Starting phenix.real_space_refine
on Sat Aug 23 21:17:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cl1_16709/08_2025/8cl1_16709.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cl1_16709/08_2025/8cl1_16709.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cl1_16709/08_2025/8cl1_16709.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cl1_16709/08_2025/8cl1_16709.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cl1_16709/08_2025/8cl1_16709.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cl1_16709/08_2025/8cl1_16709.map"
  }
  resolution = 3.35
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.002 sd=   0.067
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5472 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C    6660      2.51       5
     N    1818      2.21       5
     O    1944      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10494
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1646
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 103
          Classifications: {'peptide': 14}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 9}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    C, E, G, I, K, D, F, H, J, L
  Time building chain proxies: 1.63, per 1000 atoms: 0.16
  Number of scatterers: 10494
  At special positions: 0
  Unit cell: (116.25, 108.81, 70.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      72     16.00
     O    1944      8.00
     N    1818      7.00
     C    6660      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=6, symmetry=0
  Number of additional bonds: simple=6, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.03
  Conformation dependent library (CDL) restraints added in 396.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2544

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 6 sheets defined
      69.2% alpha, 1.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 31
    Processing helix  chain 'A' and resid 35 through 44
    Processing helix  chain 'A' and resid 48 through 58
    Processing helix  chain 'A' and resid 62 through 84
    Processing helix  chain 'A' and resid 100 through 105
    Processing helix  chain 'A' and resid 110 through 119
    Processing helix  chain 'A' and resid 125 through 146
    Processing helix  chain 'A' and resid 149 through 153
    Processing helix  chain 'A' and resid 160 through 175
      removed outlier: 3.723A  pdb=" N   ALA A 174 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 193
      removed outlier: 4.505A  pdb=" N   LEU A 190 " --> pdb=" O   THR A 186 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   VAL A 191 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 206
      removed outlier: 3.651A  pdb=" N   GLY A 206 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 219
    Processing helix  chain 'C' and resid 16 through 31
    Processing helix  chain 'C' and resid 35 through 44
    Processing helix  chain 'C' and resid 48 through 58
    Processing helix  chain 'C' and resid 62 through 84
    Processing helix  chain 'C' and resid 100 through 105
    Processing helix  chain 'C' and resid 110 through 119
    Processing helix  chain 'C' and resid 125 through 146
    Processing helix  chain 'C' and resid 149 through 153
    Processing helix  chain 'C' and resid 160 through 175
      removed outlier: 3.723A  pdb=" N   ALA C 174 " --> pdb=" O   LYS C 170 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 193
      removed outlier: 4.505A  pdb=" N   LEU C 190 " --> pdb=" O   THR C 186 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   VAL C 191 " --> pdb=" O   GLU C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 206
      removed outlier: 3.651A  pdb=" N   GLY C 206 " --> pdb=" O   LEU C 202 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 210 through 219
    Processing helix  chain 'E' and resid 16 through 31
    Processing helix  chain 'E' and resid 35 through 44
    Processing helix  chain 'E' and resid 48 through 58
    Processing helix  chain 'E' and resid 62 through 84
    Processing helix  chain 'E' and resid 100 through 105
    Processing helix  chain 'E' and resid 110 through 119
    Processing helix  chain 'E' and resid 125 through 146
    Processing helix  chain 'E' and resid 149 through 153
    Processing helix  chain 'E' and resid 160 through 175
      removed outlier: 3.723A  pdb=" N   ALA E 174 " --> pdb=" O   LYS E 170 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 178 through 193
      removed outlier: 4.505A  pdb=" N   LEU E 190 " --> pdb=" O   THR E 186 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   VAL E 191 " --> pdb=" O   GLU E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 195 through 206
      removed outlier: 3.650A  pdb=" N   GLY E 206 " --> pdb=" O   LEU E 202 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 210 through 219
    Processing helix  chain 'G' and resid 16 through 31
    Processing helix  chain 'G' and resid 35 through 44
    Processing helix  chain 'G' and resid 48 through 58
    Processing helix  chain 'G' and resid 62 through 84
    Processing helix  chain 'G' and resid 100 through 105
    Processing helix  chain 'G' and resid 110 through 119
    Processing helix  chain 'G' and resid 125 through 146
    Processing helix  chain 'G' and resid 149 through 153
    Processing helix  chain 'G' and resid 160 through 175
      removed outlier: 3.723A  pdb=" N   ALA G 174 " --> pdb=" O   LYS G 170 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 178 through 193
      removed outlier: 4.505A  pdb=" N   LEU G 190 " --> pdb=" O   THR G 186 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   VAL G 191 " --> pdb=" O   GLU G 187 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 195 through 206
      removed outlier: 3.651A  pdb=" N   GLY G 206 " --> pdb=" O   LEU G 202 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 210 through 219
    Processing helix  chain 'I' and resid 16 through 31
    Processing helix  chain 'I' and resid 35 through 44
    Processing helix  chain 'I' and resid 48 through 58
    Processing helix  chain 'I' and resid 62 through 84
    Processing helix  chain 'I' and resid 100 through 105
    Processing helix  chain 'I' and resid 110 through 119
    Processing helix  chain 'I' and resid 125 through 146
    Processing helix  chain 'I' and resid 149 through 153
    Processing helix  chain 'I' and resid 160 through 175
      removed outlier: 3.723A  pdb=" N   ALA I 174 " --> pdb=" O   LYS I 170 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 178 through 193
      removed outlier: 4.505A  pdb=" N   LEU I 190 " --> pdb=" O   THR I 186 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   VAL I 191 " --> pdb=" O   GLU I 187 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 195 through 206
      removed outlier: 3.651A  pdb=" N   GLY I 206 " --> pdb=" O   LEU I 202 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 210 through 219
    Processing helix  chain 'K' and resid 16 through 31
    Processing helix  chain 'K' and resid 35 through 44
    Processing helix  chain 'K' and resid 48 through 58
    Processing helix  chain 'K' and resid 62 through 84
    Processing helix  chain 'K' and resid 100 through 105
    Processing helix  chain 'K' and resid 110 through 119
    Processing helix  chain 'K' and resid 125 through 146
    Processing helix  chain 'K' and resid 149 through 153
    Processing helix  chain 'K' and resid 160 through 175
      removed outlier: 3.723A  pdb=" N   ALA K 174 " --> pdb=" O   LYS K 170 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 178 through 193
      removed outlier: 4.505A  pdb=" N   LEU K 190 " --> pdb=" O   THR K 186 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   VAL K 191 " --> pdb=" O   GLU K 187 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 195 through 206
      removed outlier: 3.650A  pdb=" N   GLY K 206 " --> pdb=" O   LEU K 202 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 210 through 219
    Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4
    Processing sheet with id=2, first strand: chain 'C' and resid 2 through 4
    Processing sheet with id=3, first strand: chain 'E' and resid 2 through 4
    Processing sheet with id=4, first strand: chain 'G' and resid 2 through 4
    Processing sheet with id=5, first strand: chain 'I' and resid 2 through 4
    Processing sheet with id=6, first strand: chain 'K' and resid 2 through 4

    648 hydrogen bonds defined for protein.
    1908 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: 1.61

  Time building geometry restraints manager: 1.32 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1776
        1.29 -     1.42: 2508
        1.42 -     1.55: 6312
        1.55 -     1.68: 18
        1.68 -     1.81: 132
  Bond restraints: 10746
  Sorted by residual:
  bond pdb=" CA  ALA I 177 "
       pdb=" C   ALA I 177 "
    ideal  model  delta    sigma   weight residual
    1.525  1.428  0.097 1.28e-02 6.10e+03 5.74e+01
  bond pdb=" CA  ALA C 177 "
       pdb=" C   ALA C 177 "
    ideal  model  delta    sigma   weight residual
    1.525  1.428  0.097 1.28e-02 6.10e+03 5.74e+01
  bond pdb=" CA  ALA G 177 "
       pdb=" C   ALA G 177 "
    ideal  model  delta    sigma   weight residual
    1.525  1.428  0.097 1.28e-02 6.10e+03 5.72e+01
  bond pdb=" CA  ALA A 177 "
       pdb=" C   ALA A 177 "
    ideal  model  delta    sigma   weight residual
    1.525  1.428  0.097 1.28e-02 6.10e+03 5.72e+01
  bond pdb=" CA  ALA E 177 "
       pdb=" C   ALA E 177 "
    ideal  model  delta    sigma   weight residual
    1.525  1.428  0.097 1.28e-02 6.10e+03 5.68e+01
  ... (remaining 10741 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 13266
        1.39 -     2.78: 1026
        2.78 -     4.17: 276
        4.17 -     5.56: 36
        5.56 -     6.95: 18
  Bond angle restraints: 14622
  Sorted by residual:
  angle pdb=" N   ALA C 177 "
        pdb=" CA  ALA C 177 "
        pdb=" C   ALA C 177 "
      ideal   model   delta    sigma   weight residual
     110.35  117.30   -6.95 1.36e+00 5.41e-01 2.61e+01
  angle pdb=" N   ALA I 177 "
        pdb=" CA  ALA I 177 "
        pdb=" C   ALA I 177 "
      ideal   model   delta    sigma   weight residual
     110.35  117.30   -6.95 1.36e+00 5.41e-01 2.61e+01
  angle pdb=" N   ALA K 177 "
        pdb=" CA  ALA K 177 "
        pdb=" C   ALA K 177 "
      ideal   model   delta    sigma   weight residual
     110.35  117.29   -6.94 1.36e+00 5.41e-01 2.60e+01
  angle pdb=" N   ALA E 177 "
        pdb=" CA  ALA E 177 "
        pdb=" C   ALA E 177 "
      ideal   model   delta    sigma   weight residual
     110.35  117.29   -6.94 1.36e+00 5.41e-01 2.60e+01
  angle pdb=" N   ALA G 177 "
        pdb=" CA  ALA G 177 "
        pdb=" C   ALA G 177 "
      ideal   model   delta    sigma   weight residual
     110.35  117.25   -6.90 1.36e+00 5.41e-01 2.57e+01
  ... (remaining 14617 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.12: 6012
       15.12 -    30.23: 396
       30.23 -    45.35: 96
       45.35 -    60.46: 30
       60.46 -    75.58: 12
  Dihedral angle restraints: 6546
    sinusoidal: 2634
      harmonic: 3912
  Sorted by residual:
  dihedral pdb=" CA  PHE C  32 "
           pdb=" C   PHE C  32 "
           pdb=" N   SER C  33 "
           pdb=" CA  SER C  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.91   30.09     0      5.00e+00 4.00e-02 3.62e+01
  dihedral pdb=" CA  PHE I  32 "
           pdb=" C   PHE I  32 "
           pdb=" N   SER I  33 "
           pdb=" CA  SER I  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.91   30.09     0      5.00e+00 4.00e-02 3.62e+01
  dihedral pdb=" CA  PHE K  32 "
           pdb=" C   PHE K  32 "
           pdb=" N   SER K  33 "
           pdb=" CA  SER K  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.92   30.08     0      5.00e+00 4.00e-02 3.62e+01
  ... (remaining 6543 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 1452
       0.084 -    0.167: 162
       0.167 -    0.250: 18
       0.250 -    0.334: 0
       0.334 -    0.417: 6
  Chirality restraints: 1638
  Sorted by residual:
  chirality pdb=" CA  ALA C 177 "
            pdb=" N   ALA C 177 "
            pdb=" C   ALA C 177 "
            pdb=" CB  ALA C 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.07    0.42 2.00e-01 2.50e+01 4.34e+00
  chirality pdb=" CA  ALA I 177 "
            pdb=" N   ALA I 177 "
            pdb=" C   ALA I 177 "
            pdb=" CB  ALA I 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.07    0.42 2.00e-01 2.50e+01 4.34e+00
  chirality pdb=" CA  ALA K 177 "
            pdb=" N   ALA K 177 "
            pdb=" C   ALA K 177 "
            pdb=" CB  ALA K 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.07    0.41 2.00e-01 2.50e+01 4.30e+00
  ... (remaining 1635 not shown)

  Planarity restraints: 1902
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU I 175 "    0.015 2.00e-02 2.50e+03   2.89e-02 8.34e+00
        pdb=" C   GLU I 175 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   GLU I 175 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLN I 176 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 175 "    0.015 2.00e-02 2.50e+03   2.89e-02 8.34e+00
        pdb=" C   GLU A 175 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   GLU A 175 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLN A 176 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU G 175 "   -0.015 2.00e-02 2.50e+03   2.89e-02 8.34e+00
        pdb=" C   GLU G 175 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLU G 175 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLN G 176 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1899 not shown)

  Histogram of nonbonded interaction distances:
        0.65 -     1.50: 12
        1.50 -     2.35: 78
        2.35 -     3.20: 10164
        3.20 -     4.05: 27452
        4.05 -     4.90: 49618
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 87324
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN H 319 "
            pdb=" OE1 GLN I 179 "
     model   vdw
     0.646 3.120
  nonbonded pdb=" NE2 GLN B 319 "
            pdb=" OE1 GLN C 179 "
     model   vdw
     0.646 3.120
  nonbonded pdb=" NE2 GLN J 319 "
            pdb=" OE1 GLN K 179 "
     model   vdw
     0.646 3.120
  nonbonded pdb=" NE2 GLN D 319 "
            pdb=" OE1 GLN E 179 "
     model   vdw
     0.646 3.120
  nonbonded pdb=" OE1 GLN A 179 "
            pdb=" NE2 GLN L 319 "
     model   vdw
     0.647 3.120
  ... (remaining 87319 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'I'
  selection = chain 'K'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
  selection = chain 'J'
  selection = chain 'L'
}

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:             3.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.050
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7174
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      :  0.026   1.037  10752  Z= 2.503
  Angle     :  0.929   6.951  14622  Z= 0.576
  Chirality :  0.059   0.417   1638
  Planarity :  0.008   0.055   1902
  Dihedral  : 12.178  75.578   4002
  Min Nonbonded Distance : 0.646

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  :  0.00 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  0.00 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.49 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (0.20), residues: 1326
  helix: -0.93 (0.14), residues: 870
  sheet: -3.06 (0.31), residues: 54
  loop :  0.80 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.002   ARG A  97 
 TYR   0.026   0.006   TYR C 145 
 PHE   0.014   0.003   PHE B 321 
 TRP   0.009   0.003   TRP E  23 
 HIS   0.008   0.002   HIS C  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00784 (10746)
  covalent geometry    : angle       0.92891 (14622)
  hydrogen bonds       : bond        0.10318 (  648)
  hydrogen bonds       : angle       6.60367 ( 1908)
  Misc. bond           : bond        1.03695 (    6)

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

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

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 226
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 MET cc_start: 0.7951 (tpt) cc_final: 0.7734 (tpp)
REVERT: A   75 GLU cc_start: 0.7905 (pt0) cc_final: 0.7666 (pt0)
REVERT: C   39 MET cc_start: 0.7700 (tpt) cc_final: 0.7151 (tpp)
REVERT: G   39 MET cc_start: 0.7952 (tpt) cc_final: 0.7732 (tpp)
REVERT: G   75 GLU cc_start: 0.7907 (pt0) cc_final: 0.7669 (pt0)
REVERT: I   39 MET cc_start: 0.7691 (tpt) cc_final: 0.7151 (tpp)
  outliers start: 6
  outliers final: 2
  residues processed: 226
  average time/residue: 0.1295
  time to fit residues: 39.1030
Evaluate side-chains
  142 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 140
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 GLN
Chi-restraints excluded: chain G residue  176 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    0.5980
   chunk 91 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  74 ASN
C  74 ASN
E  74 ASN
G  74 ASN
G 176 GLN
I  74 ASN
K  74 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.197785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.163702 restraints weight = 10526.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 1.82
r_work: 0.3801 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  10752  Z= 0.211
  Angle     :  0.676   7.101  14622  Z= 0.356
  Chirality :  0.045   0.172   1638
  Planarity :  0.006   0.042   1902
  Dihedral  :  5.427  45.058   1434
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  :  0.75 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  3.23 %
    Favored  : 95.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.22), residues: 1326
  helix:  0.85 (0.17), residues: 870
  sheet: -1.92 (0.36), residues: 54
  loop :  0.96 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG I 143 
 TYR   0.010   0.002   TYR C 169 
 PHE   0.007   0.001   PHE H 321 
 TRP   0.008   0.001   TRP E 117 
 HIS   0.002   0.001   HIS I  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 (10746)
  covalent geometry    : angle       0.67643 (14622)
  hydrogen bonds       : bond        0.04448 (  648)
  hydrogen bonds       : angle       4.63524 ( 1908)
  Misc. bond           : bond        0.00141 (    6)

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

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

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 170
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 MET cc_start: 0.8061 (tpt) cc_final: 0.7418 (tpp)
REVERT: A  176 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6571 (pt0)
REVERT: C   39 MET cc_start: 0.7869 (tpt) cc_final: 0.7284 (tpp)
REVERT: C   66 MET cc_start: 0.8221 (mmt) cc_final: 0.7737 (mmt)
REVERT: E   66 MET cc_start: 0.8156 (mmt) cc_final: 0.7620 (mmt)
REVERT: G   39 MET cc_start: 0.8087 (tpt) cc_final: 0.7448 (tpp)
REVERT: G  176 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6560 (pt0)
REVERT: I   39 MET cc_start: 0.7871 (tpt) cc_final: 0.7277 (tpp)
REVERT: I   66 MET cc_start: 0.8245 (mmt) cc_final: 0.7767 (mmt)
REVERT: K   66 MET cc_start: 0.8159 (mmt) cc_final: 0.7628 (mmt)
  outliers start: 18
  outliers final: 6
  residues processed: 174
  average time/residue: 0.1095
  time to fit residues: 26.5113
Evaluate side-chains
  166 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 158
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  176 GLN
Chi-restraints excluded: chain E residue  104 ILE
Chi-restraints excluded: chain E residue  115 ILE
Chi-restraints excluded: chain G residue  146 SER
Chi-restraints excluded: chain G residue  176 GLN
Chi-restraints excluded: chain K residue  104 ILE
Chi-restraints excluded: chain K residue  115 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 118 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0010
   chunk 101 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 108 optimal weight:    2.9990
   overall best weight:    0.5786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.206058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.176026 restraints weight = 10744.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 1.65
r_work: 0.3802 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3629 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.2984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10752  Z= 0.149
  Angle     :  0.578   7.049  14622  Z= 0.298
  Chirality :  0.041   0.149   1638
  Planarity :  0.005   0.042   1902
  Dihedral  :  4.992  47.853   1434
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  1.81 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  4.84 %
    Favored  : 93.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.23), residues: 1326
  helix:  1.20 (0.17), residues: 870
  sheet: -1.35 (0.37), residues: 54
  loop :  1.07 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 143 
 TYR   0.008   0.001   TYR C 169 
 PHE   0.006   0.001   PHE K  32 
 TRP   0.009   0.001   TRP G 117 
 HIS   0.002   0.001   HIS G  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (10746)
  covalent geometry    : angle       0.57814 (14622)
  hydrogen bonds       : bond        0.03742 (  648)
  hydrogen bonds       : angle       4.28012 ( 1908)
  Misc. bond           : bond        0.00033 (    6)

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

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

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8368 (mttt) cc_final: 0.8117 (mttm)
REVERT: A   39 MET cc_start: 0.8181 (tpt) cc_final: 0.7875 (mmt)
REVERT: C   25 LYS cc_start: 0.8376 (mttt) cc_final: 0.8124 (mttm)
REVERT: D  319 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7834 (pt0)
REVERT: G   25 LYS cc_start: 0.8421 (mttt) cc_final: 0.8152 (mttm)
REVERT: G   39 MET cc_start: 0.8188 (tpt) cc_final: 0.7890 (mmt)
REVERT: I   25 LYS cc_start: 0.8324 (mttt) cc_final: 0.8087 (mttm)
REVERT: J  319 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7835 (pt0)
  outliers start: 18
  outliers final: 8
  residues processed: 178
  average time/residue: 0.0990
  time to fit residues: 24.8275
Evaluate side-chains
  168 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 160
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 GLN
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain E residue  104 ILE
Chi-restraints excluded: chain E residue  212 GLU
Chi-restraints excluded: chain G residue  176 GLN
Chi-restraints excluded: chain G residue  212 GLU
Chi-restraints excluded: chain K residue  104 ILE
Chi-restraints excluded: chain K residue  212 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 110 optimal weight:    2.9990
   chunk 120 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  21 ASN
G 179 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.202438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.172431 restraints weight = 10770.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 1.66
r_work: 0.3760 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3588 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
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      :  0.005   0.034  10752  Z= 0.185
  Angle     :  0.600   6.979  14622  Z= 0.309
  Chirality :  0.042   0.160   1638
  Planarity :  0.005   0.046   1902
  Dihedral  :  4.902  48.928   1434
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  1.51 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  6.18 %
    Favored  : 92.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.23), residues: 1326
  helix:  1.24 (0.17), residues: 870
  sheet: -1.09 (0.45), residues: 54
  loop :  1.16 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 143 
 TYR   0.008   0.001   TYR I 169 
 PHE   0.006   0.001   PHE E  32 
 TRP   0.009   0.001   TRP A 117 
 HIS   0.004   0.001   HIS G  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (10746)
  covalent geometry    : angle       0.59991 (14622)
  hydrogen bonds       : bond        0.03781 (  648)
  hydrogen bonds       : angle       4.33976 ( 1908)
  Misc. bond           : bond        0.00015 (    6)

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

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

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 MET cc_start: 0.8233 (tpt) cc_final: 0.7938 (mmt)
REVERT: B  319 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7780 (pt0)
REVERT: C   25 LYS cc_start: 0.8439 (mttt) cc_final: 0.8226 (mttm)
REVERT: C   39 MET cc_start: 0.7795 (tpp) cc_final: 0.7456 (tpp)
REVERT: C  144 MET cc_start: 0.8232 (tpp) cc_final: 0.7982 (tpp)
REVERT: D  319 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7850 (pt0)
REVERT: G   39 MET cc_start: 0.8248 (tpt) cc_final: 0.7958 (mmt)
REVERT: H  319 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7780 (pt0)
REVERT: I   25 LYS cc_start: 0.8432 (mttt) cc_final: 0.8213 (mttm)
REVERT: I   39 MET cc_start: 0.7791 (tpp) cc_final: 0.7451 (tpp)
REVERT: I  144 MET cc_start: 0.8216 (tpp) cc_final: 0.7963 (tpp)
REVERT: J  319 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7861 (pt0)
  outliers start: 14
  outliers final: 10
  residues processed: 183
  average time/residue: 0.1054
  time to fit residues: 26.9926
Evaluate side-chains
  192 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 182
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 GLN
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain E residue  104 ILE
Chi-restraints excluded: chain E residue  212 GLU
Chi-restraints excluded: chain G residue  176 GLN
Chi-restraints excluded: chain G residue  212 GLU
Chi-restraints excluded: chain I residue  186 THR
Chi-restraints excluded: chain K residue  104 ILE
Chi-restraints excluded: chain K residue  212 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 47 optimal weight:    0.3980
   chunk 106 optimal weight:    1.9990
   chunk 33 optimal weight:    0.1980
   chunk 85 optimal weight:    4.9990
   chunk 116 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0270
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.6840

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.206647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.185483 restraints weight = 10533.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.4026 rms_B_bonded: 1.33
r_work: 0.3879 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3736 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  10752  Z= 0.152
  Angle     :  0.571   7.073  14622  Z= 0.294
  Chirality :  0.040   0.150   1638
  Planarity :  0.005   0.047   1902
  Dihedral  :  4.822  48.809   1434
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  1.43 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  7.26 %
    Favored  : 91.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.70 (0.23), residues: 1326
  helix:  1.36 (0.17), residues: 870
  sheet: -0.80 (0.53), residues: 54
  loop :  1.20 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 154 
 TYR   0.008   0.001   TYR C 169 
 PHE   0.008   0.001   PHE E  32 
 TRP   0.008   0.001   TRP G 117 
 HIS   0.002   0.001   HIS K  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (10746)
  covalent geometry    : angle       0.57138 (14622)
  hydrogen bonds       : bond        0.03558 (  648)
  hydrogen bonds       : angle       4.25271 ( 1908)
  Misc. bond           : bond        0.00016 (    6)

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

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

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 182
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7166 (tt0)
REVERT: C   39 MET cc_start: 0.7767 (tpp) cc_final: 0.7378 (tpp)
REVERT: C  117 TRP cc_start: 0.7702 (m-10) cc_final: 0.7342 (m-10)
REVERT: C  144 MET cc_start: 0.8074 (tpp) cc_final: 0.7812 (tpp)
REVERT: C  176 GLN cc_start: 0.6928 (pt0) cc_final: 0.6609 (pm20)
REVERT: G  113 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7162 (tt0)
REVERT: I   39 MET cc_start: 0.7779 (tpp) cc_final: 0.7390 (tpp)
REVERT: I  117 TRP cc_start: 0.7693 (m-10) cc_final: 0.7332 (m-10)
REVERT: I  144 MET cc_start: 0.8050 (tpp) cc_final: 0.7787 (tpp)
REVERT: I  176 GLN cc_start: 0.6940 (pt0) cc_final: 0.6618 (pm20)
  outliers start: 14
  outliers final: 10
  residues processed: 190
  average time/residue: 0.0880
  time to fit residues: 23.3318
Evaluate side-chains
  170 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 160
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 GLN
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain E residue  104 ILE
Chi-restraints excluded: chain E residue  212 GLU
Chi-restraints excluded: chain G residue  176 GLN
Chi-restraints excluded: chain G residue  212 GLU
Chi-restraints excluded: chain I residue  186 THR
Chi-restraints excluded: chain K residue  104 ILE
Chi-restraints excluded: chain K residue  212 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 122 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 131 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 103 optimal weight:    1.9990
   chunk 95 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0470
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 179 GLN
** I 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.185867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.150351 restraints weight = 10898.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 1.87
r_work: 0.3384 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.3645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  10752  Z= 0.150
  Angle     :  0.565   7.045  14622  Z= 0.291
  Chirality :  0.040   0.147   1638
  Planarity :  0.005   0.050   1902
  Dihedral  :  4.767  49.626   1434
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  1.81 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  7.97 %
    Favored  : 90.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.23), residues: 1326
  helix:  1.44 (0.18), residues: 870
  sheet: -0.67 (0.58), residues: 54
  loop :  1.29 (0.34), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I 154 
 TYR   0.007   0.001   TYR C 169 
 PHE   0.007   0.001   PHE K  32 
 TRP   0.007   0.001   TRP G 117 
 HIS   0.002   0.001   HIS K  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (10746)
  covalent geometry    : angle       0.56476 (14622)
  hydrogen bonds       : bond        0.03463 (  648)
  hydrogen bonds       : angle       4.21334 ( 1908)
  Misc. bond           : bond        0.00011 (    6)

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

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

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 155
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 ARG cc_start: 0.7542 (ttm170) cc_final: 0.7213 (ttm170)
REVERT: C   39 MET cc_start: 0.7625 (tpp) cc_final: 0.7183 (tpp)
REVERT: C  117 TRP cc_start: 0.7583 (m-10) cc_final: 0.7121 (m-10)
REVERT: C  144 MET cc_start: 0.8253 (tpp) cc_final: 0.7965 (tpp)
REVERT: G   82 ARG cc_start: 0.7528 (ttm170) cc_final: 0.7197 (ttm170)
REVERT: I   39 MET cc_start: 0.7654 (tpp) cc_final: 0.7210 (tpp)
REVERT: I  117 TRP cc_start: 0.7575 (m-10) cc_final: 0.7110 (m-10)
REVERT: I  144 MET cc_start: 0.8234 (tpp) cc_final: 0.7940 (tpp)
  outliers start: 18
  outliers final: 14
  residues processed: 167
  average time/residue: 0.1199
  time to fit residues: 27.8424
Evaluate side-chains
  162 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 GLN
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  212 GLU
Chi-restraints excluded: chain E residue  104 ILE
Chi-restraints excluded: chain E residue  212 GLU
Chi-restraints excluded: chain G residue  176 GLN
Chi-restraints excluded: chain G residue  186 THR
Chi-restraints excluded: chain G residue  212 GLU
Chi-restraints excluded: chain I residue  186 THR
Chi-restraints excluded: chain I residue  212 GLU
Chi-restraints excluded: chain K residue  104 ILE
Chi-restraints excluded: chain K residue  212 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 99 optimal weight:    0.4980
   chunk 85 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 46 optimal weight:    0.4980
   chunk 10 optimal weight:    0.8980
   chunk 117 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
C 176 GLN
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 176 GLN
I 179 GLN
K 179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.205588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.185170 restraints weight = 10641.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 1.25
r_work: 0.3548 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.3767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  10752  Z= 0.157
  Angle     :  0.566   7.086  14622  Z= 0.294
  Chirality :  0.041   0.150   1638
  Planarity :  0.005   0.052   1902
  Dihedral  :  4.742  50.310   1434
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  1.81 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  8.33 %
    Favored  : 90.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.24), residues: 1326
  helix:  1.48 (0.18), residues: 864
  sheet: -0.51 (0.61), residues: 54
  loop :  1.38 (0.34), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 154 
 TYR   0.007   0.001   TYR K 169 
 PHE   0.007   0.001   PHE K  32 
 TRP   0.007   0.001   TRP G 117 
 HIS   0.002   0.001   HIS E  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (10746)
  covalent geometry    : angle       0.56573 (14622)
  hydrogen bonds       : bond        0.03500 (  648)
  hydrogen bonds       : angle       4.26838 ( 1908)
  Misc. bond           : bond        0.00008 (    6)

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

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

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 ARG cc_start: 0.7485 (ttm170) cc_final: 0.7166 (ttm170)
REVERT: A  185 MET cc_start: 0.8395 (mtm) cc_final: 0.8180 (mtt)
REVERT: C   39 MET cc_start: 0.7720 (tpp) cc_final: 0.7320 (tpp)
REVERT: C  117 TRP cc_start: 0.7613 (m-10) cc_final: 0.7241 (m-10)
REVERT: C  144 MET cc_start: 0.8199 (tpp) cc_final: 0.7932 (tpp)
REVERT: G   82 ARG cc_start: 0.7488 (ttm170) cc_final: 0.7166 (ttm170)
REVERT: G  185 MET cc_start: 0.8392 (mtm) cc_final: 0.8181 (mtt)
REVERT: I   39 MET cc_start: 0.7678 (tpp) cc_final: 0.7281 (tpp)
REVERT: I  117 TRP cc_start: 0.7590 (m-10) cc_final: 0.7217 (m-10)
REVERT: I  144 MET cc_start: 0.8164 (tpp) cc_final: 0.7888 (tpp)
  outliers start: 18
  outliers final: 16
  residues processed: 164
  average time/residue: 0.1143
  time to fit residues: 26.0515
Evaluate side-chains
  169 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue  176 GLN
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  212 GLU
Chi-restraints excluded: chain E residue  104 ILE
Chi-restraints excluded: chain E residue  212 GLU
Chi-restraints excluded: chain G residue   15 ILE
Chi-restraints excluded: chain G residue  176 GLN
Chi-restraints excluded: chain G residue  186 THR
Chi-restraints excluded: chain G residue  212 GLU
Chi-restraints excluded: chain I residue  186 THR
Chi-restraints excluded: chain I residue  212 GLU
Chi-restraints excluded: chain K residue  104 ILE
Chi-restraints excluded: chain K residue  212 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 124 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 110 optimal weight:    0.0010
   chunk 20 optimal weight:    0.9980
   chunk 12 optimal weight:    0.2980
   chunk 55 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 113 optimal weight:    0.0770
   overall best weight:    0.4144

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

Flipped N/Q/H residues before XYZ refinement:
C 176 GLN
C 179 GLN
** E  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 176 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.203169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.187964 restraints weight = 10639.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 0.81
r_work: 0.3629 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3480 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.3947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10752  Z= 0.120
  Angle     :  0.529   7.252  14622  Z= 0.273
  Chirality :  0.039   0.139   1638
  Planarity :  0.005   0.052   1902
  Dihedral  :  4.615  53.284   1434
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  1.51 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  :  7.97 %
    Favored  : 90.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.23), residues: 1326
  helix:  1.60 (0.17), residues: 864
  sheet: -0.18 (0.61), residues: 54
  loop :  1.36 (0.34), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 154 
 TYR   0.007   0.001   TYR E 169 
 PHE   0.009   0.001   PHE K  32 
 TRP   0.007   0.001   TRP E  23 
 HIS   0.001   0.000   HIS K  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (10746)
  covalent geometry    : angle       0.52859 (14622)
  hydrogen bonds       : bond        0.03278 (  648)
  hydrogen bonds       : angle       4.14306 ( 1908)
  Misc. bond           : bond        0.00008 (    6)

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

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

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7659 (mmt)
REVERT: A   82 ARG cc_start: 0.7524 (ttm170) cc_final: 0.7277 (ttm170)
REVERT: C  144 MET cc_start: 0.8097 (tpp) cc_final: 0.7817 (tpp)
REVERT: E   39 MET cc_start: 0.7245 (tpp) cc_final: 0.7039 (mmt)
REVERT: G   39 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7687 (mmt)
REVERT: G   82 ARG cc_start: 0.7494 (ttm170) cc_final: 0.7246 (ttm170)
REVERT: I  144 MET cc_start: 0.8098 (tpp) cc_final: 0.7809 (tpp)
REVERT: K   39 MET cc_start: 0.7233 (tpp) cc_final: 0.7027 (mmt)
  outliers start: 20
  outliers final: 12
  residues processed: 144
  average time/residue: 0.1140
  time to fit residues: 22.3373
Evaluate side-chains
  146 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue   39 MET
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  176 GLN
Chi-restraints excluded: chain C residue  212 GLU
Chi-restraints excluded: chain E residue  104 ILE
Chi-restraints excluded: chain E residue  212 GLU
Chi-restraints excluded: chain G residue   15 ILE
Chi-restraints excluded: chain G residue   39 MET
Chi-restraints excluded: chain G residue  146 SER
Chi-restraints excluded: chain G residue  176 GLN
Chi-restraints excluded: chain I residue  212 GLU
Chi-restraints excluded: chain K residue  104 ILE
Chi-restraints excluded: chain K residue  212 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 112 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   chunk 127 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0770
   chunk 104 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0030
   chunk 65 optimal weight:    0.4980
   chunk 111 optimal weight:    0.8980
   chunk 90 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0870
   chunk 117 optimal weight:    0.9990
   overall best weight:    0.2926

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

Flipped N/Q/H residues before XYZ refinement:
A 176 GLN
C 176 GLN
E  21 ASN
I 176 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.190429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.156170 restraints weight = 10860.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 1.81
r_work: 0.3454 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.4096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10752  Z= 0.111
  Angle     :  0.522   7.081  14622  Z= 0.269
  Chirality :  0.039   0.131   1638
  Planarity :  0.005   0.051   1902
  Dihedral  :  4.486  54.280   1434
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  1.66 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  8.78 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.17 (0.23), residues: 1326
  helix:  1.72 (0.17), residues: 864
  sheet:  0.01 (0.62), residues: 54
  loop :  1.30 (0.34), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 143 
 TYR   0.007   0.001   TYR E 169 
 PHE   0.009   0.001   PHE E  32 
 TRP   0.006   0.001   TRP K  23 
 HIS   0.002   0.000   HIS E  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (10746)
  covalent geometry    : angle       0.52195 (14622)
  hydrogen bonds       : bond        0.03202 (  648)
  hydrogen bonds       : angle       4.05932 ( 1908)
  Misc. bond           : bond        0.00010 (    6)

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

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

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7565 (mmt)
REVERT: C  144 MET cc_start: 0.8158 (tpp) cc_final: 0.7891 (tpp)
REVERT: E   39 MET cc_start: 0.7237 (tpp) cc_final: 0.7006 (mmt)
REVERT: E  185 MET cc_start: 0.8303 (mtm) cc_final: 0.8055 (mtt)
REVERT: G   39 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7582 (mmt)
REVERT: I  144 MET cc_start: 0.8134 (tpp) cc_final: 0.7856 (tpp)
REVERT: K   39 MET cc_start: 0.7230 (tpp) cc_final: 0.7001 (mmt)
REVERT: K  185 MET cc_start: 0.8306 (mtm) cc_final: 0.8056 (mtt)
  outliers start: 16
  outliers final: 8
  residues processed: 146
  average time/residue: 0.1198
  time to fit residues: 24.0796
Evaluate side-chains
  138 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 MET
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  176 GLN
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain C residue  212 GLU
Chi-restraints excluded: chain G residue   39 MET
Chi-restraints excluded: chain G residue  146 SER
Chi-restraints excluded: chain G residue  176 GLN
Chi-restraints excluded: chain G residue  212 GLU
Chi-restraints excluded: chain I residue  212 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 122 optimal weight:    0.3980
   chunk 76 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0570
   chunk 55 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0980
   chunk 111 optimal weight:    0.7980
   chunk 99 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.3898

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

Flipped N/Q/H residues before XYZ refinement:
C 176 GLN
I 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.197190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.163697 restraints weight = 10789.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 1.86
r_work: 0.3440 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.4155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10752  Z= 0.118
  Angle     :  0.525   6.948  14622  Z= 0.272
  Chirality :  0.039   0.133   1638
  Planarity :  0.005   0.052   1902
  Dihedral  :  4.431  54.775   1434
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  2.11 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  8.78 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.21 (0.23), residues: 1326
  helix:  1.76 (0.17), residues: 864
  sheet:  0.07 (0.62), residues: 54
  loop :  1.26 (0.34), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 154 
 TYR   0.007   0.001   TYR A 169 
 PHE   0.009   0.001   PHE E  32 
 TRP   0.009   0.001   TRP E  23 
 HIS   0.001   0.000   HIS K  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10746)
  covalent geometry    : angle       0.52454 (14622)
  hydrogen bonds       : bond        0.03184 (  648)
  hydrogen bonds       : angle       4.07502 ( 1908)
  Misc. bond           : bond        0.00006 (    6)

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

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

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2652 Ramachandran restraints generated.
    1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7574 (mmt)
REVERT: C  144 MET cc_start: 0.8141 (tpp) cc_final: 0.7842 (tpp)
REVERT: E   39 MET cc_start: 0.7253 (tpp) cc_final: 0.7028 (mmt)
REVERT: E  185 MET cc_start: 0.8323 (mtm) cc_final: 0.7990 (mtt)
REVERT: G   39 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7571 (mmt)
REVERT: I  144 MET cc_start: 0.8118 (tpp) cc_final: 0.7810 (tpp)
REVERT: K   39 MET cc_start: 0.7225 (tpp) cc_final: 0.7005 (mmt)
REVERT: K  185 MET cc_start: 0.8321 (mtm) cc_final: 0.7985 (mtt)
  outliers start: 16
  outliers final: 10
  residues processed: 134
  average time/residue: 0.1043
  time to fit residues: 19.6953
Evaluate side-chains
  132 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 MET
Chi-restraints excluded: chain A residue  176 GLN
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain C residue  212 GLU
Chi-restraints excluded: chain E residue  200 THR
Chi-restraints excluded: chain E residue  212 GLU
Chi-restraints excluded: chain G residue   39 MET
Chi-restraints excluded: chain G residue  176 GLN
Chi-restraints excluded: chain G residue  212 GLU
Chi-restraints excluded: chain I residue  212 GLU
Chi-restraints excluded: chain K residue  200 THR
Chi-restraints excluded: chain K residue  212 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 129 optimal weight:    0.0770
   chunk 99 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    0.3980
   chunk 77 optimal weight:    0.0970
   chunk 82 optimal weight:    0.0470
   chunk 59 optimal weight:    0.3980
   chunk 29 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.2034

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.193257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.159233 restraints weight = 10877.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 1.83
r_work: 0.3491 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.4362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10752  Z= 0.103
  Angle     :  0.505   6.952  14622  Z= 0.262
  Chirality :  0.038   0.126   1638
  Planarity :  0.005   0.051   1902
  Dihedral  :  4.358  59.718   1434
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  1.21 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  9.23 %
    Favored  : 89.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.19 (0.23), residues: 1326
  helix:  1.75 (0.17), residues: 882
  sheet:  0.17 (0.62), residues: 54
  loop :  1.22 (0.35), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 143 
 TYR   0.007   0.001   TYR A 169 
 PHE   0.009   0.001   PHE K  32 
 TRP   0.012   0.001   TRP E  23 
 HIS   0.001   0.000   HIS A  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (10746)
  covalent geometry    : angle       0.50490 (14622)
  hydrogen bonds       : bond        0.03095 (  648)
  hydrogen bonds       : angle       3.99919 ( 1908)
  Misc. bond           : bond        0.00007 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2314.94 seconds
wall clock time: 40 minutes 26.48 seconds (2426.48 seconds total)