Starting phenix.real_space_refine
on Tue Sep 24 12:19:09 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwx_21425/09_2024/6vwx_21425_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwx_21425/09_2024/6vwx_21425.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwx_21425/09_2024/6vwx_21425.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwx_21425/09_2024/6vwx_21425.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwx_21425/09_2024/6vwx_21425_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwx_21425/09_2024/6vwx_21425_neut.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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: 6
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      24      5.16       5
     Na      2      4.78       5
     C    5336      2.51       5
     N    1188      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 60 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 7782
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1841
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 7, 'TRANS': 217}
    Chain: "E"
      Number of atoms: 1841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1841
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 7, 'TRANS': 217}
    Chain: "A"
      Number of atoms: 106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 106
          Unusual residues: {' NA': 2, 'POV': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "E"
      Number of atoms: 104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 104
          Unusual residues: {'POV': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    D, F
  Time building chain proxies: 5.65, per 1000 atoms: 0.73
  Number of scatterers: 7782
  At special positions: 0
  Unit cell: (121.426, 121.426, 65.726, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      24     16.00
     P       8     15.00
     Na      2     11.00
     O    1224      8.00
     N    1188      7.00
     C    5336      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.85
  Conformation dependent library (CDL) restraints added in 988.9 milliseconds
  

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1728

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 0 sheets defined
      76.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 43
      removed outlier: 3.811A  pdb=" N   THR A  26 " --> pdb=" O   HIS A  22 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   PHE A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   THR A  28 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY A  41 " --> pdb=" O   ALA A  37 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLU A  43 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 52
    Processing helix  chain 'A' and resid 55 through 77
      removed outlier: 3.881A  pdb=" N   ALA A  77 " --> pdb=" O   MET A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 103
      removed outlier: 3.750A  pdb=" N   TRP A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 122
      removed outlier: 3.670A  pdb=" N   ARG A 113 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ILE A 114 " --> pdb=" O   THR A 110 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LEU A 115 " --> pdb=" O   VAL A 111 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ARG A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 125
      No H-bonds generated for 'chain 'A' and resid 123 through 125'
    Processing helix  chain 'A' and resid 127 through 139
      removed outlier: 3.513A  pdb=" N   ARG A 132 " --> pdb=" O   PRO A 128 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU A 133 " --> pdb=" O   SER A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 164
      removed outlier: 3.763A  pdb=" N   LEU A 148 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ILE A 149 " --> pdb=" O   GLY A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 189
      removed outlier: 3.558A  pdb=" N   VAL A 188 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   THR A 189 " --> pdb=" O   PHE A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
      removed outlier: 3.724A  pdb=" N   GLU A 204 " --> pdb=" O   PRO A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 237
      removed outlier: 3.507A  pdb=" N   PHE A 212 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE A 223 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 43
      removed outlier: 3.812A  pdb=" N   THR D  26 " --> pdb=" O   HIS D  22 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   PHE D  27 " --> pdb=" O   ARG D  23 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   THR D  28 " --> pdb=" O   ALA D  24 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY D  41 " --> pdb=" O   ALA D  37 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLU D  43 " --> pdb=" O   ILE D  39 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 52
    Processing helix  chain 'D' and resid 55 through 77
      removed outlier: 3.882A  pdb=" N   ALA D  77 " --> pdb=" O   MET D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 103
      removed outlier: 3.750A  pdb=" N   TRP D  91 " --> pdb=" O   SER D  87 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE D 103 " --> pdb=" O   ALA D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 122
      removed outlier: 3.670A  pdb=" N   ARG D 113 " --> pdb=" O   VAL D 109 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE D 114 " --> pdb=" O   THR D 110 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LEU D 115 " --> pdb=" O   VAL D 111 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ARG D 116 " --> pdb=" O   LEU D 112 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 125
      No H-bonds generated for 'chain 'D' and resid 123 through 125'
    Processing helix  chain 'D' and resid 127 through 139
      removed outlier: 3.512A  pdb=" N   ARG D 132 " --> pdb=" O   PRO D 128 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU D 133 " --> pdb=" O   SER D 129 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 144 through 164
      removed outlier: 3.763A  pdb=" N   LEU D 148 " --> pdb=" O   LEU D 144 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ILE D 149 " --> pdb=" O   GLY D 145 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 178 through 189
      removed outlier: 3.558A  pdb=" N   VAL D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   THR D 189 " --> pdb=" O   PHE D 185 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
      removed outlier: 3.724A  pdb=" N   GLU D 204 " --> pdb=" O   PRO D 200 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 237
      removed outlier: 3.506A  pdb=" N   PHE D 212 " --> pdb=" O   SER D 208 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ILE D 223 " --> pdb=" O   GLY D 219 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 22 through 43
      removed outlier: 3.812A  pdb=" N   THR E  26 " --> pdb=" O   HIS E  22 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   PHE E  27 " --> pdb=" O   ARG E  23 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR E  28 " --> pdb=" O   ALA E  24 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY E  41 " --> pdb=" O   ALA E  37 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLU E  43 " --> pdb=" O   ILE E  39 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 52
    Processing helix  chain 'E' and resid 55 through 77
      removed outlier: 3.881A  pdb=" N   ALA E  77 " --> pdb=" O   MET E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 103
      removed outlier: 3.751A  pdb=" N   TRP E  91 " --> pdb=" O   SER E  87 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE E 103 " --> pdb=" O   ALA E  99 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 122
      removed outlier: 3.670A  pdb=" N   ARG E 113 " --> pdb=" O   VAL E 109 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE E 114 " --> pdb=" O   THR E 110 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   LEU E 115 " --> pdb=" O   VAL E 111 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ARG E 116 " --> pdb=" O   LEU E 112 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 123 through 125
      No H-bonds generated for 'chain 'E' and resid 123 through 125'
    Processing helix  chain 'E' and resid 127 through 139
      removed outlier: 3.513A  pdb=" N   ARG E 132 " --> pdb=" O   PRO E 128 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU E 133 " --> pdb=" O   SER E 129 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 144 through 164
      removed outlier: 3.763A  pdb=" N   LEU E 148 " --> pdb=" O   LEU E 144 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ILE E 149 " --> pdb=" O   GLY E 145 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 178 through 189
      removed outlier: 3.558A  pdb=" N   VAL E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   THR E 189 " --> pdb=" O   PHE E 185 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 198 through 205
      removed outlier: 3.725A  pdb=" N   GLU E 204 " --> pdb=" O   PRO E 200 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 208 through 237
      removed outlier: 3.507A  pdb=" N   PHE E 212 " --> pdb=" O   SER E 208 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ILE E 223 " --> pdb=" O   GLY E 219 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 22 through 43
      removed outlier: 3.811A  pdb=" N   THR F  26 " --> pdb=" O   HIS F  22 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   PHE F  27 " --> pdb=" O   ARG F  23 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   THR F  28 " --> pdb=" O   ALA F  24 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY F  41 " --> pdb=" O   ALA F  37 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLU F  43 " --> pdb=" O   ILE F  39 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 45 through 52
    Processing helix  chain 'F' and resid 55 through 77
      removed outlier: 3.881A  pdb=" N   ALA F  77 " --> pdb=" O   MET F  73 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 87 through 103
      removed outlier: 3.750A  pdb=" N   TRP F  91 " --> pdb=" O   SER F  87 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE F 103 " --> pdb=" O   ALA F  99 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 109 through 122
      removed outlier: 3.670A  pdb=" N   ARG F 113 " --> pdb=" O   VAL F 109 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE F 114 " --> pdb=" O   THR F 110 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LEU F 115 " --> pdb=" O   VAL F 111 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ARG F 116 " --> pdb=" O   LEU F 112 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 123 through 125
      No H-bonds generated for 'chain 'F' and resid 123 through 125'
    Processing helix  chain 'F' and resid 127 through 139
      removed outlier: 3.513A  pdb=" N   ARG F 132 " --> pdb=" O   PRO F 128 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU F 133 " --> pdb=" O   SER F 129 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 144 through 164
      removed outlier: 3.763A  pdb=" N   LEU F 148 " --> pdb=" O   LEU F 144 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ILE F 149 " --> pdb=" O   GLY F 145 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 178 through 189
      removed outlier: 3.559A  pdb=" N   VAL F 188 " --> pdb=" O   LEU F 184 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   THR F 189 " --> pdb=" O   PHE F 185 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 198 through 205
      removed outlier: 3.725A  pdb=" N   GLU F 204 " --> pdb=" O   PRO F 200 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 208 through 237
      removed outlier: 3.506A  pdb=" N   PHE F 212 " --> pdb=" O   SER F 208 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE F 223 " --> pdb=" O   GLY F 219 " (cutoff:3.500A)

    428 hydrogen bonds defined for protein.
    1284 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: 1.77

  Time building geometry restraints manager: 2.16 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1052
        1.30 -     1.43: 2291
        1.43 -     1.55: 4540
        1.55 -     1.68: 57
        1.68 -     1.81: 48
  Bond restraints: 7988
  Sorted by residual:
  bond pdb=" C31 POV F 302 "
       pdb=" O31 POV F 302 "
    ideal  model  delta    sigma   weight residual
    1.327  1.425 -0.098 2.00e-02 2.50e+03 2.41e+01
  bond pdb=" C31 POV A 301 "
       pdb=" O31 POV A 301 "
    ideal  model  delta    sigma   weight residual
    1.327  1.425 -0.098 2.00e-02 2.50e+03 2.39e+01
  bond pdb=" C31 POV D 301 "
       pdb=" O31 POV D 301 "
    ideal  model  delta    sigma   weight residual
    1.327  1.425 -0.098 2.00e-02 2.50e+03 2.39e+01
  bond pdb=" C31 POV E 302 "
       pdb=" O31 POV E 302 "
    ideal  model  delta    sigma   weight residual
    1.327  1.424 -0.097 2.00e-02 2.50e+03 2.36e+01
  bond pdb=" C21 POV E 302 "
       pdb=" O21 POV E 302 "
    ideal  model  delta    sigma   weight residual
    1.330  1.422 -0.092 2.00e-02 2.50e+03 2.13e+01
  ... (remaining 7983 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 10259
        2.39 -     4.79: 367
        4.79 -     7.18: 114
        7.18 -     9.58: 44
        9.58 -    11.97: 20
  Bond angle restraints: 10804
  Sorted by residual:
  angle pdb=" C   ASN E  79 "
        pdb=" N   PRO E  80 "
        pdb=" CA  PRO E  80 "
      ideal   model   delta    sigma   weight residual
     119.84  131.81  -11.97 1.25e+00 6.40e-01 9.18e+01
  angle pdb=" C   ASN F  79 "
        pdb=" N   PRO F  80 "
        pdb=" CA  PRO F  80 "
      ideal   model   delta    sigma   weight residual
     119.84  131.81  -11.97 1.25e+00 6.40e-01 9.17e+01
  angle pdb=" C   ASN A  79 "
        pdb=" N   PRO A  80 "
        pdb=" CA  PRO A  80 "
      ideal   model   delta    sigma   weight residual
     119.84  131.78  -11.94 1.25e+00 6.40e-01 9.13e+01
  angle pdb=" C   ASN D  79 "
        pdb=" N   PRO D  80 "
        pdb=" CA  PRO D  80 "
      ideal   model   delta    sigma   weight residual
     119.84  131.78  -11.94 1.25e+00 6.40e-01 9.12e+01
  angle pdb=" N   VAL E 197 "
        pdb=" CA  VAL E 197 "
        pdb=" C   VAL E 197 "
      ideal   model   delta    sigma   weight residual
     110.72  118.38   -7.66 1.01e+00 9.80e-01 5.75e+01
  ... (remaining 10799 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.68: 3948
       23.68 -    47.37: 544
       47.37 -    71.05: 136
       71.05 -    94.73: 36
       94.73 -   118.41: 4
  Dihedral angle restraints: 4668
    sinusoidal: 2020
      harmonic: 2648
  Sorted by residual:
  dihedral pdb=" C29 POV E 302 "
           pdb="C210 POV E 302 "
           pdb="C211 POV E 302 "
           pdb="C212 POV E 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
     112.25 -129.34 -118.41     1      3.00e+01 1.11e-03 1.57e+01
  dihedral pdb=" C29 POV A 301 "
           pdb="C210 POV A 301 "
           pdb="C211 POV A 301 "
           pdb="C212 POV A 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     112.25 -129.35 -118.40     1      3.00e+01 1.11e-03 1.57e+01
  dihedral pdb=" C29 POV D 301 "
           pdb="C210 POV D 301 "
           pdb="C211 POV D 301 "
           pdb="C212 POV D 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     112.25 -129.36 -118.39     1      3.00e+01 1.11e-03 1.57e+01
  ... (remaining 4665 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 935
       0.052 -    0.104: 261
       0.104 -    0.156: 32
       0.156 -    0.209: 0
       0.209 -    0.261: 4
  Chirality restraints: 1232
  Sorted by residual:
  chirality pdb=" CA  MET E 198 "
            pdb=" N   MET E 198 "
            pdb=" C   MET E 198 "
            pdb=" CB  MET E 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CA  MET F 198 "
            pdb=" N   MET F 198 "
            pdb=" C   MET F 198 "
            pdb=" CB  MET F 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CA  MET A 198 "
            pdb=" N   MET A 198 "
            pdb=" C   MET A 198 "
            pdb=" CB  MET A 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.66e+00
  ... (remaining 1229 not shown)

  Planarity restraints: 1256
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG F 199 "   -0.042 5.00e-02 4.00e+02   6.42e-02 6.60e+00
        pdb=" N   PRO F 200 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO F 200 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO F 200 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 199 "   -0.042 5.00e-02 4.00e+02   6.40e-02 6.56e+00
        pdb=" N   PRO A 200 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 200 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 200 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E 199 "    0.042 5.00e-02 4.00e+02   6.39e-02 6.52e+00
        pdb=" N   PRO E 200 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO E 200 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO E 200 "    0.037 5.00e-02 4.00e+02
  ... (remaining 1253 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1122
        2.74 -     3.28: 7813
        3.28 -     3.82: 12303
        3.82 -     4.36: 14717
        4.36 -     4.90: 24876
  Nonbonded interactions: 60831
  Sorted by model distance:
  nonbonded pdb=" O   SER D  78 "
            pdb=" OG  SER D  78 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   SER F  78 "
            pdb=" OG  SER F  78 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   SER A  78 "
            pdb=" OG  SER A  78 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   SER E  78 "
            pdb=" OG  SER E  78 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   PHE A 158 "
            pdb=" OH  TYR A 211 "
     model   vdw
     2.277 3.040
  ... (remaining 60826 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 13 through 237 or resid 301 through 302))
  selection = chain 'D'
  selection = chain 'E'
  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:             1.020
  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:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     20.290
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.020
  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:2.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
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      :  0.011   0.098   7988  Z= 0.675
  Angle     :  1.291  11.973  10804  Z= 0.639
  Chirality :  0.047   0.261   1232
  Planarity :  0.006   0.064   1256
  Dihedral  : 22.960 118.414   2940
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  8.07 %
    Favored  : 91.48 %
  Rotamer:
    Outliers : 15.83 %
    Allowed  : 15.83 %
    Favored  : 68.34 %
  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: -4.41 (0.22), residues: 892
  helix: -2.52 (0.15), residues: 644
  sheet:  None (None), residues: 0
  loop : -3.55 (0.32), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  91 
 HIS   0.001   0.000   HIS F  22 
 PHE   0.012   0.001   PHE D 174 
 TYR   0.007   0.001   TYR D 156 
 ARG   0.002   0.000   ARG F 116 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 126
    poor density    : 175
  time to evaluate  : 0.871 
Fit side-chains
REVERT: A   22 HIS cc_start: 0.7582 (t-90) cc_final: 0.7250 (t-90)
REVERT: A   90 ASN cc_start: 0.8947 (m110) cc_final: 0.8691 (m110)
REVERT: A   95 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8493 (tp)
REVERT: A  191 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7978 (tm-30)
REVERT: D   22 HIS cc_start: 0.7639 (t-90) cc_final: 0.7290 (t70)
REVERT: D   90 ASN cc_start: 0.8931 (m110) cc_final: 0.8659 (m110)
REVERT: D   95 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8485 (tp)
REVERT: D  191 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7768 (tm-30)
REVERT: E   22 HIS cc_start: 0.7651 (t-90) cc_final: 0.7286 (t70)
REVERT: E   70 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7762 (tm-30)
REVERT: E   90 ASN cc_start: 0.8910 (m110) cc_final: 0.8649 (m110)
REVERT: E  122 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8431 (ttt-90)
REVERT: E  181 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8958 (tt)
REVERT: E  191 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7766 (tm-30)
REVERT: F   22 HIS cc_start: 0.7615 (t-90) cc_final: 0.7264 (t70)
REVERT: F   53 LYS cc_start: 0.8029 (tptp) cc_final: 0.7808 (tptp)
REVERT: F   90 ASN cc_start: 0.8934 (m110) cc_final: 0.8685 (m110)
REVERT: F  191 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7911 (tm-30)
  outliers start: 126
  outliers final: 83
  residues processed: 263
  average time/residue: 0.1617
  time to fit residues: 58.8501
Evaluate side-chains
  248 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 88
    poor density    : 160
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  178 GLN
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  199 ARG
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   21 ASN
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   48 ILE
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue   82 SER
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain D residue  120 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  155 PHE
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  176 ASN
Chi-restraints excluded: chain D residue  178 GLN
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  192 SER
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain D residue  198 MET
Chi-restraints excluded: chain D residue  199 ARG
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  210 LEU
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   21 ASN
Chi-restraints excluded: chain E residue   32 LEU
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   48 ILE
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   70 GLU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue   82 SER
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  122 ARG
Chi-restraints excluded: chain E residue  147 ILE
Chi-restraints excluded: chain E residue  155 PHE
Chi-restraints excluded: chain E residue  169 VAL
Chi-restraints excluded: chain E residue  176 ASN
Chi-restraints excluded: chain E residue  178 GLN
Chi-restraints excluded: chain E residue  181 LEU
Chi-restraints excluded: chain E residue  192 SER
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain E residue  198 MET
Chi-restraints excluded: chain E residue  199 ARG
Chi-restraints excluded: chain E residue  201 ILE
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  220 THR
Chi-restraints excluded: chain F residue   19 ILE
Chi-restraints excluded: chain F residue   21 ASN
Chi-restraints excluded: chain F residue   32 LEU
Chi-restraints excluded: chain F residue   40 VAL
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   71 ILE
Chi-restraints excluded: chain F residue   82 SER
Chi-restraints excluded: chain F residue  120 VAL
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  155 PHE
Chi-restraints excluded: chain F residue  169 VAL
Chi-restraints excluded: chain F residue  176 ASN
Chi-restraints excluded: chain F residue  178 GLN
Chi-restraints excluded: chain F residue  192 SER
Chi-restraints excluded: chain F residue  195 SER
Chi-restraints excluded: chain F residue  198 MET
Chi-restraints excluded: chain F residue  199 ARG
Chi-restraints excluded: chain F residue  201 ILE
Chi-restraints excluded: chain F residue  220 THR
Chi-restraints excluded: chain F residue  235 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 66 optimal weight:   10.0000
   chunk 37 optimal weight:    0.6980
   chunk 22 optimal weight:    9.9990
   chunk 44 optimal weight:    9.9990
   chunk 35 optimal weight:    0.4980
   chunk 68 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  90 ASN
A 167 GLN
A 186 GLN
A 234 ASN
D  90 ASN
D 167 GLN
D 186 GLN
D 234 ASN
E  90 ASN
E 167 GLN
E 186 GLN
E 234 ASN
F  90 ASN
F 167 GLN
F 186 GLN
F 234 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7988  Z= 0.210
  Angle     :  0.607  10.577  10804  Z= 0.313
  Chirality :  0.040   0.191   1232
  Planarity :  0.006   0.055   1256
  Dihedral  : 21.478 107.539   1477
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  7.17 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  8.42 %
    Allowed  : 18.47 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.42 (0.27), residues: 892
  helix: -0.26 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -2.85 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP D  54 
 HIS   0.001   0.000   HIS F  22 
 PHE   0.015   0.001   PHE F 215 
 TYR   0.006   0.001   TYR D 156 
 ARG   0.003   0.000   ARG A 131 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 172
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.7226 (ppp) cc_final: 0.6278 (ppp)
REVERT: A   22 HIS cc_start: 0.7579 (t-90) cc_final: 0.7299 (t70)
REVERT: A   74 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.8004 (ttp-110)
REVERT: A   90 ASN cc_start: 0.8856 (m-40) cc_final: 0.8574 (m110)
REVERT: A  191 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7445 (tm-30)
REVERT: D   16 MET cc_start: 0.7425 (ppp) cc_final: 0.6456 (ppp)
REVERT: D   22 HIS cc_start: 0.7586 (t-90) cc_final: 0.7280 (t70)
REVERT: D   74 ARG cc_start: 0.8281 (ttm-80) cc_final: 0.8010 (ttp-110)
REVERT: D  191 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7440 (tm-30)
REVERT: E   16 MET cc_start: 0.7227 (ppp) cc_final: 0.6952 (ppp)
REVERT: E   22 HIS cc_start: 0.7548 (t-90) cc_final: 0.7219 (t70)
REVERT: E   70 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7946 (tm-30)
REVERT: E   93 ASP cc_start: 0.8609 (m-30) cc_final: 0.8391 (m-30)
REVERT: E  191 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7494 (tm-30)
REVERT: F   16 MET cc_start: 0.7228 (ppp) cc_final: 0.6409 (ppp)
REVERT: F   22 HIS cc_start: 0.7541 (t-90) cc_final: 0.7211 (t70)
REVERT: F   74 ARG cc_start: 0.8280 (ttm-80) cc_final: 0.8013 (ttp-110)
REVERT: F   90 ASN cc_start: 0.8841 (m-40) cc_final: 0.8563 (m110)
REVERT: F  191 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7449 (tm-30)
  outliers start: 67
  outliers final: 28
  residues processed: 225
  average time/residue: 0.1912
  time to fit residues: 57.1294
Evaluate side-chains
  194 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 165
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  178 GLN
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue  120 VAL
Chi-restraints excluded: chain D residue  152 SER
Chi-restraints excluded: chain D residue  155 PHE
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  178 GLN
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   70 GLU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  152 SER
Chi-restraints excluded: chain E residue  155 PHE
Chi-restraints excluded: chain E residue  169 VAL
Chi-restraints excluded: chain E residue  178 GLN
Chi-restraints excluded: chain F residue   63 LEU
Chi-restraints excluded: chain F residue   71 ILE
Chi-restraints excluded: chain F residue  120 VAL
Chi-restraints excluded: chain F residue  152 SER
Chi-restraints excluded: chain F residue  155 PHE
Chi-restraints excluded: chain F residue  169 VAL
Chi-restraints excluded: chain F residue  178 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 66 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9980
   chunk 22 optimal weight:   10.0000
   chunk 80 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 71 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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: 0.8020
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7988  Z= 0.212
  Angle     :  0.541   6.357  10804  Z= 0.280
  Chirality :  0.039   0.191   1232
  Planarity :  0.005   0.051   1256
  Dihedral  : 19.621  98.743   1355
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  5.83 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  8.29 %
    Allowed  : 18.72 %
    Favored  : 72.99 %
  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: -0.36 (0.29), residues: 892
  helix:  0.54 (0.20), residues: 676
  sheet:  None (None), residues: 0
  loop : -2.66 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E 209 
 HIS   0.001   0.000   HIS A 101 
 PHE   0.017   0.001   PHE E 215 
 TYR   0.007   0.001   TYR E 211 
 ARG   0.002   0.000   ARG E 122 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 66
    poor density    : 181
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.6528 (ppp) cc_final: 0.6230 (ppp)
REVERT: A   22 HIS cc_start: 0.7324 (t-90) cc_final: 0.7034 (t70)
REVERT: A   42 ILE cc_start: 0.9414 (tt) cc_final: 0.9213 (tt)
REVERT: A   73 MET cc_start: 0.8529 (mtp) cc_final: 0.8309 (mtp)
REVERT: A   74 ARG cc_start: 0.8310 (ttm-80) cc_final: 0.7993 (ttp-110)
REVERT: A   90 ASN cc_start: 0.8882 (m-40) cc_final: 0.8551 (m110)
REVERT: A  131 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8264 (ttm170)
REVERT: A  191 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7414 (tm-30)
REVERT: A  210 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8310 (tp)
REVERT: D   16 MET cc_start: 0.6510 (ppp) cc_final: 0.6198 (ppp)
REVERT: D   22 HIS cc_start: 0.7324 (t-90) cc_final: 0.7033 (t70)
REVERT: D  131 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8227 (ttm170)
REVERT: D  191 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7416 (tm-30)
REVERT: E   22 HIS cc_start: 0.7251 (t-90) cc_final: 0.6922 (t70)
REVERT: E   73 MET cc_start: 0.8581 (mtp) cc_final: 0.8357 (mtp)
REVERT: E  191 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7476 (tm-30)
REVERT: F   16 MET cc_start: 0.6606 (ppp) cc_final: 0.6264 (ppp)
REVERT: F   22 HIS cc_start: 0.7371 (t-90) cc_final: 0.7107 (t-170)
REVERT: F   74 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.7940 (ttp-110)
REVERT: F   90 ASN cc_start: 0.8875 (m-40) cc_final: 0.8545 (m110)
REVERT: F  191 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7435 (tm-30)
REVERT: F  210 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8328 (tp)
  outliers start: 66
  outliers final: 46
  residues processed: 224
  average time/residue: 0.1712
  time to fit residues: 53.0635
Evaluate side-chains
  223 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 173
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   54 TRP
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  178 GLN
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain D residue   48 ILE
Chi-restraints excluded: chain D residue   54 TRP
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue  108 PHE
Chi-restraints excluded: chain D residue  120 VAL
Chi-restraints excluded: chain D residue  131 ARG
Chi-restraints excluded: chain D residue  152 SER
Chi-restraints excluded: chain D residue  155 PHE
Chi-restraints excluded: chain D residue  176 ASN
Chi-restraints excluded: chain D residue  178 GLN
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain E residue   48 ILE
Chi-restraints excluded: chain E residue   54 TRP
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue  108 PHE
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  152 SER
Chi-restraints excluded: chain E residue  155 PHE
Chi-restraints excluded: chain E residue  176 ASN
Chi-restraints excluded: chain E residue  178 GLN
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   54 TRP
Chi-restraints excluded: chain F residue   63 LEU
Chi-restraints excluded: chain F residue   71 ILE
Chi-restraints excluded: chain F residue  108 PHE
Chi-restraints excluded: chain F residue  120 VAL
Chi-restraints excluded: chain F residue  152 SER
Chi-restraints excluded: chain F residue  155 PHE
Chi-restraints excluded: chain F residue  176 ASN
Chi-restraints excluded: chain F residue  178 GLN
Chi-restraints excluded: chain F residue  195 SER
Chi-restraints excluded: chain F residue  210 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 53 optimal weight:    8.9990
   chunk 80 optimal weight:    0.7980
   chunk 85 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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: 0.8032
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7988  Z= 0.249
  Angle     :  0.596  11.694  10804  Z= 0.288
  Chirality :  0.041   0.217   1232
  Planarity :  0.008   0.116   1256
  Dihedral  : 19.057  96.882   1348
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  6.50 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  8.67 %
    Allowed  : 17.71 %
    Favored  : 73.62 %
  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:  0.02 (0.28), residues: 892
  helix:  0.83 (0.20), residues: 676
  sheet:  None (None), residues: 0
  loop : -2.56 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E 209 
 HIS   0.001   0.000   HIS E  22 
 PHE   0.022   0.001   PHE A 215 
 TYR   0.008   0.001   TYR D 211 
 ARG   0.002   0.000   ARG E 116 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 69
    poor density    : 185
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 HIS cc_start: 0.7257 (t-90) cc_final: 0.6995 (t70)
REVERT: A   74 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.7975 (ttp-110)
REVERT: A  191 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7473 (tm-30)
REVERT: A  210 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8359 (tp)
REVERT: D   22 HIS cc_start: 0.7336 (t-90) cc_final: 0.7074 (t-170)
REVERT: D  191 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7461 (tm-30)
REVERT: E   22 HIS cc_start: 0.7323 (t-90) cc_final: 0.6969 (t70)
REVERT: E   90 ASN cc_start: 0.8953 (m-40) cc_final: 0.8726 (m-40)
REVERT: E  191 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7507 (tm-30)
REVERT: F   22 HIS cc_start: 0.7208 (t-90) cc_final: 0.6925 (t70)
REVERT: F   74 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.8009 (ttp-110)
REVERT: F  191 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7452 (tm-30)
REVERT: F  210 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8333 (tp)
  outliers start: 69
  outliers final: 47
  residues processed: 229
  average time/residue: 0.1637
  time to fit residues: 52.2585
Evaluate side-chains
  223 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 174
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   54 TRP
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  178 GLN
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   54 TRP
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue  108 PHE
Chi-restraints excluded: chain D residue  120 VAL
Chi-restraints excluded: chain D residue  152 SER
Chi-restraints excluded: chain D residue  155 PHE
Chi-restraints excluded: chain D residue  176 ASN
Chi-restraints excluded: chain D residue  178 GLN
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue   54 TRP
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue  108 PHE
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  152 SER
Chi-restraints excluded: chain E residue  155 PHE
Chi-restraints excluded: chain E residue  176 ASN
Chi-restraints excluded: chain E residue  178 GLN
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain E residue  235 VAL
Chi-restraints excluded: chain F residue   54 TRP
Chi-restraints excluded: chain F residue   63 LEU
Chi-restraints excluded: chain F residue   71 ILE
Chi-restraints excluded: chain F residue  108 PHE
Chi-restraints excluded: chain F residue  120 VAL
Chi-restraints excluded: chain F residue  152 SER
Chi-restraints excluded: chain F residue  155 PHE
Chi-restraints excluded: chain F residue  176 ASN
Chi-restraints excluded: chain F residue  178 GLN
Chi-restraints excluded: chain F residue  195 SER
Chi-restraints excluded: chain F residue  210 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0870
   chunk 35 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0770
   chunk 58 optimal weight:    0.7980
   chunk 0 optimal weight:    9.9990
   chunk 43 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 28 optimal weight:    7.9990
   overall best weight:    0.4516

-------------------------------------------------------------------------------
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: 0.7987
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7988  Z= 0.161
  Angle     :  0.622  14.304  10804  Z= 0.295
  Chirality :  0.042   0.267   1232
  Planarity :  0.004   0.037   1256
  Dihedral  : 18.293  92.337   1348
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 21.23 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 14.29 %
    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:  0.42 (0.29), residues: 892
  helix:  1.19 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -2.65 (0.37), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 193 
 HIS   0.001   0.000   HIS A  22 
 PHE   0.020   0.001   PHE E 215 
 TYR   0.006   0.001   TYR E 211 
 ARG   0.003   0.000   ARG A 122 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 193
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.7936 (ttp-110)
REVERT: A   90 ASN cc_start: 0.8944 (m-40) cc_final: 0.8655 (m-40)
REVERT: A  191 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7745 (tm-30)
REVERT: D   74 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.8026 (ttp-110)
REVERT: D  191 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7742 (tm-30)
REVERT: E   16 MET cc_start: 0.6774 (ppp) cc_final: 0.5998 (ppp)
REVERT: E   22 HIS cc_start: 0.7268 (t-90) cc_final: 0.7017 (t-170)
REVERT: E   90 ASN cc_start: 0.8972 (m-40) cc_final: 0.8713 (m-40)
REVERT: E  191 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7313 (tm-30)
REVERT: F   74 ARG cc_start: 0.8331 (ttm-80) cc_final: 0.7936 (ttp-110)
REVERT: F  191 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7731 (tm-30)
  outliers start: 44
  outliers final: 32
  residues processed: 220
  average time/residue: 0.1708
  time to fit residues: 51.8914
Evaluate side-chains
  208 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 176
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 TRP
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  178 GLN
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain D residue   54 TRP
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue  108 PHE
Chi-restraints excluded: chain D residue  120 VAL
Chi-restraints excluded: chain D residue  155 PHE
Chi-restraints excluded: chain D residue  176 ASN
Chi-restraints excluded: chain D residue  178 GLN
Chi-restraints excluded: chain E residue   54 TRP
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue  108 PHE
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  155 PHE
Chi-restraints excluded: chain E residue  176 ASN
Chi-restraints excluded: chain E residue  178 GLN
Chi-restraints excluded: chain F residue   54 TRP
Chi-restraints excluded: chain F residue   63 LEU
Chi-restraints excluded: chain F residue   71 ILE
Chi-restraints excluded: chain F residue  108 PHE
Chi-restraints excluded: chain F residue  120 VAL
Chi-restraints excluded: chain F residue  152 SER
Chi-restraints excluded: chain F residue  155 PHE
Chi-restraints excluded: chain F residue  176 ASN
Chi-restraints excluded: chain F residue  178 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 76 optimal weight:    0.4980
   chunk 16 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 70 optimal weight:    6.9990
   chunk 39 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 28 optimal weight:    8.9990
   chunk 44 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  22 HIS
D  22 HIS
F  22 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7988  Z= 0.183
  Angle     :  0.586  10.312  10804  Z= 0.293
  Chirality :  0.041   0.180   1232
  Planarity :  0.004   0.036   1256
  Dihedral  : 17.993  87.996   1346
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 21.61 %
    Favored  : 72.36 %
  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:  0.53 (0.29), residues: 892
  helix:  1.31 (0.20), residues: 676
  sheet:  None (None), residues: 0
  loop : -2.81 (0.36), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP D 193 
 HIS   0.010   0.001   HIS D  22 
 PHE   0.021   0.001   PHE F 215 
 TYR   0.007   0.001   TYR E 211 
 ARG   0.002   0.000   ARG F 116 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 181
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ARG cc_start: 0.8394 (ttm-80) cc_final: 0.7964 (ttp-110)
REVERT: A  191 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7771 (tm-30)
REVERT: A  220 THR cc_start: 0.9104 (m) cc_final: 0.8784 (m)
REVERT: D   74 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.7992 (ttp-110)
REVERT: D   90 ASN cc_start: 0.9022 (m-40) cc_final: 0.8774 (m-40)
REVERT: D  191 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7321 (tm-30)
REVERT: D  220 THR cc_start: 0.9062 (m) cc_final: 0.8696 (m)
REVERT: E   16 MET cc_start: 0.6392 (ppp) cc_final: 0.6035 (ppp)
REVERT: E   22 HIS cc_start: 0.7209 (t-90) cc_final: 0.6991 (t-170)
REVERT: E   90 ASN cc_start: 0.8999 (m-40) cc_final: 0.8749 (m-40)
REVERT: E  191 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7396 (tm-30)
REVERT: E  220 THR cc_start: 0.9110 (m) cc_final: 0.8794 (m)
REVERT: F   74 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.7914 (ttp-110)
REVERT: F  191 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7799 (tm-30)
REVERT: F  210 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8167 (tp)
REVERT: F  220 THR cc_start: 0.9094 (m) cc_final: 0.8775 (m)
  outliers start: 48
  outliers final: 41
  residues processed: 211
  average time/residue: 0.1512
  time to fit residues: 45.4020
Evaluate side-chains
  219 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 177
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 TRP
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  178 GLN
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain D residue   22 HIS
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   54 TRP
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue  108 PHE
Chi-restraints excluded: chain D residue  120 VAL
Chi-restraints excluded: chain D residue  152 SER
Chi-restraints excluded: chain D residue  155 PHE
Chi-restraints excluded: chain D residue  176 ASN
Chi-restraints excluded: chain D residue  178 GLN
Chi-restraints excluded: chain E residue   34 LEU
Chi-restraints excluded: chain E residue   54 TRP
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   70 GLU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue  108 PHE
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  152 SER
Chi-restraints excluded: chain E residue  155 PHE
Chi-restraints excluded: chain E residue  176 ASN
Chi-restraints excluded: chain E residue  178 GLN
Chi-restraints excluded: chain F residue   54 TRP
Chi-restraints excluded: chain F residue   63 LEU
Chi-restraints excluded: chain F residue   71 ILE
Chi-restraints excluded: chain F residue  108 PHE
Chi-restraints excluded: chain F residue  120 VAL
Chi-restraints excluded: chain F residue  152 SER
Chi-restraints excluded: chain F residue  155 PHE
Chi-restraints excluded: chain F residue  176 ASN
Chi-restraints excluded: chain F residue  178 GLN
Chi-restraints excluded: chain F residue  210 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 53 optimal weight:    0.1980
   chunk 51 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0050
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
D  22 HIS
F  22 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7988  Z= 0.176
  Angle     :  0.581   8.253  10804  Z= 0.291
  Chirality :  0.041   0.159   1232
  Planarity :  0.004   0.035   1256
  Dihedral  : 17.789  88.194   1346
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  6.66 %
    Allowed  : 20.85 %
    Favored  : 72.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.29), residues: 892
  helix:  1.43 (0.21), residues: 676
  sheet:  None (None), residues: 0
  loop : -2.83 (0.36), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP D 193 
 HIS   0.016   0.001   HIS D  22 
 PHE   0.020   0.001   PHE F 215 
 TYR   0.007   0.001   TYR E 211 
 ARG   0.002   0.000   ARG D  23 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 185
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.7906 (ttp-110)
REVERT: A   90 ASN cc_start: 0.8997 (m-40) cc_final: 0.8764 (m-40)
REVERT: A  191 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7755 (tm-30)
REVERT: A  210 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8162 (tp)
REVERT: A  220 THR cc_start: 0.9075 (m) cc_final: 0.8757 (m)
REVERT: D   73 MET cc_start: 0.8663 (mtp) cc_final: 0.8399 (mtp)
REVERT: D   74 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.7977 (ttp-110)
REVERT: D   90 ASN cc_start: 0.9029 (m-40) cc_final: 0.8798 (m-40)
REVERT: D  191 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7367 (tm-30)
REVERT: D  220 THR cc_start: 0.9061 (m) cc_final: 0.8715 (m)
REVERT: E   90 ASN cc_start: 0.9008 (m-40) cc_final: 0.8783 (m-40)
REVERT: E  191 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7357 (tm-30)
REVERT: E  220 THR cc_start: 0.9056 (m) cc_final: 0.8739 (m)
REVERT: F   74 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.7899 (ttp-110)
REVERT: F  191 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7786 (tm-30)
REVERT: F  220 THR cc_start: 0.9071 (m) cc_final: 0.8743 (m)
  outliers start: 53
  outliers final: 47
  residues processed: 217
  average time/residue: 0.1456
  time to fit residues: 45.1251
Evaluate side-chains
  226 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 178
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   54 TRP
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  178 GLN
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   54 TRP
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue  108 PHE
Chi-restraints excluded: chain D residue  120 VAL
Chi-restraints excluded: chain D residue  152 SER
Chi-restraints excluded: chain D residue  155 PHE
Chi-restraints excluded: chain D residue  176 ASN
Chi-restraints excluded: chain D residue  178 GLN
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain E residue   34 LEU
Chi-restraints excluded: chain E residue   54 TRP
Chi-restraints excluded: chain E residue   70 GLU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue  108 PHE
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  152 SER
Chi-restraints excluded: chain E residue  155 PHE
Chi-restraints excluded: chain E residue  176 ASN
Chi-restraints excluded: chain E residue  178 GLN
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain F residue   34 LEU
Chi-restraints excluded: chain F residue   54 TRP
Chi-restraints excluded: chain F residue   63 LEU
Chi-restraints excluded: chain F residue   71 ILE
Chi-restraints excluded: chain F residue  108 PHE
Chi-restraints excluded: chain F residue  120 VAL
Chi-restraints excluded: chain F residue  152 SER
Chi-restraints excluded: chain F residue  155 PHE
Chi-restraints excluded: chain F residue  176 ASN
Chi-restraints excluded: chain F residue  178 GLN
Chi-restraints excluded: chain F residue  195 SER
Chi-restraints excluded: chain F residue  226 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 53 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 66 optimal weight:   10.0000
   chunk 77 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
A  22 HIS
D  22 HIS
E  22 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   7988  Z= 0.382
  Angle     :  0.702  19.215  10804  Z= 0.342
  Chirality :  0.044   0.170   1232
  Planarity :  0.004   0.036   1256
  Dihedral  : 18.352  94.631   1344
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  7.54 %
    Allowed  : 20.98 %
    Favored  : 71.48 %
  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:  0.47 (0.29), residues: 892
  helix:  1.25 (0.20), residues: 676
  sheet:  None (None), residues: 0
  loop : -2.76 (0.37), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F  91 
 HIS   0.014   0.002   HIS D  22 
 PHE   0.021   0.002   PHE F 215 
 TYR   0.010   0.002   TYR F 156 
 ARG   0.005   0.000   ARG F 116 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 180
  time to evaluate  : 0.832 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.8355 (ttm-80) cc_final: 0.7915 (ttp-110)
REVERT: A   90 ASN cc_start: 0.8984 (m-40) cc_final: 0.8773 (m-40)
REVERT: A  191 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7593 (tm-30)
REVERT: A  210 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8347 (tp)
REVERT: A  220 THR cc_start: 0.9125 (m) cc_final: 0.8799 (m)
REVERT: D   73 MET cc_start: 0.8667 (mtp) cc_final: 0.8410 (mtp)
REVERT: D   74 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.7977 (ttp-110)
REVERT: D   90 ASN cc_start: 0.8977 (m-40) cc_final: 0.8767 (m-40)
REVERT: D  191 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7631 (tm-30)
REVERT: D  220 THR cc_start: 0.9090 (m) cc_final: 0.8738 (m)
REVERT: E   90 ASN cc_start: 0.8962 (m-40) cc_final: 0.8752 (m-40)
REVERT: E  191 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7590 (tm-30)
REVERT: E  220 THR cc_start: 0.9133 (m) cc_final: 0.8810 (m)
REVERT: F   74 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.7915 (ttp-110)
REVERT: F   90 ASN cc_start: 0.8927 (m-40) cc_final: 0.8615 (m110)
REVERT: F  191 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7610 (tm-30)
REVERT: F  210 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8328 (tp)
REVERT: F  220 THR cc_start: 0.9109 (m) cc_final: 0.8773 (m)
  outliers start: 60
  outliers final: 50
  residues processed: 218
  average time/residue: 0.1554
  time to fit residues: 48.0718
Evaluate side-chains
  233 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 52
    poor density    : 181
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 HIS
Chi-restraints excluded: chain A residue   54 TRP
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  178 GLN
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain D residue   22 HIS
Chi-restraints excluded: chain D residue   54 TRP
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue  108 PHE
Chi-restraints excluded: chain D residue  120 VAL
Chi-restraints excluded: chain D residue  152 SER
Chi-restraints excluded: chain D residue  155 PHE
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  176 ASN
Chi-restraints excluded: chain D residue  178 GLN
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain E residue   54 TRP
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   70 GLU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue  108 PHE
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  152 SER
Chi-restraints excluded: chain E residue  155 PHE
Chi-restraints excluded: chain E residue  169 VAL
Chi-restraints excluded: chain E residue  176 ASN
Chi-restraints excluded: chain E residue  178 GLN
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain E residue  235 VAL
Chi-restraints excluded: chain F residue   54 TRP
Chi-restraints excluded: chain F residue   63 LEU
Chi-restraints excluded: chain F residue   71 ILE
Chi-restraints excluded: chain F residue  108 PHE
Chi-restraints excluded: chain F residue  120 VAL
Chi-restraints excluded: chain F residue  152 SER
Chi-restraints excluded: chain F residue  155 PHE
Chi-restraints excluded: chain F residue  169 VAL
Chi-restraints excluded: chain F residue  176 ASN
Chi-restraints excluded: chain F residue  178 GLN
Chi-restraints excluded: chain F residue  195 SER
Chi-restraints excluded: chain F residue  210 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 78 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  22 HIS
D  22 HIS
F  22 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7988  Z= 0.178
  Angle     :  0.648  17.156  10804  Z= 0.310
  Chirality :  0.041   0.185   1232
  Planarity :  0.004   0.036   1256
  Dihedral  : 17.840  91.752   1344
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 22.11 %
    Favored  : 71.11 %
  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:  0.74 (0.29), residues: 892
  helix:  1.44 (0.21), residues: 676
  sheet:  None (None), residues: 0
  loop : -2.67 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP E 193 
 HIS   0.018   0.002   HIS D  22 
 PHE   0.019   0.001   PHE F 215 
 TYR   0.008   0.001   TYR D 211 
 ARG   0.004   0.000   ARG A  23 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 54
    poor density    : 187
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 ASN cc_start: 0.8954 (m-40) cc_final: 0.8666 (m110)
REVERT: A  191 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7394 (tm-30)
REVERT: A  210 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8210 (tp)
REVERT: A  220 THR cc_start: 0.9065 (m) cc_final: 0.8748 (m)
REVERT: D   73 MET cc_start: 0.8614 (mtp) cc_final: 0.8347 (mtp)
REVERT: D  191 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7379 (tm-30)
REVERT: D  220 THR cc_start: 0.9054 (m) cc_final: 0.8709 (m)
REVERT: E   36 ASN cc_start: 0.9101 (t0) cc_final: 0.8639 (t0)
REVERT: E  191 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7468 (tm-30)
REVERT: E  220 THR cc_start: 0.9047 (m) cc_final: 0.8732 (m)
REVERT: F   74 ARG cc_start: 0.8331 (ttm-80) cc_final: 0.7873 (ttp-110)
REVERT: F  191 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7424 (tm-30)
REVERT: F  220 THR cc_start: 0.9035 (m) cc_final: 0.8711 (m)
  outliers start: 54
  outliers final: 50
  residues processed: 221
  average time/residue: 0.1365
  time to fit residues: 44.1121
Evaluate side-chains
  235 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 184
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   54 TRP
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  178 GLN
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain D residue   22 HIS
Chi-restraints excluded: chain D residue   54 TRP
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain D residue  108 PHE
Chi-restraints excluded: chain D residue  120 VAL
Chi-restraints excluded: chain D residue  152 SER
Chi-restraints excluded: chain D residue  155 PHE
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  176 ASN
Chi-restraints excluded: chain D residue  178 GLN
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain E residue   54 TRP
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   70 GLU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue  108 PHE
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  152 SER
Chi-restraints excluded: chain E residue  155 PHE
Chi-restraints excluded: chain E residue  169 VAL
Chi-restraints excluded: chain E residue  176 ASN
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain F residue   54 TRP
Chi-restraints excluded: chain F residue   63 LEU
Chi-restraints excluded: chain F residue   71 ILE
Chi-restraints excluded: chain F residue  108 PHE
Chi-restraints excluded: chain F residue  120 VAL
Chi-restraints excluded: chain F residue  152 SER
Chi-restraints excluded: chain F residue  155 PHE
Chi-restraints excluded: chain F residue  176 ASN
Chi-restraints excluded: chain F residue  178 GLN
Chi-restraints excluded: chain F residue  195 SER
Chi-restraints excluded: chain F residue  226 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  22 HIS
D  22 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7988  Z= 0.203
  Angle     :  0.641  13.431  10804  Z= 0.311
  Chirality :  0.042   0.198   1232
  Planarity :  0.004   0.036   1256
  Dihedral  : 17.621  90.076   1341
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  6.91 %
    Allowed  : 22.24 %
    Favored  : 70.85 %
  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:  0.77 (0.29), residues: 892
  helix:  1.45 (0.21), residues: 676
  sheet:  None (None), residues: 0
  loop : -2.63 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 193 
 HIS   0.018   0.002   HIS D  22 
 PHE   0.020   0.001   PHE F 215 
 TYR   0.008   0.001   TYR E 211 
 ARG   0.003   0.000   ARG D  23 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 55
    poor density    : 186
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
REVERT: A  191 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7391 (tm-30)
REVERT: A  210 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8214 (tp)
REVERT: A  220 THR cc_start: 0.9002 (m) cc_final: 0.8671 (m)
REVERT: D   73 MET cc_start: 0.8628 (mtp) cc_final: 0.8348 (mtp)
REVERT: D  191 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7438 (tm-30)
REVERT: D  220 THR cc_start: 0.9062 (m) cc_final: 0.8722 (m)
REVERT: E   36 ASN cc_start: 0.9108 (t0) cc_final: 0.8654 (t0)
REVERT: E  191 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7474 (tm-30)
REVERT: E  220 THR cc_start: 0.9047 (m) cc_final: 0.8736 (m)
REVERT: F   74 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.7879 (ttp-110)
REVERT: F   90 ASN cc_start: 0.8928 (m-40) cc_final: 0.8649 (m110)
REVERT: F  191 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7428 (tm-30)
REVERT: F  220 THR cc_start: 0.9036 (m) cc_final: 0.8716 (m)
  outliers start: 55
  outliers final: 52
  residues processed: 220
  average time/residue: 0.1535
  time to fit residues: 49.5829
Evaluate side-chains
  237 residues out of total 796 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 184
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 HIS
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   54 TRP
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  178 GLN
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain D residue   22 HIS
Chi-restraints excluded: chain D residue   54 TRP
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain D residue  108 PHE
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  120 VAL
Chi-restraints excluded: chain D residue  152 SER
Chi-restraints excluded: chain D residue  155 PHE
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  176 ASN
Chi-restraints excluded: chain D residue  178 GLN
Chi-restraints excluded: chain D residue  195 SER
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain E residue   54 TRP
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   70 GLU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue  108 PHE
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  152 SER
Chi-restraints excluded: chain E residue  155 PHE
Chi-restraints excluded: chain E residue  169 VAL
Chi-restraints excluded: chain E residue  176 ASN
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain F residue   54 TRP
Chi-restraints excluded: chain F residue   63 LEU
Chi-restraints excluded: chain F residue   71 ILE
Chi-restraints excluded: chain F residue  108 PHE
Chi-restraints excluded: chain F residue  120 VAL
Chi-restraints excluded: chain F residue  152 SER
Chi-restraints excluded: chain F residue  155 PHE
Chi-restraints excluded: chain F residue  169 VAL
Chi-restraints excluded: chain F residue  176 ASN
Chi-restraints excluded: chain F residue  195 SER
Chi-restraints excluded: chain F residue  226 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A  22 HIS
D  22 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.136591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.103033 restraints weight = 11830.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.86
r_work: 0.3207 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7988  Z= 0.242
  Angle     :  0.652  13.864  10804  Z= 0.316
  Chirality :  0.042   0.213   1232
  Planarity :  0.004   0.035   1256
  Dihedral  : 17.544  90.386   1338
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 22.49 %
    Favored  : 70.48 %
  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:  0.74 (0.29), residues: 892
  helix:  1.42 (0.20), residues: 676
  sheet:  None (None), residues: 0
  loop : -2.60 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 193 
 HIS   0.020   0.001   HIS D  22 
 PHE   0.020   0.001   PHE F 215 
 TYR   0.008   0.001   TYR E 211 
 ARG   0.003   0.000   ARG D  23 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1929.87 seconds
wall clock time: 34 minutes 49.18 seconds (2089.18 seconds total)