Starting phenix.real_space_refine
on Sat Apr 26 23:53:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gzt_51734/04_2025/9gzt_51734.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gzt_51734/04_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_51734/04_2025/9gzt_51734.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gzt_51734/04_2025/9gzt_51734.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gzt_51734/04_2025/9gzt_51734.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gzt_51734/04_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-5669/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: 2.17, per 1000 atoms: 0.55
  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: 0.98
  Conformation dependent library (CDL) restraints added in 473.1 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: 0.57
  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: 1.17 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:             3.520
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.440
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.560
-------------------------------------------------------------------------------
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  : 0.461 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1310
  time to fit residues: 8.9055
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  : 0.436 
-------------------------------------------------------------------------------
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 = 0.081459 restraints weight = 5710.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.56
r_work: 0.3349 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
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   6.158   5388  Z= 0.302
  Chirality :  0.044   0.124    648
  Planarity :  0.002   0.006    696
  Dihedral  :  5.456  19.095    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   0.002   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        0.03282 (  127)
  hydrogen bonds       : angle       4.88066 (  381)
  covalent geometry    : bond        0.00389 ( 3972)
  covalent geometry    : angle       0.55990 ( 5388)
  Misc. bond           : bond        0.00135 (   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  : 0.417 
Fit side-chains
  outliers start: 18
  outliers final: 7
  residues processed: 28
  average time/residue: 0.0658
  time to fit residues: 3.3315
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  : 0.418 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 33 optimal weight:    0.8980
   chunk 11 optimal weight:   20.0000
   chunk 20 optimal weight:    5.9990
   chunk 22 optimal weight:   20.0000
   chunk 3 optimal weight:    0.5980
   chunk 5 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 6 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    2.6986

-------------------------------------------------------------------------------
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 = 0.3884 r_free = 0.3884 target = 0.112868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.086100 restraints weight = 5625.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.48
r_work: 0.3338 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3984  Z= 0.133
  Angle     :  0.485   4.891   5388  Z= 0.267
  Chirality :  0.043   0.123    648
  Planarity :  0.001   0.004    696
  Dihedral  :  5.276  19.022    516
  Min Nonbonded Distance : 2.665

Molprobity Statistics.
  All-atom Clashscore : 0.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 10.31 %
    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: -3.52 (0.24), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.19), residues: 480

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02908 (  127)
  hydrogen bonds       : angle       4.41598 (  381)
  covalent geometry    : bond        0.00294 ( 3972)
  covalent geometry    : angle       0.48506 ( 5388)
  Misc. bond           : bond        0.00117 (   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
  23 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 11
  time to evaluate  : 0.456 
Fit side-chains
  outliers start: 12
  outliers final: 12
  residues processed: 16
  average time/residue: 0.0578
  time to fit residues: 2.0713
Evaluate side-chains
  23 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 11
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   32 VAL
Chi-restraints excluded: chain D residue   32 VAL
Chi-restraints excluded: chain G residue   32 VAL
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain P residue   19 SER
Chi-restraints excluded: chain P residue   30 THR
Chi-restraints excluded: chain P residue   32 VAL
Chi-restraints excluded: chain W residue   19 SER
Chi-restraints excluded: chain X residue   19 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 23 optimal weight:   20.0000
   chunk 17 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 3 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 = 0.3842 r_free = 0.3842 target = 0.109916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.082922 restraints weight = 5883.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.51
r_work: 0.3309 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3984  Z= 0.208
  Angle     :  0.507   3.752   5388  Z= 0.287
  Chirality :  0.043   0.125    648
  Planarity :  0.002   0.005    696
  Dihedral  :  5.563  20.291    516
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 0.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 11.84 %
    Favored  : 84.65 %
  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: -3.58 (0.24), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.72 (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        0.03517 (  127)
  hydrogen bonds       : angle       4.35927 (  381)
  covalent geometry    : bond        0.00458 ( 3972)
  covalent geometry    : angle       0.50742 ( 5388)
  Misc. bond           : bond        0.00141 (   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
  29 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 13
  time to evaluate  : 0.462 
Fit side-chains
REVERT: P   30 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.7741 (p)
  outliers start: 16
  outliers final: 14
  residues processed: 22
  average time/residue: 0.0597
  time to fit residues: 2.7063
Evaluate side-chains
  28 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 13
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A 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   32 VAL
Chi-restraints excluded: chain G residue   32 VAL
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 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   19 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:   10.0000
   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:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 26 optimal weight:    8.9990
   chunk 3 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 27 optimal weight:    8.9990
   overall best weight:    6.9990

-------------------------------------------------------------------------------
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 = 0.3715 r_free = 0.3715 target = 0.103306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.077992 restraints weight = 6161.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.53
r_work: 0.3299 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.045   3984  Z= 0.348
  Angle     :  0.584   3.761   5388  Z= 0.337
  Chirality :  0.046   0.127    648
  Planarity :  0.002   0.006    696
  Dihedral  :  5.961  20.938    516
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 0.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  6.58 %
    Allowed  : 13.82 %
    Favored  : 79.61 %
  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: -3.66 (0.24), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.78 (0.18), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS J  18 
 PHE   0.014   0.003   PHE S  23 
 TYR   0.009   0.002   TYR N  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04410 (  127)
  hydrogen bonds       : angle       4.50963 (  381)
  covalent geometry    : bond        0.00762 ( 3972)
  covalent geometry    : angle       0.58377 ( 5388)
  Misc. bond           : bond        0.00226 (   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
  55 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 25
  time to evaluate  : 0.417 
Fit side-chains
REVERT: K   30 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7618 (p)
REVERT: P   30 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.7909 (p)
  outliers start: 30
  outliers final: 25
  residues processed: 47
  average time/residue: 0.0597
  time to fit residues: 4.9972
Evaluate side-chains
  52 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 25
  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 D 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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   chunk 5 optimal weight:    7.9990
   chunk 4 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.3766 r_free = 0.3766 target = 0.106080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.079691 restraints weight = 6016.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 2.64
r_work: 0.3328 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3984  Z= 0.161
  Angle     :  0.461   2.760   5388  Z= 0.267
  Chirality :  0.043   0.127    648
  Planarity :  0.001   0.005    696
  Dihedral  :  5.422  19.618    516
  Min Nonbonded Distance : 2.659

Molprobity Statistics.
  All-atom Clashscore : 0.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 18.42 %
    Favored  : 77.19 %
  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: -3.54 (0.26), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.20), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J  18 
 PHE   0.008   0.002   PHE I  15 
 TYR   0.005   0.002   TYR N  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03124 (  127)
  hydrogen bonds       : angle       4.23184 (  381)
  covalent geometry    : bond        0.00347 ( 3972)
  covalent geometry    : angle       0.46093 ( 5388)
  Misc. bond           : bond        0.00098 (   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
  35 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 15
  time to evaluate  : 0.485 
Fit side-chains
REVERT: E   34 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8554 (t)
REVERT: P   30 THR cc_start: 0.8404 (t) cc_final: 0.7895 (p)
REVERT: U   34 SER cc_start: 0.9106 (OUTLIER) cc_final: 0.8593 (t)
REVERT: W   30 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8451 (m)
  outliers start: 20
  outliers final: 17
  residues processed: 31
  average time/residue: 0.0689
  time to fit residues: 3.8429
Evaluate side-chains
  34 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 14
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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   32 VAL
Chi-restraints excluded: chain L residue   30 THR
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 S 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 9 optimal weight:    0.2980
   chunk 27 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 28 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 20 optimal weight:   10.0000
   overall best weight:    7.0590

-------------------------------------------------------------------------------
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 = 0.3726 r_free = 0.3726 target = 0.103915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.077817 restraints weight = 6186.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 2.61
r_work: 0.3275 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8703
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.047   3984  Z= 0.356
  Angle     :  0.589   6.830   5388  Z= 0.338
  Chirality :  0.044   0.128    648
  Planarity :  0.002   0.006    696
  Dihedral  :  5.975  20.876    516
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 1.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 18.64 %
    Favored  : 75.44 %
  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: -3.69 (0.25), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.19), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E  18 
 PHE   0.014   0.003   PHE S  23 
 TYR   0.012   0.003   TYR M  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04458 (  127)
  hydrogen bonds       : angle       4.54913 (  381)
  covalent geometry    : bond        0.00771 ( 3972)
  covalent geometry    : angle       0.58868 ( 5388)
  Misc. bond           : bond        0.00259 (   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  : 0.424 
Fit side-chains
REVERT: J   29 SER cc_start: 0.9278 (OUTLIER) cc_final: 0.9011 (m)
REVERT: K   30 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7627 (p)
REVERT: M   34 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8527 (t)
REVERT: P   30 THR cc_start: 0.8414 (t) cc_final: 0.7891 (p)
REVERT: U   34 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8640 (t)
  outliers start: 27
  outliers final: 23
  residues processed: 42
  average time/residue: 0.0568
  time to fit residues: 4.3412
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  : 0.417 
-------------------------------------------------------------------------------
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 O residue   32 VAL
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 35 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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 = 0.3833 r_free = 0.3833 target = 0.109572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.082699 restraints weight = 6533.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 2.65
r_work: 0.3308 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.3136

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= 0.184
  Angle     :  0.480   6.573   5388  Z= 0.275
  Chirality :  0.043   0.128    648
  Planarity :  0.001   0.005    696
  Dihedral  :  5.492  19.768    516
  Min Nonbonded Distance : 2.662

Molprobity Statistics.
  All-atom Clashscore : 0.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 19.96 %
    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: -3.61 (0.26), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.74 (0.20), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J  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        0.03303 (  127)
  hydrogen bonds       : angle       4.28997 (  381)
  covalent geometry    : bond        0.00394 ( 3972)
  covalent geometry    : angle       0.47972 ( 5388)
  Misc. bond           : bond        0.00116 (   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
  40 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 16
  time to evaluate  : 0.419 
Fit side-chains
REVERT: E   34 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8614 (t)
REVERT: P   30 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.7892 (p)
REVERT: U   34 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8625 (t)
  outliers start: 24
  outliers final: 20
  residues processed: 34
  average time/residue: 0.0578
  time to fit residues: 3.6345
Evaluate side-chains
  38 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 15
  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   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   32 VAL
Chi-restraints excluded: chain L residue   30 THR
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   19 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:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 20 optimal weight:    6.9990
   chunk 23 optimal weight:   20.0000
   chunk 4 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    7.5990

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.103232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.077878 restraints weight = 6249.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 2.53
r_work: 0.3280 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.049   3984  Z= 0.383
  Angle     :  0.599   7.273   5388  Z= 0.344
  Chirality :  0.044   0.130    648
  Planarity :  0.002   0.007    696
  Dihedral  :  6.033  20.842    516
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 0.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 19.52 %
    Favored  : 75.00 %
  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: -3.73 (0.25), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.19), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS R  18 
 PHE   0.014   0.003   PHE L  23 
 TYR   0.012   0.003   TYR M  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04603 (  127)
  hydrogen bonds       : angle       4.59910 (  381)
  covalent geometry    : bond        0.00823 ( 3972)
  covalent geometry    : angle       0.59909 ( 5388)
  Misc. bond           : bond        0.00234 (   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
  44 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 19
  time to evaluate  : 0.419 
Fit side-chains
REVERT: B   29 SER cc_start: 0.9283 (t) cc_final: 0.9007 (m)
REVERT: E   34 SER cc_start: 0.9157 (OUTLIER) cc_final: 0.8656 (t)
REVERT: I   29 SER cc_start: 0.9269 (OUTLIER) cc_final: 0.8947 (m)
REVERT: J   29 SER cc_start: 0.9292 (OUTLIER) cc_final: 0.9036 (m)
REVERT: M   34 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8577 (t)
REVERT: P   30 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.7900 (p)
REVERT: U   34 SER cc_start: 0.9185 (OUTLIER) cc_final: 0.8688 (t)
  outliers start: 25
  outliers final: 19
  residues processed: 39
  average time/residue: 0.0569
  time to fit residues: 4.0125
Evaluate side-chains
  43 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 18
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
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   32 VAL
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain M residue   29 SER
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 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:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 3 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 18 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   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 = 0.3736 r_free = 0.3736 target = 0.104302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.078408 restraints weight = 6378.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 2.61
r_work: 0.3286 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.3267

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     :  0.541   7.880   5388  Z= 0.310
  Chirality :  0.043   0.130    648
  Planarity :  0.002   0.006    696
  Dihedral  :  5.807  20.142    516
  Min Nonbonded Distance : 2.661

Molprobity Statistics.
  All-atom Clashscore : 0.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 19.30 %
    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: -3.74 (0.26), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.84 (0.20), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS M  18 
 PHE   0.011   0.002   PHE L  23 
 TYR   0.010   0.002   TYR N  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04071 (  127)
  hydrogen bonds       : angle       4.50644 (  381)
  covalent geometry    : bond        0.00609 ( 3972)
  covalent geometry    : angle       0.54068 ( 5388)
  Misc. bond           : bond        0.00173 (   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
  44 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 17
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A   29 SER cc_start: 0.9281 (t) cc_final: 0.9023 (m)
REVERT: E   34 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8649 (t)
REVERT: I   29 SER cc_start: 0.9230 (OUTLIER) cc_final: 0.8894 (m)
REVERT: J   29 SER cc_start: 0.9264 (OUTLIER) cc_final: 0.9001 (m)
REVERT: M   34 SER cc_start: 0.9031 (OUTLIER) cc_final: 0.8543 (t)
REVERT: P   30 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.7865 (p)
REVERT: U   34 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8658 (t)
REVERT: V   34 SER cc_start: 0.9160 (OUTLIER) cc_final: 0.8675 (t)
  outliers start: 27
  outliers final: 18
  residues processed: 38
  average time/residue: 0.0588
  time to fit residues: 4.0421
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  : 0.446 
-------------------------------------------------------------------------------
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   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 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:    4.9990
   chunk 23 optimal weight:   20.0000
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 19 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 11 optimal weight:   20.0000
   chunk 13 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 = 0.3751 r_free = 0.3751 target = 0.105029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.079341 restraints weight = 6112.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 2.57
r_work: 0.3236 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8704
moved from start:          0.3251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3984  Z= 0.194
  Angle     :  0.491   8.000   5388  Z= 0.280
  Chirality :  0.043   0.128    648
  Planarity :  0.002   0.005    696
  Dihedral  :  5.597  19.836    516
  Min Nonbonded Distance : 2.661

Molprobity Statistics.
  All-atom Clashscore : 0.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 20.18 %
    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: -3.71 (0.26), residues: 480
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.82 (0.20), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J  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        0.03421 (  127)
  hydrogen bonds       : angle       4.38342 (  381)
  covalent geometry    : bond        0.00414 ( 3972)
  covalent geometry    : angle       0.49115 ( 5388)
  Misc. bond           : bond        0.00120 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3266.32 seconds
wall clock time: 57 minutes 36.38 seconds (3456.38 seconds total)