Starting phenix.real_space_refine
on Thu Nov 14 16:24:31 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t06_40936/11_2024/8t06_40936.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t06_40936/11_2024/8t06_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t06_40936/11_2024/8t06_40936.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t06_40936/11_2024/8t06_40936.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t06_40936/11_2024/8t06_40936.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t06_40936/11_2024/8t06_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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 4.78, per 1000 atoms: 0.71
  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: 1.70
  Conformation dependent library (CDL) restraints added in 998.8 milliseconds
  
  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: 0.92
  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: 2.13

  Time building geometry restraints manager: 1.98 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}

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:             1.700
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     21.290
  Find NCS groups from input model:        0.190
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.540
-------------------------------------------------------------------------------
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  : 0.789 
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: 0.2139
  time to fit residues: 63.0587
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  : 0.725 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
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  : 0.720 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 GLU cc_start: 0.7790 (tt0) cc_final: 0.7517 (tt0)
REVERT: A  178 TYR cc_start: 0.7075 (m-80) cc_final: 0.6785 (m-80)
REVERT: B   67 GLU cc_start: 0.7794 (tt0) cc_final: 0.7522 (tt0)
REVERT: B  109 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.6808 (m-80)
REVERT: B  178 TYR cc_start: 0.7081 (m-80) cc_final: 0.6603 (m-80)
REVERT: C   41 LYS cc_start: 0.8828 (tttt) cc_final: 0.8464 (tttp)
REVERT: C   55 TRP cc_start: 0.7603 (p90) cc_final: 0.7367 (p90)
REVERT: C   58 ASP cc_start: 0.7793 (t70) cc_final: 0.7284 (t0)
REVERT: C   70 THR cc_start: 0.7905 (p) cc_final: 0.7674 (p)
REVERT: C   99 ARG cc_start: 0.7767 (ttp-170) cc_final: 0.7314 (tmm-80)
REVERT: C  102 TRP cc_start: 0.7938 (t60) cc_final: 0.7501 (t-100)
REVERT: C  108 ASP cc_start: 0.8451 (p0) cc_final: 0.7681 (p0)
REVERT: C  109 TYR cc_start: 0.8018 (m-80) cc_final: 0.7608 (m-80)
REVERT: D   31 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7982 (mt-10)
REVERT: D   42 LYS cc_start: 0.8004 (mttp) cc_final: 0.7671 (mmtm)
REVERT: D   77 ASN cc_start: 0.7956 (m110) cc_final: 0.7587 (p0)
REVERT: E   18 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8813 (pt)
REVERT: E   41 LYS cc_start: 0.8793 (tttt) cc_final: 0.8447 (tttp)
REVERT: E   58 ASP cc_start: 0.7907 (t70) cc_final: 0.7348 (t0)
REVERT: E   99 ARG cc_start: 0.7734 (ttp-170) cc_final: 0.7284 (tmm-80)
REVERT: E  102 TRP cc_start: 0.7937 (t60) cc_final: 0.7519 (t-100)
REVERT: E  108 ASP cc_start: 0.8450 (p0) cc_final: 0.7675 (p0)
REVERT: E  109 TYR cc_start: 0.8004 (m-80) cc_final: 0.7606 (m-80)
REVERT: F   31 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7962 (mt-10)
REVERT: F   42 LYS cc_start: 0.7991 (mttp) cc_final: 0.7658 (mmtm)
REVERT: F   77 ASN cc_start: 0.7948 (m110) cc_final: 0.7610 (p0)
REVERT: F   82 ASP cc_start: 0.7626 (m-30) cc_final: 0.7410 (m-30)
  outliers start: 20
  outliers final: 10
  residues processed: 216
  average time/residue: 0.2161
  time to fit residues: 59.5267
Evaluate side-chains
  204 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 192
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
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 41 optimal weight:   10.0000
   chunk 23 optimal weight:    0.7980
   chunk 61 optimal weight:    7.9990
   chunk 50 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 74 optimal weight:    0.3980
   chunk 80 optimal weight:    0.4980
   chunk 66 optimal weight:    0.0980
   chunk 73 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.4780

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6992
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6892  Z= 0.157
  Angle     :  0.565   8.311   9346  Z= 0.284
  Chirality :  0.042   0.152   1036
  Planarity :  0.004   0.036   1148
  Dihedral  :  6.415  52.751    936
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 13.11 %
    Favored  : 84.70 %
  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:  1.84 (0.31), residues: 840
  helix:  2.10 (0.29), residues: 280
  sheet:  1.13 (0.36), residues: 220
  loop :  0.65 (0.40), residues: 340

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   0.017   0.001   PHE A  43 
 TYR   0.009   0.001   TYR D  91 
 ARG   0.004   0.000   ARG A  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
  210 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 194
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.7752 (mmm-85) cc_final: 0.7239 (mmm-85)
REVERT: A   67 GLU cc_start: 0.7880 (tt0) cc_final: 0.7542 (tt0)
REVERT: A  109 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.6098 (m-80)
REVERT: A  178 TYR cc_start: 0.7082 (m-80) cc_final: 0.6601 (m-80)
REVERT: B   63 ARG cc_start: 0.7769 (mmm-85) cc_final: 0.7202 (mmm-85)
REVERT: B   67 GLU cc_start: 0.7877 (tt0) cc_final: 0.7538 (tt0)
REVERT: B  109 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.6122 (m-80)
REVERT: C   41 LYS cc_start: 0.8740 (tttt) cc_final: 0.8422 (tttp)
REVERT: C   58 ASP cc_start: 0.7633 (t70) cc_final: 0.7121 (t70)
REVERT: C   99 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7408 (tmm-80)
REVERT: C  102 TRP cc_start: 0.8064 (t60) cc_final: 0.7648 (t-100)
REVERT: C  108 ASP cc_start: 0.8540 (p0) cc_final: 0.7688 (p0)
REVERT: D   31 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7955 (mt-10)
REVERT: D   42 LYS cc_start: 0.7689 (mttp) cc_final: 0.7422 (mmtm)
REVERT: D   77 ASN cc_start: 0.7943 (m110) cc_final: 0.7524 (p0)
REVERT: D  105 GLU cc_start: 0.6778 (tt0) cc_final: 0.6468 (tm-30)
REVERT: E   41 LYS cc_start: 0.8683 (tttt) cc_final: 0.8399 (tttp)
REVERT: E   58 ASP cc_start: 0.7778 (t70) cc_final: 0.7237 (t0)
REVERT: E   83 MET cc_start: 0.7541 (mpp) cc_final: 0.7288 (mpp)
REVERT: E   99 ARG cc_start: 0.7836 (ttp-170) cc_final: 0.7354 (tmm-80)
REVERT: E  102 TRP cc_start: 0.8026 (t60) cc_final: 0.7618 (t-100)
REVERT: E  108 ASP cc_start: 0.8535 (p0) cc_final: 0.7652 (p0)
REVERT: F   31 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7871 (mt-10)
REVERT: F   42 LYS cc_start: 0.7701 (mttp) cc_final: 0.7430 (mmtm)
REVERT: F   77 ASN cc_start: 0.7934 (m110) cc_final: 0.7548 (p0)
REVERT: F   82 ASP cc_start: 0.7700 (m-30) cc_final: 0.7475 (m-30)
REVERT: F   87 TYR cc_start: 0.8736 (m-80) cc_final: 0.8522 (m-80)
REVERT: F  105 GLU cc_start: 0.6698 (tm-30) cc_final: 0.6172 (tm-30)
  outliers start: 16
  outliers final: 8
  residues processed: 201
  average time/residue: 0.2318
  time to fit residues: 58.3742
Evaluate side-chains
  199 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 189
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
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   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 73 optimal weight:    6.9990
   chunk 56 optimal weight:    0.0070
   chunk 38 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 35 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 74 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 39 optimal weight:   20.0000
   chunk 70 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.5002

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   6892  Z= 0.303
  Angle     :  0.617   7.755   9346  Z= 0.314
  Chirality :  0.045   0.153   1036
  Planarity :  0.004   0.036   1148
  Dihedral  :  6.590  58.544    936
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.21 %
    Favored  : 82.92 %
  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:  1.75 (0.31), residues: 840
  helix:  1.93 (0.29), residues: 284
  sheet:  1.11 (0.36), residues: 218
  loop :  0.68 (0.40), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 110 
 HIS   0.007   0.001   HIS A 110 
 PHE   0.022   0.002   PHE A  39 
 TYR   0.014   0.002   TYR A  72 
 ARG   0.002   0.000   ARG A  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
  225 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 204
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.7733 (mmm-85) cc_final: 0.7214 (mmm-85)
REVERT: A   67 GLU cc_start: 0.7916 (tt0) cc_final: 0.7508 (tt0)
REVERT: A  109 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.6450 (m-80)
REVERT: A  178 TYR cc_start: 0.7166 (m-80) cc_final: 0.6847 (m-80)
REVERT: B   63 ARG cc_start: 0.7735 (mmm-85) cc_final: 0.7370 (mmm-85)
REVERT: B   67 GLU cc_start: 0.7919 (tt0) cc_final: 0.7715 (tt0)
REVERT: B  109 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.6487 (m-80)
REVERT: B  178 TYR cc_start: 0.7179 (m-80) cc_final: 0.6866 (m-80)
REVERT: C   41 LYS cc_start: 0.8762 (tttt) cc_final: 0.8438 (tttp)
REVERT: C   73 LYS cc_start: 0.8659 (mtmm) cc_final: 0.8421 (mtmm)
REVERT: C   88 ASP cc_start: 0.6932 (t70) cc_final: 0.6530 (t70)
REVERT: D   31 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7989 (mt-10)
REVERT: D   42 LYS cc_start: 0.7701 (mttp) cc_final: 0.7431 (mmtm)
REVERT: D   61 ARG cc_start: 0.8496 (ptt-90) cc_final: 0.8264 (ptt-90)
REVERT: D   77 ASN cc_start: 0.7933 (m110) cc_final: 0.7507 (p0)
REVERT: D  105 GLU cc_start: 0.6766 (tt0) cc_final: 0.6551 (tm-30)
REVERT: E   41 LYS cc_start: 0.8723 (tttt) cc_final: 0.8398 (tttp)
REVERT: E   83 MET cc_start: 0.7591 (mpp) cc_final: 0.7305 (mpp)
REVERT: E   88 ASP cc_start: 0.7286 (t0) cc_final: 0.6994 (t70)
REVERT: F   31 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7976 (mt-10)
REVERT: F   42 LYS cc_start: 0.7730 (mttp) cc_final: 0.7461 (mmtm)
REVERT: F   77 ASN cc_start: 0.7921 (m110) cc_final: 0.7497 (p0)
REVERT: F  105 GLU cc_start: 0.6720 (tm-30) cc_final: 0.6341 (tm-30)
  outliers start: 21
  outliers final: 8
  residues processed: 215
  average time/residue: 0.2267
  time to fit residues: 61.6005
Evaluate side-chains
  203 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 193
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 44 optimal weight:    0.4980
   chunk 1 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 67 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.9982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
moved from start:          0.3612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6892  Z= 0.229
  Angle     :  0.594   7.783   9346  Z= 0.297
  Chirality :  0.044   0.158   1036
  Planarity :  0.004   0.036   1148
  Dihedral  :  5.952  54.487    932
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 15.85 %
    Favored  : 82.38 %
  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:  1.85 (0.31), residues: 840
  helix:  2.03 (0.28), residues: 296
  sheet:  1.19 (0.36), residues: 220
  loop :  0.63 (0.42), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 110 
 HIS   0.003   0.001   HIS C  52 
 PHE   0.017   0.001   PHE B  39 
 TYR   0.011   0.001   TYR D  91 
 ARG   0.003   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
  211 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 198
  time to evaluate  : 0.767 
Fit side-chains
REVERT: A   63 ARG cc_start: 0.7705 (mmm-85) cc_final: 0.7254 (mmm-85)
REVERT: A   67 GLU cc_start: 0.7874 (tt0) cc_final: 0.7439 (tt0)
REVERT: A  109 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.6293 (m-80)
REVERT: A  170 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.7039 (m-10)
REVERT: A  178 TYR cc_start: 0.7163 (m-80) cc_final: 0.6844 (m-80)
REVERT: B   63 ARG cc_start: 0.7714 (mmm-85) cc_final: 0.7267 (mmm-85)
REVERT: B   67 GLU cc_start: 0.7876 (tt0) cc_final: 0.7440 (tt0)
REVERT: B  109 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.6288 (m-80)
REVERT: B  170 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.7051 (m-10)
REVERT: B  178 TYR cc_start: 0.7185 (m-80) cc_final: 0.6857 (m-80)
REVERT: C   16 GLN cc_start: 0.7773 (tt0) cc_final: 0.7055 (mt0)
REVERT: C   41 LYS cc_start: 0.8737 (tttt) cc_final: 0.8410 (tttp)
REVERT: C   58 ASP cc_start: 0.8057 (t70) cc_final: 0.7691 (t70)
REVERT: C   60 ARG cc_start: 0.6921 (tpp-160) cc_final: 0.6499 (ttm110)
REVERT: C  102 TRP cc_start: 0.8150 (t60) cc_final: 0.6790 (t-100)
REVERT: D   42 LYS cc_start: 0.7710 (mttp) cc_final: 0.7441 (mmtm)
REVERT: D   61 ARG cc_start: 0.8484 (ptt-90) cc_final: 0.8245 (ptt-90)
REVERT: D   77 ASN cc_start: 0.7935 (m110) cc_final: 0.7532 (p0)
REVERT: E   16 GLN cc_start: 0.7765 (tt0) cc_final: 0.7035 (mt0)
REVERT: E   41 LYS cc_start: 0.8679 (tttt) cc_final: 0.8398 (tttp)
REVERT: E   88 ASP cc_start: 0.7280 (t0) cc_final: 0.7014 (t70)
REVERT: E  102 TRP cc_start: 0.8145 (t60) cc_final: 0.6799 (t-100)
REVERT: F   42 LYS cc_start: 0.7731 (mttp) cc_final: 0.7463 (mmtm)
REVERT: F   77 ASN cc_start: 0.7935 (m110) cc_final: 0.7562 (p0)
  outliers start: 13
  outliers final: 7
  residues processed: 203
  average time/residue: 0.2220
  time to fit residues: 57.3450
Evaluate side-chains
  203 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 192
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
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 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   20 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   chunk 79 optimal weight:    6.9990
   chunk 65 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.1586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          0.3781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6892  Z= 0.256
  Angle     :  0.620   7.849   9346  Z= 0.312
  Chirality :  0.044   0.158   1036
  Planarity :  0.004   0.037   1148
  Dihedral  :  5.905  54.431    932
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 15.98 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.83 (0.31), residues: 840
  helix:  2.08 (0.28), residues: 296
  sheet:  1.23 (0.36), residues: 218
  loop :  0.50 (0.41), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 110 
 HIS   0.008   0.001   HIS B 110 
 PHE   0.019   0.001   PHE B  39 
 TYR   0.017   0.001   TYR E 109 
 ARG   0.002   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
  207 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 194
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.7695 (mmm-85) cc_final: 0.7364 (mmm-85)
REVERT: A  109 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.6297 (m-80)
REVERT: A  170 PHE cc_start: 0.7400 (m-80) cc_final: 0.7108 (m-10)
REVERT: A  178 TYR cc_start: 0.7197 (m-80) cc_final: 0.6855 (m-80)
REVERT: B   63 ARG cc_start: 0.7672 (mmm-85) cc_final: 0.7351 (mmm-85)
REVERT: B  109 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.6298 (m-80)
REVERT: B  170 PHE cc_start: 0.7397 (m-80) cc_final: 0.7090 (m-10)
REVERT: B  178 TYR cc_start: 0.7195 (m-80) cc_final: 0.6885 (m-80)
REVERT: C   41 LYS cc_start: 0.8740 (tttt) cc_final: 0.8415 (tttp)
REVERT: C   60 ARG cc_start: 0.6949 (tpp-160) cc_final: 0.6603 (ttm110)
REVERT: D   42 LYS cc_start: 0.7699 (mttp) cc_final: 0.7440 (mmtm)
REVERT: D   77 ASN cc_start: 0.7902 (m110) cc_final: 0.7515 (p0)
REVERT: D   92 ASP cc_start: 0.8654 (t0) cc_final: 0.8332 (t0)
REVERT: E   16 GLN cc_start: 0.7789 (tt0) cc_final: 0.7057 (mt0)
REVERT: E   41 LYS cc_start: 0.8681 (tttt) cc_final: 0.8390 (tttp)
REVERT: E   60 ARG cc_start: 0.6740 (tpp-160) cc_final: 0.6247 (ttm110)
REVERT: E   88 ASP cc_start: 0.7284 (t0) cc_final: 0.7008 (t70)
REVERT: F   42 LYS cc_start: 0.7716 (mttp) cc_final: 0.7453 (mmtm)
REVERT: F   77 ASN cc_start: 0.7931 (m110) cc_final: 0.7510 (p0)
REVERT: F   92 ASP cc_start: 0.8633 (t0) cc_final: 0.8242 (t0)
  outliers start: 13
  outliers final: 9
  residues processed: 199
  average time/residue: 0.2219
  time to fit residues: 55.9962
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  : 0.811 
-------------------------------------------------------------------------------
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 D residue    5 THR
Chi-restraints excluded: chain D residue   20 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 45 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0670
   chunk 79 optimal weight:    7.9990
   chunk 49 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.9322

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
moved from start:          0.3928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6892  Z= 0.222
  Angle     :  0.589   7.456   9346  Z= 0.295
  Chirality :  0.043   0.154   1036
  Planarity :  0.004   0.038   1148
  Dihedral  :  5.835  53.468    932
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.20
  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:  1.90 (0.31), residues: 840
  helix:  2.19 (0.28), residues: 296
  sheet:  1.25 (0.36), residues: 220
  loop :  0.48 (0.41), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 110 
 HIS   0.002   0.001   HIS C  52 
 PHE   0.017   0.001   PHE B  39 
 TYR   0.012   0.001   TYR C 109 
 ARG   0.003   0.000   ARG B  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
  211 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 195
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 PHE cc_start: 0.7373 (m-80) cc_final: 0.7069 (m-10)
REVERT: A  178 TYR cc_start: 0.7207 (m-80) cc_final: 0.6866 (m-80)
REVERT: B  109 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.6613 (m-80)
REVERT: B  170 PHE cc_start: 0.7418 (m-80) cc_final: 0.7122 (m-10)
REVERT: B  178 TYR cc_start: 0.7197 (m-80) cc_final: 0.6876 (m-80)
REVERT: C   41 LYS cc_start: 0.8727 (tttt) cc_final: 0.8423 (tttp)
REVERT: C   60 ARG cc_start: 0.6949 (tpp-160) cc_final: 0.6626 (ttm110)
REVERT: C   66 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7631 (mttm)
REVERT: D    3 GLN cc_start: 0.7992 (mp10) cc_final: 0.7785 (mp10)
REVERT: D   42 LYS cc_start: 0.7701 (mttp) cc_final: 0.7435 (mmtm)
REVERT: D   77 ASN cc_start: 0.7925 (m110) cc_final: 0.7521 (p0)
REVERT: D  105 GLU cc_start: 0.6612 (tm-30) cc_final: 0.6030 (tm-30)
REVERT: E   16 GLN cc_start: 0.7823 (tt0) cc_final: 0.7097 (mt0)
REVERT: E   41 LYS cc_start: 0.8671 (tttt) cc_final: 0.8373 (tttp)
REVERT: E   60 ARG cc_start: 0.6829 (tpp-160) cc_final: 0.6362 (ttm110)
REVERT: E   88 ASP cc_start: 0.7290 (t0) cc_final: 0.7003 (t70)
REVERT: F   42 LYS cc_start: 0.7722 (mttp) cc_final: 0.7453 (mmtm)
REVERT: F   77 ASN cc_start: 0.7940 (m110) cc_final: 0.7551 (p0)
REVERT: F  105 GLU cc_start: 0.6643 (tm-30) cc_final: 0.6076 (tm-30)
  outliers start: 16
  outliers final: 11
  residues processed: 202
  average time/residue: 0.2235
  time to fit residues: 57.2755
Evaluate side-chains
  202 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 189
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
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   66 LYS
Chi-restraints excluded: chain C residue   68 ARG
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   20 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 7 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 73 optimal weight:    8.9990
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.4080

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= 0.211
  Angle     :  0.592   7.298   9346  Z= 0.296
  Chirality :  0.043   0.154   1036
  Planarity :  0.004   0.039   1148
  Dihedral  :  5.772  52.894    932
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 17.21 %
    Favored  : 80.87 %
  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:  1.86 (0.31), residues: 840
  helix:  2.42 (0.29), residues: 288
  sheet:  1.11 (0.36), residues: 226
  loop :  0.33 (0.40), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 110 
 HIS   0.003   0.001   HIS C  52 
 PHE   0.016   0.001   PHE A  39 
 TYR   0.009   0.001   TYR C  96 
 ARG   0.007   0.000   ARG B  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
  208 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 194
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 PHE cc_start: 0.7389 (m-80) cc_final: 0.7126 (m-10)
REVERT: A  178 TYR cc_start: 0.7216 (m-80) cc_final: 0.6865 (m-80)
REVERT: B  170 PHE cc_start: 0.7408 (m-80) cc_final: 0.7090 (m-10)
REVERT: B  178 TYR cc_start: 0.7195 (m-80) cc_final: 0.6865 (m-80)
REVERT: C   41 LYS cc_start: 0.8719 (tttt) cc_final: 0.8427 (tttp)
REVERT: C   60 ARG cc_start: 0.7033 (tpp-160) cc_final: 0.6792 (ttm110)
REVERT: C   66 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7683 (mttm)
REVERT: D    3 GLN cc_start: 0.7961 (mp10) cc_final: 0.7733 (mp10)
REVERT: D   42 LYS cc_start: 0.7707 (mttp) cc_final: 0.7437 (mmtm)
REVERT: D   52 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8317 (t)
REVERT: D   77 ASN cc_start: 0.7939 (m110) cc_final: 0.7533 (p0)
REVERT: D   92 ASP cc_start: 0.8497 (t0) cc_final: 0.8134 (t0)
REVERT: D  105 GLU cc_start: 0.6651 (tm-30) cc_final: 0.6027 (tm-30)
REVERT: E   16 GLN cc_start: 0.7890 (tt0) cc_final: 0.7143 (mt0)
REVERT: E   41 LYS cc_start: 0.8681 (tttt) cc_final: 0.8381 (tttp)
REVERT: E   60 ARG cc_start: 0.6850 (tpp-160) cc_final: 0.6383 (ttm110)
REVERT: E   88 ASP cc_start: 0.7315 (t0) cc_final: 0.7111 (t70)
REVERT: F   42 LYS cc_start: 0.7736 (mttp) cc_final: 0.7464 (mmtm)
REVERT: F   77 ASN cc_start: 0.7944 (m110) cc_final: 0.7571 (p0)
REVERT: F   92 ASP cc_start: 0.8498 (t0) cc_final: 0.8141 (t0)
REVERT: F  105 GLU cc_start: 0.6563 (tm-30) cc_final: 0.5939 (tm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 199
  average time/residue: 0.2243
  time to fit residues: 56.8333
Evaluate side-chains
  200 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 189
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
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   82 LEU
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   20 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 32 optimal weight:    0.1980
   chunk 57 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 69 optimal weight:    8.9990
   chunk 73 optimal weight:    8.9990
   chunk 48 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.5984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.4032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6892  Z= 0.332
  Angle     :  0.639   7.763   9346  Z= 0.324
  Chirality :  0.045   0.158   1036
  Planarity :  0.004   0.039   1148
  Dihedral  :  5.423  53.684    928
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 18.58 %
    Favored  : 79.64 %
  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:  1.71 (0.31), residues: 840
  helix:  2.03 (0.28), residues: 298
  sheet:  1.22 (0.36), residues: 226
  loop :  0.28 (0.41), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E 110 
 HIS   0.003   0.001   HIS C  52 
 PHE   0.021   0.002   PHE B  39 
 TYR   0.013   0.002   TYR B  72 
 ARG   0.008   0.001   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
  207 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 194
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 PHE cc_start: 0.7477 (m-80) cc_final: 0.7188 (m-10)
REVERT: A  178 TYR cc_start: 0.7272 (m-80) cc_final: 0.6947 (m-80)
REVERT: B  170 PHE cc_start: 0.7437 (m-80) cc_final: 0.7158 (m-10)
REVERT: B  178 TYR cc_start: 0.7239 (m-80) cc_final: 0.6916 (m-80)
REVERT: C   41 LYS cc_start: 0.8734 (tttt) cc_final: 0.8434 (tttp)
REVERT: C   60 ARG cc_start: 0.6974 (tpp-160) cc_final: 0.6668 (ttm110)
REVERT: C   66 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7698 (mttm)
REVERT: D    3 GLN cc_start: 0.7971 (mp10) cc_final: 0.7768 (mp10)
REVERT: D   42 LYS cc_start: 0.7755 (mttp) cc_final: 0.7470 (mmtm)
REVERT: D   77 ASN cc_start: 0.7884 (m110) cc_final: 0.7482 (p0)
REVERT: D   92 ASP cc_start: 0.8682 (t0) cc_final: 0.8293 (t0)
REVERT: D  105 GLU cc_start: 0.6607 (tm-30) cc_final: 0.5990 (tm-30)
REVERT: E    5 LYS cc_start: 0.8383 (UNCLASSIFIED) cc_final: 0.7942 (mmtm)
REVERT: E   16 GLN cc_start: 0.7911 (tt0) cc_final: 0.7209 (mt0)
REVERT: E   41 LYS cc_start: 0.8718 (tttt) cc_final: 0.8392 (tttp)
REVERT: E   60 ARG cc_start: 0.6864 (tpp-160) cc_final: 0.6399 (ttm110)
REVERT: E   74 ASP cc_start: 0.7970 (t0) cc_final: 0.7689 (t0)
REVERT: E   88 ASP cc_start: 0.7364 (t0) cc_final: 0.7089 (t70)
REVERT: F   42 LYS cc_start: 0.7764 (mttp) cc_final: 0.7475 (mmtm)
REVERT: F   77 ASN cc_start: 0.7899 (m110) cc_final: 0.7528 (p0)
REVERT: F   92 ASP cc_start: 0.8655 (t0) cc_final: 0.8284 (t0)
REVERT: F  105 GLU cc_start: 0.6533 (tm-30) cc_final: 0.5942 (tm-30)
  outliers start: 13
  outliers final: 12
  residues processed: 197
  average time/residue: 0.2286
  time to fit residues: 57.2059
Evaluate side-chains
  204 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 191
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  109 PHE
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 D residue    5 THR
Chi-restraints excluded: chain D residue   20 THR
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  108 ASP
Chi-restraints excluded: chain F residue    5 THR
Chi-restraints excluded: chain F residue   20 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0970
   chunk 81 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 51 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
E  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.4157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6892  Z= 0.221
  Angle     :  0.593   7.405   9346  Z= 0.297
  Chirality :  0.043   0.154   1036
  Planarity :  0.004   0.039   1148
  Dihedral  :  5.411  51.188    928
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 18.31 %
    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:  1.84 (0.31), residues: 840
  helix:  2.34 (0.29), residues: 288
  sheet:  1.25 (0.36), residues: 226
  loop :  0.24 (0.40), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 110 
 HIS   0.003   0.001   HIS C  52 
 PHE   0.016   0.001   PHE A  39 
 TYR   0.009   0.001   TYR B  72 
 ARG   0.009   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
  207 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 194
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 PHE cc_start: 0.7427 (m-80) cc_final: 0.7175 (m-10)
REVERT: A  178 TYR cc_start: 0.7242 (m-80) cc_final: 0.6909 (m-80)
REVERT: B  170 PHE cc_start: 0.7376 (m-80) cc_final: 0.7071 (m-10)
REVERT: B  178 TYR cc_start: 0.7217 (m-80) cc_final: 0.6873 (m-80)
REVERT: C   16 GLN cc_start: 0.8009 (tt0) cc_final: 0.7301 (mt0)
REVERT: C   41 LYS cc_start: 0.8726 (tttt) cc_final: 0.8440 (tttp)
REVERT: C   60 ARG cc_start: 0.7030 (tpp-160) cc_final: 0.6702 (ttm110)
REVERT: C   66 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7665 (mttm)
REVERT: C   88 ASP cc_start: 0.7497 (t0) cc_final: 0.7288 (t70)
REVERT: D    3 GLN cc_start: 0.7919 (mp10) cc_final: 0.7687 (mp10)
REVERT: D   42 LYS cc_start: 0.7727 (mttp) cc_final: 0.7445 (mmtm)
REVERT: D   52 SER cc_start: 0.8880 (OUTLIER) cc_final: 0.8323 (t)
REVERT: D   77 ASN cc_start: 0.7936 (m110) cc_final: 0.7554 (p0)
REVERT: D   92 ASP cc_start: 0.8542 (t0) cc_final: 0.8181 (t0)
REVERT: D  105 GLU cc_start: 0.6542 (tm-30) cc_final: 0.5937 (tm-30)
REVERT: E    5 LYS cc_start: 0.8404 (UNCLASSIFIED) cc_final: 0.7970 (mmtm)
REVERT: E   16 GLN cc_start: 0.7927 (tt0) cc_final: 0.7199 (mt0)
REVERT: E   41 LYS cc_start: 0.8699 (tttt) cc_final: 0.8392 (tttp)
REVERT: E   60 ARG cc_start: 0.6841 (tpp-160) cc_final: 0.6333 (ttm110)
REVERT: E   74 ASP cc_start: 0.8057 (t0) cc_final: 0.7758 (t0)
REVERT: E   88 ASP cc_start: 0.7406 (t0) cc_final: 0.7200 (t70)
REVERT: F   33 ILE cc_start: 0.8334 (tt) cc_final: 0.8044 (tt)
REVERT: F   42 LYS cc_start: 0.7748 (mttp) cc_final: 0.7463 (mmtm)
REVERT: F   77 ASN cc_start: 0.7871 (m110) cc_final: 0.7493 (p0)
REVERT: F   92 ASP cc_start: 0.8488 (t0) cc_final: 0.8148 (t0)
REVERT: F  105 GLU cc_start: 0.6722 (tm-30) cc_final: 0.6131 (tm-30)
  outliers start: 13
  outliers final: 9
  residues processed: 198
  average time/residue: 0.2182
  time to fit residues: 54.7757
Evaluate side-chains
  201 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 190
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
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 D residue    5 THR
Chi-restraints excluded: chain D residue   20 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
Chi-restraints excluded: chain F residue   20 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 59 optimal weight:    0.2980
   chunk 9 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 57 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
C  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.161284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.114027 restraints weight = 8876.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 2.61
r_work: 0.3234 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.4326

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= 0.182
  Angle     :  0.572   7.825   9346  Z= 0.285
  Chirality :  0.042   0.153   1036
  Planarity :  0.004   0.040   1148
  Dihedral  :  5.333  49.154    928
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 18.72 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.31), residues: 840
  helix:  2.53 (0.29), residues: 294
  sheet:  1.28 (0.36), residues: 226
  loop :  0.29 (0.40), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 110 
 HIS   0.003   0.001   HIS C 105 
 PHE   0.015   0.001   PHE A  43 
 TYR   0.007   0.001   TYR A  72 
 ARG   0.007   0.000   ARG B  63 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1997.58 seconds
wall clock time: 41 minutes 26.63 seconds (2486.63 seconds total)