal weight:   20.0000
   chunk 7 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 11 optimal weight:   20.0000
   chunk 13 optimal weight:    6.9990
   chunk 2 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    6.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.105212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.078632 restraints weight = 5958.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 2.65
r_work: 0.3281 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8720
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   3984  Z= 0.324
  Angle     :  0.549   3.385   5388  Z= 0.319
  Chirality :  0.043   0.129    648
  Planarity :  0.002   0.006    696
  Dihedral  :  5.942  20.351    516
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 0.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 20.39 %
    Favored  : 74.34 %
  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: -3.78 (0.26), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.20), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS M  18 
 PHE   0.012   0.003   PHE W  23 
 TYR   0.011   0.003   TYR N  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04260 (  127)
  hydrogen bonds       : angle       4.49843 (  381)
  covalent geometry    : bond        0.00695 ( 3972)
  covalent geometry    : angle       0.54937 ( 5388)
  Misc. bond           : bond        0.00196 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2367.77 seconds
wall clock time: 42 minutes 25.17 seconds (2545.17 seconds total)