Starting phenix.real_space_refine
on Wed Feb 12 09:00:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vvi_43560/02_2025/8vvi_43560.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vvi_43560/02_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_43560/02_2025/8vvi_43560.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vvi_43560/02_2025/8vvi_43560.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vvi_43560/02_2025/8vvi_43560.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vvi_43560/02_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-5592/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: 6.72, per 1000 atoms: 0.87
  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: 1.94
  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: 0.74
  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: 2.27

  Time building geometry restraints manager: 2.25 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:             6.930
  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:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.020
  Find NCS groups from input model:        0.270
  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:             0.000
  Load rotamer database and sin/cos tables:13.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.710
-------------------------------------------------------------------------------
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  : 0.906 
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: 1.4374
  time to fit residues: 224.7983
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  : 0.781 
-------------------------------------------------------------------------------
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 = 0.158368 restraints weight = 7428.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 1.76
r_work: 0.3618 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3494 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
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  : 0.873 
Fit side-chains
REVERT: F    1 MET cc_start: 0.5729 (pp-130) cc_final: 0.5491 (pp-130)
REVERT: F   24 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.6069 (ttp80)
REVERT: F   25 ARG cc_start: 0.7675 (mmp80) cc_final: 0.6511 (ppt170)
REVERT: A  128 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6874 (mt-10)
REVERT: A  185 MET cc_start: 0.7864 (mpt) cc_final: 0.7657 (mpt)
REVERT: A  230 ARG cc_start: 0.7012 (mmp80) cc_final: 0.6785 (mmp-170)
REVERT: C   22 MET cc_start: 0.6725 (ptp) cc_final: 0.6474 (ptt)
REVERT: D    5 MET cc_start: 0.7936 (tpt) cc_final: 0.7638 (tmm)
REVERT: D   73 LYS cc_start: 0.8299 (mttp) cc_final: 0.7630 (mtpt)
REVERT: E   73 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8177 (mtmp)
REVERT: B   21 ASP cc_start: 0.8168 (m-30) cc_final: 0.7938 (m-30)
REVERT: B   80 ASP cc_start: 0.6054 (t0) cc_final: 0.5424 (t0)
REVERT: B  108 ASP cc_start: 0.8127 (m-30) cc_final: 0.7657 (m-30)
REVERT: B  128 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6857 (tp30)
  outliers start: 15
  outliers final: 3
  residues processed: 132
  average time/residue: 1.3897
  time to fit residues: 193.3193
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  : 0.834 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 70 optimal weight:    0.8980
   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:    0.0980
   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 ** 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 = 0.4188 r_free = 0.4188 target = 0.197780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.158227 restraints weight = 7539.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3790 rms_B_bonded: 1.76
r_work: 0.3614 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3493 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1887

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= 0.220
  Angle     :  0.521   5.647  10699  Z= 0.281
  Chirality :  0.041   0.141   1236
  Planarity :  0.004   0.049   1328
  Dihedral  :  4.456  17.792   1021
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 12.85 %
    Favored  : 84.79 %
  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:  1.01 (0.27), residues: 954
  helix:  1.55 (0.20), residues: 682
  sheet: -2.00 (0.73), residues: 38
  loop : -1.46 (0.38), residues: 234

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   0.011   0.001   PHE A 151 
 TYR   0.012   0.001   TYR A  15 
 ARG   0.004   0.000   ARG A 162 

*********************** 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
  137 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.895 
Fit side-chains
REVERT: F   24 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.6062 (ttp80)
REVERT: F   25 ARG cc_start: 0.7603 (mmp80) cc_final: 0.6442 (ppt170)
REVERT: A  128 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6746 (tp30)
REVERT: C   22 MET cc_start: 0.6646 (ptp) cc_final: 0.6437 (ptt)
REVERT: D    5 MET cc_start: 0.7926 (tpt) cc_final: 0.7573 (tmm)
REVERT: D   73 LYS cc_start: 0.8333 (mttp) cc_final: 0.7659 (mtpt)
REVERT: E   73 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8158 (mttp)
REVERT: G    7 TYR cc_start: 0.7579 (m-80) cc_final: 0.7334 (m-80)
REVERT: B  128 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6814 (tp30)
REVERT: B  159 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7381 (mm-30)
REVERT: B  229 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7569 (tt0)
  outliers start: 20
  outliers final: 7
  residues processed: 127
  average time/residue: 1.3977
  time to fit residues: 186.7532
Evaluate side-chains
  125 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ARG
Chi-restraints excluded: chain A residue   27 MET
Chi-restraints excluded: chain A residue   80 ASP
Chi-restraints excluded: chain C residue   24 ARG
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain B residue  128 GLU
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:    0.8980
   chunk 83 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0370
   chunk 40 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   chunk 62 optimal weight:    0.1980
   overall best weight:    0.4658

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.185317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.138731 restraints weight = 7432.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 1.71
r_work: 0.3422 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3288 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7925  Z= 0.206
  Angle     :  0.512   6.441  10699  Z= 0.274
  Chirality :  0.041   0.139   1236
  Planarity :  0.004   0.048   1328
  Dihedral  :  4.432  17.483   1021
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 13.80 %
    Favored  : 83.49 %
  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:  1.19 (0.27), residues: 954
  helix:  1.70 (0.20), residues: 683
  sheet: -2.12 (0.71), residues: 44
  loop : -1.40 (0.38), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 183 
 HIS   0.010   0.001   HIS E   3 
 PHE   0.011   0.001   PHE A 151 
 TYR   0.011   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
  146 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.880 
Fit side-chains
REVERT: F   24 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.5865 (ttp80)
REVERT: F   25 ARG cc_start: 0.7370 (mmp80) cc_final: 0.6142 (ppt170)
REVERT: A  128 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6868 (tp30)
REVERT: C   22 MET cc_start: 0.6567 (ptp) cc_final: 0.6305 (ptt)
REVERT: D    5 MET cc_start: 0.7898 (tpt) cc_final: 0.7594 (tmm)
REVERT: D   73 LYS cc_start: 0.8186 (mttp) cc_final: 0.7398 (mtpt)
REVERT: G    7 TYR cc_start: 0.7476 (m-80) cc_final: 0.7198 (m-80)
REVERT: B   80 ASP cc_start: 0.6256 (t0) cc_final: 0.5675 (t0)
REVERT: B   86 GLN cc_start: 0.6424 (OUTLIER) cc_final: 0.5809 (mm-40)
REVERT: B  128 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6708 (tp30)
REVERT: B  159 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7093 (mm-30)
  outliers start: 23
  outliers final: 7
  residues processed: 136
  average time/residue: 1.3853
  time to fit residues: 198.2669
Evaluate side-chains
  122 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 112
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ARG
Chi-restraints excluded: chain A residue   27 MET
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   86 GLN
Chi-restraints excluded: chain B residue  128 GLU
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:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 11 optimal weight:    0.2980
   chunk 78 optimal weight:    0.1980
   chunk 48 optimal weight:    0.0870
   chunk 45 optimal weight:    0.5980
   chunk 57 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.3558

-------------------------------------------------------------------------------
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 = 0.4037 r_free = 0.4037 target = 0.186410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.139921 restraints weight = 7361.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 1.72
r_work: 0.3435 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2185

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= 0.182
  Angle     :  0.504   6.752  10699  Z= 0.270
  Chirality :  0.040   0.138   1236
  Planarity :  0.004   0.048   1328
  Dihedral  :  4.369  17.032   1021
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.98 %
    Favored  : 82.55 %
  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:  1.38 (0.27), residues: 954
  helix:  1.85 (0.20), residues: 683
  sheet: -1.75 (0.65), residues: 50
  loop : -1.39 (0.39), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 183 
 HIS   0.009   0.001   HIS E   3 
 PHE   0.017   0.001   PHE A 111 
 TYR   0.009   0.001   TYR A  15 
 ARG   0.007   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
  139 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.830 
Fit side-chains
REVERT: F   24 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.5881 (ttp80)
REVERT: A  128 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6977 (tp30)
REVERT: C   22 MET cc_start: 0.6569 (ptp) cc_final: 0.6294 (ptt)
REVERT: D    5 MET cc_start: 0.7910 (tpt) cc_final: 0.7578 (tmm)
REVERT: D   73 LYS cc_start: 0.8189 (mttp) cc_final: 0.7393 (mtpt)
REVERT: G    7 TYR cc_start: 0.7492 (m-80) cc_final: 0.7226 (m-80)
REVERT: B   80 ASP cc_start: 0.6203 (t0) cc_final: 0.5614 (t0)
REVERT: B  108 ASP cc_start: 0.7674 (m-30) cc_final: 0.7343 (m-30)
  outliers start: 21
  outliers final: 12
  residues processed: 133
  average time/residue: 1.3302
  time to fit residues: 186.4659
Evaluate side-chains
  131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ARG
Chi-restraints excluded: chain A residue   27 MET
Chi-restraints excluded: chain A residue   53 GLU
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   25 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   82 THR
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:    0.6980
   chunk 29 optimal weight:    0.0770
   chunk 44 optimal weight:    0.6980
   chunk 59 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   chunk 32 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.184937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.139480 restraints weight = 7325.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 1.65
r_work: 0.3423 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7925  Z= 0.221
  Angle     :  0.527   7.026  10699  Z= 0.281
  Chirality :  0.041   0.141   1236
  Planarity :  0.004   0.047   1328
  Dihedral  :  4.453  17.280   1021
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.68 %
    Favored  : 81.37 %
  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:  1.26 (0.27), residues: 954
  helix:  1.79 (0.20), residues: 685
  sheet: -2.04 (0.60), residues: 57
  loop : -1.48 (0.39), residues: 212

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   0.020   0.001   PHE A 111 
 TYR   0.013   0.001   TYR A  15 
 ARG   0.007   0.000   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
  140 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.884 
Fit side-chains
REVERT: F    1 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5872 (pp-130)
REVERT: F   24 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.5953 (ttp80)
REVERT: A  128 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7062 (tp30)
REVERT: C   22 MET cc_start: 0.6584 (ptp) cc_final: 0.6291 (ptt)
REVERT: D    5 MET cc_start: 0.7953 (tpt) cc_final: 0.7638 (tmm)
REVERT: D   73 LYS cc_start: 0.8277 (mttp) cc_final: 0.7447 (mtpt)
REVERT: G    7 TYR cc_start: 0.7506 (m-80) cc_final: 0.7273 (m-80)
REVERT: B   80 ASP cc_start: 0.6182 (t0) cc_final: 0.5650 (t0)
REVERT: B  108 ASP cc_start: 0.7768 (m-30) cc_final: 0.7410 (m-30)
REVERT: B  128 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6839 (tp30)
  outliers start: 25
  outliers final: 9
  residues processed: 132
  average time/residue: 1.3853
  time to fit residues: 192.3239
Evaluate side-chains
  118 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
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   53 GLU
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:    0.5980
   chunk 86 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 67 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.184087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.138351 restraints weight = 7398.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 1.66
r_work: 0.3406 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.2339

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= 0.245
  Angle     :  0.541   7.206  10699  Z= 0.287
  Chirality :  0.042   0.141   1236
  Planarity :  0.004   0.047   1328
  Dihedral  :  4.531  17.403   1021
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.86 %
    Favored  : 80.66 %
  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:  1.14 (0.27), residues: 954
  helix:  1.70 (0.20), residues: 688
  sheet: -2.17 (0.66), residues: 49
  loop : -1.58 (0.38), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 183 
 HIS   0.009   0.001   HIS E   3 
 PHE   0.018   0.001   PHE A 111 
 TYR   0.013   0.001   TYR A  15 
 ARG   0.006   0.000   ARG A 230 

*********************** 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
  135 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.860 
Fit side-chains
REVERT: F    1 MET cc_start: 0.6098 (OUTLIER) cc_final: 0.5727 (pp-130)
REVERT: F   24 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.5978 (ttp80)
REVERT: A  128 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7061 (tp30)
REVERT: C   22 MET cc_start: 0.6608 (ptp) cc_final: 0.6300 (ptt)
REVERT: D    5 MET cc_start: 0.7944 (tpt) cc_final: 0.7628 (tmm)
REVERT: D   73 LYS cc_start: 0.8273 (mttp) cc_final: 0.7446 (mtpt)
REVERT: G    7 TYR cc_start: 0.7441 (m-80) cc_final: 0.7177 (m-80)
REVERT: B   86 GLN cc_start: 0.6544 (OUTLIER) cc_final: 0.6078 (mt0)
REVERT: B  128 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6904 (tp30)
  outliers start: 21
  outliers final: 10
  residues processed: 129
  average time/residue: 1.4468
  time to fit residues: 196.1762
Evaluate side-chains
  127 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
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 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    1 MET
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:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0980
   chunk 41 optimal weight:    3.9990
   chunk 65 optimal weight:    0.4980
   chunk 68 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
D  57 ASN
E  70 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.184388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.138686 restraints weight = 7450.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 1.66
r_work: 0.3409 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3273 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7925  Z= 0.235
  Angle     :  0.542   7.368  10699  Z= 0.287
  Chirality :  0.042   0.139   1236
  Planarity :  0.004   0.047   1328
  Dihedral  :  4.538  17.381   1021
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 17.92 %
    Favored  : 80.31 %
  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:  1.14 (0.27), residues: 954
  helix:  1.69 (0.20), residues: 688
  sheet: -2.09 (0.67), residues: 49
  loop : -1.60 (0.38), residues: 217

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   0.018   0.001   PHE A 111 
 TYR   0.012   0.001   TYR A  15 
 ARG   0.005   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
  126 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.828 
Fit side-chains
REVERT: F    1 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5789 (pp-130)
REVERT: F   24 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.5997 (ttp80)
REVERT: A  128 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7049 (tp30)
REVERT: A  185 MET cc_start: 0.7984 (mpt) cc_final: 0.7591 (mpt)
REVERT: C   22 MET cc_start: 0.6623 (ptp) cc_final: 0.6317 (ptt)
REVERT: D    5 MET cc_start: 0.7945 (tpt) cc_final: 0.7632 (tmm)
REVERT: D   73 LYS cc_start: 0.8285 (mttp) cc_final: 0.7457 (mtpt)
REVERT: G    7 TYR cc_start: 0.7438 (m-80) cc_final: 0.7164 (m-80)
REVERT: B   80 ASP cc_start: 0.6173 (t0) cc_final: 0.5683 (t0)
REVERT: B   86 GLN cc_start: 0.6504 (mm-40) cc_final: 0.5880 (mt0)
REVERT: B  128 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6897 (tp30)
  outliers start: 15
  outliers final: 10
  residues processed: 122
  average time/residue: 1.4840
  time to fit residues: 190.3464
Evaluate side-chains
  122 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
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  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 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:    0.9980
   chunk 81 optimal weight:    0.2980
   chunk 13 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0570
   chunk 46 optimal weight:    1.9990
   chunk 14 optimal weight:    0.1980
   chunk 29 optimal weight:    4.9990
   chunk 60 optimal weight:    0.5980
   chunk 65 optimal weight:    0.5980
   chunk 32 optimal weight:    5.9990
   overall best weight:    0.3498

-------------------------------------------------------------------------------
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 = 0.4038 r_free = 0.4038 target = 0.186573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.141108 restraints weight = 7490.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 1.66
r_work: 0.3445 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7925  Z= 0.179
  Angle     :  0.506   7.237  10699  Z= 0.269
  Chirality :  0.040   0.136   1236
  Planarity :  0.003   0.047   1328
  Dihedral  :  4.386  17.232   1021
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 18.63 %
    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:  1.39 (0.27), residues: 954
  helix:  1.86 (0.20), residues: 687
  sheet: -1.92 (0.73), residues: 44
  loop : -1.49 (0.38), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 183 
 HIS   0.007   0.001   HIS E   3 
 PHE   0.017   0.001   PHE A 111 
 TYR   0.009   0.001   TYR A 114 
 ARG   0.005   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
  126 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.880 
Fit side-chains
REVERT: F   24 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.5988 (ttp80)
REVERT: A  128 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6988 (tp30)
REVERT: C   22 MET cc_start: 0.6571 (ptp) cc_final: 0.6291 (ptt)
REVERT: D    5 MET cc_start: 0.7901 (tpt) cc_final: 0.7575 (tmm)
REVERT: D   73 LYS cc_start: 0.8242 (mttp) cc_final: 0.7455 (mtpt)
REVERT: G    7 TYR cc_start: 0.7466 (m-80) cc_final: 0.7200 (m-80)
REVERT: B   86 GLN cc_start: 0.6478 (mm-40) cc_final: 0.6016 (mt0)
  outliers start: 13
  outliers final: 9
  residues processed: 123
  average time/residue: 1.4345
  time to fit residues: 185.6092
Evaluate side-chains
  124 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
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 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  237 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 71 optimal weight:    0.0270
   chunk 59 optimal weight:    5.9990
   chunk 26 optimal weight:    0.3980
   chunk 25 optimal weight:    0.4980
   chunk 32 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0770
   chunk 85 optimal weight:    0.7980
   chunk 73 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0970
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.2194

-------------------------------------------------------------------------------
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 = 0.4146 r_free = 0.4146 target = 0.195411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.153836 restraints weight = 7547.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 1.57
r_work: 0.3568 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3443 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.2600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7925  Z= 0.163
  Angle     :  0.507   7.860  10699  Z= 0.268
  Chirality :  0.040   0.137   1236
  Planarity :  0.003   0.046   1328
  Dihedral  :  4.306  20.977   1021
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 19.10 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.53 (0.28), residues: 954
  helix:  1.97 (0.20), residues: 687
  sheet: -1.85 (0.73), residues: 44
  loop : -1.46 (0.38), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 183 
 HIS   0.006   0.000   HIS E   3 
 PHE   0.015   0.001   PHE A 111 
 TYR   0.008   0.001   TYR A 114 
 ARG   0.004   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
  129 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.806 
Fit side-chains
REVERT: F   99 ARG cc_start: 0.5491 (tmm-80) cc_final: 0.5166 (mmt180)
REVERT: A  128 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7041 (tp30)
REVERT: C   22 MET cc_start: 0.6622 (ptp) cc_final: 0.6386 (ptt)
REVERT: D    5 MET cc_start: 0.7980 (tpt) cc_final: 0.7685 (tmm)
REVERT: D   73 LYS cc_start: 0.8355 (mttp) cc_final: 0.7679 (mtpt)
REVERT: G    7 TYR cc_start: 0.7617 (m-80) cc_final: 0.7362 (m-80)
REVERT: B   80 ASP cc_start: 0.6003 (t0) cc_final: 0.5577 (t0)
REVERT: B   86 GLN cc_start: 0.6419 (OUTLIER) cc_final: 0.6044 (mt0)
REVERT: B  186 ARG cc_start: 0.7590 (mtp180) cc_final: 0.7198 (mtm-85)
  outliers start: 14
  outliers final: 10
  residues processed: 126
  average time/residue: 1.3223
  time to fit residues: 175.8116
Evaluate side-chains
  118 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  113 ARG
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 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  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:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 18 optimal weight:    0.4980
   chunk 87 optimal weight:    9.9990
   chunk 69 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4108 r_free = 0.4108 target = 0.191665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.153264 restraints weight = 7524.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 1.56
r_work: 0.3543 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3417 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7925  Z= 0.249
  Angle     :  0.550   7.688  10699  Z= 0.290
  Chirality :  0.042   0.140   1236
  Planarity :  0.004   0.046   1328
  Dihedral  :  4.484  24.443   1021
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 19.22 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.26 (0.27), residues: 954
  helix:  1.77 (0.20), residues: 688
  sheet: -2.00 (0.60), residues: 59
  loop : -1.44 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 183 
 HIS   0.007   0.001   HIS E   3 
 PHE   0.017   0.001   PHE A 111 
 TYR   0.014   0.001   TYR A  15 
 ARG   0.004   0.000   ARG A 162 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6375.04 seconds
wall clock time: 113 minutes 21.42 seconds (6801.42 seconds total)