Starting phenix.real_space_refine
on Sun Jul 27 10:23:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7z23_14456/07_2025/7z23_14456.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7z23_14456/07_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_14456/07_2025/7z23_14456.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7z23_14456/07_2025/7z23_14456.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7z23_14456/07_2025/7z23_14456.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7z23_14456/07_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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.09, per 1000 atoms: 0.55
  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: 2.54
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.78
  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: 2.32

  Time building geometry restraints manager: 2.83 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: 0.07
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:             3.400
  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:          0.470
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     23.130
  Find NCS groups from input model:        0.200
  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:             0.010
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.160
-------------------------------------------------------------------------------
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   9507  Z= 0.195
  Angle     :  0.922   7.456  12906  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09775 (  684)
  hydrogen bonds       : angle       5.50995 ( 2034)
  SS BOND              : bond        0.00160 (    3)
  SS BOND              : angle       0.83329 (    6)
  covalent geometry    : bond        0.00361 ( 9504)
  covalent geometry    : angle       0.92160 (12900)

*********************** 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  : 1.031 
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: 0.2732
  time to fit residues: 118.5728
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  : 1.069 
-------------------------------------------------------------------------------
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 = 39)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.050919 restraints weight = 55496.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.052009 restraints weight = 43023.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.052760 restraints weight = 35049.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
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   9507  Z= 0.173
  Angle     :  0.818   9.288  12906  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04832 (  684)
  hydrogen bonds       : angle       4.97717 ( 2034)
  SS BOND              : bond        0.00203 (    3)
  SS BOND              : angle       0.91553 (    6)
  covalent geometry    : bond        0.00383 ( 9504)
  covalent geometry    : angle       0.81815 (12900)

*********************** 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  : 0.990 
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: 0.9571 (tp-100) cc_final: 0.9364 (tp-100)
REVERT: E  202 ARG cc_start: 0.8506 (tpt170) cc_final: 0.8212 (mtp-110)
REVERT: A   74 HIS cc_start: 0.9525 (m-70) cc_final: 0.9305 (m-70)
REVERT: A  105 LYS cc_start: 0.6535 (mmmt) cc_final: 0.5771 (mmmt)
REVERT: A  155 TYR cc_start: 0.9311 (t80) cc_final: 0.9096 (t80)
REVERT: A  166 GLU cc_start: 0.9400 (mt-10) cc_final: 0.9193 (pt0)
REVERT: A  202 ARG cc_start: 0.8619 (mmp-170) cc_final: 0.8264 (mtm180)
REVERT: A  206 LYS cc_start: 0.9468 (ptpt) cc_final: 0.9115 (mttp)
REVERT: A  209 PHE cc_start: 0.9753 (m-10) cc_final: 0.9457 (m-80)
REVERT: A  224 ASN cc_start: 0.9354 (p0) cc_final: 0.8911 (p0)
REVERT: B   74 HIS cc_start: 0.9512 (m-70) cc_final: 0.9269 (m-70)
REVERT: B  173 GLN cc_start: 0.9548 (tp-100) cc_final: 0.9301 (tp-100)
REVERT: B  206 LYS cc_start: 0.9344 (ptpp) cc_final: 0.9122 (mttp)
REVERT: B  209 PHE cc_start: 0.9792 (m-10) cc_final: 0.9497 (m-80)
REVERT: C  104 GLU cc_start: 0.8345 (tp30) cc_final: 0.8114 (tm-30)
REVERT: C  105 LYS cc_start: 0.6578 (mmmt) cc_final: 0.5778 (mmmt)
REVERT: C  166 GLU cc_start: 0.8980 (pt0) cc_final: 0.8775 (pt0)
REVERT: C  173 GLN cc_start: 0.9573 (tp-100) cc_final: 0.9354 (tp-100)
REVERT: C  202 ARG cc_start: 0.8574 (mmp-170) cc_final: 0.8118 (mtm180)
REVERT: C  206 LYS cc_start: 0.9473 (ptpp) cc_final: 0.9143 (mttp)
REVERT: C  209 PHE cc_start: 0.9777 (m-10) cc_final: 0.9479 (m-80)
REVERT: D   74 HIS cc_start: 0.9505 (m-70) cc_final: 0.9269 (m-70)
REVERT: D  202 ARG cc_start: 0.8734 (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: 0.9796 (m-10) cc_final: 0.9496 (m-80)
REVERT: F   74 HIS cc_start: 0.9528 (m-70) cc_final: 0.9308 (m-70)
REVERT: F  105 LYS cc_start: 0.6514 (mmmt) cc_final: 0.5726 (mmmt)
REVERT: F  155 TYR cc_start: 0.9315 (t80) cc_final: 0.9096 (t80)
REVERT: F  166 GLU cc_start: 0.9387 (mt-10) cc_final: 0.9177 (pt0)
REVERT: F  202 ARG cc_start: 0.8671 (mmp-170) cc_final: 0.8318 (mtm180)
REVERT: F  206 LYS cc_start: 0.9457 (ptpt) cc_final: 0.9120 (mttp)
REVERT: F  209 PHE cc_start: 0.9743 (m-10) cc_final: 0.9451 (m-80)
REVERT: F  224 ASN cc_start: 0.9340 (p0) cc_final: 0.8882 (p0)
  outliers start: 13
  outliers final: 6
  residues processed: 298
  average time/residue: 0.3086
  time to fit residues: 119.8054
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  : 1.277 
-------------------------------------------------------------------------------
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:    0.3980
   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:    1.9990
   chunk 84 optimal weight:    7.9990
   overall best weight:    1.6924

-------------------------------------------------------------------------------
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**
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: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.061783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.050361 restraints weight = 56691.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.051423 restraints weight = 43178.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.052201 restraints weight = 34892.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.3592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9507  Z= 0.163
  Angle     :  0.792  10.654  12906  Z= 0.408
  Chirality :  0.045   0.310   1476
  Planarity :  0.005   0.058   1548
  Dihedral  :  4.253  15.186   1218
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 20.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 16.27 %
    Favored  : 81.76 %
  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:  0.23 (0.23), residues: 1110
  helix:  0.64 (0.17), residues: 864
  sheet:  1.19 (0.60), residues: 60
  loop : -2.19 (0.34), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  78 
 HIS   0.002   0.001   HIS F  74 
 PHE   0.042   0.002   PHE D 212 
 TYR   0.017   0.002   TYR A  92 
 ARG   0.008   0.001   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04782 (  684)
  hydrogen bonds       : angle       4.85556 ( 2034)
  SS BOND              : bond        0.00176 (    3)
  SS BOND              : angle       0.92146 (    6)
  covalent geometry    : bond        0.00361 ( 9504)
  covalent geometry    : angle       0.79227 (12900)

*********************** 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
  289 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 269
  time to evaluate  : 1.033 
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: E  101 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8811 (ttp80)
REVERT: E  102 LYS cc_start: 0.9123 (pttm) cc_final: 0.8680 (pttm)
REVERT: E  173 GLN cc_start: 0.9602 (tp40) cc_final: 0.9393 (tp-100)
REVERT: E  202 ARG cc_start: 0.8492 (tpt170) cc_final: 0.8098 (mtp180)
REVERT: E  209 PHE cc_start: 0.9697 (m-10) cc_final: 0.9350 (m-80)
REVERT: A   23 LYS cc_start: 0.9062 (tptp) cc_final: 0.8821 (tptp)
REVERT: A   74 HIS cc_start: 0.9559 (m-70) cc_final: 0.9267 (m-70)
REVERT: A   92 TYR cc_start: 0.8808 (t80) cc_final: 0.8574 (t80)
REVERT: A  166 GLU cc_start: 0.9376 (mt-10) cc_final: 0.9081 (mt-10)
REVERT: A  206 LYS cc_start: 0.9456 (ptpt) cc_final: 0.9122 (mttp)
REVERT: A  209 PHE cc_start: 0.9751 (m-10) cc_final: 0.9438 (m-80)
REVERT: A  224 ASN cc_start: 0.9323 (p0) cc_final: 0.9055 (p0)
REVERT: B   74 HIS cc_start: 0.9568 (m-70) cc_final: 0.9268 (m-70)
REVERT: B  101 ARG cc_start: 0.9057 (ttp80) cc_final: 0.8742 (ttp80)
REVERT: B  102 LYS cc_start: 0.9115 (pttm) cc_final: 0.8681 (pttm)
REVERT: B  173 GLN cc_start: 0.9582 (tp-100) cc_final: 0.9346 (tp-100)
REVERT: B  206 LYS cc_start: 0.9392 (ptpp) cc_final: 0.9160 (mttp)
REVERT: B  209 PHE cc_start: 0.9752 (m-10) cc_final: 0.9440 (m-80)
REVERT: C   97 PHE cc_start: 0.9336 (t80) cc_final: 0.9132 (t80)
REVERT: C  162 LYS cc_start: 0.9665 (ttmm) cc_final: 0.9434 (mttm)
REVERT: C  173 GLN cc_start: 0.9606 (tp40) cc_final: 0.9406 (tp-100)
REVERT: C  202 ARG cc_start: 0.8612 (mmp-170) cc_final: 0.8027 (mtp-110)
REVERT: C  206 LYS cc_start: 0.9460 (ptpp) cc_final: 0.9108 (mttp)
REVERT: C  209 PHE cc_start: 0.9764 (m-10) cc_final: 0.9444 (m-80)
REVERT: D   74 HIS cc_start: 0.9562 (m-70) cc_final: 0.9273 (m-70)
REVERT: D  202 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8049 (mtp180)
REVERT: D  206 LYS cc_start: 0.9425 (ptpp) cc_final: 0.9136 (mttp)
REVERT: D  209 PHE cc_start: 0.9762 (m-10) cc_final: 0.9454 (m-80)
REVERT: F   23 LYS cc_start: 0.9059 (tptp) cc_final: 0.8817 (tptp)
REVERT: F   74 HIS cc_start: 0.9553 (m-70) cc_final: 0.9257 (m-70)
REVERT: F   92 TYR cc_start: 0.8811 (t80) cc_final: 0.8581 (t80)
REVERT: F  166 GLU cc_start: 0.9381 (mt-10) cc_final: 0.9090 (mt-10)
REVERT: F  202 ARG cc_start: 0.8628 (mmp-170) cc_final: 0.8181 (mtm180)
REVERT: F  206 LYS cc_start: 0.9468 (ptpt) cc_final: 0.9166 (mttp)
REVERT: F  209 PHE cc_start: 0.9743 (m-10) cc_final: 0.9433 (m-80)
REVERT: F  224 ASN cc_start: 0.9306 (p0) cc_final: 0.9032 (p0)
  outliers start: 20
  outliers final: 7
  residues processed: 281
  average time/residue: 0.2458
  time to fit residues: 89.8442
Evaluate side-chains
  263 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 255
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
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   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:    5.9990
   chunk 97 optimal weight:    7.9990
   chunk 26 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 55 optimal weight:    8.9990
   chunk 101 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    1.1388

-------------------------------------------------------------------------------
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 = 0.3346 r_free = 0.3346 target = 0.059981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.048898 restraints weight = 58393.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.050032 restraints weight = 43979.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.050935 restraints weight = 35048.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.4086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9507  Z= 0.154
  Angle     :  0.805  11.516  12906  Z= 0.417
  Chirality :  0.045   0.185   1476
  Planarity :  0.004   0.049   1548
  Dihedral  :  4.199  18.510   1218
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 18.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.14 %
    Favored  : 79.90 %
  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:  0.60 (0.24), residues: 1110
  helix:  0.89 (0.17), residues: 864
  sheet:  0.96 (0.58), residues: 60
  loop : -1.82 (0.36), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  78 
 HIS   0.002   0.001   HIS E  74 
 PHE   0.044   0.002   PHE F 212 
 TYR   0.025   0.002   TYR D 155 
 ARG   0.007   0.001   ARG D 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04719 (  684)
  hydrogen bonds       : angle       4.90459 ( 2034)
  SS BOND              : bond        0.00149 (    3)
  SS BOND              : angle       0.85589 (    6)
  covalent geometry    : bond        0.00331 ( 9504)
  covalent geometry    : angle       0.80502 (12900)

*********************** 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
  308 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 288
  time to evaluate  : 1.034 
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: E   74 HIS cc_start: 0.9459 (m-70) cc_final: 0.9125 (m-70)
REVERT: E   81 GLN cc_start: 0.9700 (tt0) cc_final: 0.9494 (tt0)
REVERT: E  101 ARG cc_start: 0.9144 (ttp80) cc_final: 0.8925 (ttp80)
REVERT: E  102 LYS cc_start: 0.9124 (pttm) cc_final: 0.8818 (pttm)
REVERT: E  202 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8308 (mtm180)
REVERT: E  206 LYS cc_start: 0.9483 (mttp) cc_final: 0.8943 (mttm)
REVERT: E  209 PHE cc_start: 0.9723 (m-10) cc_final: 0.9341 (m-80)
REVERT: A   23 LYS cc_start: 0.9091 (tptp) cc_final: 0.8856 (tptp)
REVERT: A   74 HIS cc_start: 0.9628 (m-70) cc_final: 0.9342 (m-70)
REVERT: A   92 TYR cc_start: 0.9023 (t80) cc_final: 0.8778 (t80)
REVERT: A  166 GLU cc_start: 0.9393 (mt-10) cc_final: 0.9088 (mt-10)
REVERT: A  202 ARG cc_start: 0.8815 (mtp-110) cc_final: 0.7891 (mtm180)
REVERT: A  206 LYS cc_start: 0.9432 (ptpt) cc_final: 0.9031 (mttp)
REVERT: A  209 PHE cc_start: 0.9747 (m-10) cc_final: 0.9435 (m-80)
REVERT: A  224 ASN cc_start: 0.9273 (p0) cc_final: 0.9055 (p0)
REVERT: B   13 LYS cc_start: 0.9515 (mmmt) cc_final: 0.9286 (mmmt)
REVERT: B   74 HIS cc_start: 0.9588 (m-70) cc_final: 0.9284 (m-70)
REVERT: B  101 ARG cc_start: 0.9087 (ttp80) cc_final: 0.8874 (ttp80)
REVERT: B  102 LYS cc_start: 0.9125 (pttm) cc_final: 0.8824 (pttm)
REVERT: B  173 GLN cc_start: 0.9591 (tp-100) cc_final: 0.9371 (tp-100)
REVERT: B  190 ASP cc_start: 0.9126 (t0) cc_final: 0.8849 (p0)
REVERT: B  206 LYS cc_start: 0.9415 (ptpp) cc_final: 0.9178 (mttp)
REVERT: B  209 PHE cc_start: 0.9709 (m-10) cc_final: 0.9424 (m-80)
REVERT: B  227 GLU cc_start: 0.9711 (mm-30) cc_final: 0.9398 (mm-30)
REVERT: C   74 HIS cc_start: 0.9438 (m-70) cc_final: 0.9124 (m-70)
REVERT: C   81 GLN cc_start: 0.9701 (tt0) cc_final: 0.9493 (tt0)
REVERT: C  202 ARG cc_start: 0.8757 (mmp-170) cc_final: 0.8098 (mtp180)
REVERT: C  206 LYS cc_start: 0.9452 (ptpp) cc_final: 0.9156 (mttp)
REVERT: C  209 PHE cc_start: 0.9763 (m-10) cc_final: 0.9449 (m-80)
REVERT: D   13 LYS cc_start: 0.9526 (mmmt) cc_final: 0.9293 (mmmt)
REVERT: D   74 HIS cc_start: 0.9579 (m-70) cc_final: 0.9295 (m-70)
REVERT: D  202 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7937 (mtp180)
REVERT: D  206 LYS cc_start: 0.9468 (ptpp) cc_final: 0.9169 (mttp)
REVERT: D  209 PHE cc_start: 0.9728 (m-10) cc_final: 0.9424 (m-80)
REVERT: D  227 GLU cc_start: 0.9705 (mm-30) cc_final: 0.9395 (mm-30)
REVERT: F   23 LYS cc_start: 0.9059 (tptp) cc_final: 0.8820 (tptp)
REVERT: F   74 HIS cc_start: 0.9628 (m-70) cc_final: 0.9333 (m-70)
REVERT: F   92 TYR cc_start: 0.9005 (t80) cc_final: 0.8759 (t80)
REVERT: F  101 ARG cc_start: 0.9049 (ttp80) cc_final: 0.8758 (ttp80)
REVERT: F  166 GLU cc_start: 0.9396 (mt-10) cc_final: 0.9082 (mt-10)
REVERT: F  202 ARG cc_start: 0.8726 (mmp-170) cc_final: 0.8212 (mtp180)
REVERT: F  206 LYS cc_start: 0.9501 (ptpt) cc_final: 0.9139 (mttp)
REVERT: F  209 PHE cc_start: 0.9749 (m-10) cc_final: 0.9422 (m-80)
REVERT: F  224 ASN cc_start: 0.9278 (p0) cc_final: 0.9058 (p0)
  outliers start: 20
  outliers final: 7
  residues processed: 294
  average time/residue: 0.2665
  time to fit residues: 100.6876
Evaluate side-chains
  269 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 260
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  202 ARG
Chi-restraints excluded: chain A residue   91 LEU
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:    0.8980
   chunk 102 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   chunk 98 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 84 optimal weight:    5.9990
   chunk 99 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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**
E  63 ASN
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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.060366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.049446 restraints weight = 57344.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.050511 restraints weight = 44177.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.051315 restraints weight = 35642.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.4470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9507  Z= 0.154
  Angle     :  0.847  11.847  12906  Z= 0.437
  Chirality :  0.048   0.375   1476
  Planarity :  0.005   0.072   1548
  Dihedral  :  4.203  20.795   1218
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 19.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 21.76 %
    Favored  : 76.47 %
  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:  0.79 (0.24), residues: 1110
  helix:  0.99 (0.17), residues: 864
  sheet:  1.02 (0.57), residues: 60
  loop : -1.64 (0.37), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP C  78 
 HIS   0.003   0.001   HIS E  74 
 PHE   0.048   0.002   PHE D 212 
 TYR   0.025   0.002   TYR B 155 
 ARG   0.015   0.001   ARG F  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04678 (  684)
  hydrogen bonds       : angle       4.88088 ( 2034)
  SS BOND              : bond        0.00167 (    3)
  SS BOND              : angle       0.85099 (    6)
  covalent geometry    : bond        0.00332 ( 9504)
  covalent geometry    : angle       0.84748 (12900)

*********************** 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
  314 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 296
  time to evaluate  : 1.179 
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   74 HIS cc_start: 0.9311 (m-70) cc_final: 0.9049 (m-70)
REVERT: E   92 TYR cc_start: 0.9013 (t80) cc_final: 0.8802 (t80)
REVERT: E  101 ARG cc_start: 0.9050 (ttp80) cc_final: 0.8794 (ttp80)
REVERT: E  173 GLN cc_start: 0.9571 (tp-100) cc_final: 0.9365 (tp-100)
REVERT: E  202 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8386 (mtp180)
REVERT: E  206 LYS cc_start: 0.9509 (mttp) cc_final: 0.8838 (mttt)
REVERT: E  209 PHE cc_start: 0.9750 (m-10) cc_final: 0.9365 (m-80)
REVERT: A   17 TYR cc_start: 0.8237 (m-10) cc_final: 0.7826 (m-10)
REVERT: A   74 HIS cc_start: 0.9481 (m-70) cc_final: 0.9133 (m-70)
REVERT: A  166 GLU cc_start: 0.9325 (mt-10) cc_final: 0.9050 (mt-10)
REVERT: A  202 ARG cc_start: 0.8852 (mtp-110) cc_final: 0.7998 (mtm180)
REVERT: A  206 LYS cc_start: 0.9419 (ptpt) cc_final: 0.9009 (mttp)
REVERT: A  209 PHE cc_start: 0.9713 (m-10) cc_final: 0.9372 (m-80)
REVERT: B   17 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7833 (m-10)
REVERT: B   74 HIS cc_start: 0.9445 (m-70) cc_final: 0.9127 (m-70)
REVERT: B   92 TYR cc_start: 0.9105 (t80) cc_final: 0.8879 (t80)
REVERT: B   98 TYR cc_start: 0.9618 (m-80) cc_final: 0.9353 (m-10)
REVERT: B  101 ARG cc_start: 0.8971 (ttp80) cc_final: 0.8611 (ttp80)
REVERT: B  102 LYS cc_start: 0.9076 (pttm) cc_final: 0.8524 (pttm)
REVERT: B  173 GLN cc_start: 0.9575 (tp-100) cc_final: 0.9371 (tp-100)
REVERT: B  190 ASP cc_start: 0.8886 (t0) cc_final: 0.8685 (p0)
REVERT: B  206 LYS cc_start: 0.9395 (ptpp) cc_final: 0.9177 (mttp)
REVERT: B  209 PHE cc_start: 0.9657 (m-10) cc_final: 0.9335 (m-80)
REVERT: B  227 GLU cc_start: 0.9668 (mm-30) cc_final: 0.9339 (mm-30)
REVERT: C   74 HIS cc_start: 0.9324 (m-70) cc_final: 0.9050 (m-70)
REVERT: C  202 ARG cc_start: 0.8814 (mmp-170) cc_final: 0.8111 (mtp180)
REVERT: C  206 LYS cc_start: 0.9418 (ptpp) cc_final: 0.9098 (mttp)
REVERT: C  209 PHE cc_start: 0.9766 (m-10) cc_final: 0.9424 (m-80)
REVERT: D   17 TYR cc_start: 0.8323 (m-80) cc_final: 0.7709 (m-10)
REVERT: D   74 HIS cc_start: 0.9415 (m-70) cc_final: 0.9105 (m-70)
REVERT: D   98 TYR cc_start: 0.9601 (m-80) cc_final: 0.9312 (m-10)
REVERT: D  101 ARG cc_start: 0.8964 (ttp80) cc_final: 0.8610 (ttp80)
REVERT: D  102 LYS cc_start: 0.9047 (pttm) cc_final: 0.8646 (pttm)
REVERT: D  202 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7828 (mtp180)
REVERT: D  206 LYS cc_start: 0.9436 (ptpp) cc_final: 0.9148 (mttp)
REVERT: D  209 PHE cc_start: 0.9721 (m-10) cc_final: 0.9363 (m-80)
REVERT: F   17 TYR cc_start: 0.8246 (m-10) cc_final: 0.7844 (m-10)
REVERT: F   23 LYS cc_start: 0.9077 (tptp) cc_final: 0.8767 (tptp)
REVERT: F   74 HIS cc_start: 0.9484 (m-70) cc_final: 0.9127 (m-70)
REVERT: F  166 GLU cc_start: 0.9343 (mt-10) cc_final: 0.9067 (mt-10)
REVERT: F  190 ASP cc_start: 0.8888 (t0) cc_final: 0.8570 (p0)
REVERT: F  206 LYS cc_start: 0.9493 (ptpt) cc_final: 0.8987 (mttp)
REVERT: F  209 PHE cc_start: 0.9728 (m-10) cc_final: 0.9416 (m-80)
REVERT: F  227 GLU cc_start: 0.9726 (mm-30) cc_final: 0.9425 (mm-30)
  outliers start: 18
  outliers final: 2
  residues processed: 303
  average time/residue: 0.2608
  time to fit residues: 103.3388
Evaluate side-chains
  268 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 263
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  202 ARG
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   91 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:    0.9990
   chunk 67 optimal weight:    0.2980
   chunk 92 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 45 optimal weight:    9.9990
   chunk 3 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 41 optimal weight:   20.0000
   chunk 97 optimal weight:    9.9990
   chunk 103 optimal weight:    6.9990
   overall best weight:    2.2588

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.055652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.044322 restraints weight = 58959.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.045218 restraints weight = 46467.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.045878 restraints weight = 38538.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.4956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9507  Z= 0.176
  Angle     :  0.820  13.068  12906  Z= 0.432
  Chirality :  0.045   0.221   1476
  Planarity :  0.005   0.080   1548
  Dihedral  :  4.281  21.743   1218
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 23.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 27.25 %
    Favored  : 71.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.24), residues: 1110
  helix:  1.01 (0.17), residues: 864
  sheet:  1.15 (0.59), residues: 60
  loop : -1.68 (0.38), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP C  78 
 HIS   0.003   0.001   HIS E  74 
 PHE   0.044   0.002   PHE E 212 
 TYR   0.015   0.001   TYR D 155 
 ARG   0.017   0.001   ARG A  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04829 (  684)
  hydrogen bonds       : angle       5.06695 ( 2034)
  SS BOND              : bond        0.00186 (    3)
  SS BOND              : angle       0.82716 (    6)
  covalent geometry    : bond        0.00384 ( 9504)
  covalent geometry    : angle       0.82045 (12900)

*********************** 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
  293 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 285
  time to evaluate  : 1.034 
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: E   17 TYR cc_start: 0.8392 (m-10) cc_final: 0.7904 (m-10)
REVERT: E   42 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8301 (mt-10)
REVERT: E   92 TYR cc_start: 0.9162 (t80) cc_final: 0.8895 (t80)
REVERT: E  173 GLN cc_start: 0.9629 (tp40) cc_final: 0.9388 (tp-100)
REVERT: E  202 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8229 (mtp-110)
REVERT: E  206 LYS cc_start: 0.9578 (mttp) cc_final: 0.9246 (mmtt)
REVERT: E  227 GLU cc_start: 0.9786 (mm-30) cc_final: 0.9491 (mm-30)
REVERT: A   17 TYR cc_start: 0.8436 (m-10) cc_final: 0.7983 (m-10)
REVERT: A   74 HIS cc_start: 0.9549 (m-70) cc_final: 0.9150 (m-70)
REVERT: A  166 GLU cc_start: 0.9275 (mt-10) cc_final: 0.9066 (mt-10)
REVERT: A  202 ARG cc_start: 0.8891 (mtp-110) cc_final: 0.8129 (mtm180)
REVERT: A  206 LYS cc_start: 0.9442 (ptpt) cc_final: 0.9077 (mttp)
REVERT: A  209 PHE cc_start: 0.9739 (m-10) cc_final: 0.9383 (m-80)
REVERT: A  227 GLU cc_start: 0.9746 (mm-30) cc_final: 0.9436 (mm-30)
REVERT: B   13 LYS cc_start: 0.9558 (mmmt) cc_final: 0.9311 (mmmt)
REVERT: B   17 TYR cc_start: 0.8474 (m-10) cc_final: 0.8026 (m-10)
REVERT: B   74 HIS cc_start: 0.9494 (m-70) cc_final: 0.9144 (m-70)
REVERT: B  173 GLN cc_start: 0.9594 (tp-100) cc_final: 0.9381 (tp-100)
REVERT: B  206 LYS cc_start: 0.9434 (ptpp) cc_final: 0.9223 (mttp)
REVERT: B  209 PHE cc_start: 0.9703 (m-10) cc_final: 0.9347 (m-80)
REVERT: B  227 GLU cc_start: 0.9742 (mm-30) cc_final: 0.9410 (mm-30)
REVERT: C   17 TYR cc_start: 0.8374 (m-10) cc_final: 0.7889 (m-10)
REVERT: C   42 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8374 (mt-10)
REVERT: C  173 GLN cc_start: 0.9604 (tp-100) cc_final: 0.9366 (tp-100)
REVERT: C  202 ARG cc_start: 0.8893 (mmp-170) cc_final: 0.8260 (mtp180)
REVERT: C  206 LYS cc_start: 0.9515 (ptpp) cc_final: 0.9263 (ptpt)
REVERT: C  209 PHE cc_start: 0.9781 (m-10) cc_final: 0.9450 (m-80)
REVERT: C  227 GLU cc_start: 0.9766 (mm-30) cc_final: 0.9475 (mm-30)
REVERT: D   13 LYS cc_start: 0.9560 (mmmt) cc_final: 0.9307 (mmmt)
REVERT: D   17 TYR cc_start: 0.8523 (m-80) cc_final: 0.7882 (m-10)
REVERT: D   42 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8454 (mt-10)
REVERT: D   74 HIS cc_start: 0.9451 (m-70) cc_final: 0.9084 (m-70)
REVERT: D  202 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7934 (mtp180)
REVERT: D  206 LYS cc_start: 0.9453 (ptpp) cc_final: 0.9211 (mttp)
REVERT: D  209 PHE cc_start: 0.9760 (m-10) cc_final: 0.9383 (m-80)
REVERT: F   17 TYR cc_start: 0.8418 (m-10) cc_final: 0.7987 (m-10)
REVERT: F   42 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8407 (mt-10)
REVERT: F   74 HIS cc_start: 0.9567 (m-70) cc_final: 0.9195 (m-70)
REVERT: F  166 GLU cc_start: 0.9280 (mt-10) cc_final: 0.9075 (mt-10)
REVERT: F  202 ARG cc_start: 0.8873 (mmp-170) cc_final: 0.8321 (mtp180)
REVERT: F  206 LYS cc_start: 0.9382 (ptpt) cc_final: 0.9038 (ptpt)
REVERT: F  209 PHE cc_start: 0.9731 (m-10) cc_final: 0.9390 (m-80)
REVERT: F  227 GLU cc_start: 0.9768 (mm-30) cc_final: 0.9456 (mm-30)
  outliers start: 8
  outliers final: 2
  residues processed: 288
  average time/residue: 0.2689
  time to fit residues: 101.4716
Evaluate side-chains
  265 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 261
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   78 TRP
Chi-restraints excluded: chain E residue  202 ARG
Chi-restraints excluded: chain C residue   78 TRP
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:    0.9990
   chunk 6 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 60 optimal weight:    5.9990
   chunk 14 optimal weight:   20.0000
   chunk 29 optimal weight:    7.9990
   chunk 15 optimal weight:    8.9990
   chunk 41 optimal weight:   20.0000
   chunk 93 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
E  15 GLN
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 ASN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.053678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.043000 restraints weight = 62942.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.043880 restraints weight = 48148.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.044642 restraints weight = 39361.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.5468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9507  Z= 0.190
  Angle     :  0.888  13.871  12906  Z= 0.457
  Chirality :  0.046   0.259   1476
  Planarity :  0.005   0.063   1548
  Dihedral  :  4.345  21.106   1218
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 23.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 30.49 %
    Favored  : 68.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.24), residues: 1110
  helix:  0.90 (0.17), residues: 864
  sheet:  1.13 (0.58), residues: 60
  loop : -1.89 (0.37), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.002   TRP C  78 
 HIS   0.004   0.001   HIS F  74 
 PHE   0.034   0.002   PHE E 212 
 TYR   0.012   0.001   TYR B 230 
 ARG   0.015   0.002   ARG D  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04931 (  684)
  hydrogen bonds       : angle       5.21587 ( 2034)
  SS BOND              : bond        0.00203 (    3)
  SS BOND              : angle       0.80510 (    6)
  covalent geometry    : bond        0.00410 ( 9504)
  covalent geometry    : angle       0.88772 (12900)

*********************** 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
  312 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 299
  time to evaluate  : 1.033 
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: E   17 TYR cc_start: 0.8416 (m-10) cc_final: 0.7971 (m-10)
REVERT: E   42 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8510 (mt-10)
REVERT: E   92 TYR cc_start: 0.9203 (t80) cc_final: 0.8960 (t80)
REVERT: E  179 PHE cc_start: 0.8388 (m-80) cc_final: 0.8139 (m-80)
REVERT: E  190 ASP cc_start: 0.9124 (t0) cc_final: 0.8614 (p0)
REVERT: E  227 GLU cc_start: 0.9789 (mm-30) cc_final: 0.9493 (mm-30)
REVERT: A   17 TYR cc_start: 0.8547 (m-10) cc_final: 0.8140 (m-10)
REVERT: A   42 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8443 (mt-10)
REVERT: A   74 HIS cc_start: 0.9530 (m-70) cc_final: 0.9139 (m-70)
REVERT: A   92 TYR cc_start: 0.9002 (t80) cc_final: 0.8765 (t80)
REVERT: A  162 LYS cc_start: 0.9616 (ttmm) cc_final: 0.9411 (ptpp)
REVERT: A  206 LYS cc_start: 0.9495 (ptpt) cc_final: 0.8997 (mttp)
REVERT: A  209 PHE cc_start: 0.9739 (m-10) cc_final: 0.9340 (m-80)
REVERT: A  227 GLU cc_start: 0.9777 (mm-30) cc_final: 0.9501 (mm-30)
REVERT: B   17 TYR cc_start: 0.8510 (m-10) cc_final: 0.8089 (m-10)
REVERT: B   42 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8404 (mt-10)
REVERT: B   74 HIS cc_start: 0.9498 (m-70) cc_final: 0.9057 (m-70)
REVERT: B  173 GLN cc_start: 0.9608 (tp-100) cc_final: 0.9380 (tp-100)
REVERT: B  190 ASP cc_start: 0.8998 (t0) cc_final: 0.8780 (p0)
REVERT: B  209 PHE cc_start: 0.9720 (m-10) cc_final: 0.9339 (m-80)
REVERT: B  227 GLU cc_start: 0.9755 (mm-30) cc_final: 0.9417 (mm-30)
REVERT: C   17 TYR cc_start: 0.8441 (m-10) cc_final: 0.7968 (m-10)
REVERT: C   42 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8520 (mt-10)
REVERT: C  202 ARG cc_start: 0.8903 (mmp-170) cc_final: 0.8542 (mtm180)
REVERT: C  206 LYS cc_start: 0.9509 (ptpp) cc_final: 0.9177 (ptpt)
REVERT: C  209 PHE cc_start: 0.9744 (m-10) cc_final: 0.9433 (m-80)
REVERT: C  227 GLU cc_start: 0.9794 (mm-30) cc_final: 0.9498 (mm-30)
REVERT: D   17 TYR cc_start: 0.8601 (m-80) cc_final: 0.8018 (m-10)
REVERT: D   33 ARG cc_start: 0.9166 (mtm110) cc_final: 0.8915 (ptt90)
REVERT: D   48 GLU cc_start: 0.8980 (mm-30) cc_final: 0.6567 (mm-30)
REVERT: D   74 HIS cc_start: 0.9445 (m-70) cc_final: 0.9050 (m-70)
REVERT: D  200 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9327 (tp)
REVERT: D  202 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8340 (mtm180)
REVERT: D  206 LYS cc_start: 0.9480 (ptpp) cc_final: 0.9272 (ptpt)
REVERT: D  209 PHE cc_start: 0.9750 (m-10) cc_final: 0.9370 (m-80)
REVERT: D  227 GLU cc_start: 0.9757 (mm-30) cc_final: 0.9424 (mm-30)
REVERT: F   17 TYR cc_start: 0.8561 (m-10) cc_final: 0.8157 (m-10)
REVERT: F   33 ARG cc_start: 0.9491 (mtm-85) cc_final: 0.9207 (ptt90)
REVERT: F   42 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8535 (mt-10)
REVERT: F   74 HIS cc_start: 0.9537 (m-70) cc_final: 0.9137 (m-70)
REVERT: F   92 TYR cc_start: 0.8971 (t80) cc_final: 0.8700 (t80)
REVERT: F  206 LYS cc_start: 0.9468 (ptpt) cc_final: 0.9110 (ptpt)
REVERT: F  209 PHE cc_start: 0.9747 (m-10) cc_final: 0.9401 (m-80)
REVERT: F  227 GLU cc_start: 0.9788 (mm-30) cc_final: 0.9507 (mm-30)
  outliers start: 13
  outliers final: 2
  residues processed: 309
  average time/residue: 0.2637
  time to fit residues: 106.7299
Evaluate side-chains
  276 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 272
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  202 ARG
Chi-restraints excluded: chain C residue  210 ILE
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:    2.9990
   chunk 94 optimal weight:    9.9990
   chunk 14 optimal weight:    0.1980
   chunk 57 optimal weight:    0.9990
   chunk 77 optimal weight:    7.9990
   chunk 64 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0970
   chunk 87 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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
** 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 = 0.3264 r_free = 0.3264 target = 0.058003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.047400 restraints weight = 62674.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.048355 restraints weight = 47567.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.049117 restraints weight = 38326.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.5731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9507  Z= 0.171
  Angle     :  1.009  14.558  12906  Z= 0.505
  Chirality :  0.049   0.339   1476
  Planarity :  0.005   0.053   1548
  Dihedral  :  4.348  26.062   1218
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 20.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 32.65 %
    Favored  : 66.86 %
  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:  0.55 (0.24), residues: 1110
  helix:  0.83 (0.17), residues: 864
  sheet:  1.32 (0.59), residues: 60
  loop : -1.94 (0.37), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.002   TRP C  78 
 HIS   0.002   0.001   HIS F  74 
 PHE   0.052   0.002   PHE E 212 
 TYR   0.009   0.001   TYR B 185 
 ARG   0.013   0.001   ARG A  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04889 (  684)
  hydrogen bonds       : angle       5.13517 ( 2034)
  SS BOND              : bond        0.00114 (    3)
  SS BOND              : angle       0.74404 (    6)
  covalent geometry    : bond        0.00365 ( 9504)
  covalent geometry    : angle       1.00900 (12900)

*********************** 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
  306 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 301
  time to evaluate  : 1.971 
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: 0.8273 (m-10) cc_final: 0.7857 (m-10)
REVERT: E   42 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8390 (mt-10)
REVERT: E   92 TYR cc_start: 0.9133 (t80) cc_final: 0.8931 (t80)
REVERT: E   98 TYR cc_start: 0.9509 (m-10) cc_final: 0.9263 (m-10)
REVERT: E  202 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8491 (mmm-85)
REVERT: E  206 LYS cc_start: 0.9581 (mttt) cc_final: 0.8930 (mttm)
REVERT: E  209 PHE cc_start: 0.9642 (m-10) cc_final: 0.9317 (m-80)
REVERT: E  227 GLU cc_start: 0.9765 (mm-30) cc_final: 0.9474 (mm-30)
REVERT: A   17 TYR cc_start: 0.8471 (m-10) cc_final: 0.8115 (m-10)
REVERT: A   33 ARG cc_start: 0.9431 (mtm-85) cc_final: 0.9210 (mtm-85)
REVERT: A   42 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8400 (mt-10)
REVERT: A   92 TYR cc_start: 0.8979 (t80) cc_final: 0.8692 (t80)
REVERT: A  190 ASP cc_start: 0.8958 (t0) cc_final: 0.8750 (p0)
REVERT: A  206 LYS cc_start: 0.9324 (ptpt) cc_final: 0.9001 (mttp)
REVERT: A  209 PHE cc_start: 0.9723 (m-10) cc_final: 0.9383 (m-80)
REVERT: A  227 GLU cc_start: 0.9756 (mm-30) cc_final: 0.9463 (mm-30)
REVERT: B   17 TYR cc_start: 0.8373 (m-10) cc_final: 0.8042 (m-10)
REVERT: B   42 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8314 (mt-10)
REVERT: B   74 HIS cc_start: 0.9330 (m-70) cc_final: 0.8903 (m-70)
REVERT: B  173 GLN cc_start: 0.9540 (tp-100) cc_final: 0.9313 (tp-100)
REVERT: B  209 PHE cc_start: 0.9650 (m-10) cc_final: 0.9230 (m-80)
REVERT: B  227 GLU cc_start: 0.9727 (mm-30) cc_final: 0.9383 (mm-30)
REVERT: C   17 TYR cc_start: 0.8316 (m-10) cc_final: 0.7918 (m-10)
REVERT: C   42 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8459 (mt-10)
REVERT: C  209 PHE cc_start: 0.9659 (m-10) cc_final: 0.9328 (m-80)
REVERT: C  227 GLU cc_start: 0.9762 (mm-30) cc_final: 0.9464 (mm-30)
REVERT: D   17 TYR cc_start: 0.8444 (m-80) cc_final: 0.7917 (m-10)
REVERT: D   33 ARG cc_start: 0.9138 (mtm110) cc_final: 0.8929 (ptt90)
REVERT: D   48 GLU cc_start: 0.8909 (mm-30) cc_final: 0.7609 (mm-30)
REVERT: D   74 HIS cc_start: 0.9299 (m-70) cc_final: 0.8904 (m-70)
REVERT: D  179 PHE cc_start: 0.8469 (m-80) cc_final: 0.8265 (m-80)
REVERT: D  190 ASP cc_start: 0.8978 (t0) cc_final: 0.8755 (p0)
REVERT: D  202 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8354 (mtm110)
REVERT: D  206 LYS cc_start: 0.9417 (ptpp) cc_final: 0.9214 (ptpt)
REVERT: D  209 PHE cc_start: 0.9707 (m-10) cc_final: 0.9238 (m-80)
REVERT: D  227 GLU cc_start: 0.9714 (mm-30) cc_final: 0.9388 (mm-30)
REVERT: F   17 TYR cc_start: 0.8409 (m-10) cc_final: 0.8073 (m-10)
REVERT: F   33 ARG cc_start: 0.9495 (mtm-85) cc_final: 0.9238 (ptt90)
REVERT: F   42 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8455 (mt-10)
REVERT: F   92 TYR cc_start: 0.9001 (t80) cc_final: 0.8718 (t80)
REVERT: F  161 PHE cc_start: 0.9538 (m-80) cc_final: 0.9128 (m-80)
REVERT: F  162 LYS cc_start: 0.9502 (ptpp) cc_final: 0.9258 (ptpp)
REVERT: F  190 ASP cc_start: 0.8958 (t0) cc_final: 0.8655 (p0)
REVERT: F  202 ARG cc_start: 0.8942 (mmp-170) cc_final: 0.8330 (mtp180)
REVERT: F  206 LYS cc_start: 0.9431 (ptpt) cc_final: 0.9068 (ptpt)
REVERT: F  209 PHE cc_start: 0.9734 (m-10) cc_final: 0.9406 (m-80)
REVERT: F  227 GLU cc_start: 0.9777 (mm-30) cc_final: 0.9483 (mm-30)
  outliers start: 5
  outliers final: 1
  residues processed: 303
  average time/residue: 0.2840
  time to fit residues: 114.6200
Evaluate side-chains
  274 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 271
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  202 ARG
Chi-restraints excluded: chain C residue   74 HIS
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:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 63 optimal weight:   10.0000
   chunk 85 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 102 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 17 optimal weight:    0.7980
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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  15 GLN
** B  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.057100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.046635 restraints weight = 62793.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.047600 restraints weight = 47318.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.048355 restraints weight = 37856.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.6020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9507  Z= 0.183
  Angle     :  1.074  15.425  12906  Z= 0.546
  Chirality :  0.051   0.363   1476
  Planarity :  0.005   0.071   1548
  Dihedral  :  4.402  23.593   1218
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 23.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 34.71 %
    Favored  : 64.71 %
  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:  0.49 (0.24), residues: 1110
  helix:  0.78 (0.17), residues: 864
  sheet:  1.42 (0.59), residues: 60
  loop : -1.94 (0.37), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.003   TRP C  78 
 HIS   0.007   0.001   HIS F  74 
 PHE   0.034   0.002   PHE E 212 
 TYR   0.023   0.001   TYR D  66 
 ARG   0.011   0.001   ARG A  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04895 (  684)
  hydrogen bonds       : angle       5.23012 ( 2034)
  SS BOND              : bond        0.00157 (    3)
  SS BOND              : angle       0.71238 (    6)
  covalent geometry    : bond        0.00412 ( 9504)
  covalent geometry    : angle       1.07416 (12900)

*********************** 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
  301 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 295
  time to evaluate  : 1.193 
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: 0.8331 (m-10) cc_final: 0.7946 (m-10)
REVERT: E   42 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8453 (mt-10)
REVERT: E   81 GLN cc_start: 0.9662 (tt0) cc_final: 0.9316 (mt0)
REVERT: E  179 PHE cc_start: 0.8552 (m-80) cc_final: 0.8167 (m-80)
REVERT: E  206 LYS cc_start: 0.9595 (mttt) cc_final: 0.9176 (mmtt)
REVERT: E  209 PHE cc_start: 0.9615 (m-10) cc_final: 0.9241 (m-80)
REVERT: E  227 GLU cc_start: 0.9760 (mm-30) cc_final: 0.9466 (mm-30)
REVERT: A   17 TYR cc_start: 0.8450 (m-10) cc_final: 0.8105 (m-10)
REVERT: A   42 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8431 (mt-10)
REVERT: A   92 TYR cc_start: 0.9077 (t80) cc_final: 0.8818 (t80)
REVERT: A  202 ARG cc_start: 0.8823 (mtm180) cc_final: 0.8308 (mtm180)
REVERT: A  206 LYS cc_start: 0.9411 (ptpt) cc_final: 0.9053 (ptpt)
REVERT: A  209 PHE cc_start: 0.9727 (m-10) cc_final: 0.9410 (m-80)
REVERT: A  227 GLU cc_start: 0.9766 (mm-30) cc_final: 0.9469 (mm-30)
REVERT: B   17 TYR cc_start: 0.8403 (m-10) cc_final: 0.8068 (m-10)
REVERT: B   42 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8339 (mt-10)
REVERT: B   74 HIS cc_start: 0.9311 (m-70) cc_final: 0.8895 (m-70)
REVERT: B   81 GLN cc_start: 0.9793 (OUTLIER) cc_final: 0.9322 (mm-40)
REVERT: B  190 ASP cc_start: 0.8964 (t0) cc_final: 0.8758 (p0)
REVERT: B  209 PHE cc_start: 0.9634 (m-10) cc_final: 0.9229 (m-80)
REVERT: B  227 GLU cc_start: 0.9737 (mm-30) cc_final: 0.9403 (mm-30)
REVERT: C   17 TYR cc_start: 0.8378 (m-10) cc_final: 0.8020 (m-10)
REVERT: C   42 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8449 (mt-10)
REVERT: C  179 PHE cc_start: 0.8567 (m-80) cc_final: 0.8163 (m-80)
REVERT: C  209 PHE cc_start: 0.9658 (m-10) cc_final: 0.9342 (m-80)
REVERT: C  227 GLU cc_start: 0.9758 (mm-30) cc_final: 0.9454 (mm-30)
REVERT: D   17 TYR cc_start: 0.8483 (m-80) cc_final: 0.7927 (m-10)
REVERT: D   33 ARG cc_start: 0.9169 (mtm110) cc_final: 0.8939 (ptt180)
REVERT: D   48 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8503 (mm-30)
REVERT: D   74 HIS cc_start: 0.9257 (m-70) cc_final: 0.8849 (m-70)
REVERT: D  190 ASP cc_start: 0.9023 (t0) cc_final: 0.8805 (p0)
REVERT: D  202 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8355 (mtp180)
REVERT: D  206 LYS cc_start: 0.9451 (ptpp) cc_final: 0.9242 (ptpt)
REVERT: D  209 PHE cc_start: 0.9703 (m-10) cc_final: 0.9281 (m-80)
REVERT: D  227 GLU cc_start: 0.9747 (mm-30) cc_final: 0.9412 (mm-30)
REVERT: F   17 TYR cc_start: 0.8415 (m-10) cc_final: 0.8080 (m-10)
REVERT: F   33 ARG cc_start: 0.9477 (mtm-85) cc_final: 0.9135 (ptt90)
REVERT: F   42 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8536 (mt-10)
REVERT: F   92 TYR cc_start: 0.9009 (t80) cc_final: 0.8740 (t80)
REVERT: F  161 PHE cc_start: 0.9527 (m-80) cc_final: 0.9076 (m-80)
REVERT: F  190 ASP cc_start: 0.8934 (t0) cc_final: 0.8648 (p0)
REVERT: F  206 LYS cc_start: 0.9452 (ptpt) cc_final: 0.9176 (ptpt)
REVERT: F  209 PHE cc_start: 0.9727 (m-10) cc_final: 0.9420 (m-80)
REVERT: F  227 GLU cc_start: 0.9767 (mm-30) cc_final: 0.9471 (mm-30)
  outliers start: 6
  outliers final: 3
  residues processed: 297
  average time/residue: 0.3062
  time to fit residues: 120.6434
Evaluate side-chains
  279 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 274
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   74 HIS
Chi-restraints excluded: chain E residue  202 ARG
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain C residue   74 HIS
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:    5.9990
   chunk 68 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 90 optimal weight:    7.9990
   chunk 46 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 29 optimal weight:    3.9990
   chunk 96 optimal weight:    7.9990
   chunk 93 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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
B  81 GLN
** C  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 = 0.3173 r_free = 0.3173 target = 0.054428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.044678 restraints weight = 66306.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.045557 restraints weight = 49886.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.046173 restraints weight = 40155.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.6389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9507  Z= 0.221
  Angle     :  1.084  13.979  12906  Z= 0.566
  Chirality :  0.052   0.334   1476
  Planarity :  0.006   0.082   1548
  Dihedral  :  4.580  23.944   1218
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 27.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 35.78 %
    Favored  : 63.53 %
  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:  0.43 (0.24), residues: 1110
  helix:  0.71 (0.17), residues: 870
  sheet:  1.46 (0.63), residues: 60
  loop : -1.94 (0.38), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.003   TRP C  78 
 HIS   0.004   0.001   HIS B  74 
 PHE   0.029   0.002   PHE E 212 
 TYR   0.018   0.001   TYR E  92 
 ARG   0.013   0.001   ARG A  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05063 (  684)
  hydrogen bonds       : angle       5.41749 ( 2034)
  SS BOND              : bond        0.00217 (    3)
  SS BOND              : angle       0.75146 (    6)
  covalent geometry    : bond        0.00490 ( 9504)
  covalent geometry    : angle       1.08443 (12900)

********************** 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
  296 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 289
  time to evaluate  : 1.034 
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: E   17 TYR cc_start: 0.8369 (m-10) cc_final: 0.8048 (m-10)
REVERT: E   42 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8566 (mt-10)
REVERT: E   81 GLN cc_start: 0.9655 (tt0) cc_final: 0.9227 (mt0)
REVERT: E  179 PHE cc_start: 0.8579 (m-80) cc_final: 0.8195 (m-80)
REVERT: E  190 ASP cc_start: 0.9049 (t0) cc_final: 0.8732 (p0)
REVERT: E  202 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8100 (mmm-85)
REVERT: E  227 GLU cc_start: 0.9770 (mm-30) cc_final: 0.9484 (mm-30)
REVERT: A   17 TYR cc_start: 0.8475 (m-10) cc_final: 0.8118 (m-10)
REVERT: A   42 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8503 (mt-10)
REVERT: A   92 TYR cc_start: 0.9090 (t80) cc_final: 0.8885 (t80)
REVERT: A  157 ILE cc_start: 0.9719 (mm) cc_final: 0.9478 (pt)
REVERT: A  161 PHE cc_start: 0.9521 (m-80) cc_final: 0.9129 (m-80)
REVERT: A  179 PHE cc_start: 0.8625 (m-80) cc_final: 0.8367 (m-80)
REVERT: A  202 ARG cc_start: 0.8816 (mtm180) cc_final: 0.8331 (mtm180)
REVERT: A  209 PHE cc_start: 0.9739 (m-10) cc_final: 0.9453 (m-80)
REVERT: A  227 GLU cc_start: 0.9799 (mm-30) cc_final: 0.9528 (mm-30)
REVERT: B   17 TYR cc_start: 0.8423 (m-10) cc_final: 0.8102 (m-10)
REVERT: B   42 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8416 (mt-10)
REVERT: B   74 HIS cc_start: 0.9287 (m-70) cc_final: 0.9035 (m90)
REVERT: B   81 GLN cc_start: 0.9735 (OUTLIER) cc_final: 0.9295 (mm-40)
REVERT: B  209 PHE cc_start: 0.9665 (m-10) cc_final: 0.9308 (m-80)
REVERT: B  227 GLU cc_start: 0.9755 (mm-30) cc_final: 0.9468 (mm-30)
REVERT: C   17 TYR cc_start: 0.8410 (m-10) cc_final: 0.8077 (m-10)
REVERT: C   37 LEU cc_start: 0.9588 (pp) cc_final: 0.9157 (pp)
REVERT: C   42 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8569 (mt-10)
REVERT: C   81 GLN cc_start: 0.9655 (tt0) cc_final: 0.9427 (tp40)
REVERT: C  179 PHE cc_start: 0.8588 (m-80) cc_final: 0.8198 (m-80)
REVERT: C  209 PHE cc_start: 0.9700 (m-10) cc_final: 0.9363 (m-80)
REVERT: C  227 GLU cc_start: 0.9773 (mm-30) cc_final: 0.9489 (mm-30)
REVERT: D   17 TYR cc_start: 0.8518 (m-80) cc_final: 0.8003 (m-10)
REVERT: D   42 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8608 (mt-10)
REVERT: D   48 GLU cc_start: 0.8923 (mm-30) cc_final: 0.7411 (mm-30)
REVERT: D   74 HIS cc_start: 0.9258 (m-70) cc_final: 0.9000 (m90)
REVERT: D  202 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8464 (mtp180)
REVERT: D  206 LYS cc_start: 0.9487 (ptpp) cc_final: 0.9276 (ptpt)
REVERT: D  209 PHE cc_start: 0.9726 (m-10) cc_final: 0.9308 (m-80)
REVERT: D  227 GLU cc_start: 0.9732 (mm-30) cc_final: 0.9433 (mm-30)
REVERT: F   17 TYR cc_start: 0.8449 (m-10) cc_final: 0.8103 (m-10)
REVERT: F   33 ARG cc_start: 0.9485 (mtm-85) cc_final: 0.9138 (ptt90)
REVERT: F   42 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8645 (mt-10)
REVERT: F  101 ARG cc_start: 0.8842 (ttp80) cc_final: 0.8596 (ttp80)
REVERT: F  161 PHE cc_start: 0.9513 (m-80) cc_final: 0.9083 (m-80)
REVERT: F  209 PHE cc_start: 0.9731 (m-10) cc_final: 0.9450 (m-80)
REVERT: F  227 GLU cc_start: 0.9787 (mm-30) cc_final: 0.9515 (mm-30)
  outliers start: 7
  outliers final: 2
  residues processed: 292
  average time/residue: 0.2411
  time to fit residues: 92.9395
Evaluate side-chains
  285 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 280
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   74 HIS
Chi-restraints excluded: chain E residue  202 ARG
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain C residue   74 HIS
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:    0.5980
   chunk 100 optimal weight:    0.8980
   chunk 73 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 54 optimal weight:    4.9990
   chunk 82 optimal weight:    8.9990
   chunk 1 optimal weight:    9.9990
   chunk 89 optimal weight:    5.9990
   chunk 78 optimal weight:    6.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.055922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.045792 restraints weight = 63734.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.046720 restraints weight = 48173.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.047443 restraints weight = 38682.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.6521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9507  Z= 0.195
  Angle     :  1.165  17.278  12906  Z= 0.597
  Chirality :  0.054   0.350   1476
  Planarity :  0.005   0.089   1548
  Dihedral  :  4.526  25.166   1218
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 25.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 37.16 %
    Favored  : 62.55 %
  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:  0.23 (0.24), residues: 1110
  helix:  0.59 (0.17), residues: 864
  sheet:  1.40 (0.61), residues: 60
  loop : -1.98 (0.37), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.003   TRP A  78 
 HIS   0.002   0.001   HIS B  74 
 PHE   0.037   0.002   PHE E 212 
 TYR   0.022   0.002   TYR F 230 
 ARG   0.020   0.002   ARG A  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05285 (  684)
  hydrogen bonds       : angle       5.30122 ( 2034)
  SS BOND              : bond        0.00127 (    3)
  SS BOND              : angle       0.68926 (    6)
  covalent geometry    : bond        0.00432 ( 9504)
  covalent geometry    : angle       1.16507 (12900)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3849.57 seconds
wall clock time: 70 minutes 13.89 seconds (4213.89 seconds total)