Starting phenix.real_space_refine
on Thu Mar  5 07:40:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mqd_23943/03_2026/7mqd_23943.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mqd_23943/03_2026/7mqd_23943.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mqd_23943/03_2026/7mqd_23943.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mqd_23943/03_2026/7mqd_23943.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mqd_23943/03_2026/7mqd_23943.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mqd_23943/03_2026/7mqd_23943.cif"
  }
  resolution = 3.25
  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=   0.001 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 10912 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P      16      5.49       5
     S      48      5.16       5
     C    7632      2.51       5
     N    2176      2.21       5
     O    2088      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11960
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1449
          Classifications: {'peptide': 199}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 5, 'TRANS': 193}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 135
          Unresolved non-hydrogen angles: 167
          Unresolved non-hydrogen dihedrals: 103
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 11, 'ASN:plan1': 4, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 101
    Chain: "B"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 46
          Classifications: {'RNA': 2}
          Modifications used: {'rna3p_pur': 2}
          Link IDs: {'rna3p': 1}
  Restraints were copied for chains:
    C, E, G, I, K, M, O, D, F, H, J, L, N, P
  Time building chain proxies: 1.21, per 1000 atoms: 0.10
  Number of scatterers: 11960
  At special positions: 0
  Unit cell: (105.4, 105.4, 85.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     P      16     15.00
     O    2088      8.00
     N    2176      7.00
     C    7632      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 534.5 milliseconds
  

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3024

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 8 sheets defined
      46.7% alpha, 13.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 71
    Processing helix  chain 'A' and resid 80 through 93
      removed outlier: 3.911A  pdb=" N   ASP A  84 " --> pdb=" O   PHE A  80 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA A  86 " --> pdb=" O   ARG A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 110
    Processing helix  chain 'A' and resid 117 through 127
    Processing helix  chain 'A' and resid 145 through 155
      removed outlier: 3.501A  pdb=" N   ASP A 155 " --> pdb=" O   TYR A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 173
    Processing helix  chain 'A' and resid 175 through 196
      Proline residue:  A 187  - end of helix
    Processing helix  chain 'C' and resid 62 through 71
    Processing helix  chain 'C' and resid 80 through 93
      removed outlier: 3.912A  pdb=" N   ASP C  84 " --> pdb=" O   PHE C  80 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA C  86 " --> pdb=" O   ARG C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 110
    Processing helix  chain 'C' and resid 117 through 127
    Processing helix  chain 'C' and resid 145 through 155
    Processing helix  chain 'C' and resid 158 through 173
    Processing helix  chain 'C' and resid 175 through 196
      Proline residue:  C 187  - end of helix
    Processing helix  chain 'E' and resid 62 through 71
    Processing helix  chain 'E' and resid 80 through 93
      removed outlier: 3.911A  pdb=" N   ASP E  84 " --> pdb=" O   PHE E  80 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA E  86 " --> pdb=" O   ARG E  82 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 102 through 110
    Processing helix  chain 'E' and resid 117 through 127
    Processing helix  chain 'E' and resid 145 through 155
      removed outlier: 3.501A  pdb=" N   ASP E 155 " --> pdb=" O   TYR E 151 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 158 through 173
    Processing helix  chain 'E' and resid 175 through 196
      Proline residue:  E 187  - end of helix
    Processing helix  chain 'G' and resid 62 through 71
    Processing helix  chain 'G' and resid 80 through 93
      removed outlier: 3.912A  pdb=" N   ASP G  84 " --> pdb=" O   PHE G  80 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA G  86 " --> pdb=" O   ARG G  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 102 through 110
    Processing helix  chain 'G' and resid 117 through 127
    Processing helix  chain 'G' and resid 145 through 155
      removed outlier: 3.501A  pdb=" N   ASP G 155 " --> pdb=" O   TYR G 151 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 158 through 173
    Processing helix  chain 'G' and resid 175 through 196
      Proline residue:  G 187  - end of helix
    Processing helix  chain 'I' and resid 62 through 71
    Processing helix  chain 'I' and resid 80 through 93
      removed outlier: 3.911A  pdb=" N   ASP I  84 " --> pdb=" O   PHE I  80 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA I  86 " --> pdb=" O   ARG I  82 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 102 through 110
    Processing helix  chain 'I' and resid 117 through 127
    Processing helix  chain 'I' and resid 145 through 155
      removed outlier: 3.501A  pdb=" N   ASP I 155 " --> pdb=" O   TYR I 151 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 158 through 173
    Processing helix  chain 'I' and resid 175 through 196
      Proline residue:  I 187  - end of helix
    Processing helix  chain 'K' and resid 62 through 71
    Processing helix  chain 'K' and resid 80 through 93
      removed outlier: 3.912A  pdb=" N   ASP K  84 " --> pdb=" O   PHE K  80 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA K  86 " --> pdb=" O   ARG K  82 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 102 through 110
    Processing helix  chain 'K' and resid 117 through 127
    Processing helix  chain 'K' and resid 145 through 155
      removed outlier: 3.501A  pdb=" N   ASP K 155 " --> pdb=" O   TYR K 151 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 158 through 173
    Processing helix  chain 'K' and resid 175 through 196
      Proline residue:  K 187  - end of helix
    Processing helix  chain 'M' and resid 62 through 71
    Processing helix  chain 'M' and resid 80 through 93
      removed outlier: 3.912A  pdb=" N   ASP M  84 " --> pdb=" O   PHE M  80 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA M  86 " --> pdb=" O   ARG M  82 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 102 through 110
    Processing helix  chain 'M' and resid 117 through 127
    Processing helix  chain 'M' and resid 145 through 155
      removed outlier: 3.501A  pdb=" N   ASP M 155 " --> pdb=" O   TYR M 151 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 158 through 173
    Processing helix  chain 'M' and resid 175 through 196
      Proline residue:  M 187  - end of helix
    Processing helix  chain 'O' and resid 62 through 71
    Processing helix  chain 'O' and resid 80 through 93
      removed outlier: 3.911A  pdb=" N   ASP O  84 " --> pdb=" O   PHE O  80 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA O  86 " --> pdb=" O   ARG O  82 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 102 through 110
    Processing helix  chain 'O' and resid 117 through 127
    Processing helix  chain 'O' and resid 145 through 155
      removed outlier: 3.501A  pdb=" N   ASP O 155 " --> pdb=" O   TYR O 151 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 158 through 173
    Processing helix  chain 'O' and resid 175 through 196
      Proline residue:  O 187  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8
      removed outlier: 6.181A  pdb=" N   ARG A   5 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   GLN A  54 " --> pdb=" O   ARG A   5 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   HIS A   7 " --> pdb=" O   GLN A  54 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLU A  27 " --> pdb=" O   CYS A  39 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   VAL A  41 " --> pdb=" O   ASP A  25 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASP A  25 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU A  43 " --> pdb=" O   ALA A  23 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA A  23 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 8
      removed outlier: 6.181A  pdb=" N   ARG C   5 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   GLN C  54 " --> pdb=" O   ARG C   5 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   HIS C   7 " --> pdb=" O   GLN C  54 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLU C  27 " --> pdb=" O   CYS C  39 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   VAL C  41 " --> pdb=" O   ASP C  25 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASP C  25 " --> pdb=" O   VAL C  41 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU C  43 " --> pdb=" O   ALA C  23 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA C  23 " --> pdb=" O   LEU C  43 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 8
      removed outlier: 6.180A  pdb=" N   ARG E   5 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   GLN E  54 " --> pdb=" O   ARG E   5 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   HIS E   7 " --> pdb=" O   GLN E  54 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   GLU E  27 " --> pdb=" O   CYS E  39 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   VAL E  41 " --> pdb=" O   ASP E  25 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASP E  25 " --> pdb=" O   VAL E  41 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU E  43 " --> pdb=" O   ALA E  23 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA E  23 " --> pdb=" O   LEU E  43 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 4 through 8
      removed outlier: 6.180A  pdb=" N   ARG G   5 " --> pdb=" O   VAL G  52 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   GLN G  54 " --> pdb=" O   ARG G   5 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   HIS G   7 " --> pdb=" O   GLN G  54 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLU G  27 " --> pdb=" O   CYS G  39 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   VAL G  41 " --> pdb=" O   ASP G  25 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASP G  25 " --> pdb=" O   VAL G  41 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU G  43 " --> pdb=" O   ALA G  23 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA G  23 " --> pdb=" O   LEU G  43 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'I' and resid 4 through 8
      removed outlier: 6.181A  pdb=" N   ARG I   5 " --> pdb=" O   VAL I  52 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   GLN I  54 " --> pdb=" O   ARG I   5 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   HIS I   7 " --> pdb=" O   GLN I  54 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLU I  27 " --> pdb=" O   CYS I  39 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   VAL I  41 " --> pdb=" O   ASP I  25 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASP I  25 " --> pdb=" O   VAL I  41 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU I  43 " --> pdb=" O   ALA I  23 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ALA I  23 " --> pdb=" O   LEU I  43 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'K' and resid 4 through 8
      removed outlier: 6.181A  pdb=" N   ARG K   5 " --> pdb=" O   VAL K  52 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   GLN K  54 " --> pdb=" O   ARG K   5 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   HIS K   7 " --> pdb=" O   GLN K  54 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLU K  27 " --> pdb=" O   CYS K  39 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   VAL K  41 " --> pdb=" O   ASP K  25 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ASP K  25 " --> pdb=" O   VAL K  41 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   LEU K  43 " --> pdb=" O   ALA K  23 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA K  23 " --> pdb=" O   LEU K  43 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'M' and resid 4 through 8
      removed outlier: 6.181A  pdb=" N   ARG M   5 " --> pdb=" O   VAL M  52 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   GLN M  54 " --> pdb=" O   ARG M   5 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   HIS M   7 " --> pdb=" O   GLN M  54 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   GLU M  27 " --> pdb=" O   CYS M  39 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   VAL M  41 " --> pdb=" O   ASP M  25 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASP M  25 " --> pdb=" O   VAL M  41 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU M  43 " --> pdb=" O   ALA M  23 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA M  23 " --> pdb=" O   LEU M  43 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'O' and resid 4 through 8
      removed outlier: 6.181A  pdb=" N   ARG O   5 " --> pdb=" O   VAL O  52 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   GLN O  54 " --> pdb=" O   ARG O   5 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   HIS O   7 " --> pdb=" O   GLN O  54 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLU O  27 " --> pdb=" O   CYS O  39 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   VAL O  41 " --> pdb=" O   ASP O  25 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASP O  25 " --> pdb=" O   VAL O  41 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU O  43 " --> pdb=" O   ALA O  23 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA O  23 " --> pdb=" O   LEU O  43 " (cutoff:3.500A)

    553 hydrogen bonds defined for protein.
    1659 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: 1.74

  Time building geometry restraints manager: 1.32 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3841
        1.34 -     1.45: 1632
        1.45 -     1.57: 6655
        1.57 -     1.69: 24
        1.69 -     1.81: 64
  Bond restraints: 12216
  Sorted by residual:
  bond pdb=" N   VAL A 156 "
       pdb=" CA  VAL A 156 "
    ideal  model  delta    sigma   weight residual
    1.456  1.463 -0.007 1.08e-02 8.57e+03 4.43e-01
  bond pdb=" N   VAL M 156 "
       pdb=" CA  VAL M 156 "
    ideal  model  delta    sigma   weight residual
    1.456  1.463 -0.007 1.08e-02 8.57e+03 4.28e-01
  bond pdb=" CB  VAL I  40 "
       pdb=" CG1 VAL I  40 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 3.30e-02 9.18e+02 4.13e-01
  bond pdb=" CB  VAL C  40 "
       pdb=" CG1 VAL C  40 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 3.30e-02 9.18e+02 4.02e-01
  bond pdb=" C   ARG M 161 "
       pdb=" O   ARG M 161 "
    ideal  model  delta    sigma   weight residual
    1.237  1.244 -0.007 1.17e-02 7.31e+03 3.94e-01
  ... (remaining 12211 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 15748
        1.13 -     2.26: 771
        2.26 -     3.40: 140
        3.40 -     4.53: 21
        4.53 -     5.66: 32
  Bond angle restraints: 16712
  Sorted by residual:
  angle pdb=" CA  GLN A  42 "
        pdb=" CB  GLN A  42 "
        pdb=" CG  GLN A  42 "
      ideal   model   delta    sigma   weight residual
     114.10  119.76   -5.66 2.00e+00 2.50e-01 8.01e+00
  angle pdb=" CA  GLN C  42 "
        pdb=" CB  GLN C  42 "
        pdb=" CG  GLN C  42 "
      ideal   model   delta    sigma   weight residual
     114.10  119.75   -5.65 2.00e+00 2.50e-01 7.99e+00
  angle pdb=" CA  GLN M  42 "
        pdb=" CB  GLN M  42 "
        pdb=" CG  GLN M  42 "
      ideal   model   delta    sigma   weight residual
     114.10  119.73   -5.63 2.00e+00 2.50e-01 7.92e+00
  angle pdb=" CA  GLN I  42 "
        pdb=" CB  GLN I  42 "
        pdb=" CG  GLN I  42 "
      ideal   model   delta    sigma   weight residual
     114.10  119.72   -5.62 2.00e+00 2.50e-01 7.89e+00
  angle pdb=" CA  GLN O  42 "
        pdb=" CB  GLN O  42 "
        pdb=" CG  GLN O  42 "
      ideal   model   delta    sigma   weight residual
     114.10  119.71   -5.61 2.00e+00 2.50e-01 7.88e+00
  ... (remaining 16707 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 6754
       17.83 -    35.66: 318
       35.66 -    53.49: 80
       53.49 -    71.32: 64
       71.32 -    89.15: 16
  Dihedral angle restraints: 7232
    sinusoidal: 2600
      harmonic: 4632
  Sorted by residual:
  dihedral pdb=" CA  PHE A  78 "
           pdb=" C   PHE A  78 "
           pdb=" N   HIS A  79 "
           pdb=" CA  HIS A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.64   22.36     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  PHE C  78 "
           pdb=" C   PHE C  78 "
           pdb=" N   HIS C  79 "
           pdb=" CA  HIS C  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.66   22.34     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  PHE G  78 "
           pdb=" C   PHE G  78 "
           pdb=" N   HIS G  79 "
           pdb=" CA  HIS G  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.68   22.32     0      5.00e+00 4.00e-02 1.99e+01
  ... (remaining 7229 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1071
       0.028 -    0.056: 526
       0.056 -    0.083: 256
       0.083 -    0.111: 131
       0.111 -    0.139: 64
  Chirality restraints: 2048
  Sorted by residual:
  chirality pdb=" CA  ILE G   4 "
            pdb=" N   ILE G   4 "
            pdb=" C   ILE G   4 "
            pdb=" CB  ILE G   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.83e-01
  chirality pdb=" CA  ILE M   4 "
            pdb=" N   ILE M   4 "
            pdb=" C   ILE M   4 "
            pdb=" CB  ILE M   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.79e-01
  chirality pdb=" CA  ILE I   4 "
            pdb=" N   ILE I   4 "
            pdb=" C   ILE I   4 "
            pdb=" CB  ILE I   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.76e-01
  ... (remaining 2045 not shown)

  Planarity restraints: 2048
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE G  83 "   -0.007 2.00e-02 2.50e+03   1.32e-02 1.76e+00
        pdb=" C   PHE G  83 "    0.023 2.00e-02 2.50e+03
        pdb=" O   PHE G  83 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASP G  84 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE E  83 "   -0.007 2.00e-02 2.50e+03   1.32e-02 1.73e+00
        pdb=" C   PHE E  83 "    0.023 2.00e-02 2.50e+03
        pdb=" O   PHE E  83 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASP E  84 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE O  83 "   -0.007 2.00e-02 2.50e+03   1.31e-02 1.72e+00
        pdb=" C   PHE O  83 "    0.023 2.00e-02 2.50e+03
        pdb=" O   PHE O  83 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASP O  84 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2045 not shown)

  Histogram of nonbonded interaction distances:
        2.46 -     2.94: 5116
        2.94 -     3.43: 11286
        3.43 -     3.92: 19745
        3.92 -     4.41: 23107
        4.41 -     4.90: 37981
  Nonbonded interactions: 97235
  Sorted by model distance:
  nonbonded pdb=" O   HIS G 205 "
            pdb=" NZ  LYS O 103 "
     model   vdw
     2.456 3.120
  nonbonded pdb=" NZ  LYS E 103 "
            pdb=" O   HIS I 205 "
     model   vdw
     2.490 3.120
  nonbonded pdb=" OG1 THR G  26 "
            pdb=" OD1 ASP G  84 "
     model   vdw
     2.499 3.040
  nonbonded pdb=" OG1 THR C  26 "
            pdb=" OD1 ASP C  84 "
     model   vdw
     2.499 3.040
  nonbonded pdb=" OG1 THR I  26 "
            pdb=" OD1 ASP I  84 "
     model   vdw
     2.499 3.040
  ... (remaining 97230 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 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'I'
  selection = chain 'K'
  selection = chain 'M'
  selection = chain 'O'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
  selection = chain 'J'
  selection = chain 'L'
  selection = chain 'N'
  selection = chain 'P'
}

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:             0.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     10.050
  Find NCS groups from input model:        0.100
  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:             0.010
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
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      :  0.003   0.021  12216  Z= 0.148
  Angle     :  0.617   5.660  16712  Z= 0.372
  Chirality :  0.046   0.139   2048
  Planarity :  0.004   0.026   2048
  Dihedral  : 14.589  89.151   4208
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  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 are not related in a simple way.
  whole:  1.04 (0.21), residues: 1560
  helix:  0.79 (0.19), residues: 704
  sheet:  0.50 (0.22), residues: 240
  loop :  0.94 (0.28), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG C  37 
 TYR   0.005   0.001   TYR M  17 
 PHE   0.013   0.002   PHE K  78 
 TRP   0.016   0.002   TRP M 197 
 HIS   0.002   0.001   HIS E 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (12216)
  covalent geometry    : angle       0.61652 (16712)
  hydrogen bonds       : bond        0.10484 (  553)
  hydrogen bonds       : angle       7.48907 ( 1659)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.423 
Fit side-chains
REVERT: A  137 SER cc_start: 0.8402 (t) cc_final: 0.8122 (p)
REVERT: A  146 ARG cc_start: 0.7689 (tpt170) cc_final: 0.7413 (tpp-160)
REVERT: C  146 ARG cc_start: 0.7610 (tpt170) cc_final: 0.7176 (tpp-160)
REVERT: E  146 ARG cc_start: 0.7698 (tpt170) cc_final: 0.7277 (tpp-160)
REVERT: G  146 ARG cc_start: 0.7808 (tpt170) cc_final: 0.7471 (tpp-160)
REVERT: I  146 ARG cc_start: 0.7775 (tpt170) cc_final: 0.7423 (tpp-160)
REVERT: K  137 SER cc_start: 0.8430 (t) cc_final: 0.8148 (p)
REVERT: M  146 ARG cc_start: 0.7579 (tpt170) cc_final: 0.7288 (tpp-160)
REVERT: O  146 ARG cc_start: 0.7612 (tpt170) cc_final: 0.7170 (tpp-160)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1204
  time to fit residues: 24.2027
Evaluate side-chains
  137 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
K 184 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.118636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.100822 restraints weight = 13656.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 1.27
r_work: 0.2958 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2807 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  12216  Z= 0.227
  Angle     :  0.542   4.616  16712  Z= 0.285
  Chirality :  0.047   0.129   2048
  Planarity :  0.004   0.032   2048
  Dihedral  : 11.271  63.758   1968
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  1.33 %
    Favored  : 97.92 %
  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 are not related in a simple way.
  whole:  1.73 (0.22), residues: 1560
  helix:  1.67 (0.20), residues: 704
  sheet:  0.67 (0.26), residues: 240
  loop :  0.92 (0.29), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G 172 
 TYR   0.011   0.002   TYR G  17 
 PHE   0.016   0.002   PHE A  78 
 TRP   0.012   0.002   TRP I 197 
 HIS   0.004   0.001   HIS I 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 (12216)
  covalent geometry    : angle       0.54177 (16712)
  hydrogen bonds       : bond        0.04277 (  553)
  hydrogen bonds       : angle       6.07042 ( 1659)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 135
  time to evaluate  : 0.447 
Fit side-chains
REVERT: K  146 ARG cc_start: 0.7418 (tpp-160) cc_final: 0.7201 (tpp-160)
  outliers start: 8
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1177
  time to fit residues: 22.8584
Evaluate side-chains
  125 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 102 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 131 optimal weight:    0.6980
   chunk 77 optimal weight:    7.9990
   chunk 149 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 133 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 121 optimal weight:    6.9990
   chunk 49 optimal weight:    6.9990
   overall best weight:    4.7388

-------------------------------------------------------------------------------
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 = 0.3225 r_free = 0.3225 target = 0.117300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.098338 restraints weight = 13901.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 1.39
r_work: 0.2918 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044  12216  Z= 0.286
  Angle     :  0.564   4.510  16712  Z= 0.295
  Chirality :  0.048   0.131   2048
  Planarity :  0.004   0.036   2048
  Dihedral  : 11.379  63.753   1968
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  3.03 %
    Favored  : 96.21 %
  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 are not related in a simple way.
  whole:  1.24 (0.22), residues: 1560
  helix:  1.18 (0.20), residues: 704
  sheet:  0.89 (0.28), residues: 240
  loop :  0.57 (0.28), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG O 189 
 TYR   0.014   0.002   TYR O  17 
 PHE   0.012   0.002   PHE O  78 
 TRP   0.009   0.002   TRP G 197 
 HIS   0.005   0.001   HIS G 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00697 (12216)
  covalent geometry    : angle       0.56431 (16712)
  hydrogen bonds       : bond        0.04450 (  553)
  hydrogen bonds       : angle       6.04508 ( 1659)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.424 
Fit side-chains
  outliers start: 8
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1132
  time to fit residues: 19.3150
Evaluate side-chains
  118 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 148 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 128 optimal weight:    0.9980
   chunk 137 optimal weight:    8.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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 = 0.3248 r_free = 0.3248 target = 0.118749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.099527 restraints weight = 13876.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.43
r_work: 0.3010 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  12216  Z= 0.211
  Angle     :  0.497   4.411  16712  Z= 0.262
  Chirality :  0.045   0.126   2048
  Planarity :  0.004   0.035   2048
  Dihedral  : 11.295  63.769   1968
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.03 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.21), residues: 1560
  helix:  1.14 (0.20), residues: 704
  sheet:  1.00 (0.27), residues: 240
  loop :  0.42 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  35 
 TYR   0.011   0.002   TYR K  17 
 PHE   0.012   0.002   PHE G  78 
 TRP   0.006   0.001   TRP I 197 
 HIS   0.003   0.001   HIS E 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 (12216)
  covalent geometry    : angle       0.49681 (16712)
  hydrogen bonds       : bond        0.03901 (  553)
  hydrogen bonds       : angle       5.81174 ( 1659)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.458 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.7860 (tpt-90) cc_final: 0.7376 (tpp-160)
REVERT: G  146 ARG cc_start: 0.7865 (tpt170) cc_final: 0.7199 (tpp-160)
REVERT: I  146 ARG cc_start: 0.7880 (tpt-90) cc_final: 0.7380 (tpp-160)
REVERT: M  146 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7204 (tpp-160)
REVERT: O  146 ARG cc_start: 0.7904 (tpt-90) cc_final: 0.7221 (tpp-160)
  outliers start: 1
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1299
  time to fit residues: 22.8820
Evaluate side-chains
  127 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  146 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 148 optimal weight:    4.9990
   chunk 137 optimal weight:    7.9990
   chunk 99 optimal weight:    6.9990
   chunk 35 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   chunk 24 optimal weight:    0.5980
   chunk 151 optimal weight:    3.9990
   chunk 87 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 32 optimal weight:    7.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    3.9188

-------------------------------------------------------------------------------
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 = 0.3255 r_free = 0.3255 target = 0.119068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.100294 restraints weight = 13864.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 1.39
r_work: 0.3005 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037  12216  Z= 0.239
  Angle     :  0.514   4.419  16712  Z= 0.270
  Chirality :  0.046   0.129   2048
  Planarity :  0.004   0.036   2048
  Dihedral  : 11.317  63.777   1968
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  2.84 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.21), residues: 1560
  helix:  1.06 (0.20), residues: 704
  sheet:  1.02 (0.28), residues: 240
  loop :  0.28 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 189 
 TYR   0.013   0.002   TYR K  17 
 PHE   0.012   0.002   PHE O  78 
 TRP   0.006   0.001   TRP G 197 
 HIS   0.003   0.001   HIS E 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00583 (12216)
  covalent geometry    : angle       0.51398 (16712)
  hydrogen bonds       : bond        0.04082 (  553)
  hydrogen bonds       : angle       5.88541 ( 1659)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 126
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.7895 (tpt170) cc_final: 0.7206 (tpp-160)
REVERT: I  146 ARG cc_start: 0.7928 (tpt170) cc_final: 0.7417 (tpp-160)
REVERT: M  146 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7213 (tpp-160)
  outliers start: 3
  outliers final: 1
  residues processed: 128
  average time/residue: 0.1335
  time to fit residues: 23.5877
Evaluate side-chains
  128 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 126
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   42 GLN
Chi-restraints excluded: chain M residue  146 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 102 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 145 optimal weight:    7.9990
   chunk 107 optimal weight:    6.9990
   chunk 133 optimal weight:   10.0000
   chunk 132 optimal weight:    3.9990
   chunk 135 optimal weight:    1.9990
   chunk 61 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    3.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.119126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.100046 restraints weight = 13904.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 1.43
r_work: 0.2921 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2765 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036  12216  Z= 0.243
  Angle     :  0.512   4.409  16712  Z= 0.270
  Chirality :  0.046   0.128   2048
  Planarity :  0.004   0.036   2048
  Dihedral  : 11.330  63.780   1968
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  2.18 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.21), residues: 1560
  helix:  1.03 (0.20), residues: 704
  sheet:  0.98 (0.28), residues: 240
  loop :  0.17 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 189 
 TYR   0.013   0.002   TYR K  17 
 PHE   0.012   0.002   PHE G  78 
 TRP   0.005   0.001   TRP G 197 
 HIS   0.003   0.001   HIS K 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 (12216)
  covalent geometry    : angle       0.51236 (16712)
  hydrogen bonds       : bond        0.04064 (  553)
  hydrogen bonds       : angle       5.88288 ( 1659)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.7927 (tpt170) cc_final: 0.7247 (tpp-160)
REVERT: I  146 ARG cc_start: 0.7916 (tpt170) cc_final: 0.7386 (tpp-160)
REVERT: M  146 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7191 (tpp-160)
  outliers start: 10
  outliers final: 1
  residues processed: 134
  average time/residue: 0.1247
  time to fit residues: 23.2422
Evaluate side-chains
  127 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   42 GLN
Chi-restraints excluded: chain M residue  146 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 151 optimal weight:    3.9990
   chunk 146 optimal weight:    0.0570
   chunk 111 optimal weight:    8.9990
   chunk 114 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 140 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 127 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 70 optimal weight:   10.0000
   overall best weight:    3.8106

-------------------------------------------------------------------------------
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 = 0.3258 r_free = 0.3258 target = 0.119367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.100276 restraints weight = 13783.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 1.42
r_work: 0.3007 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034  12216  Z= 0.233
  Angle     :  0.502   4.398  16712  Z= 0.265
  Chirality :  0.046   0.127   2048
  Planarity :  0.004   0.036   2048
  Dihedral  : 11.327  63.783   1968
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  2.46 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.21), residues: 1560
  helix:  1.03 (0.19), residues: 704
  sheet:  0.91 (0.28), residues: 240
  loop :  0.16 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG O  35 
 TYR   0.013   0.002   TYR K  17 
 PHE   0.012   0.002   PHE K  78 
 TRP   0.005   0.001   TRP I 197 
 HIS   0.003   0.001   HIS E 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00568 (12216)
  covalent geometry    : angle       0.50231 (16712)
  hydrogen bonds       : bond        0.03995 (  553)
  hydrogen bonds       : angle       5.86343 ( 1659)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.7908 (tpt170) cc_final: 0.7214 (tpp-160)
REVERT: G  146 ARG cc_start: 0.7852 (tpt-90) cc_final: 0.7335 (tpp-160)
REVERT: I  146 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7350 (tpp-160)
REVERT: M  146 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7211 (tpp-160)
REVERT: O  146 ARG cc_start: 0.7926 (tpt170) cc_final: 0.7265 (tpp-160)
  outliers start: 12
  outliers final: 1
  residues processed: 133
  average time/residue: 0.1241
  time to fit residues: 23.2896
Evaluate side-chains
  126 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 123
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain I residue  146 ARG
Chi-restraints excluded: chain M residue  146 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 120 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 146 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 136 optimal weight:    0.9990
   chunk 135 optimal weight:    1.9990
   chunk 128 optimal weight:    0.9990
   chunk 80 optimal weight:   10.0000
   chunk 113 optimal weight:    1.9990
   chunk 111 optimal weight:    8.9990
   overall best weight:    1.5990

-------------------------------------------------------------------------------
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 = 0.3293 r_free = 0.3293 target = 0.121921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.103069 restraints weight = 13718.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 1.41
r_work: 0.2950 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2796 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020  12216  Z= 0.117
  Angle     :  0.408   4.347  16712  Z= 0.223
  Chirality :  0.043   0.121   2048
  Planarity :  0.003   0.033   2048
  Dihedral  : 11.204  63.836   1968
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  2.56 %
    Favored  : 96.12 %
  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 are not related in a simple way.
  whole:  1.35 (0.22), residues: 1560
  helix:  1.38 (0.20), residues: 704
  sheet:  1.15 (0.28), residues: 240
  loop :  0.37 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  35 
 TYR   0.006   0.001   TYR K  17 
 PHE   0.013   0.001   PHE O  78 
 TRP   0.004   0.001   TRP M 139 
 HIS   0.001   0.000   HIS M 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (12216)
  covalent geometry    : angle       0.40806 (16712)
  hydrogen bonds       : bond        0.03174 (  553)
  hydrogen bonds       : angle       5.46084 ( 1659)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.443 
Fit side-chains
REVERT: I  146 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7423 (tpp-160)
REVERT: M  146 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7413 (tpp-160)
  outliers start: 14
  outliers final: 4
  residues processed: 120
  average time/residue: 0.0886
  time to fit residues: 16.9006
Evaluate side-chains
  112 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain G residue  156 VAL
Chi-restraints excluded: chain I residue  146 ARG
Chi-restraints excluded: chain I residue  156 VAL
Chi-restraints excluded: chain M residue  146 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 99 optimal weight:    9.9990
   chunk 15 optimal weight:    2.9990
   chunk 137 optimal weight:   10.0000
   chunk 120 optimal weight:    1.9990
   chunk 103 optimal weight:    7.9990
   chunk 148 optimal weight:    6.9990
   chunk 102 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 68 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   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 = 0.3256 r_free = 0.3256 target = 0.119211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.100420 restraints weight = 13854.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 1.40
r_work: 0.2927 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036  12216  Z= 0.254
  Angle     :  0.516   4.536  16712  Z= 0.271
  Chirality :  0.046   0.126   2048
  Planarity :  0.004   0.035   2048
  Dihedral  : 11.276  63.773   1968
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  2.84 %
    Favored  : 96.12 %
  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 are not related in a simple way.
  whole:  0.95 (0.21), residues: 1560
  helix:  1.06 (0.19), residues: 704
  sheet:  0.96 (0.28), residues: 240
  loop :  0.14 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG M 189 
 TYR   0.014   0.002   TYR G  17 
 PHE   0.012   0.002   PHE A  78 
 TRP   0.005   0.001   TRP G 197 
 HIS   0.004   0.001   HIS I 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00620 (12216)
  covalent geometry    : angle       0.51562 (16712)
  hydrogen bonds       : bond        0.04101 (  553)
  hydrogen bonds       : angle       5.84302 ( 1659)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7140 (tpp-160)
REVERT: G  146 ARG cc_start: 0.7942 (tpt170) cc_final: 0.7420 (tpp-160)
REVERT: I  146 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7241 (tpp-160)
REVERT: M  146 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7194 (tpp-160)
  outliers start: 11
  outliers final: 1
  residues processed: 122
  average time/residue: 0.1160
  time to fit residues: 20.4653
Evaluate side-chains
  118 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 114
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain C residue   42 GLN
Chi-restraints excluded: chain I residue  146 ARG
Chi-restraints excluded: chain M residue  146 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 122 optimal weight:    4.9990
   chunk 144 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 13 optimal weight:    0.3980
   chunk 1 optimal weight:    9.9990
   chunk 111 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3312 r_free = 0.3312 target = 0.123505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.104514 restraints weight = 13802.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 1.43
r_work: 0.2976 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2822 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018  12216  Z= 0.092
  Angle     :  0.390   4.369  16712  Z= 0.215
  Chirality :  0.042   0.120   2048
  Planarity :  0.003   0.032   2048
  Dihedral  : 11.116  63.811   1968
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  3.50 %
    Favored  : 96.21 %
  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 are not related in a simple way.
  whole:  1.50 (0.22), residues: 1560
  helix:  1.49 (0.20), residues: 704
  sheet:  1.32 (0.28), residues: 240
  loop :  0.41 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  82 
 TYR   0.005   0.001   TYR C 151 
 PHE   0.014   0.001   PHE K  78 
 TRP   0.004   0.001   TRP K 139 
 HIS   0.001   0.000   HIS K  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 (12216)
  covalent geometry    : angle       0.39021 (16712)
  hydrogen bonds       : bond        0.02954 (  553)
  hydrogen bonds       : angle       5.28832 ( 1659)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 111
  time to evaluate  : 0.434 
Fit side-chains
REVERT: C  191 ASN cc_start: 0.8621 (t0) cc_final: 0.8404 (t0)
REVERT: E  191 ASN cc_start: 0.8632 (t0) cc_final: 0.8416 (t0)
REVERT: G  191 ASN cc_start: 0.8704 (t0) cc_final: 0.8496 (t0)
REVERT: I  146 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7438 (tpp-160)
REVERT: I  191 ASN cc_start: 0.8648 (t0) cc_final: 0.8431 (t0)
REVERT: O  191 ASN cc_start: 0.8625 (t0) cc_final: 0.8412 (t0)
  outliers start: 3
  outliers final: 1
  residues processed: 114
  average time/residue: 0.0852
  time to fit residues: 15.8333
Evaluate side-chains
  108 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain I residue  146 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 150 optimal weight:    0.8980
   chunk 66 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 135 optimal weight:    8.9990
   chunk 68 optimal weight:    9.9990
   chunk 80 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   chunk 58 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    2.7384

-------------------------------------------------------------------------------
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 = 0.3262 r_free = 0.3262 target = 0.119754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.100080 restraints weight = 13797.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 1.49
r_work: 0.2991 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  12216  Z= 0.176
  Angle     :  0.452   4.467  16712  Z= 0.241
  Chirality :  0.044   0.123   2048
  Planarity :  0.004   0.033   2048
  Dihedral  : 11.192  63.786   1968
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  3.79 %
    Favored  : 95.74 %
  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 are not related in a simple way.
  whole:  1.31 (0.21), residues: 1560
  helix:  1.32 (0.20), residues: 704
  sheet:  1.23 (0.27), residues: 240
  loop :  0.33 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 189 
 TYR   0.010   0.002   TYR M  17 
 PHE   0.011   0.001   PHE K  78 
 TRP   0.004   0.001   TRP G 139 
 HIS   0.002   0.001   HIS I 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 (12216)
  covalent geometry    : angle       0.45195 (16712)
  hydrogen bonds       : bond        0.03613 (  553)
  hydrogen bonds       : angle       5.56088 ( 1659)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2354.89 seconds
wall clock time: 41 minutes 7.30 seconds (2467.30 seconds total)