Starting phenix.real_space_refine
on Wed Sep 17 05:04:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qv6_14168/09_2025/7qv6_14168.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qv6_14168/09_2025/7qv6_14168.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qv6_14168/09_2025/7qv6_14168.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qv6_14168/09_2025/7qv6_14168.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qv6_14168/09_2025/7qv6_14168.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qv6_14168/09_2025/7qv6_14168.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     C    1512      2.51       5
     N     378      2.21       5
     O     396      1.98       5
     H    2556      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4842
  Number of models: 1
  Model: ""
    Number of chains: 18
    Chain: "B"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "A"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "E"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "D"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "C"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "F"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "H"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "G"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "K"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "J"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "I"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "L"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "N"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "M"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "Q"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "P"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "O"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "R"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 269
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 16}
  Time building chain proxies: 1.30, per 1000 atoms: 0.27
  Number of scatterers: 4842
  At special positions: 0
  Unit cell: (94.35, 78.2, 33.15, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O     396      8.00
     N     378      7.00
     C    1512      6.00
     H    2556      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 132.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  540

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 9 sheets defined
      0.0% alpha, 58.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 10
    Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 16
      removed outlier: 6.582A  pdb=" N   ILE B  13 " --> pdb=" O   VAL H  14 " (cutoff:3.500A)
      removed outlier: 8.258A  pdb=" N   SER H  16 " --> pdb=" O   ILE B  13 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   SER B  15 " --> pdb=" O   SER H  16 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ILE H  13 " --> pdb=" O   VAL N  14 " (cutoff:3.500A)
      removed outlier: 8.257A  pdb=" N   SER N  16 " --> pdb=" O   ILE H  13 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   SER H  15 " --> pdb=" O   SER N  16 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 2 through 8
      removed outlier: 6.293A  pdb=" N   PHE A   3 " --> pdb=" O   ASP G   4 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   VAL G   6 " --> pdb=" O   PHE A   3 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   ILE A   5 " --> pdb=" O   VAL G   6 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   LYS G   8 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   LYS A   7 " --> pdb=" O   LYS G   8 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   PHE G   3 " --> pdb=" O   ASP M   4 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   VAL M   6 " --> pdb=" O   PHE G   3 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   ILE G   5 " --> pdb=" O   VAL M   6 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   LYS M   8 " --> pdb=" O   ILE G   5 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   LYS G   7 " --> pdb=" O   LYS M   8 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 13 through 14
    Processing sheet with id=AA5, first strand: chain 'E' and resid 5 through 7
    Processing sheet with id=AA6, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.322A  pdb=" N   ALA E  10 " --> pdb=" O   GLY K  11 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   ALA K  10 " --> pdb=" O   GLY Q  11 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'D' and resid 2 through 16
      removed outlier: 9.319A  pdb=" N   PHE D   3 " --> pdb=" O   ASP J   4 " (cutoff:3.500A)
      removed outlier: 10.367A  pdb=" N   VAL J   6 " --> pdb=" O   PHE D   3 " (cutoff:3.500A)
      removed outlier: 9.033A  pdb=" N   ILE D   5 " --> pdb=" O   VAL J   6 " (cutoff:3.500A)
      removed outlier: 10.271A  pdb=" N   LYS J   8 " --> pdb=" O   ILE D   5 " (cutoff:3.500A)
      removed outlier: 9.063A  pdb=" N   LYS D   7 " --> pdb=" O   LYS J   8 " (cutoff:3.500A)
      removed outlier: 10.437A  pdb=" N   ALA J  10 " --> pdb=" O   LYS D   7 " (cutoff:3.500A)
      removed outlier: 9.064A  pdb=" N   ILE D   9 " --> pdb=" O   ALA J  10 " (cutoff:3.500A)
      removed outlier: 10.262A  pdb=" N   HIS J  12 " --> pdb=" O   ILE D   9 " (cutoff:3.500A)
      removed outlier: 5.652A  pdb=" N   GLY D  11 " --> pdb=" O   HIS J  12 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   VAL J  14 " --> pdb=" O   GLY D  11 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ILE D  13 " --> pdb=" O   VAL J  14 " (cutoff:3.500A)
      removed outlier: 8.159A  pdb=" N   SER J  16 " --> pdb=" O   ILE D  13 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   SER D  15 " --> pdb=" O   SER J  16 " (cutoff:3.500A)
      removed outlier: 9.319A  pdb=" N   PHE J   3 " --> pdb=" O   ASP P   4 " (cutoff:3.500A)
      removed outlier: 10.367A  pdb=" N   VAL P   6 " --> pdb=" O   PHE J   3 " (cutoff:3.500A)
      removed outlier: 9.033A  pdb=" N   ILE J   5 " --> pdb=" O   VAL P   6 " (cutoff:3.500A)
      removed outlier: 10.271A  pdb=" N   LYS P   8 " --> pdb=" O   ILE J   5 " (cutoff:3.500A)
      removed outlier: 9.064A  pdb=" N   LYS J   7 " --> pdb=" O   LYS P   8 " (cutoff:3.500A)
      removed outlier: 10.437A  pdb=" N   ALA P  10 " --> pdb=" O   LYS J   7 " (cutoff:3.500A)
      removed outlier: 9.064A  pdb=" N   ILE J   9 " --> pdb=" O   ALA P  10 " (cutoff:3.500A)
      removed outlier: 10.262A  pdb=" N   HIS P  12 " --> pdb=" O   ILE J   9 " (cutoff:3.500A)
      removed outlier: 5.652A  pdb=" N   GLY J  11 " --> pdb=" O   HIS P  12 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   VAL P  14 " --> pdb=" O   GLY J  11 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ILE J  13 " --> pdb=" O   VAL P  14 " (cutoff:3.500A)
      removed outlier: 8.158A  pdb=" N   SER P  16 " --> pdb=" O   ILE J  13 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   SER J  15 " --> pdb=" O   SER P  16 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 15
      removed outlier: 5.970A  pdb=" N   PHE C   3 " --> pdb=" O   ASP I   4 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   VAL I   6 " --> pdb=" O   PHE C   3 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ILE C   5 " --> pdb=" O   VAL I   6 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   LYS I   8 " --> pdb=" O   ILE C   5 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   LYS C   7 " --> pdb=" O   LYS I   8 " (cutoff:3.500A)
      removed outlier: 8.384A  pdb=" N   ALA I  10 " --> pdb=" O   LYS C   7 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ILE C   9 " --> pdb=" O   ALA I  10 " (cutoff:3.500A)
      removed outlier: 8.940A  pdb=" N   HIS I  12 " --> pdb=" O   ILE C   9 " (cutoff:3.500A)
      removed outlier: 9.379A  pdb=" N   GLY C  11 " --> pdb=" O   HIS I  12 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   VAL I  14 " --> pdb=" O   GLY C  11 " (cutoff:3.500A)
      removed outlier: 9.049A  pdb=" N   ILE C  13 " --> pdb=" O   VAL I  14 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   PHE I   3 " --> pdb=" O   ASP O   4 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   VAL O   6 " --> pdb=" O   PHE I   3 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ILE I   5 " --> pdb=" O   VAL O   6 " (cutoff:3.500A)
      removed outlier: 8.170A  pdb=" N   LYS O   8 " --> pdb=" O   ILE I   5 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   LYS I   7 " --> pdb=" O   LYS O   8 " (cutoff:3.500A)
      removed outlier: 8.384A  pdb=" N   ALA O  10 " --> pdb=" O   LYS I   7 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ILE I   9 " --> pdb=" O   ALA O  10 " (cutoff:3.500A)
      removed outlier: 8.940A  pdb=" N   HIS O  12 " --> pdb=" O   ILE I   9 " (cutoff:3.500A)
      removed outlier: 9.378A  pdb=" N   GLY I  11 " --> pdb=" O   HIS O  12 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   VAL O  14 " --> pdb=" O   GLY I  11 " (cutoff:3.500A)
      removed outlier: 9.048A  pdb=" N   ILE I  13 " --> pdb=" O   VAL O  14 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'F' and resid 3 through 15

    46 hydrogen bonds defined for protein.
    138 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: 0.99

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        0.84 -     0.98: 2556
        0.98 -     1.12: 0
        1.12 -     1.26: 360
        1.26 -     1.40: 486
        1.40 -     1.54: 1458
  Bond restraints: 4860
  Sorted by residual:
  bond pdb=" CB  VAL C  14 "
       pdb=" CG2 VAL C  14 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.01e+00
  bond pdb=" CB  VAL I  14 "
       pdb=" CG2 VAL I  14 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 1.99e+00
  bond pdb=" CB  VAL O  14 "
       pdb=" CG2 VAL O  14 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.93e+00
  bond pdb=" CG1 ILE F  13 "
       pdb=" CD1 ILE F  13 "
    ideal  model  delta    sigma   weight residual
    1.513  1.461  0.052 3.90e-02 6.57e+02 1.77e+00
  bond pdb=" CG1 ILE L  13 "
       pdb=" CD1 ILE L  13 "
    ideal  model  delta    sigma   weight residual
    1.513  1.462  0.051 3.90e-02 6.57e+02 1.74e+00
  ... (remaining 4855 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.90: 8229
        0.90 -     1.80: 615
        1.80 -     2.70: 50
        2.70 -     3.59: 7
        3.59 -     4.49: 9
  Bond angle restraints: 8910
  Sorted by residual:
  angle pdb=" N   GLY Q  11 "
        pdb=" CA  GLY Q  11 "
        pdb=" C   GLY Q  11 "
      ideal   model   delta    sigma   weight residual
     110.45  114.94   -4.49 1.30e+00 5.92e-01 1.19e+01
  angle pdb=" N   GLY K  11 "
        pdb=" CA  GLY K  11 "
        pdb=" C   GLY K  11 "
      ideal   model   delta    sigma   weight residual
     110.45  114.93   -4.48 1.30e+00 5.92e-01 1.19e+01
  angle pdb=" N   GLY E  11 "
        pdb=" CA  GLY E  11 "
        pdb=" C   GLY E  11 "
      ideal   model   delta    sigma   weight residual
     110.45  114.93   -4.48 1.30e+00 5.92e-01 1.19e+01
  angle pdb=" N   GLY R  11 "
        pdb=" CA  GLY R  11 "
        pdb=" C   GLY R  11 "
      ideal   model   delta    sigma   weight residual
     110.29  114.31   -4.02 1.28e+00 6.10e-01 9.84e+00
  angle pdb=" N   GLY F  11 "
        pdb=" CA  GLY F  11 "
        pdb=" C   GLY F  11 "
      ideal   model   delta    sigma   weight residual
     110.29  114.31   -4.02 1.28e+00 6.10e-01 9.84e+00
  ... (remaining 8905 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.69: 1896
       12.69 -    25.37: 119
       25.37 -    38.06: 61
       38.06 -    50.74: 54
       50.74 -    63.43: 30
  Dihedral angle restraints: 2160
    sinusoidal: 1188
      harmonic: 972
  Sorted by residual:
  dihedral pdb=" CA  ASP L   4 "
           pdb=" C   ASP L   4 "
           pdb=" N   ILE L   5 "
           pdb=" CA  ILE L   5 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.32   14.68     0      5.00e+00 4.00e-02 8.62e+00
  dihedral pdb=" CA  ASP F   4 "
           pdb=" C   ASP F   4 "
           pdb=" N   ILE F   5 "
           pdb=" CA  ILE F   5 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.33   14.67     0      5.00e+00 4.00e-02 8.60e+00
  dihedral pdb=" CA  ASP R   4 "
           pdb=" C   ASP R   4 "
           pdb=" N   ILE R   5 "
           pdb=" CA  ILE R   5 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.35   14.65     0      5.00e+00 4.00e-02 8.59e+00
  ... (remaining 2157 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 141
       0.024 -    0.047: 87
       0.047 -    0.071: 66
       0.071 -    0.094: 75
       0.094 -    0.118: 27
  Chirality restraints: 396
  Sorted by residual:
  chirality pdb=" CA  ILE Q   5 "
            pdb=" N   ILE Q   5 "
            pdb=" C   ILE Q   5 "
            pdb=" CB  ILE Q   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.48e-01
  chirality pdb=" CA  ILE F   9 "
            pdb=" N   ILE F   9 "
            pdb=" C   ILE F   9 "
            pdb=" CB  ILE F   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.47e-01
  chirality pdb=" CA  ILE L   9 "
            pdb=" N   ILE L   9 "
            pdb=" C   ILE L   9 "
            pdb=" CB  ILE L   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.47e-01
  ... (remaining 393 not shown)

  Planarity restraints: 648
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS J  12 "    0.007 2.00e-02 2.50e+03   4.46e-03 4.48e-01
        pdb=" CG  HIS J  12 "   -0.011 2.00e-02 2.50e+03
        pdb=" ND1 HIS J  12 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS J  12 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS J  12 "    0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS J  12 "   -0.000 2.00e-02 2.50e+03
        pdb=" HD2 HIS J  12 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE1 HIS J  12 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 HIS J  12 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS P  12 "    0.007 2.00e-02 2.50e+03   4.38e-03 4.31e-01
        pdb=" CG  HIS P  12 "   -0.011 2.00e-02 2.50e+03
        pdb=" ND1 HIS P  12 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS P  12 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS P  12 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS P  12 "    0.000 2.00e-02 2.50e+03
        pdb=" HD2 HIS P  12 "    0.000 2.00e-02 2.50e+03
        pdb=" HE1 HIS P  12 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 HIS P  12 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS D  12 "    0.006 2.00e-02 2.50e+03   4.35e-03 4.26e-01
        pdb=" CG  HIS D  12 "   -0.011 2.00e-02 2.50e+03
        pdb=" ND1 HIS D  12 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS D  12 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS D  12 "    0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS D  12 "   -0.000 2.00e-02 2.50e+03
        pdb=" HD2 HIS D  12 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE1 HIS D  12 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 HIS D  12 "    0.002 2.00e-02 2.50e+03
  ... (remaining 645 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.45: 3232
        2.45 -     2.97: 10383
        2.97 -     3.48: 9111
        3.48 -     3.99: 13759
        3.99 -     4.50: 18178
  Nonbonded interactions: 54663
  Sorted by model distance:
  nonbonded pdb=" O   GLY F   1 "
            pdb=" H2  GLY L   1 "
     model   vdw
     1.943 2.450
  nonbonded pdb=" O   GLY L   1 "
            pdb=" H2  GLY R   1 "
     model   vdw
     1.943 2.450
  nonbonded pdb="HD23 LEU J   2 "
            pdb="HD13 LEU P   2 "
     model   vdw
     1.954 2.440
  nonbonded pdb="HD23 LEU D   2 "
            pdb="HD13 LEU J   2 "
     model   vdw
     1.954 2.440
  nonbonded pdb=" O   PHE C   3 "
            pdb=" H   ASP I   4 "
     model   vdw
     2.008 2.450
  ... (remaining 54658 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  selection = chain 'R'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.610
  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:             0.030
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.170
  Find NCS groups from input model:        0.070
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
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      :  0.011   0.052   2304  Z= 0.435
  Angle     :  0.587   4.492   3078  Z= 0.355
  Chirality :  0.054   0.118    396
  Planarity :  0.001   0.005    360
  Dihedral  : 11.565  54.871    810
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.85 (0.39), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.40 (0.30), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.002   PHE M   3 
 HIS   0.005   0.001   HIS J  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.01063 ( 2304)
  covalent geometry    : angle       0.58679 ( 3078)
  hydrogen bonds       : bond        0.22231 (   46)
  hydrogen bonds       : angle       7.62708 (  138)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.176 
Fit side-chains
REVERT: D    8 LYS cc_start: 0.8600 (mtpt) cc_final: 0.8347 (ttmm)
REVERT: J    8 LYS cc_start: 0.8534 (mtpt) cc_final: 0.8292 (mtpp)
REVERT: P    8 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8594 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.3936
  time to fit residues: 8.9476
Evaluate side-chains
  20 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
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 = 0.3877 r_free = 0.3877 target = 0.123677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.099326 restraints weight = 9941.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.105363 restraints weight = 4391.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.109162 restraints weight = 2581.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.111506 restraints weight = 1760.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.112827 restraints weight = 1338.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2304  Z= 0.167
  Angle     :  0.425   2.871   3078  Z= 0.244
  Chirality :  0.062   0.146    396
  Planarity :  0.002   0.007    360
  Dihedral  :  8.573  46.071    306
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 1.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.66 (0.45), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.49 (0.34), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.001   PHE B   3 
 HIS   0.002   0.001   HIS P  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 2304)
  covalent geometry    : angle       0.42498 ( 3078)
  hydrogen bonds       : bond        0.03129 (   46)
  hydrogen bonds       : angle       4.76719 (  138)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.179 
Fit side-chains
REVERT: D    7 LYS cc_start: 0.8547 (mttt) cc_final: 0.8194 (mttm)
REVERT: D    8 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8370 (ttmm)
REVERT: J    8 LYS cc_start: 0.8643 (mtpt) cc_final: 0.8371 (mtpp)
REVERT: P    8 LYS cc_start: 0.8941 (mtpt) cc_final: 0.8586 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.3402
  time to fit residues: 7.5108
Evaluate side-chains
  18 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 4 optimal weight:    5.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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 = 0.3915 r_free = 0.3915 target = 0.126320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.101947 restraints weight = 9581.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.108121 restraints weight = 4218.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.111965 restraints weight = 2461.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.114352 restraints weight = 1664.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.116144 restraints weight = 1260.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2304  Z= 0.114
  Angle     :  0.366   2.124   3078  Z= 0.207
  Chirality :  0.061   0.140    396
  Planarity :  0.001   0.006    360
  Dihedral  :  6.658  36.578    306
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 1.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.49), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.06 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.007   0.001   PHE J   3 
 HIS   0.001   0.000   HIS K  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 2304)
  covalent geometry    : angle       0.36608 ( 3078)
  hydrogen bonds       : bond        0.02613 (   46)
  hydrogen bonds       : angle       4.42003 (  138)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.148 
Fit side-chains
REVERT: D    8 LYS cc_start: 0.8605 (mtpt) cc_final: 0.8041 (mttm)
REVERT: J    7 LYS cc_start: 0.8258 (mttt) cc_final: 0.7964 (mttp)
REVERT: J    8 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8370 (mtpp)
REVERT: P    8 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8631 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.3338
  time to fit residues: 8.3957
Evaluate side-chains
  20 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 15 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 0 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3919 r_free = 0.3919 target = 0.126930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.102284 restraints weight = 9563.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.108542 restraints weight = 4218.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.112402 restraints weight = 2456.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.114798 restraints weight = 1663.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.116634 restraints weight = 1259.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   2304  Z= 0.089
  Angle     :  0.353   2.926   3078  Z= 0.196
  Chirality :  0.062   0.140    396
  Planarity :  0.001   0.004    360
  Dihedral  :  5.745  29.431    306
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 0.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.50), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.26 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.003   0.001   PHE Q   3 
 HIS   0.001   0.000   HIS K  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00177 ( 2304)
  covalent geometry    : angle       0.35338 ( 3078)
  hydrogen bonds       : bond        0.01770 (   46)
  hydrogen bonds       : angle       4.30514 (  138)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.143 
Fit side-chains
REVERT: D    8 LYS cc_start: 0.8609 (mtpt) cc_final: 0.8082 (mttm)
REVERT: J    7 LYS cc_start: 0.8257 (mttt) cc_final: 0.7972 (mttp)
REVERT: J    8 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8412 (mtpp)
REVERT: P    8 LYS cc_start: 0.8956 (mtpt) cc_final: 0.8587 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.3767
  time to fit residues: 8.1820
Evaluate side-chains
  20 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    2.1388

-------------------------------------------------------------------------------
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 = 0.3933 r_free = 0.3933 target = 0.129426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.105185 restraints weight = 9570.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.111292 restraints weight = 4306.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.115103 restraints weight = 2518.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.117614 restraints weight = 1712.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.119180 restraints weight = 1281.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2304  Z= 0.135
  Angle     :  0.361   2.705   3078  Z= 0.203
  Chirality :  0.061   0.137    396
  Planarity :  0.001   0.004    360
  Dihedral  :  5.944  30.622    306
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 1.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.51), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.33 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE B   3 
 HIS   0.001   0.000   HIS K  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 2304)
  covalent geometry    : angle       0.36107 ( 3078)
  hydrogen bonds       : bond        0.02201 (   46)
  hydrogen bonds       : angle       4.27856 (  138)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.146 
Fit side-chains
REVERT: D    8 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8021 (mttm)
REVERT: J    7 LYS cc_start: 0.8256 (mttt) cc_final: 0.7973 (mttp)
REVERT: P    8 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8484 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.3171
  time to fit residues: 7.9539
Evaluate side-chains
  20 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    8.9990
   chunk 7 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.3956 r_free = 0.3956 target = 0.130814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.106100 restraints weight = 9474.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.112515 restraints weight = 4058.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.116468 restraints weight = 2319.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.118951 restraints weight = 1554.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.120335 restraints weight = 1163.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2304  Z= 0.076
  Angle     :  0.358   3.533   3078  Z= 0.197
  Chirality :  0.062   0.142    396
  Planarity :  0.001   0.004    360
  Dihedral  :  5.245  24.998    306
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 1.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.52), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.41 (0.40), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.003   0.000   PHE K   3 
 HIS   0.001   0.000   HIS K  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00155 ( 2304)
  covalent geometry    : angle       0.35849 ( 3078)
  hydrogen bonds       : bond        0.01536 (   46)
  hydrogen bonds       : angle       4.09489 (  138)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.092 
Fit side-chains
REVERT: D    8 LYS cc_start: 0.8564 (mtpt) cc_final: 0.8075 (mttm)
REVERT: J    7 LYS cc_start: 0.8265 (mttt) cc_final: 0.7985 (mttp)
REVERT: P    8 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8496 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.3558
  time to fit residues: 8.1112
Evaluate side-chains
  20 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   overall best weight:    2.5186

-------------------------------------------------------------------------------
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 = 0.3934 r_free = 0.3934 target = 0.129336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.105036 restraints weight = 9483.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.111080 restraints weight = 4284.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.114869 restraints weight = 2515.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.117179 restraints weight = 1716.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.118886 restraints weight = 1307.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2304  Z= 0.150
  Angle     :  0.383   3.369   3078  Z= 0.212
  Chirality :  0.061   0.141    396
  Planarity :  0.001   0.004    360
  Dihedral  :  5.787  31.693    306
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 1.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.52), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.34 (0.40), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.005   0.001   PHE O   3 
 HIS   0.001   0.000   HIS O  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 2304)
  covalent geometry    : angle       0.38300 ( 3078)
  hydrogen bonds       : bond        0.02177 (   46)
  hydrogen bonds       : angle       4.21115 (  138)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.140 
Fit side-chains
REVERT: D    8 LYS cc_start: 0.8529 (mtpt) cc_final: 0.8056 (mttm)
REVERT: J    7 LYS cc_start: 0.8245 (mttt) cc_final: 0.7967 (mttp)
REVERT: P    8 LYS cc_start: 0.8931 (mtpt) cc_final: 0.8491 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.3550
  time to fit residues: 8.1155
Evaluate side-chains
  20 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   overall best weight:    2.3186

-------------------------------------------------------------------------------
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 = 0.3995 r_free = 0.3995 target = 0.135432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.111802 restraints weight = 9343.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.118383 restraints weight = 3889.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.122367 restraints weight = 2174.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.124743 restraints weight = 1431.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.126588 restraints weight = 1066.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2304  Z= 0.136
  Angle     :  0.374   3.333   3078  Z= 0.207
  Chirality :  0.061   0.144    396
  Planarity :  0.001   0.004    360
  Dihedral  :  5.837  34.459    306
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.52), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.34 (0.40), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE O   3 
 HIS   0.001   0.000   HIS O  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 2304)
  covalent geometry    : angle       0.37423 ( 3078)
  hydrogen bonds       : bond        0.02039 (   46)
  hydrogen bonds       : angle       4.16919 (  138)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.132 
Fit side-chains
REVERT: D    8 LYS cc_start: 0.8502 (mtpt) cc_final: 0.8096 (mttm)
REVERT: J    7 LYS cc_start: 0.8240 (mttt) cc_final: 0.7975 (mttp)
REVERT: P    8 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8484 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.3509
  time to fit residues: 8.3638
Evaluate side-chains
  21 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   overall best weight:    2.5584

-------------------------------------------------------------------------------
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 = 0.3984 r_free = 0.3984 target = 0.134304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.110853 restraints weight = 9222.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.117357 restraints weight = 3888.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.121174 restraints weight = 2189.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.123757 restraints weight = 1466.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.125166 restraints weight = 1069.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2304  Z= 0.156
  Angle     :  0.384   3.326   3078  Z= 0.213
  Chirality :  0.061   0.147    396
  Planarity :  0.001   0.003    360
  Dihedral  :  6.027  36.939    306
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.52), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.25 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.005   0.001   PHE O   3 
 HIS   0.001   0.000   HIS C  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 2304)
  covalent geometry    : angle       0.38416 ( 3078)
  hydrogen bonds       : bond        0.02211 (   46)
  hydrogen bonds       : angle       4.20118 (  138)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.141 
Fit side-chains
REVERT: D    8 LYS cc_start: 0.8477 (mtpt) cc_final: 0.8132 (mttm)
REVERT: J    7 LYS cc_start: 0.8278 (mttt) cc_final: 0.8016 (mttp)
REVERT: P    8 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8498 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.3032
  time to fit residues: 7.9170
Evaluate side-chains
  22 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 0 optimal weight:    0.6980
   overall best weight:    1.1982

-------------------------------------------------------------------------------
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 = 0.4017 r_free = 0.4017 target = 0.136098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.113459 restraints weight = 9163.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.119808 restraints weight = 3935.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.123672 restraints weight = 2220.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.126094 restraints weight = 1464.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.127622 restraints weight = 1076.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.2714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2304  Z= 0.083
  Angle     :  0.360   3.426   3078  Z= 0.197
  Chirality :  0.062   0.141    396
  Planarity :  0.001   0.004    360
  Dihedral  :  5.194  28.866    306
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.53), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.44 (0.40), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.003   0.000   PHE O   3 
 HIS   0.001   0.000   HIS K  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00169 ( 2304)
  covalent geometry    : angle       0.35953 ( 3078)
  hydrogen bonds       : bond        0.01522 (   46)
  hydrogen bonds       : angle       3.99211 (  138)

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

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

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  540 Ramachandran restraints generated.
    270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.116 
Fit side-chains
REVERT: D    8 LYS cc_start: 0.8549 (mtpt) cc_final: 0.8251 (mttm)
REVERT: J    7 LYS cc_start: 0.8297 (mttt) cc_final: 0.8031 (mttp)
REVERT: P    8 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8482 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.3364
  time to fit residues: 7.7375
Evaluate side-chains
  20 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 6 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 0 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    1.9388

-------------------------------------------------------------------------------
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 = 0.4007 r_free = 0.4007 target = 0.135193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.111668 restraints weight = 9291.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.118323 restraints weight = 3882.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.122248 restraints weight = 2159.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.124846 restraints weight = 1429.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.126216 restraints weight = 1036.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2304  Z= 0.120
  Angle     :  0.365   3.346   3078  Z= 0.202
  Chirality :  0.061   0.147    396
  Planarity :  0.001   0.004    360
  Dihedral  :  5.263  30.668    306
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.53), residues: 270
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.40 (0.40), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE E   3 
 HIS   0.001   0.000   HIS E  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 2304)
  covalent geometry    : angle       0.36514 ( 3078)
  hydrogen bonds       : bond        0.01877 (   46)
  hydrogen bonds       : angle       4.05056 (  138)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1245.91 seconds
wall clock time: 21 minutes 54.04 seconds (1314.04 seconds total)