Starting phenix.real_space_refine
on Tue Mar  3 23:23:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ajq_11806/03_2026/7ajq_11806.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ajq_11806/03_2026/7ajq_11806.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ajq_11806/03_2026/7ajq_11806.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ajq_11806/03_2026/7ajq_11806.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ajq_11806/03_2026/7ajq_11806.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ajq_11806/03_2026/7ajq_11806.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.074
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      29      5.16       5
     C    5817      2.51       5
     N    1675      2.21       5
     O    1689      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9210
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1729
          Classifications: {'peptide': 230}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1777
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 231}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1777
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 231}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1777
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 231}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1777
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 231}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 177
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 177
          Classifications: {'peptide': 23}
          Link IDs: {'PTRANS': 2, 'TRANS': 20}
    Chain: "G"
      Number of atoms: 196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 196
          Classifications: {'peptide': 25}
          Link IDs: {'PTRANS': 2, 'TRANS': 22}
  Time building chain proxies: 2.11, per 1000 atoms: 0.23
  Number of scatterers: 9210
  At special positions: 0
  Unit cell: (84.293, 87.494, 133.375, 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      29     16.00
     O    1689      8.00
     N    1675      7.00
     C    5817      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 372.6 milliseconds
  

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2246

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 0 sheets defined
      87.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 100
    Processing helix  chain 'A' and resid 104 through 113
      removed outlier: 3.530A  pdb=" N   ALA A 108 " --> pdb=" O   SER A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 136
    Processing helix  chain 'A' and resid 140 through 164
    Processing helix  chain 'A' and resid 166 through 199
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 206 through 272
      removed outlier: 4.633A  pdb=" N   GLY A 210 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      Proline residue:  A 227  - end of helix
      removed outlier: 4.246A  pdb=" N   ALA A 267 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLU A 268 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   SER A 272 " --> pdb=" O   GLU A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 280
      removed outlier: 3.509A  pdb=" N   HIS A 276 " --> pdb=" O   SER A 272 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLN A 277 " --> pdb=" O   GLN A 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 100
    Processing helix  chain 'B' and resid 104 through 114
      removed outlier: 4.395A  pdb=" N   ASN B 114 " --> pdb=" O   GLU B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 136
    Processing helix  chain 'B' and resid 140 through 164
    Processing helix  chain 'B' and resid 165 through 199
      removed outlier: 4.107A  pdb=" N   PHE B 169 " --> pdb=" O   ARG B 165 " (cutoff:3.500A)
      Proline residue:  B 178  - end of helix
    Processing helix  chain 'B' and resid 206 through 280
      removed outlier: 4.098A  pdb=" N   GLY B 210 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE B 211 " --> pdb=" O   VAL B 207 " (cutoff:3.500A)
      Proline residue:  B 227  - end of helix
      removed outlier: 4.524A  pdb=" N   ALA B 267 " --> pdb=" O   LEU B 263 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   GLU B 268 " --> pdb=" O   ALA B 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 53
      removed outlier: 4.207A  pdb=" N   TYR C  53 " --> pdb=" O   ILE C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 57 through 100
    Processing helix  chain 'C' and resid 105 through 113
    Processing helix  chain 'C' and resid 119 through 135
    Processing helix  chain 'C' and resid 140 through 164
      removed outlier: 3.608A  pdb=" N   ILE C 144 " --> pdb=" O   ASP C 140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 199
      Proline residue:  C 178  - end of helix
    Processing helix  chain 'C' and resid 207 through 280
      Proline residue:  C 227  - end of helix
      removed outlier: 4.447A  pdb=" N   ALA C 267 " --> pdb=" O   LEU C 263 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   GLU C 268 " --> pdb=" O   ALA C 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 52
    Processing helix  chain 'D' and resid 57 through 99
    Processing helix  chain 'D' and resid 100 through 102
      No H-bonds generated for 'chain 'D' and resid 100 through 102'
    Processing helix  chain 'D' and resid 104 through 114
      removed outlier: 3.515A  pdb=" N   ASN D 114 " --> pdb=" O   GLU D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 135
    Processing helix  chain 'D' and resid 140 through 164
    Processing helix  chain 'D' and resid 165 through 199
      removed outlier: 4.232A  pdb=" N   PHE D 169 " --> pdb=" O   ARG D 165 " (cutoff:3.500A)
      Proline residue:  D 178  - end of helix
    Processing helix  chain 'D' and resid 204 through 206
      No H-bonds generated for 'chain 'D' and resid 204 through 206'
    Processing helix  chain 'D' and resid 207 through 272
      removed outlier: 3.506A  pdb=" N   ILE D 211 " --> pdb=" O   VAL D 207 " (cutoff:3.500A)
      Proline residue:  D 227  - end of helix
      removed outlier: 3.908A  pdb=" N   ALA D 267 " --> pdb=" O   LEU D 263 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   GLU D 268 " --> pdb=" O   ALA D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 272 through 277
      removed outlier: 4.551A  pdb=" N   GLN D 277 " --> pdb=" O   GLN D 273 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 59 through 100
    Processing helix  chain 'E' and resid 104 through 113
    Processing helix  chain 'E' and resid 119 through 135
    Processing helix  chain 'E' and resid 140 through 164
    Processing helix  chain 'E' and resid 166 through 199
      Proline residue:  E 178  - end of helix
    Processing helix  chain 'E' and resid 207 through 277
      removed outlier: 3.945A  pdb=" N   ILE E 211 " --> pdb=" O   VAL E 207 " (cutoff:3.500A)
      Proline residue:  E 227  - end of helix
    Processing helix  chain 'F' and resid 22 through 38
      removed outlier: 4.068A  pdb=" N   VAL F  26 " --> pdb=" O   PRO F  22 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 21 through 38
      removed outlier: 4.168A  pdb=" N   ASP G  25 " --> pdb=" O   THR G  21 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   VAL G  26 " --> pdb=" O   PRO G  22 " (cutoff:3.500A)

    865 hydrogen bonds defined for protein.
    2589 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.43

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3175
        1.34 -     1.46: 1464
        1.46 -     1.57: 4643
        1.57 -     1.69: 0
        1.69 -     1.81: 58
  Bond restraints: 9340
  Sorted by residual:
  bond pdb=" C   THR F  21 "
       pdb=" N   PRO F  22 "
    ideal  model  delta    sigma   weight residual
    1.337  1.369 -0.033 9.80e-03 1.04e+04 1.11e+01
  bond pdb=" C   HIS E 276 "
       pdb=" O   HIS E 276 "
    ideal  model  delta    sigma   weight residual
    1.235  1.249 -0.014 1.43e-02 4.89e+03 1.00e+00
  bond pdb=" CA  ALA A 136 "
       pdb=" C   ALA A 136 "
    ideal  model  delta    sigma   weight residual
    1.532  1.523  0.009 9.60e-03 1.09e+04 9.64e-01
  bond pdb=" CA  THR F  21 "
       pdb=" C   THR F  21 "
    ideal  model  delta    sigma   weight residual
    1.524  1.534 -0.010 1.26e-02 6.30e+03 6.14e-01
  bond pdb=" C   ALA F  38 "
       pdb=" N   PRO F  39 "
    ideal  model  delta    sigma   weight residual
    1.334  1.351 -0.017 2.34e-02 1.83e+03 5.33e-01
  ... (remaining 9335 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 12474
        1.64 -     3.28: 128
        3.28 -     4.92: 31
        4.92 -     6.56: 22
        6.56 -     8.20: 2
  Bond angle restraints: 12657
  Sorted by residual:
  angle pdb=" N   THR G  21 "
        pdb=" CA  THR G  21 "
        pdb=" C   THR G  21 "
      ideal   model   delta    sigma   weight residual
     109.81  116.15   -6.34 2.21e+00 2.05e-01 8.23e+00
  angle pdb=" N   THR F  21 "
        pdb=" CA  THR F  21 "
        pdb=" C   THR F  21 "
      ideal   model   delta    sigma   weight residual
     109.81  116.10   -6.29 2.21e+00 2.05e-01 8.10e+00
  angle pdb=" CA  LEU B 278 "
        pdb=" CB  LEU B 278 "
        pdb=" CG  LEU B 278 "
      ideal   model   delta    sigma   weight residual
     116.30  108.10    8.20 3.50e+00 8.16e-02 5.49e+00
  angle pdb=" N   SER A 135 "
        pdb=" CA  SER A 135 "
        pdb=" C   SER A 135 "
      ideal   model   delta    sigma   weight residual
     111.11  108.33    2.78 1.20e+00 6.94e-01 5.37e+00
  angle pdb=" C   ALA D 136 "
        pdb=" N   GLU D 137 "
        pdb=" CA  GLU D 137 "
      ideal   model   delta    sigma   weight residual
     121.54  125.90   -4.36 1.91e+00 2.74e-01 5.20e+00
  ... (remaining 12652 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 5113
       17.43 -    34.86: 395
       34.86 -    52.29: 69
       52.29 -    69.72: 9
       69.72 -    87.14: 8
  Dihedral angle restraints: 5594
    sinusoidal: 2118
      harmonic: 3476
  Sorted by residual:
  dihedral pdb=" CA  LEU B 278 "
           pdb=" C   LEU B 278 "
           pdb=" N   ARG B 279 "
           pdb=" CA  ARG B 279 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.98   23.02     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  HIS E 276 "
           pdb=" C   HIS E 276 "
           pdb=" N   GLN E 277 "
           pdb=" CA  GLN E 277 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.27  -22.73     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  THR G  21 "
           pdb=" C   THR G  21 "
           pdb=" N   PRO G  22 "
           pdb=" CA  PRO G  22 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.70  -21.30     0      5.00e+00 4.00e-02 1.82e+01
  ... (remaining 5591 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 935
       0.025 -    0.051: 339
       0.051 -    0.076: 164
       0.076 -    0.102: 46
       0.102 -    0.127: 18
  Chirality restraints: 1502
  Sorted by residual:
  chirality pdb=" CA  THR F  21 "
            pdb=" N   THR F  21 "
            pdb=" C   THR F  21 "
            pdb=" CB  THR F  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.03e-01
  chirality pdb=" CB  VAL A 223 "
            pdb=" CA  VAL A 223 "
            pdb=" CG1 VAL A 223 "
            pdb=" CG2 VAL A 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.51   -0.12 2.00e-01 2.50e+01 3.79e-01
  chirality pdb=" CB  VAL G  29 "
            pdb=" CA  VAL G  29 "
            pdb=" CG1 VAL G  29 "
            pdb=" CG2 VAL G  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.51   -0.12 2.00e-01 2.50e+01 3.73e-01
  ... (remaining 1499 not shown)

  Planarity restraints: 1642
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS C 274 "    0.008 2.00e-02 2.50e+03   1.66e-02 2.75e+00
        pdb=" C   HIS C 274 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   HIS C 274 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ALA C 275 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE G  33 "    0.006 2.00e-02 2.50e+03   1.18e-02 1.38e+00
        pdb=" C   ILE G  33 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   ILE G  33 "    0.008 2.00e-02 2.50e+03
        pdb=" N   PHE G  34 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP C 248 "   -0.006 2.00e-02 2.50e+03   1.15e-02 1.32e+00
        pdb=" CG  ASP C 248 "    0.020 2.00e-02 2.50e+03
        pdb=" OD1 ASP C 248 "   -0.007 2.00e-02 2.50e+03
        pdb=" OD2 ASP C 248 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1639 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1227
        2.75 -     3.28: 10405
        3.28 -     3.82: 16218
        3.82 -     4.36: 17160
        4.36 -     4.90: 28997
  Nonbonded interactions: 74007
  Sorted by model distance:
  nonbonded pdb=" OG1 THR E 185 "
            pdb=" OG1 THR E 218 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   GLU D 268 "
            pdb=" OG  SER D 272 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OG  SER B 104 "
            pdb=" OD1 ASP B 106 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   ASP C 262 "
            pdb=" OG1 THR C 266 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   ASN D 162 "
            pdb=" NH1 ARG D 165 "
     model   vdw
     2.263 3.120
  ... (remaining 74002 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 52 through 281)
  selection = (chain 'C' and resid 52 through 281)
  selection = (chain 'D' and resid 52 through 281)
  selection = (chain 'E' and resid 52 through 281)
}
ncs_group {
  reference = chain 'F'
  selection = (chain 'G' and resid 18 through 40)
}

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:             1.500
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.230
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
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      :  0.002   0.033   9340  Z= 0.126
  Angle     :  0.553   8.204  12657  Z= 0.315
  Chirality :  0.035   0.127   1502
  Planarity :  0.003   0.029   1642
  Dihedral  : 13.098  87.144   3348
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.22), residues: 1208
  helix: -0.03 (0.15), residues: 1015
  sheet:  None (None), residues: 0
  loop : -3.52 (0.36), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 271 
 TYR   0.007   0.001   TYR A 232 
 PHE   0.006   0.001   PHE C 193 
 TRP   0.010   0.001   TRP C 187 
 HIS   0.003   0.001   HIS C 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 9340)
  covalent geometry    : angle       0.55305 (12657)
  hydrogen bonds       : bond        0.06438 (  865)
  hydrogen bonds       : angle       4.23437 ( 2589)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 304
  time to evaluate  : 0.236 
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: A   79 PHE cc_start: 0.8721 (m-10) cc_final: 0.8437 (m-10)
REVERT: A   81 LYS cc_start: 0.8074 (mmmm) cc_final: 0.7860 (mmmm)
REVERT: A  126 ASN cc_start: 0.8808 (t0) cc_final: 0.8238 (p0)
REVERT: A  193 PHE cc_start: 0.8916 (m-10) cc_final: 0.8472 (m-10)
REVERT: A  252 GLN cc_start: 0.8769 (tt0) cc_final: 0.8548 (tm-30)
REVERT: B   61 LYS cc_start: 0.3875 (tttt) cc_final: 0.2932 (mmmt)
REVERT: B   81 LYS cc_start: 0.9321 (tppt) cc_final: 0.8531 (mmmt)
REVERT: B  150 PHE cc_start: 0.8937 (t80) cc_final: 0.8701 (t80)
REVERT: B  187 TRP cc_start: 0.8553 (t60) cc_final: 0.8308 (t-100)
REVERT: B  270 LYS cc_start: 0.7512 (pttt) cc_final: 0.7072 (tptp)
REVERT: C  169 PHE cc_start: 0.8946 (t80) cc_final: 0.8730 (t80)
REVERT: C  220 MET cc_start: 0.8990 (ptm) cc_final: 0.7956 (ptm)
REVERT: C  232 TYR cc_start: 0.7957 (t80) cc_final: 0.7754 (t80)
REVERT: C  245 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8013 (mm-40)
REVERT: C  248 ASP cc_start: 0.8370 (m-30) cc_final: 0.7991 (t70)
REVERT: C  252 GLN cc_start: 0.8417 (mt0) cc_final: 0.7887 (mt0)
REVERT: D  169 PHE cc_start: 0.9004 (t80) cc_final: 0.8729 (t80)
REVERT: D  190 MET cc_start: 0.9085 (ppp) cc_final: 0.8740 (tmm)
REVERT: D  216 LEU cc_start: 0.8898 (pp) cc_final: 0.8661 (pp)
REVERT: D  220 MET cc_start: 0.9033 (mmt) cc_final: 0.8725 (mpp)
REVERT: E  231 ILE cc_start: 0.9236 (mm) cc_final: 0.8991 (tp)
REVERT: F   27 MET cc_start: 0.7647 (mmt) cc_final: 0.7389 (mmp)
REVERT: F   34 PHE cc_start: 0.3922 (m-10) cc_final: 0.3168 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 304
  average time/residue: 0.0992
  time to fit residues: 40.7024
Evaluate side-chains
  224 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0770
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    2.9990
   overall best weight:    2.0146

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

Flipped N/Q/H residues before XYZ refinement:
A 139 ASN
A 245 GLN
B 257 GLN
C  96 GLN
C 129 GLN
** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  96 GLN
E 191 ASN
E 273 GLN
** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  19 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.077733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.063831 restraints weight = 47300.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.065137 restraints weight = 34155.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.066082 restraints weight = 26813.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.066782 restraints weight = 22507.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.067269 restraints weight = 19731.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9340  Z= 0.168
  Angle     :  0.699  11.774  12657  Z= 0.359
  Chirality :  0.042   0.217   1502
  Planarity :  0.004   0.037   1642
  Dihedral  :  4.168  23.618   1320
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 15.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 15.42 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.24), residues: 1208
  helix:  0.94 (0.16), residues: 1021
  sheet:  None (None), residues: 0
  loop : -3.24 (0.40), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 155 
 TYR   0.016   0.002   TYR B  53 
 PHE   0.025   0.002   PHE B 179 
 TRP   0.014   0.001   TRP B  75 
 HIS   0.012   0.002   HIS C 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9340)
  covalent geometry    : angle       0.69944 (12657)
  hydrogen bonds       : bond        0.03740 (  865)
  hydrogen bonds       : angle       4.31773 ( 2589)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 247
  time to evaluate  : 0.253 
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: A   61 LYS cc_start: 0.9344 (pttp) cc_final: 0.8987 (tppt)
REVERT: A   79 PHE cc_start: 0.8620 (m-10) cc_final: 0.8402 (m-10)
REVERT: A  126 ASN cc_start: 0.8894 (t0) cc_final: 0.8279 (p0)
REVERT: A  140 ASP cc_start: 0.6673 (m-30) cc_final: 0.6355 (m-30)
REVERT: A  193 PHE cc_start: 0.8871 (m-10) cc_final: 0.8559 (m-10)
REVERT: A  235 PHE cc_start: 0.9201 (m-80) cc_final: 0.8824 (m-80)
REVERT: B   52 MET cc_start: 0.6839 (ttm) cc_final: 0.6632 (ttm)
REVERT: B   61 LYS cc_start: 0.3742 (tttt) cc_final: 0.3067 (mmmt)
REVERT: B   81 LYS cc_start: 0.9211 (tppt) cc_final: 0.8949 (mttt)
REVERT: B  163 MET cc_start: 0.8528 (mmm) cc_final: 0.8128 (mmm)
REVERT: B  187 TRP cc_start: 0.8552 (t60) cc_final: 0.8351 (t-100)
REVERT: B  257 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8530 (pt0)
REVERT: B  270 LYS cc_start: 0.7528 (pttt) cc_final: 0.7074 (tptp)
REVERT: C  169 PHE cc_start: 0.8884 (t80) cc_final: 0.8647 (t80)
REVERT: C  235 PHE cc_start: 0.8578 (t80) cc_final: 0.8261 (m-80)
REVERT: C  245 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8180 (mm-40)
REVERT: C  248 ASP cc_start: 0.8619 (m-30) cc_final: 0.8220 (t70)
REVERT: C  252 GLN cc_start: 0.8670 (mt0) cc_final: 0.8053 (mt0)
REVERT: D  169 PHE cc_start: 0.8792 (t80) cc_final: 0.8490 (t80)
REVERT: D  189 ILE cc_start: 0.9409 (tp) cc_final: 0.9136 (pt)
REVERT: D  190 MET cc_start: 0.9045 (ppp) cc_final: 0.8826 (tmm)
REVERT: E   64 MET cc_start: 0.8010 (ppp) cc_final: 0.7727 (ppp)
REVERT: E  235 PHE cc_start: 0.8860 (m-80) cc_final: 0.8626 (m-80)
  outliers start: 17
  outliers final: 9
  residues processed: 252
  average time/residue: 0.0931
  time to fit residues: 32.3869
Evaluate side-chains
  231 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 221
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  257 GLN
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain E residue  248 ASP
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain G residue   21 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 105 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 114 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 233 ASN
B 257 GLN
C 139 ASN
C 191 ASN
** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 276 HIS ** 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 = 0.3822 r_free = 0.3822 target = 0.079077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.064873 restraints weight = 47420.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.066255 restraints weight = 34212.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.067249 restraints weight = 26858.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.067947 restraints weight = 22445.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.068470 restraints weight = 19658.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9340  Z= 0.144
  Angle     :  0.700  11.742  12657  Z= 0.355
  Chirality :  0.043   0.186   1502
  Planarity :  0.004   0.046   1642
  Dihedral  :  4.233  23.147   1320
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.91 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.24), residues: 1208
  helix:  1.22 (0.16), residues: 1021
  sheet:  None (None), residues: 0
  loop : -3.15 (0.40), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 151 
 TYR   0.016   0.002   TYR C 232 
 PHE   0.041   0.002   PHE B  79 
 TRP   0.018   0.001   TRP B  75 
 HIS   0.009   0.001   HIS C 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9340)
  covalent geometry    : angle       0.69973 (12657)
  hydrogen bonds       : bond        0.03675 (  865)
  hydrogen bonds       : angle       4.26837 ( 2589)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 244
  time to evaluate  : 0.354 
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: A  126 ASN cc_start: 0.8888 (t0) cc_final: 0.8253 (p0)
REVERT: A  140 ASP cc_start: 0.6861 (m-30) cc_final: 0.6360 (m-30)
REVERT: A  193 PHE cc_start: 0.8866 (m-10) cc_final: 0.8427 (m-10)
REVERT: A  220 MET cc_start: 0.8292 (tpt) cc_final: 0.8090 (tpt)
REVERT: A  235 PHE cc_start: 0.9187 (m-80) cc_final: 0.8438 (m-80)
REVERT: A  270 LYS cc_start: 0.6067 (mttt) cc_final: 0.5509 (tmtt)
REVERT: B   61 LYS cc_start: 0.3609 (tttt) cc_final: 0.3019 (mmmt)
REVERT: B   81 LYS cc_start: 0.9277 (tppt) cc_final: 0.9005 (mttt)
REVERT: B  163 MET cc_start: 0.8529 (mmm) cc_final: 0.8154 (mmm)
REVERT: B  187 TRP cc_start: 0.8498 (t60) cc_final: 0.8221 (t-100)
REVERT: B  270 LYS cc_start: 0.7504 (pttt) cc_final: 0.7077 (tptp)
REVERT: C  169 PHE cc_start: 0.8875 (t80) cc_final: 0.8637 (t80)
REVERT: C  235 PHE cc_start: 0.8671 (t80) cc_final: 0.8329 (m-80)
REVERT: C  245 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8252 (mm-40)
REVERT: C  248 ASP cc_start: 0.8599 (m-30) cc_final: 0.8243 (t70)
REVERT: C  252 GLN cc_start: 0.8715 (mt0) cc_final: 0.8125 (mt0)
REVERT: D   67 LEU cc_start: 0.9374 (mt) cc_final: 0.9095 (pp)
REVERT: D  169 PHE cc_start: 0.8821 (t80) cc_final: 0.8457 (t80)
REVERT: E   64 MET cc_start: 0.8024 (ppp) cc_final: 0.7693 (ppp)
REVERT: E  140 ASP cc_start: 0.7397 (t0) cc_final: 0.7119 (t0)
REVERT: E  187 TRP cc_start: 0.8273 (t-100) cc_final: 0.7870 (t60)
REVERT: E  237 ARG cc_start: 0.8400 (mmt180) cc_final: 0.7864 (mmt180)
REVERT: E  270 LYS cc_start: 0.7246 (pptt) cc_final: 0.6379 (pttt)
REVERT: G   24 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8397 (mp)
REVERT: G   35 MET cc_start: 0.8306 (mtm) cc_final: 0.8013 (mtm)
  outliers start: 23
  outliers final: 16
  residues processed: 255
  average time/residue: 0.0862
  time to fit residues: 30.8857
Evaluate side-chains
  232 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 215
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain E residue  150 PHE
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain E residue  248 ASP
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue   26 VAL
Chi-restraints excluded: chain G residue   21 THR
Chi-restraints excluded: chain G residue   24 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 35 optimal weight:    7.9990
   chunk 1 optimal weight:    0.8980
   chunk 72 optimal weight:    7.9990
   chunk 101 optimal weight:    8.9990
   chunk 61 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0970
   chunk 81 optimal weight:    1.9990
   chunk 70 optimal weight:    7.9990
   chunk 110 optimal weight:    0.5980
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 257 GLN
** E 276 HIS ** 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 = 0.3812 r_free = 0.3812 target = 0.078186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.064124 restraints weight = 48323.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.065426 restraints weight = 35487.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.066328 restraints weight = 28082.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.066983 restraints weight = 23690.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.067491 restraints weight = 20959.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9340  Z= 0.145
  Angle     :  0.720  13.270  12657  Z= 0.360
  Chirality :  0.043   0.205   1502
  Planarity :  0.004   0.027   1642
  Dihedral  :  4.235  23.593   1320
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 16.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 20.77 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.25), residues: 1208
  helix:  1.29 (0.16), residues: 1027
  sheet:  None (None), residues: 0
  loop : -3.02 (0.42), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 151 
 TYR   0.025   0.002   TYR C 232 
 PHE   0.038   0.002   PHE B  79 
 TRP   0.017   0.001   TRP B  75 
 HIS   0.006   0.001   HIS C 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9340)
  covalent geometry    : angle       0.71965 (12657)
  hydrogen bonds       : bond        0.03647 (  865)
  hydrogen bonds       : angle       4.30620 ( 2589)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 232
  time to evaluate  : 0.335 
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: A   61 LYS cc_start: 0.9328 (pttp) cc_final: 0.8973 (tppt)
REVERT: A  126 ASN cc_start: 0.8856 (t0) cc_final: 0.8240 (p0)
REVERT: A  140 ASP cc_start: 0.6847 (m-30) cc_final: 0.6359 (m-30)
REVERT: A  187 TRP cc_start: 0.8088 (t-100) cc_final: 0.7592 (t-100)
REVERT: A  190 MET cc_start: 0.8032 (ptp) cc_final: 0.7648 (ptp)
REVERT: A  193 PHE cc_start: 0.8935 (m-10) cc_final: 0.8470 (m-10)
REVERT: A  220 MET cc_start: 0.8363 (tpt) cc_final: 0.8089 (tpt)
REVERT: A  270 LYS cc_start: 0.6225 (mttt) cc_final: 0.5760 (tmtt)
REVERT: B   61 LYS cc_start: 0.3599 (tttt) cc_final: 0.3040 (mmmt)
REVERT: B   81 LYS cc_start: 0.9248 (tppt) cc_final: 0.8924 (mttt)
REVERT: B  163 MET cc_start: 0.8599 (mmm) cc_final: 0.8158 (mmm)
REVERT: B  187 TRP cc_start: 0.8514 (t60) cc_final: 0.8247 (t-100)
REVERT: B  200 GLN cc_start: 0.8347 (mp10) cc_final: 0.7538 (tp40)
REVERT: B  270 LYS cc_start: 0.7494 (pttt) cc_final: 0.7085 (tptp)
REVERT: C  169 PHE cc_start: 0.8853 (t80) cc_final: 0.8616 (t80)
REVERT: C  220 MET cc_start: 0.9125 (ptm) cc_final: 0.8694 (ppp)
REVERT: C  235 PHE cc_start: 0.8637 (t80) cc_final: 0.8287 (m-80)
REVERT: C  245 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8210 (mm-40)
REVERT: C  248 ASP cc_start: 0.8498 (m-30) cc_final: 0.8229 (t70)
REVERT: C  252 GLN cc_start: 0.8683 (mt0) cc_final: 0.8126 (mt0)
REVERT: E   64 MET cc_start: 0.8017 (ppp) cc_final: 0.7632 (ppp)
REVERT: E  140 ASP cc_start: 0.7395 (t0) cc_final: 0.7155 (t0)
REVERT: E  187 TRP cc_start: 0.8253 (t-100) cc_final: 0.7860 (t60)
REVERT: E  237 ARG cc_start: 0.8354 (mmt180) cc_final: 0.7691 (mmt180)
REVERT: F   35 MET cc_start: 0.3039 (mmm) cc_final: 0.2658 (mmm)
REVERT: G   24 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8436 (mp)
REVERT: G   27 MET cc_start: 0.8659 (mmm) cc_final: 0.8382 (mpp)
  outliers start: 27
  outliers final: 18
  residues processed: 245
  average time/residue: 0.0854
  time to fit residues: 29.6580
Evaluate side-chains
  231 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 212
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   75 TRP
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain E residue  248 ASP
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue   26 VAL
Chi-restraints excluded: chain G residue   24 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 55 optimal weight:    7.9990
   chunk 47 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 8 optimal weight:    6.9990
   chunk 110 optimal weight:    0.2980
   chunk 71 optimal weight:    0.9990
   chunk 96 optimal weight:    4.9990
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 276 HIS ** 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 = 0.3827 r_free = 0.3827 target = 0.078960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.064608 restraints weight = 47407.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.065863 restraints weight = 35089.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.066747 restraints weight = 27748.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.067395 restraints weight = 23422.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.067883 restraints weight = 20803.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9340  Z= 0.137
  Angle     :  0.730  12.116  12657  Z= 0.363
  Chirality :  0.043   0.200   1502
  Planarity :  0.003   0.026   1642
  Dihedral  :  4.216  22.668   1320
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 22.70 %
    Favored  : 74.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.25), residues: 1208
  helix:  1.36 (0.16), residues: 1028
  sheet:  None (None), residues: 0
  loop : -3.04 (0.40), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 165 
 TYR   0.016   0.002   TYR D 159 
 PHE   0.046   0.002   PHE D 193 
 TRP   0.015   0.001   TRP B  75 
 HIS   0.006   0.001   HIS C 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9340)
  covalent geometry    : angle       0.73022 (12657)
  hydrogen bonds       : bond        0.03619 (  865)
  hydrogen bonds       : angle       4.34578 ( 2589)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 233
  time to evaluate  : 0.275 
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: A  126 ASN cc_start: 0.8819 (t0) cc_final: 0.8244 (p0)
REVERT: A  140 ASP cc_start: 0.6765 (m-30) cc_final: 0.6301 (m-30)
REVERT: A  163 MET cc_start: 0.8947 (mmm) cc_final: 0.8673 (mmm)
REVERT: A  190 MET cc_start: 0.8125 (ptp) cc_final: 0.7529 (ptp)
REVERT: A  193 PHE cc_start: 0.8978 (m-10) cc_final: 0.8461 (m-10)
REVERT: A  220 MET cc_start: 0.8313 (tpt) cc_final: 0.8059 (tpt)
REVERT: A  235 PHE cc_start: 0.8791 (m-80) cc_final: 0.8589 (m-80)
REVERT: A  270 LYS cc_start: 0.6149 (mttt) cc_final: 0.5833 (tmtt)
REVERT: B   61 LYS cc_start: 0.3606 (tttt) cc_final: 0.3123 (mmmt)
REVERT: B  163 MET cc_start: 0.8627 (mmm) cc_final: 0.8162 (mmm)
REVERT: B  167 ASN cc_start: 0.8907 (p0) cc_final: 0.7874 (t0)
REVERT: B  187 TRP cc_start: 0.8469 (t60) cc_final: 0.8229 (t-100)
REVERT: B  200 GLN cc_start: 0.8355 (mp10) cc_final: 0.7547 (tp40)
REVERT: B  220 MET cc_start: 0.8847 (mtp) cc_final: 0.8520 (mtt)
REVERT: B  270 LYS cc_start: 0.7489 (pttt) cc_final: 0.7099 (tptp)
REVERT: C  113 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7630 (tm-30)
REVERT: C  169 PHE cc_start: 0.8850 (t80) cc_final: 0.8625 (t80)
REVERT: C  179 PHE cc_start: 0.8793 (m-10) cc_final: 0.8553 (m-80)
REVERT: C  235 PHE cc_start: 0.8570 (t80) cc_final: 0.8180 (m-80)
REVERT: C  245 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8140 (mm-40)
REVERT: C  248 ASP cc_start: 0.8421 (m-30) cc_final: 0.8183 (t70)
REVERT: C  252 GLN cc_start: 0.8590 (mt0) cc_final: 0.8079 (mt0)
REVERT: D   67 LEU cc_start: 0.9354 (mt) cc_final: 0.9054 (pp)
REVERT: D  163 MET cc_start: 0.8848 (mpp) cc_final: 0.8628 (mpp)
REVERT: D  190 MET cc_start: 0.8906 (tmm) cc_final: 0.8646 (ptm)
REVERT: E   64 MET cc_start: 0.8047 (ppp) cc_final: 0.7633 (ppp)
REVERT: E  140 ASP cc_start: 0.7365 (t0) cc_final: 0.7144 (t0)
REVERT: E  150 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.8262 (t80)
REVERT: E  187 TRP cc_start: 0.8283 (t-100) cc_final: 0.7891 (t60)
REVERT: E  237 ARG cc_start: 0.8292 (mmt180) cc_final: 0.7648 (mmt180)
REVERT: E  270 LYS cc_start: 0.7338 (pptt) cc_final: 0.6438 (ptpt)
REVERT: F   35 MET cc_start: 0.2437 (mmm) cc_final: 0.2011 (mmm)
REVERT: G   35 MET cc_start: 0.8070 (mtm) cc_final: 0.7801 (mtt)
  outliers start: 29
  outliers final: 21
  residues processed: 250
  average time/residue: 0.0808
  time to fit residues: 28.8131
Evaluate side-chains
  233 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 211
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   75 TRP
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain E residue   69 LEU
Chi-restraints excluded: chain E residue  150 PHE
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain E residue  248 ASP
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue   26 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 117 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 39 optimal weight:   10.0000
   chunk 102 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 80 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 71 optimal weight:    9.9990
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 276 HIS ** 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 = 0.3815 r_free = 0.3815 target = 0.078462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.064055 restraints weight = 47640.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.065368 restraints weight = 34789.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.066331 restraints weight = 27631.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.067041 restraints weight = 23308.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.067490 restraints weight = 20447.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9340  Z= 0.144
  Angle     :  0.742  12.478  12657  Z= 0.368
  Chirality :  0.043   0.201   1502
  Planarity :  0.004   0.026   1642
  Dihedral  :  4.229  22.826   1320
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 16.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 24.20 %
    Favored  : 72.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.25), residues: 1208
  helix:  1.40 (0.16), residues: 1027
  sheet:  None (None), residues: 0
  loop : -2.85 (0.42), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 151 
 TYR   0.025   0.002   TYR C 232 
 PHE   0.041   0.002   PHE B  79 
 TRP   0.019   0.001   TRP B  75 
 HIS   0.006   0.001   HIS C 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9340)
  covalent geometry    : angle       0.74171 (12657)
  hydrogen bonds       : bond        0.03675 (  865)
  hydrogen bonds       : angle       4.33743 ( 2589)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 224
  time to evaluate  : 0.327 
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: A   61 LYS cc_start: 0.9270 (pttp) cc_final: 0.8943 (tppt)
REVERT: A  126 ASN cc_start: 0.8866 (t0) cc_final: 0.8286 (p0)
REVERT: A  140 ASP cc_start: 0.6858 (m-30) cc_final: 0.6367 (m-30)
REVERT: A  190 MET cc_start: 0.8238 (ptp) cc_final: 0.7554 (ptp)
REVERT: A  193 PHE cc_start: 0.8999 (m-10) cc_final: 0.8463 (m-10)
REVERT: A  220 MET cc_start: 0.8287 (tpt) cc_final: 0.8046 (tpt)
REVERT: A  235 PHE cc_start: 0.8860 (m-80) cc_final: 0.8427 (m-80)
REVERT: A  237 ARG cc_start: 0.8908 (ptm160) cc_final: 0.8587 (ptt180)
REVERT: A  270 LYS cc_start: 0.6204 (mttt) cc_final: 0.5890 (tmtt)
REVERT: B   61 LYS cc_start: 0.3640 (tttt) cc_final: 0.3237 (tttt)
REVERT: B  146 GLU cc_start: 0.8859 (pt0) cc_final: 0.8157 (pt0)
REVERT: B  163 MET cc_start: 0.8657 (mmm) cc_final: 0.8237 (mmm)
REVERT: B  167 ASN cc_start: 0.8972 (p0) cc_final: 0.7951 (t0)
REVERT: B  200 GLN cc_start: 0.8283 (mp10) cc_final: 0.7511 (tp40)
REVERT: B  270 LYS cc_start: 0.7466 (pttt) cc_final: 0.6992 (tptp)
REVERT: C   92 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8336 (pp)
REVERT: C  169 PHE cc_start: 0.8872 (t80) cc_final: 0.8652 (t80)
REVERT: C  220 MET cc_start: 0.9260 (ptm) cc_final: 0.8803 (ppp)
REVERT: C  235 PHE cc_start: 0.8559 (t80) cc_final: 0.8142 (m-80)
REVERT: C  248 ASP cc_start: 0.8452 (m-30) cc_final: 0.8223 (t70)
REVERT: C  252 GLN cc_start: 0.8673 (mt0) cc_final: 0.8158 (mt0)
REVERT: D  129 GLN cc_start: 0.7614 (tp40) cc_final: 0.7391 (tp40)
REVERT: D  163 MET cc_start: 0.8754 (mpp) cc_final: 0.8490 (mpp)
REVERT: D  190 MET cc_start: 0.8923 (tmm) cc_final: 0.8624 (ptm)
REVERT: E   64 MET cc_start: 0.8089 (ppp) cc_final: 0.7692 (ppp)
REVERT: E  140 ASP cc_start: 0.7533 (t0) cc_final: 0.7276 (t0)
REVERT: E  187 TRP cc_start: 0.8171 (t-100) cc_final: 0.7822 (t60)
REVERT: E  237 ARG cc_start: 0.8399 (mmt180) cc_final: 0.8074 (tpt90)
REVERT: F   35 MET cc_start: 0.1950 (mmm) cc_final: 0.1725 (mmm)
REVERT: G   27 MET cc_start: 0.8758 (mmm) cc_final: 0.8471 (mpp)
REVERT: G   35 MET cc_start: 0.8089 (mtm) cc_final: 0.7867 (mtt)
  outliers start: 30
  outliers final: 24
  residues processed: 241
  average time/residue: 0.0844
  time to fit residues: 28.7558
Evaluate side-chains
  240 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 215
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   75 TRP
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  191 ASN
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain E residue   69 LEU
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain E residue  248 ASP
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue   26 VAL
Chi-restraints excluded: chain G residue   21 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 106 optimal weight:    4.9990
   chunk 101 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 11 optimal weight:    9.9990
   chunk 110 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 47 optimal weight:   10.0000
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 276 HIS ** 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 = 0.3817 r_free = 0.3817 target = 0.078339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.064350 restraints weight = 48277.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.065671 restraints weight = 34497.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.066638 restraints weight = 26973.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.067287 restraints weight = 22560.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.067667 restraints weight = 19894.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9340  Z= 0.144
  Angle     :  0.763  14.370  12657  Z= 0.382
  Chirality :  0.043   0.209   1502
  Planarity :  0.007   0.227   1642
  Dihedral  :  4.307  30.678   1320
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 16.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 25.48 %
    Favored  : 71.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.25), residues: 1208
  helix:  1.38 (0.16), residues: 1028
  sheet:  None (None), residues: 0
  loop : -2.80 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG E 154 
 TYR   0.031   0.003   TYR C 232 
 PHE   0.045   0.002   PHE D 193 
 TRP   0.023   0.002   TRP B  75 
 HIS   0.004   0.001   HIS B 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9340)
  covalent geometry    : angle       0.76314 (12657)
  hydrogen bonds       : bond        0.03709 (  865)
  hydrogen bonds       : angle       4.32882 ( 2589)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 227
  time to evaluate  : 0.290 
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: A   61 LYS cc_start: 0.9269 (pttp) cc_final: 0.8937 (tppt)
REVERT: A  126 ASN cc_start: 0.8912 (t0) cc_final: 0.8285 (p0)
REVERT: A  140 ASP cc_start: 0.6816 (m-30) cc_final: 0.6315 (m-30)
REVERT: A  190 MET cc_start: 0.8305 (ptp) cc_final: 0.7642 (ptp)
REVERT: A  193 PHE cc_start: 0.9018 (m-10) cc_final: 0.8607 (m-10)
REVERT: A  220 MET cc_start: 0.8245 (tpt) cc_final: 0.8021 (tpt)
REVERT: A  235 PHE cc_start: 0.8901 (m-80) cc_final: 0.8513 (m-80)
REVERT: A  237 ARG cc_start: 0.8902 (ptm160) cc_final: 0.8569 (ptt180)
REVERT: A  270 LYS cc_start: 0.6164 (mttt) cc_final: 0.5947 (tmtt)
REVERT: B   61 LYS cc_start: 0.3860 (tttt) cc_final: 0.3585 (tttt)
REVERT: B   81 LYS cc_start: 0.9236 (tppt) cc_final: 0.8868 (mttt)
REVERT: B  150 PHE cc_start: 0.8737 (t80) cc_final: 0.8462 (t80)
REVERT: B  163 MET cc_start: 0.8673 (mmm) cc_final: 0.8209 (mmm)
REVERT: B  167 ASN cc_start: 0.8908 (p0) cc_final: 0.7929 (t0)
REVERT: B  200 GLN cc_start: 0.8288 (mp10) cc_final: 0.7505 (tp40)
REVERT: B  220 MET cc_start: 0.8997 (mtm) cc_final: 0.8681 (mtt)
REVERT: B  270 LYS cc_start: 0.7455 (pttt) cc_final: 0.6987 (tptp)
REVERT: C   92 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8120 (pp)
REVERT: C  113 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7617 (tm-30)
REVERT: C  169 PHE cc_start: 0.8864 (t80) cc_final: 0.8645 (t80)
REVERT: C  179 PHE cc_start: 0.8782 (m-10) cc_final: 0.8536 (m-80)
REVERT: C  220 MET cc_start: 0.9216 (ptm) cc_final: 0.8775 (ppp)
REVERT: C  232 TYR cc_start: 0.7977 (t80) cc_final: 0.7613 (t80)
REVERT: C  248 ASP cc_start: 0.8670 (m-30) cc_final: 0.8356 (t70)
REVERT: C  252 GLN cc_start: 0.8727 (mt0) cc_final: 0.8255 (mt0)
REVERT: D   67 LEU cc_start: 0.9384 (mt) cc_final: 0.9062 (pp)
REVERT: D  129 GLN cc_start: 0.7604 (tp40) cc_final: 0.7354 (tp40)
REVERT: D  163 MET cc_start: 0.8693 (mpp) cc_final: 0.8445 (mpp)
REVERT: E   52 MET cc_start: 0.5816 (mmp) cc_final: 0.5142 (mmp)
REVERT: E   64 MET cc_start: 0.8082 (ppp) cc_final: 0.7701 (ppp)
REVERT: E  187 TRP cc_start: 0.8180 (t-100) cc_final: 0.7839 (t60)
REVERT: E  216 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8432 (tt)
REVERT: E  237 ARG cc_start: 0.8388 (mmt180) cc_final: 0.8097 (tpt90)
  outliers start: 29
  outliers final: 22
  residues processed: 244
  average time/residue: 0.0838
  time to fit residues: 29.2852
Evaluate side-chains
  245 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 221
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   75 TRP
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  191 ASN
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain E residue   69 LEU
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  248 ASP
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue   26 VAL
Chi-restraints excluded: chain G residue   21 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 73 optimal weight:    0.3980
   chunk 55 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0670
   chunk 102 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 69 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.8322

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

Flipped N/Q/H residues before XYZ refinement:
** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 245 GLN
** E 276 HIS ** 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 = 0.3822 r_free = 0.3822 target = 0.078951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.064444 restraints weight = 46788.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.065733 restraints weight = 34229.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.066542 restraints weight = 27129.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.067261 restraints weight = 23303.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.067754 restraints weight = 20556.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9340  Z= 0.141
  Angle     :  0.782  13.476  12657  Z= 0.386
  Chirality :  0.044   0.220   1502
  Planarity :  0.004   0.054   1642
  Dihedral  :  4.226  23.171   1320
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 16.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 27.30 %
    Favored  : 70.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.25), residues: 1208
  helix:  1.40 (0.16), residues: 1028
  sheet:  None (None), residues: 0
  loop : -2.71 (0.43), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 154 
 TYR   0.024   0.002   TYR C 232 
 PHE   0.048   0.003   PHE D 193 
 TRP   0.021   0.002   TRP B  75 
 HIS   0.004   0.001   HIS C 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9340)
  covalent geometry    : angle       0.78235 (12657)
  hydrogen bonds       : bond        0.03720 (  865)
  hydrogen bonds       : angle       4.34731 ( 2589)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 226
  time to evaluate  : 0.310 
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: A   61 LYS cc_start: 0.9274 (pttp) cc_final: 0.8937 (tppt)
REVERT: A  106 ASP cc_start: 0.8281 (m-30) cc_final: 0.7873 (p0)
REVERT: A  126 ASN cc_start: 0.8846 (t0) cc_final: 0.8264 (p0)
REVERT: A  140 ASP cc_start: 0.6759 (m-30) cc_final: 0.6268 (m-30)
REVERT: A  190 MET cc_start: 0.8328 (ptp) cc_final: 0.7494 (ptp)
REVERT: A  193 PHE cc_start: 0.9017 (m-10) cc_final: 0.8414 (m-80)
REVERT: A  220 MET cc_start: 0.8278 (tpt) cc_final: 0.8056 (tpt)
REVERT: A  235 PHE cc_start: 0.8890 (m-80) cc_final: 0.8605 (m-80)
REVERT: A  237 ARG cc_start: 0.8897 (ptm160) cc_final: 0.8610 (ptt180)
REVERT: B   81 LYS cc_start: 0.9287 (tppt) cc_final: 0.9027 (mttt)
REVERT: B  163 MET cc_start: 0.8707 (mmm) cc_final: 0.8305 (mmm)
REVERT: B  167 ASN cc_start: 0.8918 (p0) cc_final: 0.7987 (t0)
REVERT: B  200 GLN cc_start: 0.8275 (mp10) cc_final: 0.7502 (tp-100)
REVERT: B  270 LYS cc_start: 0.7503 (pttt) cc_final: 0.7041 (tptp)
REVERT: C  113 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7613 (tm-30)
REVERT: C  169 PHE cc_start: 0.8889 (t80) cc_final: 0.8670 (t80)
REVERT: C  179 PHE cc_start: 0.8756 (m-10) cc_final: 0.8547 (m-80)
REVERT: C  220 MET cc_start: 0.9210 (ptm) cc_final: 0.8760 (ppp)
REVERT: C  232 TYR cc_start: 0.7966 (t80) cc_final: 0.7650 (t80)
REVERT: C  248 ASP cc_start: 0.8526 (m-30) cc_final: 0.8258 (t70)
REVERT: C  252 GLN cc_start: 0.8687 (mt0) cc_final: 0.8254 (mt0)
REVERT: D   67 LEU cc_start: 0.9391 (mt) cc_final: 0.9080 (pp)
REVERT: D  129 GLN cc_start: 0.7617 (tp40) cc_final: 0.7347 (tp40)
REVERT: D  163 MET cc_start: 0.8644 (mpp) cc_final: 0.8305 (mpp)
REVERT: E   52 MET cc_start: 0.5832 (mmp) cc_final: 0.5517 (mmp)
REVERT: E   64 MET cc_start: 0.8076 (ppp) cc_final: 0.7704 (ppp)
REVERT: E  187 TRP cc_start: 0.8178 (t-100) cc_final: 0.7794 (t60)
REVERT: E  237 ARG cc_start: 0.8336 (mmt180) cc_final: 0.8095 (tpt90)
  outliers start: 24
  outliers final: 23
  residues processed: 239
  average time/residue: 0.0808
  time to fit residues: 27.6487
Evaluate side-chains
  240 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 217
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   75 TRP
Chi-restraints excluded: chain C residue  191 ASN
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain E residue   69 LEU
Chi-restraints excluded: chain E residue  150 PHE
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain E residue  248 ASP
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue   26 VAL
Chi-restraints excluded: chain G residue   21 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 112 optimal weight:    0.0870
   chunk 66 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0010
   chunk 15 optimal weight:    7.9990
   chunk 79 optimal weight:    1.9990
   chunk 95 optimal weight:    6.9990
   chunk 113 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 81 optimal weight:    7.9990
   chunk 71 optimal weight:   10.0000
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.4966

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

Flipped N/Q/H residues before XYZ refinement:
** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 276 HIS ** 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 = 0.3831 r_free = 0.3831 target = 0.079374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.064750 restraints weight = 46761.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.066016 restraints weight = 34723.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.066913 restraints weight = 27581.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.067562 restraints weight = 23370.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.067991 restraints weight = 20770.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9340  Z= 0.144
  Angle     :  0.844  19.256  12657  Z= 0.406
  Chirality :  0.045   0.240   1502
  Planarity :  0.004   0.027   1642
  Dihedral  :  4.204  22.830   1320
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 16.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 28.27 %
    Favored  : 69.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.25), residues: 1208
  helix:  1.38 (0.16), residues: 1029
  sheet:  None (None), residues: 0
  loop : -2.82 (0.42), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 154 
 TYR   0.023   0.002   TYR C 232 
 PHE   0.048   0.002   PHE B  79 
 TRP   0.020   0.002   TRP B  75 
 HIS   0.008   0.001   HIS E 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9340)
  covalent geometry    : angle       0.84401 (12657)
  hydrogen bonds       : bond        0.03743 (  865)
  hydrogen bonds       : angle       4.39019 ( 2589)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 227
  time to evaluate  : 0.330 
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: A   61 LYS cc_start: 0.9247 (pttp) cc_final: 0.8912 (tppt)
REVERT: A  106 ASP cc_start: 0.8352 (m-30) cc_final: 0.7917 (p0)
REVERT: A  126 ASN cc_start: 0.8899 (t0) cc_final: 0.8355 (p0)
REVERT: A  140 ASP cc_start: 0.6840 (m-30) cc_final: 0.6311 (m-30)
REVERT: A  190 MET cc_start: 0.8350 (ptp) cc_final: 0.7475 (ptp)
REVERT: A  193 PHE cc_start: 0.9011 (m-10) cc_final: 0.8402 (m-80)
REVERT: A  220 MET cc_start: 0.8295 (tpt) cc_final: 0.8070 (tpt)
REVERT: A  235 PHE cc_start: 0.9092 (m-80) cc_final: 0.8683 (m-80)
REVERT: A  237 ARG cc_start: 0.8975 (ptm160) cc_final: 0.8684 (ptt180)
REVERT: B  150 PHE cc_start: 0.8879 (t80) cc_final: 0.8664 (t80)
REVERT: B  163 MET cc_start: 0.8813 (mmm) cc_final: 0.8359 (mmm)
REVERT: B  167 ASN cc_start: 0.8979 (p0) cc_final: 0.7966 (t0)
REVERT: B  200 GLN cc_start: 0.8299 (mp10) cc_final: 0.7489 (tp-100)
REVERT: B  270 LYS cc_start: 0.7496 (pttt) cc_final: 0.7041 (tptp)
REVERT: C  113 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7692 (tm-30)
REVERT: C  169 PHE cc_start: 0.8958 (t80) cc_final: 0.8697 (t80)
REVERT: C  220 MET cc_start: 0.9177 (ptm) cc_final: 0.8724 (ppp)
REVERT: C  232 TYR cc_start: 0.8021 (t80) cc_final: 0.7721 (t80)
REVERT: C  233 ASN cc_start: 0.8489 (t0) cc_final: 0.8003 (t0)
REVERT: C  248 ASP cc_start: 0.8558 (m-30) cc_final: 0.8154 (t70)
REVERT: C  252 GLN cc_start: 0.8733 (mt0) cc_final: 0.8223 (mt0)
REVERT: D   89 LYS cc_start: 0.8703 (pttt) cc_final: 0.8402 (pttm)
REVERT: D  163 MET cc_start: 0.8733 (mpp) cc_final: 0.8369 (mpp)
REVERT: E   64 MET cc_start: 0.8013 (ppp) cc_final: 0.7720 (ppp)
REVERT: E   89 LYS cc_start: 0.9274 (tppt) cc_final: 0.8847 (tptt)
REVERT: E  187 TRP cc_start: 0.8244 (t-100) cc_final: 0.7836 (t60)
REVERT: E  193 PHE cc_start: 0.8536 (m-10) cc_final: 0.8326 (m-10)
REVERT: E  237 ARG cc_start: 0.8418 (mmt180) cc_final: 0.8081 (tpt90)
  outliers start: 20
  outliers final: 19
  residues processed: 236
  average time/residue: 0.0833
  time to fit residues: 28.0799
Evaluate side-chains
  236 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 217
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain C residue   75 TRP
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  229 VAL
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain E residue   69 LEU
Chi-restraints excluded: chain E residue  150 PHE
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain E residue  248 ASP
Chi-restraints excluded: chain F residue   26 VAL
Chi-restraints excluded: chain G residue   21 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 68 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 112 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 86 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  54 GLN
** E 276 HIS ** 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 = 0.3828 r_free = 0.3828 target = 0.078380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.064002 restraints weight = 47127.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.065239 restraints weight = 34906.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.066016 restraints weight = 27702.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.066749 restraints weight = 23646.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.067177 restraints weight = 20935.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9340  Z= 0.153
  Angle     :  0.879  18.623  12657  Z= 0.421
  Chirality :  0.046   0.275   1502
  Planarity :  0.004   0.031   1642
  Dihedral  :  4.255  23.242   1320
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 17.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 28.27 %
    Favored  : 69.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.25), residues: 1208
  helix:  1.36 (0.16), residues: 1028
  sheet:  None (None), residues: 0
  loop : -2.78 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 154 
 TYR   0.021   0.002   TYR C 232 
 PHE   0.051   0.003   PHE B  79 
 TRP   0.017   0.002   TRP B  75 
 HIS   0.006   0.001   HIS E 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 9340)
  covalent geometry    : angle       0.87889 (12657)
  hydrogen bonds       : bond        0.03856 (  865)
  hydrogen bonds       : angle       4.46611 ( 2589)

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

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

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2416 Ramachandran restraints generated.
    1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 217
  time to evaluate  : 0.331 
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: A   61 LYS cc_start: 0.9265 (pttp) cc_final: 0.8943 (tppt)
REVERT: A  106 ASP cc_start: 0.8260 (m-30) cc_final: 0.7827 (p0)
REVERT: A  126 ASN cc_start: 0.8830 (t0) cc_final: 0.8263 (p0)
REVERT: A  140 ASP cc_start: 0.6679 (m-30) cc_final: 0.6198 (m-30)
REVERT: A  190 MET cc_start: 0.8365 (ptp) cc_final: 0.7688 (ptp)
REVERT: A  193 PHE cc_start: 0.9020 (m-10) cc_final: 0.8625 (m-10)
REVERT: A  220 MET cc_start: 0.8266 (tpt) cc_final: 0.8047 (tpt)
REVERT: A  235 PHE cc_start: 0.9129 (m-80) cc_final: 0.8666 (m-80)
REVERT: A  237 ARG cc_start: 0.8915 (ptm160) cc_final: 0.8611 (ptt180)
REVERT: B   77 ILE cc_start: 0.8434 (mm) cc_final: 0.8221 (mm)
REVERT: B   81 LYS cc_start: 0.9251 (tppt) cc_final: 0.9022 (mttt)
REVERT: B  163 MET cc_start: 0.8727 (mmm) cc_final: 0.8355 (mmm)
REVERT: B  167 ASN cc_start: 0.8923 (p0) cc_final: 0.7983 (t0)
REVERT: B  200 GLN cc_start: 0.8275 (mp10) cc_final: 0.7475 (tp-100)
REVERT: B  220 MET cc_start: 0.9029 (mtm) cc_final: 0.8749 (mtt)
REVERT: B  270 LYS cc_start: 0.7462 (pttt) cc_final: 0.7010 (tptp)
REVERT: C  113 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7654 (tm-30)
REVERT: C  169 PHE cc_start: 0.8883 (t80) cc_final: 0.8660 (t80)
REVERT: C  220 MET cc_start: 0.9129 (ptm) cc_final: 0.8701 (ppp)
REVERT: C  233 ASN cc_start: 0.8349 (t0) cc_final: 0.7927 (t0)
REVERT: C  248 ASP cc_start: 0.8448 (m-30) cc_final: 0.8127 (t70)
REVERT: C  252 GLN cc_start: 0.8659 (mt0) cc_final: 0.8220 (mt0)
REVERT: D  129 GLN cc_start: 0.7788 (tp40) cc_final: 0.7362 (tp40)
REVERT: E   64 MET cc_start: 0.7988 (ppp) cc_final: 0.7618 (ppp)
REVERT: E  187 TRP cc_start: 0.8212 (t-100) cc_final: 0.7832 (t60)
REVERT: E  237 ARG cc_start: 0.8373 (mmt180) cc_final: 0.8099 (tpt90)
  outliers start: 21
  outliers final: 21
  residues processed: 227
  average time/residue: 0.0830
  time to fit residues: 27.0522
Evaluate side-chains
  235 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 214
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain C residue   75 TRP
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  229 VAL
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain E residue   69 LEU
Chi-restraints excluded: chain E residue  150 PHE
Chi-restraints excluded: chain E residue  177 SER
Chi-restraints excluded: chain E residue  248 ASP
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue   26 VAL
Chi-restraints excluded: chain G residue   21 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 97 optimal weight:   10.0000
   chunk 107 optimal weight:    7.9990
   chunk 109 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 114 optimal weight:    0.7980
   chunk 105 optimal weight:    0.6980
   chunk 112 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 276 HIS ** 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 = 0.3831 r_free = 0.3831 target = 0.078605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.064345 restraints weight = 46718.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.065564 restraints weight = 34813.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.066313 restraints weight = 27777.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.066976 restraints weight = 23754.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.067448 restraints weight = 21297.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.3793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9340  Z= 0.151
  Angle     :  0.895  18.305  12657  Z= 0.429
  Chirality :  0.047   0.296   1502
  Planarity :  0.004   0.025   1642
  Dihedral  :  4.270  22.874   1320
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 17.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 29.01 %
    Favored  : 68.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.25), residues: 1208
  helix:  1.32 (0.16), residues: 1028
  sheet:  None (None), residues: 0
  loop : -2.84 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 154 
 TYR   0.016   0.002   TYR D 232 
 PHE   0.051   0.002   PHE B  79 
 TRP   0.014   0.001   TRP B  75 
 HIS   0.005   0.001   HIS C 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9340)
  covalent geometry    : angle       0.89456 (12657)
  hydrogen bonds       : bond        0.03892 (  865)
  hydrogen bonds       : angle       4.52289 ( 2589)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1554.34 seconds
wall clock time: 27 minutes 31.24 seconds (1651.24 seconds total)