Starting phenix.real_space_refine
on Tue Mar 11 22:13:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t06_40936/03_2025/8t06_40936.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t06_40936/03_2025/8t06_40936.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t06_40936/03_2025/8t06_40936.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t06_40936/03_2025/8t06_40936.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t06_40936/03_2025/8t06_40936.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t06_40936/03_2025/8t06_40936.cif"
  }
  resolution = 3.32
  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=   0.003 sd=   0.054
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: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      44      5.16       5
     C    4358      2.51       5
     N    1084      2.21       5
     O    1224      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 6712
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1587
          Classifications: {'peptide': 199}
          Link IDs: {'PTRANS': 8, 'TRANS': 190}
    Chain: "B"
      Number of atoms: 1587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1587
          Classifications: {'peptide': 199}
          Link IDs: {'PTRANS': 8, 'TRANS': 190}
    Chain: "C"
      Number of atoms: 936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 936
          Classifications: {'peptide': 120}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "D"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 832
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
    Chain: "E"
      Number of atoms: 936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 936
          Classifications: {'peptide': 120}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "F"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 832
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.08, per 1000 atoms: 0.76
  Number of scatterers: 6712
  At special positions: 0
  Unit cell: (87.15, 108.73, 104.58, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      44     16.00
     O    1224      8.00
     N    1084      7.00
     C    4358      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  59 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B  59 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  97 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  97 " distance=2.04

  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: 1.66
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 301 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A 184 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A 180 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A  48 "
      pdb="  ZN B 301 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B 184 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B 180 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B  48 "


  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1572

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      43.5% alpha, 27.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 14
      removed outlier: 4.285A  pdb=" N   LEU A   9 " --> pdb=" O   VAL A   5 " (cutoff:3.500A)
      Proline residue:  A  11  - end of helix
    Processing helix  chain 'A' and resid 15 through 17
      No H-bonds generated for 'chain 'A' and resid 15 through 17'
    Processing helix  chain 'A' and resid 18 through 28
    Processing helix  chain 'A' and resid 30 through 52
      removed outlier: 3.970A  pdb=" N   ASP A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 86
      removed outlier: 3.519A  pdb=" N   LEU A  66 " --> pdb=" O   ARG A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 111
    Processing helix  chain 'A' and resid 115 through 141
      Proline residue:  A 121  - end of helix
    Processing helix  chain 'A' and resid 146 through 153
    Processing helix  chain 'A' and resid 153 through 170
    Processing helix  chain 'A' and resid 171 through 174
    Processing helix  chain 'A' and resid 178 through 194
    Processing helix  chain 'A' and resid 199 through 203
    Processing helix  chain 'B' and resid 6 through 14
      Proline residue:  B  11  - end of helix
    Processing helix  chain 'B' and resid 15 through 17
      No H-bonds generated for 'chain 'B' and resid 15 through 17'
    Processing helix  chain 'B' and resid 18 through 28
    Processing helix  chain 'B' and resid 30 through 52
      removed outlier: 3.969A  pdb=" N   ASP B  51 " --> pdb=" O   SER B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 86
      removed outlier: 3.519A  pdb=" N   LEU B  66 " --> pdb=" O   ARG B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 111
    Processing helix  chain 'B' and resid 115 through 141
      Proline residue:  B 121  - end of helix
    Processing helix  chain 'B' and resid 146 through 153
    Processing helix  chain 'B' and resid 153 through 170
    Processing helix  chain 'B' and resid 171 through 174
    Processing helix  chain 'B' and resid 178 through 194
    Processing helix  chain 'B' and resid 199 through 203
    Processing helix  chain 'C' and resid 65 through 67
      No H-bonds generated for 'chain 'C' and resid 65 through 67'
    Processing helix  chain 'C' and resid 88 through 91
    Processing helix  chain 'D' and resid 79 through 83
      removed outlier: 3.566A  pdb=" N   ILE D  83 " --> pdb=" O   PRO D  80 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 65 through 67
      No H-bonds generated for 'chain 'E' and resid 65 through 67'
    Processing helix  chain 'E' and resid 88 through 91
    Processing helix  chain 'F' and resid 79 through 83
      removed outlier: 3.567A  pdb=" N   ILE F  83 " --> pdb=" O   PRO F  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12
      removed outlier: 6.980A  pdb=" N   VAL C  36 " --> pdb=" O   HIS C  52 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   HIS C  52 " --> pdb=" O   VAL C  36 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   TRP C  38 " --> pdb=" O   LEU C  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.849A  pdb=" N   TYR C 109 " --> pdb=" O   ARG C  99 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6
    Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 14
      removed outlier: 6.719A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 14
    Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12
      removed outlier: 6.980A  pdb=" N   VAL E  36 " --> pdb=" O   HIS E  52 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   HIS E  52 " --> pdb=" O   VAL E  36 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   TRP E  38 " --> pdb=" O   LEU E  50 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12
      removed outlier: 3.849A  pdb=" N   TYR E 109 " --> pdb=" O   ARG E  99 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 6
    Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 14
      removed outlier: 6.721A  pdb=" N   TRP F  35 " --> pdb=" O   LEU F  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 14

    398 hydrogen bonds defined for protein.
    1074 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.99

  Time building geometry restraints manager: 1.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1251
        1.34 -     1.46: 1807
        1.46 -     1.58: 3762
        1.58 -     1.70: 0
        1.70 -     1.82: 72
  Bond restraints: 6892
  Sorted by residual:
  bond pdb=" N   ILE D  29 "
       pdb=" CA  ILE D  29 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.041 1.09e-02 8.42e+03 1.39e+01
  bond pdb=" N   ILE F  29 "
       pdb=" CA  ILE F  29 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.041 1.09e-02 8.42e+03 1.38e+01
  bond pdb=" N   ILE D  58 "
       pdb=" CA  ILE D  58 "
    ideal  model  delta    sigma   weight residual
    1.462  1.496 -0.035 1.01e-02 9.80e+03 1.18e+01
  bond pdb=" N   VAL A 198 "
       pdb=" CA  VAL A 198 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.038 1.14e-02 7.69e+03 1.13e+01
  bond pdb=" N   SER D   7 "
       pdb=" CA  SER D   7 "
    ideal  model  delta    sigma   weight residual
    1.462  1.488 -0.026 7.70e-03 1.69e+04 1.12e+01
  ... (remaining 6887 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 5347
        1.32 -     2.64: 2720
        2.64 -     3.96: 1034
        3.96 -     5.29: 225
        5.29 -     6.61: 20
  Bond angle restraints: 9346
  Sorted by residual:
  angle pdb=" C   PHE C  54 "
        pdb=" N   TRP C  55 "
        pdb=" CA  TRP C  55 "
      ideal   model   delta    sigma   weight residual
     120.38  126.99   -6.61 1.37e+00 5.33e-01 2.33e+01
  angle pdb=" C   PHE E  54 "
        pdb=" N   TRP E  55 "
        pdb=" CA  TRP E  55 "
      ideal   model   delta    sigma   weight residual
     120.38  126.96   -6.58 1.37e+00 5.33e-01 2.31e+01
  angle pdb=" C   PHE B 160 "
        pdb=" N   GLY B 161 "
        pdb=" CA  GLY B 161 "
      ideal   model   delta    sigma   weight residual
     119.94  124.87   -4.93 1.11e+00 8.12e-01 1.97e+01
  angle pdb=" C   TYR A 115 "
        pdb=" N   GLY A 116 "
        pdb=" CA  GLY A 116 "
      ideal   model   delta    sigma   weight residual
     120.13  125.70   -5.57 1.26e+00 6.30e-01 1.95e+01
  angle pdb=" C   TYR B 115 "
        pdb=" N   GLY B 116 "
        pdb=" CA  GLY B 116 "
      ideal   model   delta    sigma   weight residual
     120.13  125.67   -5.54 1.26e+00 6.30e-01 1.93e+01
  ... (remaining 9341 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.05: 3624
       16.05 -    32.10: 326
       32.10 -    48.15: 52
       48.15 -    64.20: 26
       64.20 -    80.25: 2
  Dihedral angle restraints: 4030
    sinusoidal: 1568
      harmonic: 2462
  Sorted by residual:
  dihedral pdb=" CA  PHE B 170 "
           pdb=" C   PHE B 170 "
           pdb=" N   PHE B 171 "
           pdb=" CA  PHE B 171 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.87  -25.13     0      5.00e+00 4.00e-02 2.53e+01
  dihedral pdb=" CA  PHE A 170 "
           pdb=" C   PHE A 170 "
           pdb=" N   PHE A 171 "
           pdb=" CA  PHE A 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.01  -24.99     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  CYS B  59 "
           pdb=" C   CYS B  59 "
           pdb=" N   PHE B  60 "
           pdb=" CA  PHE B  60 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.36  -24.64     0      5.00e+00 4.00e-02 2.43e+01
  ... (remaining 4027 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 430
       0.046 -    0.092: 319
       0.092 -    0.138: 207
       0.138 -    0.184: 68
       0.184 -    0.230: 12
  Chirality restraints: 1036
  Sorted by residual:
  chirality pdb=" CA  ILE E  39 "
            pdb=" N   ILE E  39 "
            pdb=" C   ILE E  39 "
            pdb=" CB  ILE E  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  ILE C  39 "
            pdb=" N   ILE C  39 "
            pdb=" C   ILE C  39 "
            pdb=" CB  ILE C  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  ILE F  21 "
            pdb=" N   ILE F  21 "
            pdb=" C   ILE F  21 "
            pdb=" CB  ILE F  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1033 not shown)

  Planarity restraints: 1148
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 144 "   -0.021 2.00e-02 2.50e+03   1.21e-02 2.92e+00
        pdb=" CG  TYR A 144 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 144 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 144 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 144 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 144 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 144 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR A 144 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 144 "    0.021 2.00e-02 2.50e+03   1.20e-02 2.90e+00
        pdb=" CG  TYR B 144 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 144 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 144 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 144 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 144 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 144 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR B 144 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F  50 "    0.013 2.00e-02 2.50e+03   1.08e-02 2.35e+00
        pdb=" CG  TYR F  50 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR F  50 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR F  50 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR F  50 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR F  50 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR F  50 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR F  50 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1145 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 2961
        2.99 -     3.47: 6785
        3.47 -     3.94: 11304
        3.94 -     4.42: 12527
        4.42 -     4.90: 21451
  Nonbonded interactions: 55028
  Sorted by model distance:
  nonbonded pdb=" O   ASP F  82 "
            pdb=" OH  TYR F  86 "
     model   vdw
     2.510 3.040
  nonbonded pdb=" O   ASP D  82 "
            pdb=" OH  TYR D  86 "
     model   vdw
     2.511 3.040
  nonbonded pdb=" NH2 ARG C  99 "
            pdb=" OD2 ASP C 108 "
     model   vdw
     2.528 3.120
  nonbonded pdb=" N   TYR D  50 "
            pdb=" O   TYR D  50 "
     model   vdw
     2.528 2.496
  nonbonded pdb=" O   MET E 107 "
            pdb=" OH  TYR F  36 "
     model   vdw
     2.528 3.040
  ... (remaining 55023 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             2.240
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.110
  Find NCS groups from input model:        0.130
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
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      :  0.014   0.049   6892  Z= 0.881
  Angle     :  1.727   6.607   9346  Z= 1.286
  Chirality :  0.081   0.230   1036
  Planarity :  0.003   0.023   1148
  Dihedral  : 13.195  80.246   2446
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 0.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  5.60 %
    Favored  : 93.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.29), residues: 840
  helix: -1.58 (0.25), residues: 284
  sheet:  0.56 (0.36), residues: 184
  loop : -0.01 (0.36), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP E 110 
 HIS   0.008   0.002   HIS D  49 
 PHE   0.023   0.003   PHE B  43 
 TYR   0.027   0.003   TYR F  50 
 ARG   0.002   0.000   ARG E  68 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 225
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 PHE cc_start: 0.6557 (t80) cc_final: 0.6314 (m-10)
REVERT: A   63 ARG cc_start: 0.7542 (mtp85) cc_final: 0.7125 (mmm-85)
REVERT: A   67 GLU cc_start: 0.7829 (tt0) cc_final: 0.7592 (tt0)
REVERT: A  109 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.6898 (m-80)
REVERT: B   42 PHE cc_start: 0.6594 (t80) cc_final: 0.6310 (m-10)
REVERT: B   63 ARG cc_start: 0.7568 (mtp85) cc_final: 0.7163 (mmm-85)
REVERT: B   67 GLU cc_start: 0.7849 (tt0) cc_final: 0.7605 (tt0)
REVERT: B  109 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.6927 (m-80)
REVERT: B  168 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6640 (tpt-90)
REVERT: C   65 LEU cc_start: 0.8359 (mt) cc_final: 0.8066 (mt)
REVERT: C   69 LEU cc_start: 0.7860 (mp) cc_final: 0.7640 (mt)
REVERT: C   73 LYS cc_start: 0.8458 (ptmm) cc_final: 0.8212 (ptmm)
REVERT: C   99 ARG cc_start: 0.7521 (ttp-170) cc_final: 0.6798 (tmm-80)
REVERT: C  102 TRP cc_start: 0.7553 (t60) cc_final: 0.7352 (t-100)
REVERT: C  108 ASP cc_start: 0.7791 (p0) cc_final: 0.7009 (p0)
REVERT: D   22 THR cc_start: 0.7914 (m) cc_final: 0.7640 (p)
REVERT: D   42 LYS cc_start: 0.8030 (mttp) cc_final: 0.7577 (mmtp)
REVERT: D   82 ASP cc_start: 0.7584 (m-30) cc_final: 0.7270 (m-30)
REVERT: D  105 GLU cc_start: 0.6745 (tt0) cc_final: 0.6531 (tm-30)
REVERT: E   52 HIS cc_start: 0.8054 (m170) cc_final: 0.7649 (m90)
REVERT: E   69 LEU cc_start: 0.7882 (mp) cc_final: 0.7653 (mt)
REVERT: E   73 LYS cc_start: 0.8528 (ptmm) cc_final: 0.8236 (ptmm)
REVERT: E   99 ARG cc_start: 0.7522 (ttp-170) cc_final: 0.6805 (tmm-80)
REVERT: E  108 ASP cc_start: 0.7809 (p0) cc_final: 0.7050 (p0)
REVERT: F   22 THR cc_start: 0.7905 (m) cc_final: 0.7656 (p)
REVERT: F   42 LYS cc_start: 0.8060 (mttp) cc_final: 0.7605 (mmtp)
REVERT: F   82 ASP cc_start: 0.7574 (m-30) cc_final: 0.7270 (m-30)
  outliers start: 7
  outliers final: 4
  residues processed: 232
  average time/residue: 0.2075
  time to fit residues: 61.3062
Evaluate side-chains
  201 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 194
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain B residue  109 PHE
Chi-restraints excluded: chain B residue  168 ARG
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain D residue   33 ILE
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain F residue   33 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 24 optimal weight:    6.9990
   chunk 39 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 152 GLN
B 152 GLN
D  27 GLN
F  27 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.160368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.112530 restraints weight = 8951.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.73
r_work: 0.3190 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6892  Z= 0.214
  Angle     :  0.631   5.843   9346  Z= 0.328
  Chirality :  0.044   0.154   1036
  Planarity :  0.004   0.030   1148
  Dihedral  :  6.831  54.361    940
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 11.75 %
    Favored  : 85.52 %
  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:  1.13 (0.30), residues: 840
  helix:  1.03 (0.29), residues: 290
  sheet:  0.83 (0.35), residues: 224
  loop :  0.65 (0.40), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 110 
 HIS   0.003   0.001   HIS B  48 
 PHE   0.018   0.002   PHE D  73 
 TYR   0.015   0.001   TYR D  91 
 ARG   0.003   0.000   ARG A  93 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 210
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 GLU cc_start: 0.8296 (tt0) cc_final: 0.8094 (tt0)
REVERT: A  178 TYR cc_start: 0.7851 (m-80) cc_final: 0.7571 (m-80)
REVERT: B  109 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8007 (m-80)
REVERT: B  178 TYR cc_start: 0.7825 (m-80) cc_final: 0.7335 (m-80)
REVERT: C   58 ASP cc_start: 0.8474 (t70) cc_final: 0.8102 (t0)
REVERT: C   88 ASP cc_start: 0.7575 (t0) cc_final: 0.7350 (t70)
REVERT: C  108 ASP cc_start: 0.8871 (p0) cc_final: 0.8271 (p0)
REVERT: C  109 TYR cc_start: 0.8595 (m-80) cc_final: 0.8329 (m-80)
REVERT: E   18 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8594 (pt)
REVERT: E   58 ASP cc_start: 0.8495 (t70) cc_final: 0.8117 (t0)
REVERT: E  108 ASP cc_start: 0.8861 (p0) cc_final: 0.8269 (p0)
REVERT: E  109 TYR cc_start: 0.8597 (m-80) cc_final: 0.8335 (m-80)
  outliers start: 20
  outliers final: 10
  residues processed: 216
  average time/residue: 0.2213
  time to fit residues: 61.1742
Evaluate side-chains
  199 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 187
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain B residue  109 PHE
Chi-restraints excluded: chain B residue  170 PHE
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   33 ILE
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   68 ARG
Chi-restraints excluded: chain F residue    5 THR
Chi-restraints excluded: chain F residue   33 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0770
   chunk 42 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    0.7542

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

Flipped N/Q/H residues before XYZ refinement:
A 110 HIS
B 110 HIS
C  16 GLN
D  77 ASN
E  16 GLN
F  77 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.160765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.112764 restraints weight = 9082.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.68
r_work: 0.3198 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6892  Z= 0.192
  Angle     :  0.587   8.270   9346  Z= 0.298
  Chirality :  0.043   0.147   1036
  Planarity :  0.004   0.036   1148
  Dihedral  :  6.514  53.133    936
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 13.52 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.78 (0.31), residues: 840
  helix:  1.82 (0.29), residues: 288
  sheet:  1.19 (0.36), residues: 216
  loop :  0.75 (0.40), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 110 
 HIS   0.003   0.001   HIS A 110 
 PHE   0.016   0.001   PHE B  39 
 TYR   0.011   0.001   TYR D  91 
 ARG   0.006   0.000   ARG B  63 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 189
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.8390 (mmm-85) cc_final: 0.8175 (mmm-85)
REVERT: A  109 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.7639 (m-80)
REVERT: A  178 TYR cc_start: 0.7836 (m-80) cc_final: 0.7520 (m-80)
REVERT: B  109 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.7647 (m-80)
REVERT: B  178 TYR cc_start: 0.7825 (m-80) cc_final: 0.7528 (m-80)
REVERT: C   58 ASP cc_start: 0.8342 (t70) cc_final: 0.8066 (t0)
REVERT: C   88 ASP cc_start: 0.7600 (t0) cc_final: 0.7307 (t70)
REVERT: E   58 ASP cc_start: 0.8408 (t70) cc_final: 0.8038 (t0)
REVERT: E   83 MET cc_start: 0.7587 (mpp) cc_final: 0.7210 (mpp)
REVERT: F  105 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6583 (tm-30)
  outliers start: 19
  outliers final: 10
  residues processed: 198
  average time/residue: 0.2161
  time to fit residues: 54.5235
Evaluate side-chains
  197 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 185
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain B residue  109 PHE
Chi-restraints excluded: chain B residue  170 PHE
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   33 ILE
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   68 ARG
Chi-restraints excluded: chain F residue   33 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 50 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 110 HIS
B 110 HIS
C  16 GLN
E  16 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.158036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.109483 restraints weight = 9166.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 2.68
r_work: 0.3148 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.3538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6892  Z= 0.282
  Angle     :  0.621   6.547   9346  Z= 0.317
  Chirality :  0.045   0.157   1036
  Planarity :  0.004   0.034   1148
  Dihedral  :  6.615  58.358    936
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 13.93 %
    Favored  : 82.79 %
  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:  1.68 (0.30), residues: 840
  helix:  1.90 (0.29), residues: 286
  sheet:  1.21 (0.36), residues: 216
  loop :  0.47 (0.39), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 110 
 HIS   0.007   0.001   HIS B 110 
 PHE   0.021   0.002   PHE A  39 
 TYR   0.013   0.001   TYR A  72 
 ARG   0.006   0.000   ARG B  63 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 197
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.7542 (m-80)
REVERT: A  178 TYR cc_start: 0.7899 (m-80) cc_final: 0.7594 (m-80)
REVERT: B  109 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.7597 (m-80)
REVERT: B  178 TYR cc_start: 0.7878 (m-80) cc_final: 0.7557 (m-80)
REVERT: C   41 LYS cc_start: 0.9160 (tttm) cc_final: 0.8950 (tptp)
REVERT: C   88 ASP cc_start: 0.7614 (t0) cc_final: 0.7323 (t70)
REVERT: D  107 LYS cc_start: 0.4906 (tptt) cc_final: 0.4673 (tptt)
REVERT: E   88 ASP cc_start: 0.7651 (t0) cc_final: 0.7360 (t70)
  outliers start: 24
  outliers final: 12
  residues processed: 208
  average time/residue: 0.2234
  time to fit residues: 59.3039
Evaluate side-chains
  200 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 186
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain B residue  109 PHE
Chi-restraints excluded: chain B residue  170 PHE
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   68 ARG
Chi-restraints excluded: chain F residue    5 THR
Chi-restraints excluded: chain F residue   20 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   chunk 76 optimal weight:    0.8980
   chunk 63 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 110 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.159413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.111686 restraints weight = 9046.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 2.67
r_work: 0.3196 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.3857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6892  Z= 0.211
  Angle     :  0.604   6.384   9346  Z= 0.303
  Chirality :  0.044   0.152   1036
  Planarity :  0.004   0.035   1148
  Dihedral  :  5.887  53.498    932
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 16.39 %
    Favored  : 81.42 %
  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:  1.87 (0.31), residues: 840
  helix:  2.10 (0.29), residues: 296
  sheet:  1.34 (0.36), residues: 216
  loop :  0.48 (0.40), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 110 
 HIS   0.008   0.001   HIS A 110 
 PHE   0.016   0.001   PHE B  39 
 TYR   0.010   0.001   TYR D  91 
 ARG   0.006   0.000   ARG B  63 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 194
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.7371 (m-80)
REVERT: A  170 PHE cc_start: 0.7580 (m-10) cc_final: 0.7266 (m-10)
REVERT: A  178 TYR cc_start: 0.7877 (m-80) cc_final: 0.7541 (m-80)
REVERT: B  109 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.7359 (m-80)
REVERT: B  170 PHE cc_start: 0.7589 (m-80) cc_final: 0.7294 (m-10)
REVERT: B  178 TYR cc_start: 0.7847 (m-80) cc_final: 0.7514 (m-80)
REVERT: C   60 ARG cc_start: 0.8103 (tpp-160) cc_final: 0.7694 (ttm110)
REVERT: C   88 ASP cc_start: 0.7609 (t0) cc_final: 0.7311 (t70)
REVERT: D  105 GLU cc_start: 0.6489 (tm-30) cc_final: 0.6126 (tm-30)
REVERT: E   16 GLN cc_start: 0.7561 (tt0) cc_final: 0.6971 (mt0)
REVERT: E   88 ASP cc_start: 0.7624 (t0) cc_final: 0.7397 (t70)
  outliers start: 16
  outliers final: 9
  residues processed: 202
  average time/residue: 0.2079
  time to fit residues: 53.9654
Evaluate side-chains
  195 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 184
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain B residue  109 PHE
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   48 GLU
Chi-restraints excluded: chain E residue   68 ARG
Chi-restraints excluded: chain F residue    5 THR
Chi-restraints excluded: chain F residue   20 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 75 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 40 optimal weight:    6.9990
   chunk 71 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 37 optimal weight:    0.5980
   chunk 69 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
D  30 ASN
F  30 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.161104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.113729 restraints weight = 9046.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.64
r_work: 0.3228 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.4077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6892  Z= 0.189
  Angle     :  0.580   7.111   9346  Z= 0.292
  Chirality :  0.043   0.154   1036
  Planarity :  0.004   0.036   1148
  Dihedral  :  5.779  52.224    932
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 16.39 %
    Favored  : 81.28 %
  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:  1.89 (0.30), residues: 840
  helix:  2.43 (0.29), residues: 288
  sheet:  1.28 (0.35), residues: 216
  loop :  0.26 (0.39), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 110 
 HIS   0.003   0.001   HIS C  52 
 PHE   0.015   0.001   PHE B  39 
 TYR   0.010   0.001   TYR C 109 
 ARG   0.006   0.000   ARG A  63 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 195
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 PHE cc_start: 0.7586 (m-10) cc_final: 0.7319 (m-10)
REVERT: A  178 TYR cc_start: 0.7869 (m-80) cc_final: 0.7540 (m-80)
REVERT: B  170 PHE cc_start: 0.7597 (m-80) cc_final: 0.7314 (m-10)
REVERT: B  178 TYR cc_start: 0.7853 (m-80) cc_final: 0.7356 (m-80)
REVERT: C   60 ARG cc_start: 0.8112 (tpp-160) cc_final: 0.7747 (ttm110)
REVERT: C   88 ASP cc_start: 0.7591 (t0) cc_final: 0.7357 (t70)
REVERT: D  105 GLU cc_start: 0.6753 (tm-30) cc_final: 0.6460 (tm-30)
REVERT: E   88 ASP cc_start: 0.7610 (t0) cc_final: 0.7388 (t70)
REVERT: F  105 GLU cc_start: 0.6836 (tm-30) cc_final: 0.6456 (tm-30)
  outliers start: 17
  outliers final: 13
  residues processed: 204
  average time/residue: 0.2106
  time to fit residues: 55.1917
Evaluate side-chains
  201 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 188
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain B residue  109 PHE
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   48 GLU
Chi-restraints excluded: chain E residue   68 ARG
Chi-restraints excluded: chain F residue    5 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 67 optimal weight:    0.1980
   chunk 50 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 68 optimal weight:    7.9990
   chunk 18 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.161920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.119748 restraints weight = 9003.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 2.63
r_work: 0.3222 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.4256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6892  Z= 0.194
  Angle     :  0.590   7.227   9346  Z= 0.294
  Chirality :  0.043   0.150   1036
  Planarity :  0.004   0.037   1148
  Dihedral  :  5.701  51.366    932
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.49 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.93 (0.30), residues: 840
  helix:  2.54 (0.29), residues: 288
  sheet:  1.27 (0.35), residues: 218
  loop :  0.22 (0.38), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 110 
 HIS   0.003   0.001   HIS C  52 
 PHE   0.015   0.001   PHE B  39 
 TYR   0.008   0.001   TYR B  72 
 ARG   0.005   0.000   ARG A  63 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 191
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 PHE cc_start: 0.7574 (m-10) cc_final: 0.7336 (m-10)
REVERT: A  178 TYR cc_start: 0.7864 (m-80) cc_final: 0.7533 (m-80)
REVERT: B  170 PHE cc_start: 0.7583 (m-80) cc_final: 0.7318 (m-10)
REVERT: C   16 GLN cc_start: 0.8070 (tt0) cc_final: 0.7146 (mt0)
REVERT: C   60 ARG cc_start: 0.8154 (tpp-160) cc_final: 0.7764 (ttm110)
REVERT: C   83 MET cc_start: 0.7365 (mpp) cc_final: 0.6774 (mpp)
REVERT: C   88 ASP cc_start: 0.7588 (t0) cc_final: 0.7340 (t70)
REVERT: C  104 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8606 (pp)
REVERT: D  105 GLU cc_start: 0.6885 (tm-30) cc_final: 0.6556 (tm-30)
REVERT: E   88 ASP cc_start: 0.7526 (t0) cc_final: 0.7313 (t70)
REVERT: F  105 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6342 (tm-30)
  outliers start: 19
  outliers final: 10
  residues processed: 201
  average time/residue: 0.2159
  time to fit residues: 55.2304
Evaluate side-chains
  195 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 184
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   48 GLU
Chi-restraints excluded: chain E residue   68 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 56 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9980
   chunk 1 optimal weight:    0.1980
   chunk 60 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 7 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 39 optimal weight:    6.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.161297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.113495 restraints weight = 8999.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 2.63
r_work: 0.3225 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.4324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6892  Z= 0.210
  Angle     :  0.600   8.401   9346  Z= 0.301
  Chirality :  0.043   0.149   1036
  Planarity :  0.004   0.038   1148
  Dihedral  :  5.156  49.904    928
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 18.85 %
    Favored  : 79.51 %
  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:  1.92 (0.30), residues: 840
  helix:  2.52 (0.29), residues: 288
  sheet:  1.31 (0.35), residues: 218
  loop :  0.19 (0.38), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C  55 
 HIS   0.003   0.001   HIS C  52 
 PHE   0.016   0.001   PHE B  39 
 TYR   0.009   0.001   TYR B  72 
 ARG   0.008   0.000   ARG A  63 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 194
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 PHE cc_start: 0.7604 (m-10) cc_final: 0.7366 (m-10)
REVERT: A  178 TYR cc_start: 0.7866 (m-80) cc_final: 0.7533 (m-80)
REVERT: B  170 PHE cc_start: 0.7567 (m-80) cc_final: 0.7309 (m-10)
REVERT: B  178 TYR cc_start: 0.7849 (m-80) cc_final: 0.7367 (m-80)
REVERT: C   60 ARG cc_start: 0.8134 (tpp-160) cc_final: 0.7715 (ttm110)
REVERT: C   83 MET cc_start: 0.7235 (mpp) cc_final: 0.6591 (mpp)
REVERT: C   88 ASP cc_start: 0.7558 (t0) cc_final: 0.7325 (t70)
REVERT: D   79 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8530 (mm-30)
REVERT: D   92 ASP cc_start: 0.8706 (t0) cc_final: 0.8504 (t0)
REVERT: D  105 GLU cc_start: 0.6806 (tm-30) cc_final: 0.6491 (tm-30)
REVERT: D  107 LYS cc_start: 0.4658 (tptt) cc_final: 0.4435 (tptt)
REVERT: E   73 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8515 (mtmm)
REVERT: E   88 ASP cc_start: 0.7545 (t0) cc_final: 0.7322 (t70)
REVERT: F  105 GLU cc_start: 0.6930 (tm-30) cc_final: 0.6518 (tm-30)
  outliers start: 12
  outliers final: 10
  residues processed: 200
  average time/residue: 0.2445
  time to fit residues: 62.0339
Evaluate side-chains
  200 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 190
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   48 GLU
Chi-restraints excluded: chain E residue   68 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 12 optimal weight:    0.4980
   chunk 68 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 41 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 39 optimal weight:    0.1980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.162254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.114766 restraints weight = 9068.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 2.64
r_work: 0.3246 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.4463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6892  Z= 0.193
  Angle     :  0.594   7.741   9346  Z= 0.297
  Chirality :  0.043   0.151   1036
  Planarity :  0.004   0.038   1148
  Dihedral  :  5.083  52.127    928
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.85 %
    Favored  : 78.96 %
  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:  1.96 (0.30), residues: 840
  helix:  2.61 (0.29), residues: 288
  sheet:  1.34 (0.36), residues: 218
  loop :  0.13 (0.38), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP C  55 
 HIS   0.003   0.001   HIS C  52 
 PHE   0.014   0.001   PHE A  39 
 TYR   0.008   0.001   TYR F  91 
 ARG   0.006   0.000   ARG B  63 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 194
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 PHE cc_start: 0.7600 (m-10) cc_final: 0.7384 (m-10)
REVERT: A  178 TYR cc_start: 0.7869 (m-80) cc_final: 0.7533 (m-80)
REVERT: B  170 PHE cc_start: 0.7587 (m-80) cc_final: 0.7344 (m-10)
REVERT: C    5 LYS cc_start: 0.8509 (mmmm) cc_final: 0.8242 (mmtp)
REVERT: C   60 ARG cc_start: 0.8174 (tpp-160) cc_final: 0.7699 (ttm110)
REVERT: C   83 MET cc_start: 0.7131 (mpp) cc_final: 0.6568 (mpp)
REVERT: D   79 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8668 (mp0)
REVERT: D   92 ASP cc_start: 0.8669 (t0) cc_final: 0.8462 (t0)
REVERT: D  105 GLU cc_start: 0.6828 (tm-30) cc_final: 0.6519 (tm-30)
REVERT: E   41 LYS cc_start: 0.9039 (tptm) cc_final: 0.8766 (tptt)
REVERT: E   66 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7626 (mttm)
REVERT: E   73 LYS cc_start: 0.8722 (mtpp) cc_final: 0.8487 (ttmm)
REVERT: E   88 ASP cc_start: 0.7441 (t0) cc_final: 0.7236 (t70)
REVERT: F  105 GLU cc_start: 0.6855 (tm-30) cc_final: 0.6554 (tm-30)
  outliers start: 16
  outliers final: 10
  residues processed: 202
  average time/residue: 0.2152
  time to fit residues: 55.2948
Evaluate side-chains
  199 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 188
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   48 GLU
Chi-restraints excluded: chain E residue   66 LYS
Chi-restraints excluded: chain E residue   68 ARG
Chi-restraints excluded: chain E residue   82 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 35 optimal weight:    4.9990
   chunk 50 optimal weight:    0.4980
   chunk 30 optimal weight:    0.0770
   chunk 38 optimal weight:    5.9990
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.5138

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.163737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.119395 restraints weight = 9087.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 2.46
r_work: 0.3243 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.4635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6892  Z= 0.180
  Angle     :  0.579   7.574   9346  Z= 0.292
  Chirality :  0.042   0.155   1036
  Planarity :  0.005   0.049   1148
  Dihedral  :  5.180  54.058    928
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 19.40 %
    Favored  : 78.96 %
  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:  2.08 (0.31), residues: 840
  helix:  2.68 (0.29), residues: 288
  sheet:  1.62 (0.36), residues: 210
  loop :  0.10 (0.38), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP C  55 
 HIS   0.002   0.001   HIS E 105 
 PHE   0.014   0.001   PHE B  39 
 TYR   0.010   0.001   TYR F  91 
 ARG   0.008   0.000   ARG B  63 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 193
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 PHE cc_start: 0.7610 (m-80) cc_final: 0.7371 (m-10)
REVERT: C    5 LYS cc_start: 0.8490 (mmmm) cc_final: 0.8215 (mmtp)
REVERT: C   16 GLN cc_start: 0.8146 (tt0) cc_final: 0.7582 (mt0)
REVERT: C   60 ARG cc_start: 0.8130 (tpp-160) cc_final: 0.7671 (ttm110)
REVERT: C   83 MET cc_start: 0.7266 (mpp) cc_final: 0.6678 (mpp)
REVERT: D  105 GLU cc_start: 0.6762 (tm-30) cc_final: 0.6483 (tm-30)
REVERT: E   16 GLN cc_start: 0.8123 (tt0) cc_final: 0.7572 (mt0)
REVERT: E   41 LYS cc_start: 0.9021 (tptm) cc_final: 0.8750 (tptt)
REVERT: E   73 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8511 (ttmm)
REVERT: E   88 ASP cc_start: 0.7587 (t0) cc_final: 0.7315 (t70)
REVERT: F   94 LEU cc_start: 0.8350 (mm) cc_final: 0.8127 (mm)
REVERT: F  105 GLU cc_start: 0.6874 (tm-30) cc_final: 0.6594 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 199
  average time/residue: 0.2108
  time to fit residues: 53.3433
Evaluate side-chains
  200 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 191
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   96 TYR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   48 GLU
Chi-restraints excluded: chain F residue    5 THR
Chi-restraints excluded: chain F residue   52 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 65 optimal weight:    0.0980
   chunk 31 optimal weight:    0.6980
   chunk 48 optimal weight:    5.9990
   chunk 77 optimal weight:    0.0670
   chunk 42 optimal weight:    0.5980
   chunk 51 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 56 optimal weight:    7.9990
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
B 110 HIS
C  13 GLN
D  30 ASN
E  79 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.163882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.116381 restraints weight = 8994.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 2.62
r_work: 0.3267 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.4761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6892  Z= 0.176
  Angle     :  0.596   7.843   9346  Z= 0.297
  Chirality :  0.042   0.209   1036
  Planarity :  0.004   0.039   1148
  Dihedral  :  4.761  55.114    926
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 19.95 %
    Favored  : 78.83 %
  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:  2.11 (0.31), residues: 840
  helix:  2.76 (0.29), residues: 288
  sheet:  1.61 (0.36), residues: 210
  loop :  0.08 (0.38), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP C  55 
 HIS   0.011   0.001   HIS B 110 
 PHE   0.013   0.001   PHE A  39 
 TYR   0.007   0.001   TYR C 109 
 ARG   0.008   0.001   ARG A  63 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3682.39 seconds
wall clock time: 63 minutes 57.97 seconds (3837.97 seconds total)