Starting phenix.real_space_refine
on Thu Feb 13 18:39:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7z23_14456/02_2025/7z23_14456.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7z23_14456/02_2025/7z23_14456.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7z23_14456/02_2025/7z23_14456.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7z23_14456/02_2025/7z23_14456.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7z23_14456/02_2025/7z23_14456.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7z23_14456/02_2025/7z23_14456.cif"
  }
  resolution = 3.98
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    6198      2.51       5
     N    1446      2.21       5
     O    1554      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-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9246
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1541
          Classifications: {'peptide': 189}
          Link IDs: {'PTRANS': 6, 'TRANS': 182}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 4.40, per 1000 atoms: 0.48
  Number of scatterers: 9246
  At special positions: 0
  Unit cell: (101.37, 105.294, 86.328, 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      48     16.00
     O    1554      8.00
     N    1446      7.00
     C    6198      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  54 " - pdb=" SG  CYS E 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  61 " - pdb=" SG  CYS E 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  65 " - pdb=" SG  CYS E 187 " distance=2.03

  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: 2.35
  Conformation dependent library (CDL) restraints added in 942.2 milliseconds
  

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 6 sheets defined
      77.8% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'E' and resid 3 through 15
      removed outlier: 4.297A  pdb=" N   LEU E   7 " --> pdb=" O   ASP E   3 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 21 through 45
      removed outlier: 4.404A  pdb=" N   TRP E  25 " --> pdb=" O   GLY E  21 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   VAL E  41 " --> pdb=" O   LEU E  37 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   GLU E  42 " --> pdb=" O   GLY E  38 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 47 through 52
    Processing helix  chain 'E' and resid 60 through 70
    Processing helix  chain 'E' and resid 73 through 103
      Proline residue:  E  88  - end of helix
    Processing helix  chain 'E' and resid 152 through 178
    Processing helix  chain 'E' and resid 202 through 235
    Processing helix  chain 'A' and resid 3 through 15
      removed outlier: 4.298A  pdb=" N   LEU A   7 " --> pdb=" O   ASP A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 45
      removed outlier: 4.404A  pdb=" N   TRP A  25 " --> pdb=" O   GLY A  21 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   VAL A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   GLU A  42 " --> pdb=" O   GLY A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 52
    Processing helix  chain 'A' and resid 60 through 70
    Processing helix  chain 'A' and resid 73 through 103
      Proline residue:  A  88  - end of helix
    Processing helix  chain 'A' and resid 152 through 178
    Processing helix  chain 'A' and resid 202 through 235
    Processing helix  chain 'B' and resid 3 through 15
      removed outlier: 4.298A  pdb=" N   LEU B   7 " --> pdb=" O   ASP B   3 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 45
      removed outlier: 4.404A  pdb=" N   TRP B  25 " --> pdb=" O   GLY B  21 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   VAL B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   GLU B  42 " --> pdb=" O   GLY B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 52
    Processing helix  chain 'B' and resid 60 through 70
    Processing helix  chain 'B' and resid 73 through 103
      Proline residue:  B  88  - end of helix
    Processing helix  chain 'B' and resid 152 through 178
    Processing helix  chain 'B' and resid 202 through 235
    Processing helix  chain 'C' and resid 3 through 15
      removed outlier: 4.297A  pdb=" N   LEU C   7 " --> pdb=" O   ASP C   3 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 45
      removed outlier: 4.404A  pdb=" N   TRP C  25 " --> pdb=" O   GLY C  21 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   VAL C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   GLU C  42 " --> pdb=" O   GLY C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 52
    Processing helix  chain 'C' and resid 60 through 70
    Processing helix  chain 'C' and resid 73 through 103
      Proline residue:  C  88  - end of helix
    Processing helix  chain 'C' and resid 152 through 178
    Processing helix  chain 'C' and resid 202 through 235
    Processing helix  chain 'D' and resid 3 through 15
      removed outlier: 4.297A  pdb=" N   LEU D   7 " --> pdb=" O   ASP D   3 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 21 through 45
      removed outlier: 4.404A  pdb=" N   TRP D  25 " --> pdb=" O   GLY D  21 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   VAL D  41 " --> pdb=" O   LEU D  37 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   GLU D  42 " --> pdb=" O   GLY D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 52
    Processing helix  chain 'D' and resid 60 through 70
    Processing helix  chain 'D' and resid 73 through 103
      Proline residue:  D  88  - end of helix
    Processing helix  chain 'D' and resid 152 through 178
    Processing helix  chain 'D' and resid 202 through 235
    Processing helix  chain 'F' and resid 3 through 15
      removed outlier: 4.297A  pdb=" N   LEU F   7 " --> pdb=" O   ASP F   3 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 21 through 45
      removed outlier: 4.404A  pdb=" N   TRP F  25 " --> pdb=" O   GLY F  21 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   VAL F  41 " --> pdb=" O   LEU F  37 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   GLU F  42 " --> pdb=" O   GLY F  38 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 47 through 52
    Processing helix  chain 'F' and resid 60 through 70
    Processing helix  chain 'F' and resid 73 through 103
      Proline residue:  F  88  - end of helix
    Processing helix  chain 'F' and resid 152 through 178
    Processing helix  chain 'F' and resid 202 through 235
    Processing sheet with id=AA1, first strand: chain 'E' and resid 53 through 54
      removed outlier: 4.532A  pdb=" N   ARG E  53 " --> pdb=" O   PHE E 199 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   PHE E 199 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54
      removed outlier: 4.532A  pdb=" N   ARG A  53 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   PHE A 199 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54
      removed outlier: 4.532A  pdb=" N   ARG B  53 " --> pdb=" O   PHE B 199 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   PHE B 199 " --> pdb=" O   ARG B  53 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 54
      removed outlier: 4.532A  pdb=" N   ARG C  53 " --> pdb=" O   PHE C 199 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   PHE C 199 " --> pdb=" O   ARG C  53 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 53 through 54
      removed outlier: 4.532A  pdb=" N   ARG D  53 " --> pdb=" O   PHE D 199 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   PHE D 199 " --> pdb=" O   ARG D  53 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54
      removed outlier: 4.532A  pdb=" N   ARG F  53 " --> pdb=" O   PHE F 199 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   PHE F 199 " --> pdb=" O   ARG F  53 " (cutoff:3.500A)

    684 hydrogen bonds defined for protein.
    2034 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.50

  Time building geometry restraints manager: 2.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2676
        1.34 -     1.46: 2079
        1.46 -     1.58: 4689
        1.58 -     1.70: 0
        1.70 -     1.81: 60
  Bond restraints: 9504
  Sorted by residual:
  bond pdb=" C   VAL D  87 "
       pdb=" N   PRO D  88 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.025 1.28e-02 6.10e+03 3.72e+00
  bond pdb=" C   VAL E  87 "
       pdb=" N   PRO E  88 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.025 1.28e-02 6.10e+03 3.68e+00
  bond pdb=" C   ASP C 190 "
       pdb=" N   PRO C 191 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.023 1.19e-02 7.06e+03 3.58e+00
  bond pdb=" C   VAL C  87 "
       pdb=" N   PRO C  88 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.28e-02 6.10e+03 3.54e+00
  bond pdb=" C   VAL F  87 "
       pdb=" N   PRO F  88 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.28e-02 6.10e+03 3.50e+00
  ... (remaining 9499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 11921
        1.49 -     2.98: 772
        2.98 -     4.47: 120
        4.47 -     5.96: 75
        5.96 -     7.46: 12
  Bond angle restraints: 12900
  Sorted by residual:
  angle pdb=" N   ARG D  76 "
        pdb=" CA  ARG D  76 "
        pdb=" C   ARG D  76 "
      ideal   model   delta    sigma   weight residual
     111.36  107.02    4.34 1.09e+00 8.42e-01 1.59e+01
  angle pdb=" N   ARG B  76 "
        pdb=" CA  ARG B  76 "
        pdb=" C   ARG B  76 "
      ideal   model   delta    sigma   weight residual
     111.36  107.05    4.31 1.09e+00 8.42e-01 1.56e+01
  angle pdb=" N   ARG A  76 "
        pdb=" CA  ARG A  76 "
        pdb=" C   ARG A  76 "
      ideal   model   delta    sigma   weight residual
     111.36  107.06    4.30 1.09e+00 8.42e-01 1.56e+01
  angle pdb=" N   ARG E  76 "
        pdb=" CA  ARG E  76 "
        pdb=" C   ARG E  76 "
      ideal   model   delta    sigma   weight residual
     111.36  107.06    4.30 1.09e+00 8.42e-01 1.55e+01
  angle pdb=" N   ARG C  76 "
        pdb=" CA  ARG C  76 "
        pdb=" C   ARG C  76 "
      ideal   model   delta    sigma   weight residual
     111.36  107.07    4.29 1.09e+00 8.42e-01 1.55e+01
  ... (remaining 12895 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 4809
       15.94 -    31.87: 544
       31.87 -    47.81: 109
       47.81 -    63.75: 13
       63.75 -    79.68: 12
  Dihedral angle restraints: 5487
    sinusoidal: 2151
      harmonic: 3336
  Sorted by residual:
  dihedral pdb=" CB  CYS E  61 "
           pdb=" SG  CYS E  61 "
           pdb=" SG  CYS E 192 "
           pdb=" CB  CYS E 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   35.13   57.87     1      1.00e+01 1.00e-02 4.49e+01
  dihedral pdb=" CA  GLY F  21 "
           pdb=" C   GLY F  21 "
           pdb=" N   GLY F  22 "
           pdb=" CA  GLY F  22 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.20  -26.80     0      5.00e+00 4.00e-02 2.87e+01
  dihedral pdb=" CA  GLY B  21 "
           pdb=" C   GLY B  21 "
           pdb=" N   GLY B  22 "
           pdb=" CA  GLY B  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.23  -26.77     0      5.00e+00 4.00e-02 2.87e+01
  ... (remaining 5484 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1168
       0.049 -    0.097: 236
       0.097 -    0.146: 57
       0.146 -    0.194: 4
       0.194 -    0.243: 11
  Chirality restraints: 1476
  Sorted by residual:
  chirality pdb=" CA  TRP C  78 "
            pdb=" N   TRP C  78 "
            pdb=" C   TRP C  78 "
            pdb=" CB  TRP C  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  TRP F  78 "
            pdb=" N   TRP F  78 "
            pdb=" C   TRP F  78 "
            pdb=" CB  TRP F  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  TRP D  78 "
            pdb=" N   TRP D  78 "
            pdb=" C   TRP D  78 "
            pdb=" CB  TRP D  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 1473 not shown)

  Planarity restraints: 1548
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 212 "    0.020 2.00e-02 2.50e+03   1.93e-02 6.51e+00
        pdb=" CG  PHE C 212 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 212 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 212 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 212 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 212 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 212 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 212 "    0.021 2.00e-02 2.50e+03   1.93e-02 6.49e+00
        pdb=" CG  PHE B 212 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 212 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 212 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 212 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 212 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 212 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 212 "   -0.021 2.00e-02 2.50e+03   1.92e-02 6.44e+00
        pdb=" CG  PHE D 212 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 212 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 212 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 212 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 212 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 212 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1545 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 121
        2.60 -     3.18: 8834
        3.18 -     3.75: 15192
        3.75 -     4.33: 18816
        4.33 -     4.90: 29802
  Nonbonded interactions: 72765
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B  61 "
            pdb=" SG  CYS B 192 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS A  61 "
            pdb=" SG  CYS A 192 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS C  61 "
            pdb=" SG  CYS C 192 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS D  61 "
            pdb=" SG  CYS D 192 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS F  61 "
            pdb=" SG  CYS F 192 "
     model   vdw
     2.029 3.760
  ... (remaining 72760 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: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             3.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     21.340
  Find NCS groups from input model:        0.230
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
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      :  0.004   0.033   9504  Z= 0.227
  Angle     :  0.922   7.456  12900  Z= 0.559
  Chirality :  0.047   0.243   1476
  Planarity :  0.006   0.055   1548
  Dihedral  : 14.001  79.684   3318
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 18.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -0.34 (0.25), residues: 1110
  helix:  0.28 (0.18), residues: 864
  sheet:  0.15 (0.69), residues: 60
  loop : -2.31 (0.36), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP E 174 
 HIS   0.009   0.002   HIS B  74 
 PHE   0.045   0.003   PHE C 212 
 TYR   0.009   0.001   TYR E  66 
 ARG   0.004   0.001   ARG F  76 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 339
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  100 MET cc_start: 0.9292 (mpp) cc_final: 0.9054 (mpp)
REVERT: E  224 ASN cc_start: 0.9358 (p0) cc_final: 0.8822 (p0)
REVERT: A  100 MET cc_start: 0.9243 (mpp) cc_final: 0.8991 (mpp)
REVERT: A  166 GLU cc_start: 0.9379 (mt-10) cc_final: 0.9157 (pt0)
REVERT: A  224 ASN cc_start: 0.9365 (p0) cc_final: 0.8832 (p0)
REVERT: B  100 MET cc_start: 0.9155 (mpp) cc_final: 0.8934 (mpp)
REVERT: B  224 ASN cc_start: 0.9298 (p0) cc_final: 0.8725 (p0)
REVERT: C  100 MET cc_start: 0.9306 (mpp) cc_final: 0.9042 (mpp)
REVERT: C  224 ASN cc_start: 0.9348 (p0) cc_final: 0.8789 (p0)
REVERT: D   66 TYR cc_start: 0.8846 (t80) cc_final: 0.8616 (t80)
REVERT: D  100 MET cc_start: 0.9146 (mpp) cc_final: 0.8936 (mpp)
REVERT: D  224 ASN cc_start: 0.9307 (p0) cc_final: 0.8771 (p0)
REVERT: F  100 MET cc_start: 0.9263 (mpp) cc_final: 0.8983 (mpp)
REVERT: F  166 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9161 (pt0)
REVERT: F  224 ASN cc_start: 0.9358 (p0) cc_final: 0.8805 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 339
  average time/residue: 0.2884
  time to fit residues: 125.5117
Evaluate side-chains
  251 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    8.9990
   chunk 81 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 43 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 32 optimal weight:    9.9990
   chunk 51 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   chunk 98 optimal weight:    0.0970
   overall best weight:    1.9984

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

Flipped N/Q/H residues before XYZ refinement:
** E  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 ASN
** C  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  63 ASN ** 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 = 0.3337 r_free = 0.3337 target = 0.062534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.050918 restraints weight = 55496.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.051961 restraints weight = 43025.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 15)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.052720 restraints weight = 35147.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.2661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9504  Z= 0.241
  Angle     :  0.818   9.288  12900  Z= 0.416
  Chirality :  0.047   0.218   1476
  Planarity :  0.005   0.041   1548
  Dihedral  :  4.478  14.726   1218
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 19.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.63 %
    Favored  : 85.10 %
  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: -0.03 (0.24), residues: 1110
  helix:  0.49 (0.17), residues: 870
  sheet:  0.89 (0.61), residues: 60
  loop : -2.47 (0.34), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 174 
 HIS   0.004   0.001   HIS C  74 
 PHE   0.045   0.002   PHE E 212 
 TYR   0.019   0.002   TYR B  66 
 ARG   0.005   0.001   ARG A  76 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 292
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  166 GLU cc_start: 0.8994 (pt0) cc_final: 0.8791 (pt0)
REVERT: E  173 GLN cc_start: 0.9572 (tp-100) cc_final: 0.9366 (tp-100)
REVERT: E  202 ARG cc_start: 0.8503 (tpt170) cc_final: 0.8211 (mtp-110)
REVERT: A   74 HIS cc_start: 0.9522 (m-70) cc_final: 0.9303 (m-70)
REVERT: A  105 LYS cc_start: 0.6536 (mmmt) cc_final: 0.5769 (mmmt)
REVERT: A  155 TYR cc_start: 0.9309 (t80) cc_final: 0.9094 (t80)
REVERT: A  166 GLU cc_start: 0.9400 (mt-10) cc_final: 0.9192 (pt0)
REVERT: A  202 ARG cc_start: 0.8620 (mmp-170) cc_final: 0.8264 (mtm180)
REVERT: A  206 LYS cc_start: 0.9468 (ptpt) cc_final: 0.9114 (mttp)
REVERT: A  209 PHE cc_start: 0.9753 (m-10) cc_final: 0.9458 (m-80)
REVERT: A  224 ASN cc_start: 0.9355 (p0) cc_final: 0.8913 (p0)
REVERT: B   74 HIS cc_start: 0.9510 (m-70) cc_final: 0.9268 (m-70)
REVERT: B  173 GLN cc_start: 0.9549 (tp-100) cc_final: 0.9302 (tp-100)
REVERT: B  206 LYS cc_start: 0.9344 (ptpp) cc_final: 0.9122 (mttp)
REVERT: B  209 PHE cc_start: 0.9791 (m-10) cc_final: 0.9497 (m-80)
REVERT: C  104 GLU cc_start: 0.8342 (tp30) cc_final: 0.8110 (tm-30)
REVERT: C  105 LYS cc_start: 0.6577 (mmmt) cc_final: 0.5775 (mmmt)
REVERT: C  166 GLU cc_start: 0.8980 (pt0) cc_final: 0.8776 (pt0)
REVERT: C  173 GLN cc_start: 0.9574 (tp-100) cc_final: 0.9354 (tp-100)
REVERT: C  202 ARG cc_start: 0.8569 (mmp-170) cc_final: 0.8116 (mtm180)
REVERT: C  206 LYS cc_start: 0.9472 (ptpp) cc_final: 0.9142 (mttp)
REVERT: C  209 PHE cc_start: 0.9777 (m-10) cc_final: 0.9479 (m-80)
REVERT: D   74 HIS cc_start: 0.9504 (m-70) cc_final: 0.9269 (m-70)
REVERT: D  202 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8203 (mtp-110)
REVERT: D  206 LYS cc_start: 0.9439 (ptpp) cc_final: 0.9192 (mttp)
REVERT: D  209 PHE cc_start: 0.9795 (m-10) cc_final: 0.9495 (m-80)
REVERT: F   74 HIS cc_start: 0.9529 (m-70) cc_final: 0.9309 (m-70)
REVERT: F  105 LYS cc_start: 0.6514 (mmmt) cc_final: 0.5724 (mmmt)
REVERT: F  155 TYR cc_start: 0.9314 (t80) cc_final: 0.9095 (t80)
REVERT: F  166 GLU cc_start: 0.9387 (mt-10) cc_final: 0.9178 (pt0)
REVERT: F  202 ARG cc_start: 0.8671 (mmp-170) cc_final: 0.8317 (mtm180)
REVERT: F  206 LYS cc_start: 0.9457 (ptpt) cc_final: 0.9118 (mttp)
REVERT: F  209 PHE cc_start: 0.9742 (m-10) cc_final: 0.9450 (m-80)
REVERT: F  224 ASN cc_start: 0.9340 (p0) cc_final: 0.8881 (p0)
  outliers start: 13
  outliers final: 6
  residues processed: 298
  average time/residue: 0.2875
  time to fit residues: 110.5747
Evaluate side-chains
  267 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 260
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  202 ARG
Chi-restraints excluded: chain F residue   91 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 50 optimal weight:    8.9990
   chunk 55 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 94 optimal weight:    7.9990
   chunk 19 optimal weight:    0.0670
   chunk 13 optimal weight:   10.0000
   chunk 78 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 84 optimal weight:    8.9990
   overall best weight:    1.5722

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

Flipped N/Q/H residues before XYZ refinement:
E  63 ASN
E  95 HIS
E 173 GLN
A  63 ASN
A  95 HIS
B  63 ASN
B  95 HIS
** C  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  95 HIS
C 173 GLN
D  63 ASN
D  95 HIS
F  63 ASN
F  95 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.058472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.047175 restraints weight = 57048.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.048212 restraints weight = 44148.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.048981 restraints weight = 36028.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.3653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9504  Z= 0.220
  Angle     :  0.780  10.902  12900  Z= 0.399
  Chirality :  0.045   0.293   1476
  Planarity :  0.004   0.056   1548
  Dihedral  :  4.198  15.244   1218
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 20.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.88 %
    Favored  : 82.16 %
  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:  0.28 (0.23), residues: 1110
  helix:  0.67 (0.17), residues: 864
  sheet:  1.20 (0.59), residues: 60
  loop : -2.14 (0.34), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  78 
 HIS   0.003   0.001   HIS C  74 
 PHE   0.040   0.002   PHE B 212 
 TYR   0.016   0.002   TYR F  92 
 ARG   0.007   0.001   ARG A 101 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 270
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   81 GLN cc_start: 0.9697 (tt0) cc_final: 0.9230 (mt0)
REVERT: E  102 LYS cc_start: 0.9105 (pttm) cc_final: 0.8794 (pttm)
REVERT: E  202 ARG cc_start: 0.8480 (tpt170) cc_final: 0.8114 (mtp180)
REVERT: A   23 LYS cc_start: 0.9059 (tptp) cc_final: 0.8813 (tptp)
REVERT: A   74 HIS cc_start: 0.9543 (m-70) cc_final: 0.9247 (m-70)
REVERT: A   92 TYR cc_start: 0.8811 (t80) cc_final: 0.8510 (t80)
REVERT: A  166 GLU cc_start: 0.9390 (mt-10) cc_final: 0.9084 (mt-10)
REVERT: A  206 LYS cc_start: 0.9440 (ptpt) cc_final: 0.9141 (mttp)
REVERT: A  209 PHE cc_start: 0.9736 (m-10) cc_final: 0.9432 (m-80)
REVERT: A  224 ASN cc_start: 0.9313 (p0) cc_final: 0.9062 (p0)
REVERT: B   74 HIS cc_start: 0.9552 (m-70) cc_final: 0.9248 (m-70)
REVERT: B  101 ARG cc_start: 0.9040 (ttp80) cc_final: 0.8697 (ttp80)
REVERT: B  102 LYS cc_start: 0.9101 (pttm) cc_final: 0.8684 (pttm)
REVERT: B  173 GLN cc_start: 0.9580 (tp-100) cc_final: 0.9357 (tp-100)
REVERT: B  206 LYS cc_start: 0.9379 (ptpp) cc_final: 0.9072 (mttp)
REVERT: B  209 PHE cc_start: 0.9730 (m-10) cc_final: 0.9413 (m-80)
REVERT: C   81 GLN cc_start: 0.9697 (tt0) cc_final: 0.9246 (mt0)
REVERT: C  202 ARG cc_start: 0.8594 (mmp-170) cc_final: 0.7804 (mtm-85)
REVERT: C  206 LYS cc_start: 0.9450 (ptpp) cc_final: 0.9085 (mttp)
REVERT: C  209 PHE cc_start: 0.9754 (m-10) cc_final: 0.9410 (m-80)
REVERT: D   74 HIS cc_start: 0.9541 (m-70) cc_final: 0.9250 (m-70)
REVERT: D  202 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7673 (mtm180)
REVERT: D  206 LYS cc_start: 0.9423 (ptpp) cc_final: 0.9199 (mttp)
REVERT: D  209 PHE cc_start: 0.9740 (m-10) cc_final: 0.9429 (m-80)
REVERT: F   23 LYS cc_start: 0.9055 (tptp) cc_final: 0.8812 (tptp)
REVERT: F   74 HIS cc_start: 0.9538 (m-70) cc_final: 0.9240 (m-70)
REVERT: F   92 TYR cc_start: 0.8810 (t80) cc_final: 0.8483 (t80)
REVERT: F  166 GLU cc_start: 0.9374 (mt-10) cc_final: 0.9084 (mt-10)
REVERT: F  206 LYS cc_start: 0.9450 (ptpt) cc_final: 0.9111 (mttp)
REVERT: F  209 PHE cc_start: 0.9724 (m-10) cc_final: 0.9413 (m-80)
REVERT: F  224 ASN cc_start: 0.9304 (p0) cc_final: 0.9025 (p0)
  outliers start: 20
  outliers final: 8
  residues processed: 282
  average time/residue: 0.2679
  time to fit residues: 97.8300
Evaluate side-chains
  266 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 257
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain B residue   63 ASN
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain C residue   84 PHE
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  202 ARG
Chi-restraints excluded: chain F residue   91 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 97 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 101 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 93 optimal weight:    0.1980
   chunk 27 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
E  63 ASN
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  63 ASN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.059307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.048071 restraints weight = 56980.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.049210 restraints weight = 43095.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.050079 restraints weight = 34517.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9504  Z= 0.213
  Angle     :  0.795  11.968  12900  Z= 0.412
  Chirality :  0.044   0.186   1476
  Planarity :  0.004   0.056   1548
  Dihedral  :  4.096  15.512   1218
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 19.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 16.96 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.24), residues: 1110
  helix:  0.92 (0.17), residues: 864
  sheet:  1.04 (0.59), residues: 60
  loop : -1.79 (0.36), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E  78 
 HIS   0.001   0.001   HIS B  74 
 PHE   0.045   0.002   PHE D 212 
 TYR   0.024   0.002   TYR D 155 
 ARG   0.008   0.001   ARG E 202 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 289
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  202 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8420 (mtp180)
REVERT: E  206 LYS cc_start: 0.9474 (mttp) cc_final: 0.8927 (mttm)
REVERT: E  209 PHE cc_start: 0.9678 (m-10) cc_final: 0.9288 (m-80)
REVERT: A   23 LYS cc_start: 0.9110 (tptp) cc_final: 0.8859 (tptp)
REVERT: A   33 ARG cc_start: 0.9457 (mpp80) cc_final: 0.9255 (mtm-85)
REVERT: A   74 HIS cc_start: 0.9665 (m-70) cc_final: 0.9377 (m-70)
REVERT: A   92 TYR cc_start: 0.9049 (t80) cc_final: 0.8845 (t80)
REVERT: A  101 ARG cc_start: 0.9001 (ttp80) cc_final: 0.8725 (ttp80)
REVERT: A  102 LYS cc_start: 0.9129 (pttm) cc_final: 0.8847 (pttm)
REVERT: A  166 GLU cc_start: 0.9408 (mt-10) cc_final: 0.9115 (pt0)
REVERT: A  202 ARG cc_start: 0.8865 (mtm180) cc_final: 0.8163 (mtm180)
REVERT: A  206 LYS cc_start: 0.9463 (ptpt) cc_final: 0.9110 (mttp)
REVERT: A  209 PHE cc_start: 0.9763 (m-10) cc_final: 0.9451 (m-80)
REVERT: A  224 ASN cc_start: 0.9280 (p0) cc_final: 0.8838 (p0)
REVERT: B   13 LYS cc_start: 0.9518 (mmmt) cc_final: 0.9283 (mmmt)
REVERT: B   74 HIS cc_start: 0.9628 (m-70) cc_final: 0.9344 (m-70)
REVERT: B  101 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8815 (ttp80)
REVERT: B  102 LYS cc_start: 0.9098 (pttm) cc_final: 0.8797 (pttm)
REVERT: B  173 GLN cc_start: 0.9602 (tp-100) cc_final: 0.9396 (tp-100)
REVERT: B  190 ASP cc_start: 0.9116 (t0) cc_final: 0.8843 (p0)
REVERT: B  206 LYS cc_start: 0.9422 (ptpp) cc_final: 0.9214 (mttp)
REVERT: B  209 PHE cc_start: 0.9708 (m-10) cc_final: 0.9430 (m-80)
REVERT: C  202 ARG cc_start: 0.8813 (mmp-170) cc_final: 0.8113 (mtp180)
REVERT: C  206 LYS cc_start: 0.9448 (ptpp) cc_final: 0.9109 (mttp)
REVERT: C  209 PHE cc_start: 0.9738 (m-10) cc_final: 0.9432 (m-80)
REVERT: D   13 LYS cc_start: 0.9532 (mmmt) cc_final: 0.9299 (mmmt)
REVERT: D   74 HIS cc_start: 0.9611 (m-70) cc_final: 0.9322 (m-70)
REVERT: D  202 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7987 (mtp180)
REVERT: D  206 LYS cc_start: 0.9411 (ptpp) cc_final: 0.9133 (mttp)
REVERT: D  209 PHE cc_start: 0.9711 (m-10) cc_final: 0.9406 (m-80)
REVERT: F   23 LYS cc_start: 0.9098 (tptp) cc_final: 0.8844 (tptp)
REVERT: F   74 HIS cc_start: 0.9657 (m-70) cc_final: 0.9358 (m-70)
REVERT: F   92 TYR cc_start: 0.9058 (t80) cc_final: 0.8807 (t80)
REVERT: F  101 ARG cc_start: 0.9124 (ttp80) cc_final: 0.8766 (ttp80)
REVERT: F  166 GLU cc_start: 0.9413 (mt-10) cc_final: 0.9119 (pt0)
REVERT: F  202 ARG cc_start: 0.8410 (mtm180) cc_final: 0.7639 (mtm180)
REVERT: F  206 LYS cc_start: 0.9445 (ptpt) cc_final: 0.9034 (mttp)
REVERT: F  209 PHE cc_start: 0.9744 (m-10) cc_final: 0.9421 (m-80)
REVERT: F  224 ASN cc_start: 0.9278 (p0) cc_final: 0.8824 (p0)
  outliers start: 22
  outliers final: 6
  residues processed: 296
  average time/residue: 0.2661
  time to fit residues: 101.6440
Evaluate side-chains
  268 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 260
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  202 ARG
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain C residue   84 PHE
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  202 ARG
Chi-restraints excluded: chain F residue   91 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   chunk 17 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 84 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  15 GLN
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  63 ASN ** 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 = 0.3324 r_free = 0.3324 target = 0.059707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.048949 restraints weight = 60076.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.049994 restraints weight = 46952.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.050797 restraints weight = 38098.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.4572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9504  Z= 0.205
  Angle     :  0.835  11.876  12900  Z= 0.424
  Chirality :  0.046   0.370   1476
  Planarity :  0.005   0.072   1548
  Dihedral  :  4.109  17.333   1218
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 19.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 22.65 %
    Favored  : 75.78 %
  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:  0.76 (0.24), residues: 1110
  helix:  0.96 (0.17), residues: 864
  sheet:  1.07 (0.58), residues: 60
  loop : -1.63 (0.37), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  78 
 HIS   0.002   0.001   HIS C  74 
 PHE   0.038   0.002   PHE C 212 
 TYR   0.038   0.002   TYR F  66 
 ARG   0.013   0.001   ARG F  33 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 293
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  162 LYS cc_start: 0.9701 (ptmt) cc_final: 0.9433 (ptpp)
REVERT: E  202 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7996 (mtm180)
REVERT: E  206 LYS cc_start: 0.9520 (mttp) cc_final: 0.8952 (mmtt)
REVERT: E  209 PHE cc_start: 0.9677 (m-10) cc_final: 0.9327 (m-80)
REVERT: A   17 TYR cc_start: 0.8479 (m-10) cc_final: 0.8002 (m-10)
REVERT: A   23 LYS cc_start: 0.9120 (tptp) cc_final: 0.8860 (tptp)
REVERT: A   74 HIS cc_start: 0.9629 (m-70) cc_final: 0.9282 (m-70)
REVERT: A  101 ARG cc_start: 0.8976 (ttp80) cc_final: 0.8664 (ttp80)
REVERT: A  102 LYS cc_start: 0.9120 (pttm) cc_final: 0.8646 (pttm)
REVERT: A  166 GLU cc_start: 0.9394 (mt-10) cc_final: 0.9084 (mt-10)
REVERT: A  202 ARG cc_start: 0.8813 (mtm180) cc_final: 0.8350 (mtm180)
REVERT: A  206 LYS cc_start: 0.9465 (ptpt) cc_final: 0.9134 (mttp)
REVERT: A  209 PHE cc_start: 0.9758 (m-10) cc_final: 0.9421 (m-80)
REVERT: A  224 ASN cc_start: 0.9319 (p0) cc_final: 0.9108 (p0)
REVERT: B   17 TYR cc_start: 0.8527 (m-80) cc_final: 0.7857 (m-10)
REVERT: B   74 HIS cc_start: 0.9576 (m-70) cc_final: 0.9265 (m-70)
REVERT: B  101 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8806 (ttp80)
REVERT: B  102 LYS cc_start: 0.9091 (pttm) cc_final: 0.8852 (pttm)
REVERT: B  206 LYS cc_start: 0.9423 (ptpp) cc_final: 0.9211 (mttp)
REVERT: B  209 PHE cc_start: 0.9673 (m-10) cc_final: 0.9356 (m-80)
REVERT: C   17 TYR cc_start: 0.8382 (m-10) cc_final: 0.7877 (m-10)
REVERT: C  102 LYS cc_start: 0.9055 (pttm) cc_final: 0.8805 (pttm)
REVERT: C  202 ARG cc_start: 0.8878 (mmp-170) cc_final: 0.8108 (mtp180)
REVERT: C  206 LYS cc_start: 0.9446 (ptpp) cc_final: 0.9143 (mttp)
REVERT: C  209 PHE cc_start: 0.9710 (m-10) cc_final: 0.9408 (m-80)
REVERT: C  214 LEU cc_start: 0.9873 (mm) cc_final: 0.9632 (mm)
REVERT: D   17 TYR cc_start: 0.8522 (m-80) cc_final: 0.7846 (m-10)
REVERT: D   74 HIS cc_start: 0.9549 (m-70) cc_final: 0.9235 (m-70)
REVERT: D  202 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7893 (mtp180)
REVERT: D  206 LYS cc_start: 0.9421 (ptpp) cc_final: 0.9175 (mttp)
REVERT: D  209 PHE cc_start: 0.9692 (m-10) cc_final: 0.9326 (m-80)
REVERT: F   17 TYR cc_start: 0.8452 (m-10) cc_final: 0.8008 (m-80)
REVERT: F   23 LYS cc_start: 0.9114 (tptp) cc_final: 0.8812 (tptp)
REVERT: F   74 HIS cc_start: 0.9609 (m-70) cc_final: 0.9265 (m-70)
REVERT: F  166 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9093 (mt-10)
REVERT: F  190 ASP cc_start: 0.9069 (t0) cc_final: 0.8706 (p0)
REVERT: F  202 ARG cc_start: 0.8420 (mtm180) cc_final: 0.7954 (mtm180)
REVERT: F  206 LYS cc_start: 0.9444 (ptpt) cc_final: 0.9076 (mttp)
REVERT: F  209 PHE cc_start: 0.9732 (m-10) cc_final: 0.9405 (m-80)
REVERT: F  227 GLU cc_start: 0.9755 (mm-30) cc_final: 0.9451 (mm-30)
  outliers start: 16
  outliers final: 3
  residues processed: 299
  average time/residue: 0.2675
  time to fit residues: 103.6242
Evaluate side-chains
  263 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 258
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  200 LEU
Chi-restraints excluded: chain E residue  202 ARG
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain D residue  202 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 67 optimal weight:    7.9990
   chunk 92 optimal weight:    0.7980
   chunk 59 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 6 optimal weight:    7.9990
   chunk 77 optimal weight:    5.9990
   chunk 41 optimal weight:   20.0000
   chunk 97 optimal weight:    0.5980
   chunk 103 optimal weight:    6.9990
   overall best weight:    3.4786

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

Flipped N/Q/H residues before XYZ refinement:
E  15 GLN
E 173 GLN
A  63 ASN
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 ASN
C  15 GLN
C  63 ASN
C 173 GLN
** D  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  15 GLN
** F  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 173 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.054746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.044024 restraints weight = 62323.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.044948 restraints weight = 48150.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.045623 restraints weight = 39131.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.5243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9504  Z= 0.286
  Angle     :  0.814  13.065  12900  Z= 0.437
  Chirality :  0.045   0.202   1476
  Planarity :  0.005   0.066   1548
  Dihedral  :  4.303  22.266   1218
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 25.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 26.86 %
    Favored  : 72.06 %
  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:  0.87 (0.24), residues: 1110
  helix:  1.08 (0.17), residues: 870
  sheet:  1.03 (0.60), residues: 60
  loop : -1.87 (0.38), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A  78 
 HIS   0.003   0.001   HIS B  74 
 PHE   0.037   0.002   PHE C 212 
 TYR   0.027   0.002   TYR F  66 
 ARG   0.013   0.001   ARG A  33 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 292
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   17 TYR cc_start: 0.8470 (m-10) cc_final: 0.7980 (m-10)
REVERT: E   42 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8483 (mt-10)
REVERT: E   74 HIS cc_start: 0.9240 (m-70) cc_final: 0.8844 (t-90)
REVERT: E  179 PHE cc_start: 0.8403 (m-80) cc_final: 0.8071 (m-80)
REVERT: E  202 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8370 (mtp180)
REVERT: E  206 LYS cc_start: 0.9599 (mttp) cc_final: 0.9080 (mttp)
REVERT: E  214 LEU cc_start: 0.9873 (OUTLIER) cc_final: 0.9644 (mm)
REVERT: E  227 GLU cc_start: 0.9797 (mm-30) cc_final: 0.9507 (mm-30)
REVERT: A   17 TYR cc_start: 0.8554 (m-10) cc_final: 0.8076 (m-10)
REVERT: A   42 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8392 (mt-10)
REVERT: A   74 HIS cc_start: 0.9593 (m-70) cc_final: 0.9363 (m90)
REVERT: A  166 GLU cc_start: 0.9268 (mt-10) cc_final: 0.9064 (mt-10)
REVERT: A  202 ARG cc_start: 0.8955 (mtm180) cc_final: 0.8321 (mtm180)
REVERT: A  206 LYS cc_start: 0.9484 (ptpt) cc_final: 0.9140 (mttp)
REVERT: A  209 PHE cc_start: 0.9766 (m-10) cc_final: 0.9384 (m-80)
REVERT: A  227 GLU cc_start: 0.9794 (mm-30) cc_final: 0.9587 (mm-30)
REVERT: B   17 TYR cc_start: 0.8643 (m-80) cc_final: 0.8032 (m-10)
REVERT: B   42 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8420 (mt-10)
REVERT: B   74 HIS cc_start: 0.9491 (m-70) cc_final: 0.9091 (m-70)
REVERT: B  190 ASP cc_start: 0.8957 (t0) cc_final: 0.8742 (p0)
REVERT: B  206 LYS cc_start: 0.9465 (ptpp) cc_final: 0.9214 (mttp)
REVERT: B  209 PHE cc_start: 0.9673 (m-10) cc_final: 0.9307 (m-80)
REVERT: B  227 GLU cc_start: 0.9775 (mm-30) cc_final: 0.9442 (mm-30)
REVERT: C   17 TYR cc_start: 0.8482 (m-10) cc_final: 0.8031 (m-10)
REVERT: C   42 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8468 (mt-10)
REVERT: C   74 HIS cc_start: 0.9257 (m-70) cc_final: 0.8873 (t-90)
REVERT: C  179 PHE cc_start: 0.8429 (m-80) cc_final: 0.8043 (m-80)
REVERT: C  202 ARG cc_start: 0.8899 (mmp-170) cc_final: 0.8336 (mtp180)
REVERT: C  206 LYS cc_start: 0.9548 (ptpp) cc_final: 0.9156 (ptpt)
REVERT: C  209 PHE cc_start: 0.9708 (m-10) cc_final: 0.9419 (m-80)
REVERT: C  214 LEU cc_start: 0.9874 (OUTLIER) cc_final: 0.9647 (mm)
REVERT: C  227 GLU cc_start: 0.9800 (mm-30) cc_final: 0.9507 (mm-30)
REVERT: D   17 TYR cc_start: 0.8628 (m-80) cc_final: 0.7955 (m-10)
REVERT: D   74 HIS cc_start: 0.9489 (m-70) cc_final: 0.9074 (m-70)
REVERT: D  202 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7901 (mtp180)
REVERT: D  206 LYS cc_start: 0.9482 (ptpp) cc_final: 0.9191 (ptpt)
REVERT: D  209 PHE cc_start: 0.9744 (m-10) cc_final: 0.9354 (m-80)
REVERT: D  227 GLU cc_start: 0.9767 (mm-30) cc_final: 0.9435 (mm-30)
REVERT: F   17 TYR cc_start: 0.8528 (m-10) cc_final: 0.8076 (m-10)
REVERT: F   33 ARG cc_start: 0.9490 (mtm-85) cc_final: 0.9239 (mtm-85)
REVERT: F   42 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8479 (mt-10)
REVERT: F   74 HIS cc_start: 0.9567 (m-70) cc_final: 0.9192 (m-70)
REVERT: F  102 LYS cc_start: 0.9210 (pttm) cc_final: 0.8977 (pttm)
REVERT: F  160 LEU cc_start: 0.9890 (mt) cc_final: 0.9689 (pp)
REVERT: F  166 GLU cc_start: 0.9266 (mt-10) cc_final: 0.9053 (mt-10)
REVERT: F  202 ARG cc_start: 0.8482 (mtm180) cc_final: 0.7808 (mtm180)
REVERT: F  206 LYS cc_start: 0.9478 (ptpt) cc_final: 0.9057 (mttp)
REVERT: F  209 PHE cc_start: 0.9727 (m-10) cc_final: 0.9369 (m-80)
REVERT: F  227 GLU cc_start: 0.9791 (mm-30) cc_final: 0.9515 (mm-30)
  outliers start: 11
  outliers final: 2
  residues processed: 298
  average time/residue: 0.2497
  time to fit residues: 97.7509
Evaluate side-chains
  270 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 264
  time to evaluate  : 1.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  200 LEU
Chi-restraints excluded: chain E residue  202 ARG
Chi-restraints excluded: chain E residue  207 THR
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain D residue  202 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 69 optimal weight:    0.0980
   chunk 6 optimal weight:   10.0000
   chunk 65 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 41 optimal weight:   10.0000
   chunk 93 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0170
   overall best weight:    1.2022

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

Flipped N/Q/H residues before XYZ refinement:
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.057421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.046601 restraints weight = 61097.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.047591 restraints weight = 45823.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.048370 restraints weight = 36584.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.5540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9504  Z= 0.218
  Angle     :  0.922  14.340  12900  Z= 0.463
  Chirality :  0.046   0.229   1476
  Planarity :  0.004   0.038   1548
  Dihedral  :  4.193  19.491   1218
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 20.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 30.88 %
    Favored  : 67.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.24), residues: 1110
  helix:  1.01 (0.17), residues: 864
  sheet:  1.10 (0.58), residues: 60
  loop : -1.91 (0.36), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP F  78 
 HIS   0.002   0.001   HIS F  74 
 PHE   0.044   0.002   PHE C 212 
 TYR   0.025   0.001   TYR F  66 
 ARG   0.009   0.001   ARG E 202 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 300
  time to evaluate  : 1.072 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   17 TYR cc_start: 0.8476 (m-10) cc_final: 0.8003 (m-10)
REVERT: E   42 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8517 (mt-10)
REVERT: E   74 HIS cc_start: 0.9293 (m-70) cc_final: 0.8946 (t-90)
REVERT: E   77 PHE cc_start: 0.9675 (t80) cc_final: 0.9464 (t80)
REVERT: E  179 PHE cc_start: 0.8337 (m-80) cc_final: 0.7826 (m-80)
REVERT: E  190 ASP cc_start: 0.9166 (t0) cc_final: 0.8640 (p0)
REVERT: E  202 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8282 (mtp180)
REVERT: E  206 LYS cc_start: 0.9604 (mttp) cc_final: 0.9203 (mttt)
REVERT: E  213 MET cc_start: 0.9325 (tmm) cc_final: 0.9110 (tmm)
REVERT: E  214 LEU cc_start: 0.9849 (OUTLIER) cc_final: 0.9483 (mm)
REVERT: E  227 GLU cc_start: 0.9813 (mm-30) cc_final: 0.9522 (mm-30)
REVERT: A   17 TYR cc_start: 0.8590 (m-10) cc_final: 0.8171 (m-10)
REVERT: A   42 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8364 (mt-10)
REVERT: A  101 ARG cc_start: 0.8915 (ttp80) cc_final: 0.8488 (ttp80)
REVERT: A  102 LYS cc_start: 0.9090 (pttm) cc_final: 0.8623 (pttm)
REVERT: A  166 GLU cc_start: 0.9228 (mt-10) cc_final: 0.9017 (mt-10)
REVERT: A  202 ARG cc_start: 0.8804 (mtm180) cc_final: 0.8401 (mtm180)
REVERT: A  206 LYS cc_start: 0.9517 (ptpt) cc_final: 0.9226 (mttp)
REVERT: A  209 PHE cc_start: 0.9785 (m-10) cc_final: 0.9416 (m-80)
REVERT: A  227 GLU cc_start: 0.9810 (mm-30) cc_final: 0.9587 (mm-30)
REVERT: B   17 TYR cc_start: 0.8662 (m-80) cc_final: 0.8095 (m-10)
REVERT: B   42 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8391 (mt-10)
REVERT: B   74 HIS cc_start: 0.9548 (m-70) cc_final: 0.9153 (m-70)
REVERT: B  209 PHE cc_start: 0.9704 (m-10) cc_final: 0.9333 (m-80)
REVERT: B  227 GLU cc_start: 0.9781 (mm-30) cc_final: 0.9443 (mm-30)
REVERT: C   17 TYR cc_start: 0.8481 (m-10) cc_final: 0.8029 (m-10)
REVERT: C   42 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8515 (mt-10)
REVERT: C   74 HIS cc_start: 0.9301 (m-70) cc_final: 0.8961 (t-90)
REVERT: C   77 PHE cc_start: 0.9690 (t80) cc_final: 0.9474 (t80)
REVERT: C  202 ARG cc_start: 0.8945 (mmp-170) cc_final: 0.8541 (mtm-85)
REVERT: C  209 PHE cc_start: 0.9713 (m-10) cc_final: 0.9418 (m-80)
REVERT: C  214 LEU cc_start: 0.9848 (OUTLIER) cc_final: 0.9602 (mt)
REVERT: C  227 GLU cc_start: 0.9805 (mm-30) cc_final: 0.9515 (mm-30)
REVERT: D   17 TYR cc_start: 0.8664 (m-80) cc_final: 0.8061 (m-10)
REVERT: D   48 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8499 (mm-30)
REVERT: D   74 HIS cc_start: 0.9521 (m-70) cc_final: 0.9131 (m-70)
REVERT: D  100 MET cc_start: 0.9627 (tpt) cc_final: 0.9416 (mmm)
REVERT: D  200 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9132 (tp)
REVERT: D  202 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8223 (mtp180)
REVERT: D  206 LYS cc_start: 0.9475 (ptpp) cc_final: 0.9271 (mttp)
REVERT: D  209 PHE cc_start: 0.9745 (m-10) cc_final: 0.9317 (m-80)
REVERT: D  227 GLU cc_start: 0.9767 (mm-30) cc_final: 0.9439 (mm-30)
REVERT: F   17 TYR cc_start: 0.8580 (m-10) cc_final: 0.8176 (m-10)
REVERT: F   33 ARG cc_start: 0.9535 (mtm-85) cc_final: 0.9271 (ptt90)
REVERT: F   42 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8485 (mt-10)
REVERT: F   48 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8286 (mm-30)
REVERT: F   74 HIS cc_start: 0.9600 (m-70) cc_final: 0.9249 (m-70)
REVERT: F  202 ARG cc_start: 0.8473 (mtm180) cc_final: 0.8007 (mtm180)
REVERT: F  206 LYS cc_start: 0.9472 (ptpt) cc_final: 0.9051 (mttp)
REVERT: F  209 PHE cc_start: 0.9732 (m-10) cc_final: 0.9357 (m-80)
REVERT: F  227 GLU cc_start: 0.9801 (mm-30) cc_final: 0.9527 (mm-30)
  outliers start: 16
  outliers final: 1
  residues processed: 311
  average time/residue: 0.2522
  time to fit residues: 103.1140
Evaluate side-chains
  286 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 280
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  202 ARG
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  202 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 94 optimal weight:    5.9990
   chunk 14 optimal weight:   20.0000
   chunk 57 optimal weight:    0.4980
   chunk 77 optimal weight:    8.9990
   chunk 64 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 87 optimal weight:    9.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    1.8988

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

Flipped N/Q/H residues before XYZ refinement:
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  74 HIS
** B  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  63 ASN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.056399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.045954 restraints weight = 62636.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 17)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.046919 restraints weight = 46685.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.047646 restraints weight = 37197.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.5864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9504  Z= 0.240
  Angle     :  0.971  14.220  12900  Z= 0.491
  Chirality :  0.048   0.342   1476
  Planarity :  0.005   0.091   1548
  Dihedral  :  4.270  19.809   1218
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 22.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 32.75 %
    Favored  : 66.47 %
  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 (0.24), residues: 1110
  helix:  1.01 (0.17), residues: 864
  sheet:  1.25 (0.58), residues: 60
  loop : -2.01 (0.36), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A  78 
 HIS   0.002   0.001   HIS F  74 
 PHE   0.043   0.002   PHE E 212 
 TYR   0.018   0.001   TYR F  66 
 ARG   0.018   0.001   ARG A  33 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 304
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   17 TYR cc_start: 0.8557 (m-10) cc_final: 0.8135 (m-10)
REVERT: E   42 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8535 (mt-10)
REVERT: E   74 HIS cc_start: 0.9321 (m-70) cc_final: 0.8971 (t-90)
REVERT: E  162 LYS cc_start: 0.9609 (ptmt) cc_final: 0.9347 (ptpp)
REVERT: E  179 PHE cc_start: 0.8257 (m-80) cc_final: 0.7698 (m-80)
REVERT: E  202 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8303 (mtp-110)
REVERT: E  206 LYS cc_start: 0.9656 (mttp) cc_final: 0.9034 (mttm)
REVERT: E  209 PHE cc_start: 0.9653 (m-10) cc_final: 0.9296 (m-80)
REVERT: E  214 LEU cc_start: 0.9845 (OUTLIER) cc_final: 0.9524 (mm)
REVERT: E  227 GLU cc_start: 0.9824 (mm-30) cc_final: 0.9534 (mm-30)
REVERT: A   17 TYR cc_start: 0.8664 (m-10) cc_final: 0.8260 (m-10)
REVERT: A   42 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8415 (mt-10)
REVERT: A  101 ARG cc_start: 0.8939 (ttp80) cc_final: 0.8525 (ttp80)
REVERT: A  102 LYS cc_start: 0.9098 (pttm) cc_final: 0.8644 (pttm)
REVERT: A  202 ARG cc_start: 0.8907 (mtm180) cc_final: 0.8389 (mtm180)
REVERT: A  206 LYS cc_start: 0.9492 (ptpt) cc_final: 0.9224 (mttp)
REVERT: A  209 PHE cc_start: 0.9786 (m-10) cc_final: 0.9421 (m-80)
REVERT: A  227 GLU cc_start: 0.9810 (mm-30) cc_final: 0.9572 (mm-30)
REVERT: B   17 TYR cc_start: 0.8693 (m-80) cc_final: 0.8139 (m-10)
REVERT: B   42 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8404 (mt-10)
REVERT: B   74 HIS cc_start: 0.9604 (m-70) cc_final: 0.9148 (m-70)
REVERT: B  100 MET cc_start: 0.9669 (tpt) cc_final: 0.9455 (mmm)
REVERT: B  209 PHE cc_start: 0.9669 (m-10) cc_final: 0.9304 (m-80)
REVERT: B  227 GLU cc_start: 0.9805 (mm-30) cc_final: 0.9482 (mm-30)
REVERT: C   17 TYR cc_start: 0.8582 (m-10) cc_final: 0.8139 (m-10)
REVERT: C   42 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8584 (mt-10)
REVERT: C   74 HIS cc_start: 0.9315 (m-70) cc_final: 0.8953 (t-90)
REVERT: C   77 PHE cc_start: 0.9692 (t80) cc_final: 0.9485 (t80)
REVERT: C  100 MET cc_start: 0.9695 (tpt) cc_final: 0.9493 (mmm)
REVERT: C  179 PHE cc_start: 0.8290 (m-80) cc_final: 0.7717 (m-80)
REVERT: C  202 ARG cc_start: 0.8922 (mmp-170) cc_final: 0.8538 (mtp180)
REVERT: C  206 LYS cc_start: 0.9370 (ptpt) cc_final: 0.9153 (mttp)
REVERT: C  209 PHE cc_start: 0.9673 (m-10) cc_final: 0.9336 (m-80)
REVERT: C  214 LEU cc_start: 0.9863 (OUTLIER) cc_final: 0.9586 (mm)
REVERT: C  227 GLU cc_start: 0.9832 (mm-30) cc_final: 0.9520 (mm-30)
REVERT: D   17 TYR cc_start: 0.8695 (m-80) cc_final: 0.8118 (m-10)
REVERT: D   33 ARG cc_start: 0.9193 (mtm110) cc_final: 0.8988 (mtm110)
REVERT: D   42 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8610 (mt-10)
REVERT: D   48 GLU cc_start: 0.9061 (mm-30) cc_final: 0.7847 (mm-30)
REVERT: D   74 HIS cc_start: 0.9567 (m-70) cc_final: 0.9132 (m-70)
REVERT: D  100 MET cc_start: 0.9681 (tpt) cc_final: 0.9448 (mmm)
REVERT: D  190 ASP cc_start: 0.9281 (t0) cc_final: 0.8996 (p0)
REVERT: D  200 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9247 (tp)
REVERT: D  202 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8451 (mtp180)
REVERT: D  209 PHE cc_start: 0.9741 (m-10) cc_final: 0.9332 (m-80)
REVERT: D  227 GLU cc_start: 0.9783 (mm-30) cc_final: 0.9453 (mm-30)
REVERT: F   17 TYR cc_start: 0.8637 (m-10) cc_final: 0.8242 (m-10)
REVERT: F   33 ARG cc_start: 0.9559 (mtm-85) cc_final: 0.9282 (ptt90)
REVERT: F   42 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8512 (mt-10)
REVERT: F   48 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8193 (mm-30)
REVERT: F   98 TYR cc_start: 0.9616 (m-10) cc_final: 0.9371 (m-10)
REVERT: F  161 PHE cc_start: 0.9511 (m-80) cc_final: 0.9191 (m-80)
REVERT: F  179 PHE cc_start: 0.8333 (m-80) cc_final: 0.8114 (m-80)
REVERT: F  190 ASP cc_start: 0.9257 (t0) cc_final: 0.8913 (p0)
REVERT: F  202 ARG cc_start: 0.8396 (mtm180) cc_final: 0.7974 (mtm180)
REVERT: F  206 LYS cc_start: 0.9483 (ptpt) cc_final: 0.9039 (mttp)
REVERT: F  209 PHE cc_start: 0.9740 (m-10) cc_final: 0.9371 (m-80)
REVERT: F  227 GLU cc_start: 0.9811 (mm-30) cc_final: 0.9522 (mm-30)
  outliers start: 8
  outliers final: 1
  residues processed: 307
  average time/residue: 0.2542
  time to fit residues: 102.2364
Evaluate side-chains
  285 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 279
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  202 ARG
Chi-restraints excluded: chain E residue  207 THR
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  202 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   chunk 63 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0970
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.057041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.046608 restraints weight = 61352.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.047569 restraints weight = 45969.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.048304 restraints weight = 36770.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.6059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9504  Z= 0.247
  Angle     :  1.042  16.734  12900  Z= 0.527
  Chirality :  0.050   0.365   1476
  Planarity :  0.005   0.054   1548
  Dihedral  :  4.183  19.030   1218
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 23.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 33.92 %
    Favored  : 65.29 %
  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:  0.64 (0.24), residues: 1110
  helix:  0.92 (0.17), residues: 864
  sheet:  1.26 (0.59), residues: 60
  loop : -1.98 (0.36), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP D  78 
 HIS   0.003   0.001   HIS A  74 
 PHE   0.047   0.002   PHE E 212 
 TYR   0.017   0.001   TYR F  66 
 ARG   0.017   0.001   ARG A  33 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 298
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   17 TYR cc_start: 0.8489 (m-10) cc_final: 0.8105 (m-10)
REVERT: E   42 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8486 (mt-10)
REVERT: E   74 HIS cc_start: 0.9262 (m-70) cc_final: 0.8896 (t-90)
REVERT: E   81 GLN cc_start: 0.9727 (tt0) cc_final: 0.9374 (tp40)
REVERT: E  162 LYS cc_start: 0.9672 (ptmt) cc_final: 0.9389 (ptpp)
REVERT: E  179 PHE cc_start: 0.8395 (m-80) cc_final: 0.7898 (m-80)
REVERT: E  202 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8389 (mtp180)
REVERT: E  209 PHE cc_start: 0.9587 (m-10) cc_final: 0.9346 (m-80)
REVERT: E  214 LEU cc_start: 0.9901 (OUTLIER) cc_final: 0.9439 (mm)
REVERT: E  227 GLU cc_start: 0.9801 (mm-30) cc_final: 0.9507 (mm-30)
REVERT: A   17 TYR cc_start: 0.8562 (m-10) cc_final: 0.8193 (m-10)
REVERT: A   42 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8388 (mt-10)
REVERT: A  101 ARG cc_start: 0.8854 (ttp80) cc_final: 0.8431 (ttp80)
REVERT: A  102 LYS cc_start: 0.9080 (pttm) cc_final: 0.8574 (pttm)
REVERT: A  157 ILE cc_start: 0.9696 (mm) cc_final: 0.9410 (pt)
REVERT: A  161 PHE cc_start: 0.9474 (m-80) cc_final: 0.9163 (m-80)
REVERT: A  202 ARG cc_start: 0.8861 (mtm180) cc_final: 0.8477 (mtm180)
REVERT: A  206 LYS cc_start: 0.9485 (ptpt) cc_final: 0.9231 (mttp)
REVERT: A  209 PHE cc_start: 0.9784 (m-10) cc_final: 0.9442 (m-80)
REVERT: A  227 GLU cc_start: 0.9794 (mm-30) cc_final: 0.9562 (mm-30)
REVERT: B   17 TYR cc_start: 0.8638 (m-80) cc_final: 0.8083 (m-10)
REVERT: B   33 ARG cc_start: 0.9159 (mtm110) cc_final: 0.8957 (ptt90)
REVERT: B   42 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8501 (mt-10)
REVERT: B  209 PHE cc_start: 0.9669 (m-10) cc_final: 0.9304 (m-80)
REVERT: B  227 GLU cc_start: 0.9791 (mm-30) cc_final: 0.9499 (mm-30)
REVERT: C   17 TYR cc_start: 0.8523 (m-10) cc_final: 0.8126 (m-10)
REVERT: C   42 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8558 (mt-10)
REVERT: C   74 HIS cc_start: 0.9249 (m-70) cc_final: 0.8878 (t-90)
REVERT: C   77 PHE cc_start: 0.9636 (t80) cc_final: 0.9186 (t80)
REVERT: C   81 GLN cc_start: 0.9734 (tt0) cc_final: 0.9384 (mt0)
REVERT: C  100 MET cc_start: 0.9637 (tpt) cc_final: 0.9410 (mmm)
REVERT: C  202 ARG cc_start: 0.8955 (mmp-170) cc_final: 0.8676 (mtm-85)
REVERT: C  209 PHE cc_start: 0.9629 (m-10) cc_final: 0.9313 (m-80)
REVERT: C  214 LEU cc_start: 0.9853 (OUTLIER) cc_final: 0.9647 (mm)
REVERT: C  227 GLU cc_start: 0.9809 (mm-30) cc_final: 0.9511 (mm-30)
REVERT: D   17 TYR cc_start: 0.8604 (m-80) cc_final: 0.8045 (m-10)
REVERT: D   33 ARG cc_start: 0.9180 (mtm110) cc_final: 0.8926 (mtm110)
REVERT: D   42 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8582 (mt-10)
REVERT: D   48 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8376 (mm-30)
REVERT: D   74 HIS cc_start: 0.9432 (m-70) cc_final: 0.8999 (m-70)
REVERT: D  200 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9157 (tp)
REVERT: D  202 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8452 (mtp180)
REVERT: D  206 LYS cc_start: 0.9554 (ptpt) cc_final: 0.9246 (mttp)
REVERT: D  209 PHE cc_start: 0.9726 (m-10) cc_final: 0.9261 (m-80)
REVERT: D  227 GLU cc_start: 0.9771 (mm-30) cc_final: 0.9446 (mm-30)
REVERT: F   17 TYR cc_start: 0.8556 (m-10) cc_final: 0.8194 (m-10)
REVERT: F   33 ARG cc_start: 0.9547 (mtm-85) cc_final: 0.9308 (ptt90)
REVERT: F   42 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8470 (mt-10)
REVERT: F   48 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8252 (mm-30)
REVERT: F  161 PHE cc_start: 0.9504 (m-80) cc_final: 0.9088 (m-80)
REVERT: F  190 ASP cc_start: 0.9098 (t0) cc_final: 0.8777 (p0)
REVERT: F  202 ARG cc_start: 0.8428 (mtm180) cc_final: 0.8016 (mtm180)
REVERT: F  206 LYS cc_start: 0.9469 (ptpt) cc_final: 0.9036 (mttp)
REVERT: F  209 PHE cc_start: 0.9741 (m-10) cc_final: 0.9389 (m-80)
REVERT: F  227 GLU cc_start: 0.9805 (mm-30) cc_final: 0.9515 (mm-30)
  outliers start: 8
  outliers final: 1
  residues processed: 301
  average time/residue: 0.2653
  time to fit residues: 105.1746
Evaluate side-chains
  293 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 287
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  202 ARG
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  202 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 68 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 90 optimal weight:    7.9990
   chunk 46 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 29 optimal weight:    0.9980
   chunk 96 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  63 ASN ** 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 = 0.3202 r_free = 0.3202 target = 0.055936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.045838 restraints weight = 64310.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.046776 restraints weight = 47980.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.047494 restraints weight = 38282.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.6256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9504  Z= 0.264
  Angle     :  1.071  15.355  12900  Z= 0.550
  Chirality :  0.050   0.342   1476
  Planarity :  0.005   0.054   1548
  Dihedral  :  4.246  19.126   1218
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 26.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 34.31 %
    Favored  : 64.80 %
  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:  0.65 (0.24), residues: 1110
  helix:  0.92 (0.17), residues: 864
  sheet:  1.46 (0.61), residues: 60
  loop : -2.00 (0.36), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP B  78 
 HIS   0.003   0.001   HIS B  74 
 PHE   0.056   0.002   PHE E 212 
 TYR   0.014   0.001   TYR F  66 
 ARG   0.016   0.001   ARG A  33 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 300
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   17 TYR cc_start: 0.8434 (m-10) cc_final: 0.8082 (m-10)
REVERT: E   42 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8533 (mt-10)
REVERT: E   74 HIS cc_start: 0.9161 (m-70) cc_final: 0.8810 (t-90)
REVERT: E  162 LYS cc_start: 0.9708 (ptmt) cc_final: 0.9421 (ptpp)
REVERT: E  190 ASP cc_start: 0.9109 (t0) cc_final: 0.8780 (p0)
REVERT: E  202 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8591 (mtp180)
REVERT: E  206 LYS cc_start: 0.9620 (mttp) cc_final: 0.8972 (mttm)
REVERT: E  209 PHE cc_start: 0.9641 (m-10) cc_final: 0.9296 (m-80)
REVERT: E  214 LEU cc_start: 0.9825 (OUTLIER) cc_final: 0.9624 (mm)
REVERT: E  227 GLU cc_start: 0.9780 (mm-30) cc_final: 0.9478 (mm-30)
REVERT: A   17 TYR cc_start: 0.8530 (m-10) cc_final: 0.8163 (m-10)
REVERT: A   42 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8386 (mt-10)
REVERT: A  101 ARG cc_start: 0.8725 (ttp80) cc_final: 0.8300 (ttp80)
REVERT: A  102 LYS cc_start: 0.9106 (pttm) cc_final: 0.8570 (pttm)
REVERT: A  157 ILE cc_start: 0.9702 (mm) cc_final: 0.9394 (pt)
REVERT: A  161 PHE cc_start: 0.9467 (m-80) cc_final: 0.9114 (m-80)
REVERT: A  162 LYS cc_start: 0.9436 (ptpp) cc_final: 0.9198 (ptpp)
REVERT: A  202 ARG cc_start: 0.8878 (mtm180) cc_final: 0.8487 (mtm180)
REVERT: A  206 LYS cc_start: 0.9453 (ptpt) cc_final: 0.9194 (mttp)
REVERT: A  209 PHE cc_start: 0.9770 (m-10) cc_final: 0.9445 (m-80)
REVERT: A  227 GLU cc_start: 0.9789 (mm-30) cc_final: 0.9494 (mm-30)
REVERT: B   17 TYR cc_start: 0.8589 (m-80) cc_final: 0.8068 (m-10)
REVERT: B   42 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8530 (mt-10)
REVERT: B  101 ARG cc_start: 0.9113 (ttp80) cc_final: 0.8792 (ttp80)
REVERT: B  102 LYS cc_start: 0.9067 (ptpp) cc_final: 0.8638 (mtmm)
REVERT: B  190 ASP cc_start: 0.9035 (t0) cc_final: 0.8808 (p0)
REVERT: B  209 PHE cc_start: 0.9646 (m-10) cc_final: 0.9307 (m-80)
REVERT: B  227 GLU cc_start: 0.9773 (mm-30) cc_final: 0.9469 (mm-30)
REVERT: C   17 TYR cc_start: 0.8451 (m-10) cc_final: 0.8103 (m-10)
REVERT: C   42 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8564 (mt-10)
REVERT: C   74 HIS cc_start: 0.9144 (m-70) cc_final: 0.8806 (t-90)
REVERT: C   77 PHE cc_start: 0.9549 (t80) cc_final: 0.9131 (t80)
REVERT: C   81 GLN cc_start: 0.9710 (tt0) cc_final: 0.9389 (mt0)
REVERT: C  202 ARG cc_start: 0.8880 (mmp-170) cc_final: 0.8675 (mtm-85)
REVERT: C  209 PHE cc_start: 0.9588 (m-10) cc_final: 0.9254 (m-80)
REVERT: C  214 LEU cc_start: 0.9846 (OUTLIER) cc_final: 0.9644 (mm)
REVERT: C  227 GLU cc_start: 0.9801 (mm-30) cc_final: 0.9503 (mm-30)
REVERT: D   17 TYR cc_start: 0.8554 (m-80) cc_final: 0.8033 (m-10)
REVERT: D   33 ARG cc_start: 0.9268 (mtm110) cc_final: 0.9004 (mtm110)
REVERT: D   42 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8597 (mt-10)
REVERT: D   48 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8353 (mm-30)
REVERT: D   74 HIS cc_start: 0.9334 (m-70) cc_final: 0.9088 (m90)
REVERT: D  190 ASP cc_start: 0.9060 (t0) cc_final: 0.8741 (p0)
REVERT: D  200 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9218 (tp)
REVERT: D  202 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8242 (mtp180)
REVERT: D  205 GLU cc_start: 0.9143 (pm20) cc_final: 0.8706 (pm20)
REVERT: D  206 LYS cc_start: 0.9543 (ptpt) cc_final: 0.9174 (mttp)
REVERT: D  209 PHE cc_start: 0.9710 (m-10) cc_final: 0.9239 (m-80)
REVERT: D  227 GLU cc_start: 0.9753 (mm-30) cc_final: 0.9415 (mm-30)
REVERT: F   17 TYR cc_start: 0.8498 (m-10) cc_final: 0.8150 (m-10)
REVERT: F   33 ARG cc_start: 0.9507 (mtm-85) cc_final: 0.9183 (ptt90)
REVERT: F   42 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8491 (mt-10)
REVERT: F  161 PHE cc_start: 0.9517 (m-80) cc_final: 0.9074 (m-80)
REVERT: F  202 ARG cc_start: 0.8489 (mtm180) cc_final: 0.8167 (mtm180)
REVERT: F  206 LYS cc_start: 0.9447 (ptpt) cc_final: 0.9012 (mttp)
REVERT: F  209 PHE cc_start: 0.9724 (m-10) cc_final: 0.9391 (m-80)
REVERT: F  227 GLU cc_start: 0.9795 (mm-30) cc_final: 0.9514 (mm-30)
  outliers start: 9
  outliers final: 1
  residues processed: 306
  average time/residue: 0.2536
  time to fit residues: 101.3754
Evaluate side-chains
  295 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 289
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  202 ARG
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  202 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 100 optimal weight:   10.0000
   chunk 73 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 82 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0870
   chunk 89 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.7960

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

Flipped N/Q/H residues before XYZ refinement:
E  81 GLN
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  15 GLN
** B  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  15 GLN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.056374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.046058 restraints weight = 62831.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.046970 restraints weight = 47642.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.047679 restraints weight = 38439.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.6439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9504  Z= 0.255
  Angle     :  1.138  16.269  12900  Z= 0.579
  Chirality :  0.052   0.351   1476
  Planarity :  0.005   0.054   1548
  Dihedral  :  4.255  18.897   1218
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 24.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 35.29 %
    Favored  : 64.02 %
  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:  0.50 (0.24), residues: 1110
  helix:  0.79 (0.17), residues: 864
  sheet:  1.52 (0.61), residues: 60
  loop : -1.99 (0.37), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP B  78 
 HIS   0.002   0.001   HIS D  74 
 PHE   0.058   0.002   PHE E 212 
 TYR   0.023   0.001   TYR F 230 
 ARG   0.016   0.001   ARG A  33 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3153.59 seconds
wall clock time: 57 minutes 41.13 seconds (3461.13 seconds total)