Starting phenix.real_space_refine
on Wed Mar 12 09:04:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vvi_43560/03_2025/8vvi_43560.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vvi_43560/03_2025/8vvi_43560.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vvi_43560/03_2025/8vvi_43560.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vvi_43560/03_2025/8vvi_43560.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vvi_43560/03_2025/8vvi_43560.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vvi_43560/03_2025/8vvi_43560.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.065
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    5074      2.51       5
     N    1263      2.21       5
     O    1381      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7762
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "F"
      Number of atoms: 775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 775
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "A"
      Number of atoms: 1958
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1958
          Classifications: {'peptide': 238}
          Link IDs: {'PTRANS': 5, 'TRANS': 232}
    Chain: "C"
      Number of atoms: 775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 775
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "D"
      Number of atoms: 775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 775
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "E"
      Number of atoms: 775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 775
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "G"
      Number of atoms: 775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 775
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "B"
      Number of atoms: 1929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1929
          Classifications: {'peptide': 235}
          Link IDs: {'PTRANS': 5, 'TRANS': 229}
  Time building chain proxies: 6.59, per 1000 atoms: 0.85
  Number of scatterers: 7762
  At special positions: 0
  Unit cell: (67.962, 73.746, 124.356, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1381      8.00
     N    1263      7.00
     C    5074      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: 1.93
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1808

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 3 sheets defined
      73.7% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'F' and resid 4 through 23
    Processing helix  chain 'F' and resid 24 through 27
      removed outlier: 3.664A  pdb=" N   LYS F  27 " --> pdb=" O   ARG F  24 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 24 through 27'
    Processing helix  chain 'F' and resid 32 through 54
    Processing helix  chain 'F' and resid 61 through 63
      No H-bonds generated for 'chain 'F' and resid 61 through 63'
    Processing helix  chain 'F' and resid 64 through 99
    Processing helix  chain 'A' and resid 14 through 41
      removed outlier: 3.668A  pdb=" N   SER A  18 " --> pdb=" O   ASP A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 67
      Proline residue:  A  48  - end of helix
    Processing helix  chain 'A' and resid 69 through 74
    Processing helix  chain 'A' and resid 100 through 119
      removed outlier: 3.588A  pdb=" N   LYS A 104 " --> pdb=" O   THR A 100 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLU A 105 " --> pdb=" O   PRO A 101 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE A 106 " --> pdb=" O   ARG A 102 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   ILE A 112 " --> pdb=" O   ASP A 108 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   ARG A 113 " --> pdb=" O   ASP A 109 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LYS A 116 " --> pdb=" O   ILE A 112 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ILE A 117 " --> pdb=" O   ARG A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 171
      removed outlier: 4.123A  pdb=" N   MET A 169 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR A 170 " --> pdb=" O   GLU A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 187
      removed outlier: 3.950A  pdb=" N   TRP A 183 " --> pdb=" O   GLU A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 246
      removed outlier: 3.592A  pdb=" N   LYS A 231 " --> pdb=" O   ASN A 227 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN A 246 " --> pdb=" O   TYR A 242 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 24
      removed outlier: 3.624A  pdb=" N   ASN C  23 " --> pdb=" O   ILE C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 55
      Proline residue:  C  34  - end of helix
      removed outlier: 3.549A  pdb=" N   HIS C  55 " --> pdb=" O   ILE C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 99
      Proline residue:  C  66  - end of helix
      removed outlier: 3.885A  pdb=" N   THR C  74 " --> pdb=" O   ASN C  70 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   PHE C  76 " --> pdb=" O   ILE C  72 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   TRP C  77 " --> pdb=" O   LYS C  73 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   ALA C  78 " --> pdb=" O   THR C  74 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   SER C  79 " --> pdb=" O   ALA C  75 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ARG C  99 " --> pdb=" O   PHE C  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 4
      No H-bonds generated for 'chain 'D' and resid 2 through 4'
    Processing helix  chain 'D' and resid 5 through 24
      removed outlier: 3.799A  pdb=" N   ASN D  23 " --> pdb=" O   ILE D  19 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG D  24 " --> pdb=" O   PHE D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 53
      removed outlier: 3.557A  pdb=" N   LEU D  32 " --> pdb=" O   SER D  28 " (cutoff:3.500A)
      Proline residue:  D  34  - end of helix
    Processing helix  chain 'D' and resid 64 through 99
    Processing helix  chain 'E' and resid 2 through 24
      removed outlier: 3.633A  pdb=" N   ASN E  23 " --> pdb=" O   ILE E  19 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ARG E  24 " --> pdb=" O   PHE E  20 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 53
      removed outlier: 3.767A  pdb=" N   LEU E  32 " --> pdb=" O   SER E  28 " (cutoff:3.500A)
      Proline residue:  E  34  - end of helix
      removed outlier: 3.592A  pdb=" N   ILE E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY E  52 " --> pdb=" O   GLY E  48 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 60 through 98
      Proline residue:  E  66  - end of helix
      removed outlier: 4.600A  pdb=" N   PHE E  76 " --> pdb=" O   ILE E  72 " (cutoff:3.500A)
      removed outlier: 5.669A  pdb=" N   TRP E  77 " --> pdb=" O   LYS E  73 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   ALA E  78 " --> pdb=" O   THR E  74 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   SER E  79 " --> pdb=" O   ALA E  75 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 2 through 24
      removed outlier: 3.652A  pdb=" N   TYR G   7 " --> pdb=" O   HIS G   3 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ASN G  23 " --> pdb=" O   ILE G  19 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 54
      removed outlier: 3.749A  pdb=" N   LEU G  32 " --> pdb=" O   SER G  28 " (cutoff:3.500A)
      Proline residue:  G  34  - end of helix
    Processing helix  chain 'G' and resid 60 through 72
      Proline residue:  G  66  - end of helix
    Processing helix  chain 'G' and resid 75 through 98
      removed outlier: 4.315A  pdb=" N   SER G  79 " --> pdb=" O   ALA G  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 41
      removed outlier: 4.212A  pdb=" N   SER B  18 " --> pdb=" O   ASP B  14 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ASP B  21 " --> pdb=" O   ILE B  17 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   PHE B  30 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 67
      removed outlier: 3.505A  pdb=" N   VAL B  47 " --> pdb=" O   ASP B  43 " (cutoff:3.500A)
      Proline residue:  B  48  - end of helix
    Processing helix  chain 'B' and resid 69 through 74
    Processing helix  chain 'B' and resid 100 through 119
      removed outlier: 4.073A  pdb=" N   ILE B 112 " --> pdb=" O   ASP B 108 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ARG B 113 " --> pdb=" O   ASP B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 125
      removed outlier: 4.661A  pdb=" N   ASN B 125 " --> pdb=" O   LYS B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 170
      removed outlier: 4.120A  pdb=" N   PHE B 151 " --> pdb=" O   GLY B 147 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   LYS B 152 " --> pdb=" O   LYS B 148 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   ASN B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 187
      removed outlier: 3.951A  pdb=" N   TRP B 183 " --> pdb=" O   GLU B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 246
      removed outlier: 3.512A  pdb=" N   ILE B 235 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   VAL B 236 " --> pdb=" O   VAL B 232 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLN B 246 " --> pdb=" O   TYR B 242 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 77
      removed outlier: 3.530A  pdb=" N   VAL A 220 " --> pdb=" O   PHE A  85 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLU A 129 " --> pdb=" O   ARG A 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 75 through 77
    Processing sheet with id=AA3, first strand: chain 'B' and resid 188 through 192

    531 hydrogen bonds defined for protein.
    1584 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: 2.23

  Time building geometry restraints manager: 2.29 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2424
        1.34 -     1.46: 1657
        1.46 -     1.58: 3756
        1.58 -     1.69: 0
        1.69 -     1.81: 88
  Bond restraints: 7925
  Sorted by residual:
  bond pdb=" C   LEU D  65 "
       pdb=" N   PRO D  66 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.011 1.36e-02 5.41e+03 6.00e-01
  bond pdb=" CB  PRO A 198 "
       pdb=" CG  PRO A 198 "
    ideal  model  delta    sigma   weight residual
    1.492  1.529 -0.037 5.00e-02 4.00e+02 5.37e-01
  bond pdb=" CA  ASP B  89 "
       pdb=" CB  ASP B  89 "
    ideal  model  delta    sigma   weight residual
    1.530  1.542 -0.012 1.69e-02 3.50e+03 5.28e-01
  bond pdb=" CB  ASP A 109 "
       pdb=" CG  ASP A 109 "
    ideal  model  delta    sigma   weight residual
    1.516  1.534 -0.018 2.50e-02 1.60e+03 5.05e-01
  bond pdb=" N   LYS A  79 "
       pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.462  1.472 -0.010 1.48e-02 4.57e+03 4.99e-01
  ... (remaining 7920 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 10517
        1.34 -     2.68: 139
        2.68 -     4.02: 25
        4.02 -     5.37: 17
        5.37 -     6.71: 1
  Bond angle restraints: 10699
  Sorted by residual:
  angle pdb=" C   PRO B  88 "
        pdb=" N   ASP B  89 "
        pdb=" CA  ASP B  89 "
      ideal   model   delta    sigma   weight residual
     121.54  128.25   -6.71 1.91e+00 2.74e-01 1.23e+01
  angle pdb=" C   ASN D  26 "
        pdb=" N   LYS D  27 "
        pdb=" CA  LYS D  27 "
      ideal   model   delta    sigma   weight residual
     121.54  126.84   -5.30 1.91e+00 2.74e-01 7.70e+00
  angle pdb=" C   ASN G  26 "
        pdb=" N   LYS G  27 "
        pdb=" CA  LYS G  27 "
      ideal   model   delta    sigma   weight residual
     121.54  126.36   -4.82 1.91e+00 2.74e-01 6.38e+00
  angle pdb=" CA  LYS A  79 "
        pdb=" CB  LYS A  79 "
        pdb=" CG  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     114.10  118.21   -4.11 2.00e+00 2.50e-01 4.23e+00
  angle pdb=" C   PRO A  88 "
        pdb=" N   ASP A  89 "
        pdb=" CA  ASP A  89 "
      ideal   model   delta    sigma   weight residual
     121.54  125.26   -3.72 1.91e+00 2.74e-01 3.80e+00
  ... (remaining 10694 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 4217
       17.88 -    35.77: 369
       35.77 -    53.65: 62
       53.65 -    71.54: 14
       71.54 -    89.42: 4
  Dihedral angle restraints: 4666
    sinusoidal: 1876
      harmonic: 2790
  Sorted by residual:
  dihedral pdb=" CB  GLU B 239 "
           pdb=" CG  GLU B 239 "
           pdb=" CD  GLU B 239 "
           pdb=" OE1 GLU B 239 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.42  -89.42     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CA  ASP A  14 "
           pdb=" CB  ASP A  14 "
           pdb=" CG  ASP A  14 "
           pdb=" OD1 ASP A  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.20   54.20     1      2.00e+01 2.50e-03 9.96e+00
  dihedral pdb=" CG  LYS B 181 "
           pdb=" CD  LYS B 181 "
           pdb=" CE  LYS B 181 "
           pdb=" NZ  LYS B 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.66  -57.66     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 4663 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 718
       0.026 -    0.052: 309
       0.052 -    0.078: 149
       0.078 -    0.104: 41
       0.104 -    0.130: 19
  Chirality restraints: 1236
  Sorted by residual:
  chirality pdb=" CA  ILE A 132 "
            pdb=" N   ILE A 132 "
            pdb=" C   ILE A 132 "
            pdb=" CB  ILE A 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.20e-01
  chirality pdb=" CA  ILE B 132 "
            pdb=" N   ILE B 132 "
            pdb=" C   ILE B 132 "
            pdb=" CB  ILE B 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  chirality pdb=" CA  ILE A 130 "
            pdb=" N   ILE A 130 "
            pdb=" C   ILE A 130 "
            pdb=" CB  ILE A 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.94e-01
  ... (remaining 1233 not shown)

  Planarity restraints: 1328
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C  33 "   -0.039 5.00e-02 4.00e+02   5.98e-02 5.71e+00
        pdb=" N   PRO C  34 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO C  34 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C  34 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 100 "   -0.031 5.00e-02 4.00e+02   4.78e-02 3.66e+00
        pdb=" N   PRO A 101 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 101 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 101 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A  87 "    0.019 5.00e-02 4.00e+02   2.88e-02 1.33e+00
        pdb=" N   PRO A  88 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A  88 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A  88 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1325 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 494
        2.74 -     3.28: 8140
        3.28 -     3.82: 13128
        3.82 -     4.36: 16602
        4.36 -     4.90: 27998
  Nonbonded interactions: 66362
  Sorted by model distance:
  nonbonded pdb=" O   GLY F  35 "
            pdb=" OG1 THR F  39 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   ALA B 149 "
            pdb=" ND2 ASN B 153 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" OH  TYR A 242 "
            pdb=" OD2 ASP C  63 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   ILE B  90 "
            pdb=" OG1 THR B 100 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   PHE C  20 "
            pdb=" NE2 GLN C  30 "
     model   vdw
     2.267 3.120
  ... (remaining 66357 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' and resid 13 through 247)
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

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:             6.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.160
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.030
  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:13.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
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      :  0.002   0.037   7925  Z= 0.130
  Angle     :  0.445   6.707  10699  Z= 0.239
  Chirality :  0.038   0.130   1236
  Planarity :  0.003   0.060   1328
  Dihedral  : 13.855  89.424   2858
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.27), residues: 954
  helix:  0.60 (0.20), residues: 664
  sheet: -2.99 (0.61), residues: 46
  loop : -1.10 (0.37), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 183 
 HIS   0.002   0.000   HIS F   3 
 PHE   0.009   0.001   PHE B 111 
 TYR   0.008   0.001   TYR B 150 
 ARG   0.003   0.000   ARG A 230 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.865 
Fit side-chains
REVERT: F   25 ARG cc_start: 0.7539 (mmp80) cc_final: 0.6604 (ppt170)
REVERT: F   67 THR cc_start: 0.8161 (m) cc_final: 0.7957 (t)
REVERT: A  128 GLU cc_start: 0.6401 (mt-10) cc_final: 0.6124 (mt-10)
REVERT: D    5 MET cc_start: 0.7507 (tpt) cc_final: 0.7029 (tpt)
REVERT: B   21 ASP cc_start: 0.7936 (m-30) cc_final: 0.7675 (m-30)
REVERT: B   80 ASP cc_start: 0.5833 (t0) cc_final: 0.5155 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 1.4462
  time to fit residues: 226.0531
Evaluate side-chains
  119 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 68 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 82 optimal weight:    0.4980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
F   3 HIS
F  26 ASN
D   3 HIS
** E  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.197573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.158367 restraints weight = 7428.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 1.76
r_work: 0.3618 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3495 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7925  Z= 0.250
  Angle     :  0.572   5.874  10699  Z= 0.309
  Chirality :  0.043   0.146   1236
  Planarity :  0.004   0.049   1328
  Dihedral  :  4.480  20.605   1021
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 10.50 %
    Favored  : 87.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.27), residues: 954
  helix:  1.30 (0.19), residues: 680
  sheet: -2.26 (0.71), residues: 38
  loop : -1.47 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 183 
 HIS   0.013   0.001   HIS E   3 
 PHE   0.012   0.001   PHE B 151 
 TYR   0.014   0.001   TYR A  15 
 ARG   0.006   0.001   ARG B 186 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.927 
Fit side-chains
REVERT: F    1 MET cc_start: 0.5731 (pp-130) cc_final: 0.5495 (pp-130)
REVERT: F   24 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.6072 (ttp80)
REVERT: F   25 ARG cc_start: 0.7680 (mmp80) cc_final: 0.6518 (ppt170)
REVERT: A  128 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6868 (mt-10)
REVERT: A  185 MET cc_start: 0.7863 (mpt) cc_final: 0.7657 (mpt)
REVERT: A  230 ARG cc_start: 0.7013 (mmp80) cc_final: 0.6785 (mmp-170)
REVERT: C   22 MET cc_start: 0.6722 (ptp) cc_final: 0.6472 (ptt)
REVERT: D    5 MET cc_start: 0.7942 (tpt) cc_final: 0.7644 (tmm)
REVERT: D   73 LYS cc_start: 0.8299 (mttp) cc_final: 0.7629 (mtpt)
REVERT: E   73 LYS cc_start: 0.8406 (mtpt) cc_final: 0.8181 (mtmp)
REVERT: B   21 ASP cc_start: 0.8167 (m-30) cc_final: 0.7938 (m-30)
REVERT: B   80 ASP cc_start: 0.6051 (t0) cc_final: 0.5423 (t0)
REVERT: B  108 ASP cc_start: 0.8128 (m-30) cc_final: 0.7659 (m-30)
REVERT: B  128 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6854 (tp30)
  outliers start: 15
  outliers final: 3
  residues processed: 132
  average time/residue: 1.3855
  time to fit residues: 192.6033
Evaluate side-chains
  118 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 113
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ARG
Chi-restraints excluded: chain C residue   24 ARG
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain B residue  128 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 71 optimal weight:    0.1980
   chunk 70 optimal weight:    0.7980
   chunk 60 optimal weight:    0.2980
   chunk 36 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 8 optimal weight:    0.1980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
** E  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  49 GLN
B 218 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.199093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.159671 restraints weight = 7534.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 1.73
r_work: 0.3637 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3514 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7925  Z= 0.192
  Angle     :  0.506   5.430  10699  Z= 0.273
  Chirality :  0.041   0.139   1236
  Planarity :  0.004   0.049   1328
  Dihedral  :  4.387  17.604   1021
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.21 %
    Favored  : 84.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.27), residues: 954
  helix:  1.63 (0.20), residues: 682
  sheet: -2.38 (0.66), residues: 46
  loop : -1.39 (0.39), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 183 
 HIS   0.011   0.001   HIS E   3 
 PHE   0.010   0.001   PHE F  76 
 TYR   0.010   0.001   TYR A  15 
 ARG   0.004   0.000   ARG G  99 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.832 
Fit side-chains
REVERT: F   24 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.5986 (ttp80)
REVERT: F   25 ARG cc_start: 0.7575 (mmp80) cc_final: 0.6416 (ppt170)
REVERT: A  128 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6694 (tp30)
REVERT: C   22 MET cc_start: 0.6564 (ptp) cc_final: 0.6361 (ptt)
REVERT: D    5 MET cc_start: 0.7921 (tpt) cc_final: 0.7645 (tmm)
REVERT: D   73 LYS cc_start: 0.8283 (mttp) cc_final: 0.7621 (mtpt)
REVERT: E   73 LYS cc_start: 0.8357 (mtpt) cc_final: 0.8120 (mttp)
REVERT: G    7 TYR cc_start: 0.7538 (m-80) cc_final: 0.7289 (m-80)
REVERT: B  159 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7318 (mm-30)
REVERT: B  229 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7517 (tt0)
  outliers start: 18
  outliers final: 5
  residues processed: 126
  average time/residue: 1.4598
  time to fit residues: 193.1561
Evaluate side-chains
  121 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ARG
Chi-restraints excluded: chain A residue   27 MET
Chi-restraints excluded: chain C residue   24 ARG
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain B residue  229 GLU
Chi-restraints excluded: chain B residue  237 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0980
   chunk 15 optimal weight:    0.0030
   chunk 40 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0870
   chunk 74 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.2968

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

Flipped N/Q/H residues before XYZ refinement:
D  57 ASN
E  70 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.187438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.141467 restraints weight = 7427.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 1.71
r_work: 0.3448 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7925  Z= 0.170
  Angle     :  0.492   6.397  10699  Z= 0.263
  Chirality :  0.040   0.138   1236
  Planarity :  0.004   0.048   1328
  Dihedral  :  4.298  16.829   1021
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.62 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.27), residues: 954
  helix:  1.87 (0.20), residues: 678
  sheet: -2.11 (0.71), residues: 44
  loop : -1.42 (0.37), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 183 
 HIS   0.009   0.001   HIS E   3 
 PHE   0.010   0.001   PHE A 151 
 TYR   0.009   0.001   TYR A  15 
 ARG   0.005   0.000   ARG A 230 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 0.848 
Fit side-chains
REVERT: F   24 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.5858 (ttp80)
REVERT: F   25 ARG cc_start: 0.7384 (mmp80) cc_final: 0.6142 (ppt170)
REVERT: A  128 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6841 (tp30)
REVERT: C   22 MET cc_start: 0.6497 (ptp) cc_final: 0.6246 (ptt)
REVERT: D    5 MET cc_start: 0.7861 (tpt) cc_final: 0.7535 (tmm)
REVERT: D   73 LYS cc_start: 0.8183 (mttp) cc_final: 0.7418 (mtpt)
REVERT: G    7 TYR cc_start: 0.7473 (m-80) cc_final: 0.7187 (m-80)
REVERT: B   21 ASP cc_start: 0.8166 (m-30) cc_final: 0.7925 (m-30)
REVERT: B   80 ASP cc_start: 0.6124 (t0) cc_final: 0.5527 (t0)
REVERT: B   86 GLN cc_start: 0.6303 (OUTLIER) cc_final: 0.5721 (mm-40)
REVERT: B  159 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7109 (mm-30)
REVERT: B  185 MET cc_start: 0.7729 (mtt) cc_final: 0.7447 (mtm)
  outliers start: 19
  outliers final: 6
  residues processed: 132
  average time/residue: 1.3038
  time to fit residues: 181.5323
Evaluate side-chains
  119 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ARG
Chi-restraints excluded: chain A residue   27 MET
Chi-restraints excluded: chain C residue   24 ARG
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain B residue   86 GLN
Chi-restraints excluded: chain B residue  237 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 88 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 78 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 7 optimal weight:    0.2980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
D  57 ASN
E  26 ASN
E  70 ASN
B  86 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.185167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.138994 restraints weight = 7379.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 1.68
r_work: 0.3422 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7925  Z= 0.226
  Angle     :  0.527   6.784  10699  Z= 0.281
  Chirality :  0.041   0.142   1236
  Planarity :  0.004   0.047   1328
  Dihedral  :  4.416  17.060   1021
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.33 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.27), residues: 954
  helix:  1.79 (0.20), residues: 684
  sheet: -1.91 (0.64), residues: 52
  loop : -1.35 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 183 
 HIS   0.009   0.001   HIS E   3 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.013   0.001   TYR A  15 
 ARG   0.006   0.000   ARG B 186 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.832 
Fit side-chains
REVERT: F   24 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.5904 (ttp80)
REVERT: F   25 ARG cc_start: 0.7393 (mmp80) cc_final: 0.6213 (ppt170)
REVERT: A  128 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7070 (tp30)
REVERT: C   22 MET cc_start: 0.6569 (ptp) cc_final: 0.6292 (ptt)
REVERT: D    5 MET cc_start: 0.7944 (tpt) cc_final: 0.7623 (tmm)
REVERT: D   73 LYS cc_start: 0.8271 (mttp) cc_final: 0.7439 (mtpt)
REVERT: G    7 TYR cc_start: 0.7501 (m-80) cc_final: 0.7242 (m-80)
REVERT: B  128 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6841 (tp30)
REVERT: B  185 MET cc_start: 0.7752 (mtt) cc_final: 0.7449 (mtm)
  outliers start: 21
  outliers final: 7
  residues processed: 130
  average time/residue: 1.3985
  time to fit residues: 191.1396
Evaluate side-chains
  126 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ARG
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue   80 ASP
Chi-restraints excluded: chain C residue   24 ARG
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  237 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 29 optimal weight:    0.3980
   chunk 44 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
D  57 ASN
E  70 ASN
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.182992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.137152 restraints weight = 7335.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 1.65
r_work: 0.3393 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7925  Z= 0.285
  Angle     :  0.563   6.953  10699  Z= 0.299
  Chirality :  0.043   0.143   1236
  Planarity :  0.004   0.046   1328
  Dihedral  :  4.615  17.839   1021
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 15.33 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.27), residues: 954
  helix:  1.60 (0.20), residues: 688
  sheet: -1.99 (0.61), residues: 57
  loop : -1.55 (0.39), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 183 
 HIS   0.010   0.001   HIS E   3 
 PHE   0.022   0.002   PHE A 111 
 TYR   0.016   0.001   TYR A  15 
 ARG   0.007   0.001   ARG B 186 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.832 
Fit side-chains
REVERT: F    1 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5855 (pp-130)
REVERT: F   24 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.6072 (ttp80)
REVERT: A  128 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7127 (tp30)
REVERT: C   22 MET cc_start: 0.6691 (ptp) cc_final: 0.6370 (ptt)
REVERT: D    5 MET cc_start: 0.7960 (tpt) cc_final: 0.7649 (tmm)
REVERT: D   73 LYS cc_start: 0.8283 (mttp) cc_final: 0.7456 (mtpt)
REVERT: G    7 TYR cc_start: 0.7492 (m-80) cc_final: 0.7225 (m-80)
REVERT: B   80 ASP cc_start: 0.6159 (t0) cc_final: 0.5652 (t0)
REVERT: B   86 GLN cc_start: 0.6461 (mm-40) cc_final: 0.6035 (mt0)
REVERT: B  128 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6895 (tp30)
  outliers start: 26
  outliers final: 8
  residues processed: 131
  average time/residue: 1.7223
  time to fit residues: 238.2722
Evaluate side-chains
  119 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 1.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   24 ARG
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   80 ASP
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain C residue   24 ARG
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  237 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 67 optimal weight:    0.3980
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
E  70 ASN
B  86 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.183758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.138015 restraints weight = 7410.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 1.65
r_work: 0.3405 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7925  Z= 0.254
  Angle     :  0.545   7.180  10699  Z= 0.290
  Chirality :  0.042   0.141   1236
  Planarity :  0.004   0.047   1328
  Dihedral  :  4.594  17.672   1021
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.86 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.27), residues: 954
  helix:  1.61 (0.20), residues: 688
  sheet: -1.99 (0.60), residues: 57
  loop : -1.53 (0.39), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 183 
 HIS   0.009   0.001   HIS E   3 
 PHE   0.020   0.001   PHE A 111 
 TYR   0.012   0.001   TYR A  15 
 ARG   0.005   0.000   ARG A 162 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.959 
Fit side-chains
REVERT: F    1 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.5710 (pp-130)
REVERT: F   24 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.5992 (ttp80)
REVERT: A  128 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7108 (tp30)
REVERT: C   22 MET cc_start: 0.6651 (ptp) cc_final: 0.6350 (ptt)
REVERT: D    5 MET cc_start: 0.7963 (tpt) cc_final: 0.7655 (tmm)
REVERT: D   70 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8241 (m-40)
REVERT: D   73 LYS cc_start: 0.8260 (mttp) cc_final: 0.7437 (mtpt)
REVERT: G    7 TYR cc_start: 0.7494 (m-80) cc_final: 0.7235 (m-80)
REVERT: B   86 GLN cc_start: 0.6541 (OUTLIER) cc_final: 0.6076 (mt0)
REVERT: B  128 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6909 (tp30)
REVERT: B  186 ARG cc_start: 0.7614 (mtp180) cc_final: 0.7184 (mtm-85)
  outliers start: 19
  outliers final: 10
  residues processed: 125
  average time/residue: 1.5090
  time to fit residues: 198.6621
Evaluate side-chains
  128 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   24 ARG
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   80 ASP
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain C residue   24 ARG
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain D residue   70 ASN
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   86 GLN
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  237 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 47 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0980
   chunk 73 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
E  70 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.183756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.137113 restraints weight = 7470.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 1.71
r_work: 0.3399 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3263 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7925  Z= 0.250
  Angle     :  0.549   7.327  10699  Z= 0.290
  Chirality :  0.042   0.140   1236
  Planarity :  0.004   0.047   1328
  Dihedral  :  4.595  17.719   1021
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 17.33 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.27), residues: 954
  helix:  1.60 (0.20), residues: 688
  sheet: -1.98 (0.60), residues: 57
  loop : -1.54 (0.39), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 183 
 HIS   0.008   0.001   HIS E   3 
 PHE   0.019   0.001   PHE A 111 
 TYR   0.012   0.001   TYR A  15 
 ARG   0.009   0.000   ARG A 162 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 1.020 
Fit side-chains
REVERT: F    1 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.5731 (pp-130)
REVERT: F   24 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.6009 (ttp80)
REVERT: A  128 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7114 (tp30)
REVERT: C   22 MET cc_start: 0.6660 (ptp) cc_final: 0.6350 (ptt)
REVERT: D    5 MET cc_start: 0.7964 (tpt) cc_final: 0.7645 (tmm)
REVERT: D   70 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8233 (m-40)
REVERT: D   73 LYS cc_start: 0.8264 (mttp) cc_final: 0.7426 (mtpt)
REVERT: G    7 TYR cc_start: 0.7455 (m-80) cc_final: 0.7169 (m-80)
REVERT: B   80 ASP cc_start: 0.6192 (t0) cc_final: 0.5676 (t0)
REVERT: B   86 GLN cc_start: 0.6455 (mm-40) cc_final: 0.5786 (mt0)
REVERT: B  128 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6927 (tp30)
  outliers start: 15
  outliers final: 9
  residues processed: 127
  average time/residue: 1.8171
  time to fit residues: 243.1342
Evaluate side-chains
  125 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   24 ARG
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   80 ASP
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain C residue   24 ARG
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain D residue   70 ASN
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  237 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 81 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 14 optimal weight:    0.4980
   chunk 29 optimal weight:    0.1980
   chunk 60 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
E  70 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.184685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.138965 restraints weight = 7514.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 1.65
r_work: 0.3413 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7925  Z= 0.214
  Angle     :  0.530   7.196  10699  Z= 0.281
  Chirality :  0.041   0.138   1236
  Planarity :  0.004   0.047   1328
  Dihedral  :  4.528  17.410   1021
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.69 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.27), residues: 954
  helix:  1.69 (0.20), residues: 688
  sheet: -1.82 (0.61), residues: 55
  loop : -1.56 (0.39), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 183 
 HIS   0.007   0.001   HIS E   3 
 PHE   0.019   0.001   PHE A 111 
 TYR   0.010   0.001   TYR A  15 
 ARG   0.009   0.000   ARG A 162 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.943 
Fit side-chains
REVERT: F    1 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.5819 (pp-130)
REVERT: F   24 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.6022 (ttp80)
REVERT: A  128 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7125 (tp30)
REVERT: C   22 MET cc_start: 0.6607 (ptp) cc_final: 0.6298 (ptt)
REVERT: D    5 MET cc_start: 0.7946 (tpt) cc_final: 0.7631 (tmm)
REVERT: D   73 LYS cc_start: 0.8278 (mttp) cc_final: 0.7464 (mtpt)
REVERT: G    7 TYR cc_start: 0.7498 (m-80) cc_final: 0.7228 (m-80)
REVERT: B   86 GLN cc_start: 0.6547 (mm-40) cc_final: 0.6000 (mt0)
REVERT: B  128 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6920 (tp30)
REVERT: B  186 ARG cc_start: 0.7623 (mtp180) cc_final: 0.7220 (mtm-85)
  outliers start: 16
  outliers final: 10
  residues processed: 126
  average time/residue: 1.3937
  time to fit residues: 185.0243
Evaluate side-chains
  128 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   24 ARG
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   80 ASP
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain C residue   24 ARG
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  237 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 71 optimal weight:    0.5980
   chunk 59 optimal weight:    5.9990
   chunk 26 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0030
   chunk 85 optimal weight:    0.8980
   chunk 73 optimal weight:    0.3980
   chunk 51 optimal weight:    0.6980
   chunk 62 optimal weight:    0.2980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.3990

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

Flipped N/Q/H residues before XYZ refinement:
E  70 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.185049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.138453 restraints weight = 7453.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.72
r_work: 0.3425 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3288 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7925  Z= 0.194
  Angle     :  0.526   7.842  10699  Z= 0.277
  Chirality :  0.041   0.138   1236
  Planarity :  0.004   0.047   1328
  Dihedral  :  4.447  17.307   1021
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.92 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.27), residues: 954
  helix:  1.77 (0.20), residues: 687
  sheet: -1.67 (0.66), residues: 50
  loop : -1.45 (0.39), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 183 
 HIS   0.006   0.001   HIS E   3 
 PHE   0.018   0.001   PHE A 111 
 TYR   0.009   0.001   TYR A  15 
 ARG   0.009   0.000   ARG A 162 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.946 
Fit side-chains
REVERT: F   24 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.5947 (ttp80)
REVERT: A   43 ASP cc_start: 0.7049 (m-30) cc_final: 0.6813 (p0)
REVERT: A  128 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7086 (tp30)
REVERT: C   22 MET cc_start: 0.6593 (ptp) cc_final: 0.6297 (ptt)
REVERT: D    5 MET cc_start: 0.7904 (tpt) cc_final: 0.7565 (tmm)
REVERT: D   70 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8206 (m-40)
REVERT: D   73 LYS cc_start: 0.8234 (mttp) cc_final: 0.7406 (mtpt)
REVERT: G    7 TYR cc_start: 0.7509 (m-80) cc_final: 0.7189 (m-80)
REVERT: B   80 ASP cc_start: 0.6192 (t0) cc_final: 0.5723 (t0)
REVERT: B   86 GLN cc_start: 0.6468 (mm-40) cc_final: 0.5958 (mt0)
REVERT: B  128 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6921 (tp30)
REVERT: B  186 ARG cc_start: 0.7631 (mtp180) cc_final: 0.7213 (mtm-85)
  outliers start: 16
  outliers final: 10
  residues processed: 129
  average time/residue: 1.3128
  time to fit residues: 178.6320
Evaluate side-chains
  126 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ARG
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   80 ASP
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain C residue   24 ARG
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain D residue   70 ASN
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  237 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 83 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 87 optimal weight:    9.9990
   chunk 69 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
E  70 ASN
B  86 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.191172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.150241 restraints weight = 7549.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 1.72
r_work: 0.3525 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3397 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7925  Z= 0.258
  Angle     :  0.559   7.789  10699  Z= 0.294
  Chirality :  0.042   0.146   1236
  Planarity :  0.004   0.046   1328
  Dihedral  :  4.569  21.351   1021
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.04 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.27), residues: 954
  helix:  1.64 (0.19), residues: 688
  sheet: -1.92 (0.60), residues: 57
  loop : -1.49 (0.39), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 183 
 HIS   0.007   0.001   HIS E   3 
 PHE   0.019   0.001   PHE A 111 
 TYR   0.013   0.001   TYR A  15 
 ARG   0.009   0.000   ARG A 162 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6731.21 seconds
wall clock time: 118 minutes 10.64 seconds (7090.64 seconds total)