Starting phenix.real_space_refine
on Tue Mar  3 12:33:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v0y_26953/03_2026/7v0y_26953.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v0y_26953/03_2026/7v0y_26953.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v0y_26953/03_2026/7v0y_26953.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v0y_26953/03_2026/7v0y_26953.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v0y_26953/03_2026/7v0y_26953.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v0y_26953/03_2026/7v0y_26953.cif"
  }
  resolution = 3.0
  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=   0.000 sd=   0.239
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      12      5.16       5
     C    2840      2.51       5
     N     777      2.21       5
     O     825      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 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: 4454
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "E"
      Number of atoms: 2270
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2270
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 267}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "C"
      Number of atoms: 2183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2183
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 14, 'TRANS': 258}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 1.32, per 1000 atoms: 0.30
  Number of scatterers: 4454
  At special positions: 0
  Unit cell: (93.375, 75.53, 64.325, 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      12     16.00
     O     825      8.00
     N     777      7.00
     C    2840      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: 0.39
  Conformation dependent library (CDL) restraints added in 387.9 milliseconds
  

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1056

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 6 sheets defined
      40.9% alpha, 26.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'E' and resid 104 through 116
      removed outlier: 3.765A  pdb=" N   LYS E 116 " --> pdb=" O   ARG E 112 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 127 through 142
    Processing helix  chain 'E' and resid 146 through 148
      No H-bonds generated for 'chain 'E' and resid 146 through 148'
    Processing helix  chain 'E' and resid 149 through 158
    Processing helix  chain 'E' and resid 165 through 170
      removed outlier: 4.262A  pdb=" N   ALA E 169 " --> pdb=" O   GLY E 165 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 194 through 200
    Processing helix  chain 'E' and resid 277 through 291
    Processing helix  chain 'E' and resid 291 through 301
    Processing helix  chain 'E' and resid 303 through 317
      removed outlier: 3.765A  pdb=" N   LEU E 307 " --> pdb=" O   SER E 303 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 332 through 334
      No H-bonds generated for 'chain 'E' and resid 332 through 334'
    Processing helix  chain 'E' and resid 335 through 349
    Processing helix  chain 'C' and resid 103 through 116
      removed outlier: 3.668A  pdb=" N   LYS C 116 " --> pdb=" O   ARG C 112 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 127 through 142
    Processing helix  chain 'C' and resid 146 through 148
      No H-bonds generated for 'chain 'C' and resid 146 through 148'
    Processing helix  chain 'C' and resid 149 through 158
    Processing helix  chain 'C' and resid 167 through 171
    Processing helix  chain 'C' and resid 194 through 201
    Processing helix  chain 'C' and resid 277 through 291
    Processing helix  chain 'C' and resid 291 through 300
    Processing helix  chain 'C' and resid 303 through 317
      removed outlier: 3.748A  pdb=" N   LEU C 307 " --> pdb=" O   SER C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 327 through 334
    Processing helix  chain 'C' and resid 334 through 343
      removed outlier: 4.439A  pdb=" N   VAL C 338 " --> pdb=" O   SER C 334 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 85 through 87
      removed outlier: 6.737A  pdb=" N   LEU E  61 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   ARG E  80 " --> pdb=" O   VAL E  59 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   VAL E  59 " --> pdb=" O   ARG E  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 118 through 123
      removed outlier: 6.423A  pdb=" N   THR E 118 " --> pdb=" O   PHE E 244 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   ARG E 246 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   LEU E 120 " --> pdb=" O   ARG E 246 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   GLN E 248 " --> pdb=" O   LEU E 120 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   ASP E 122 " --> pdb=" O   GLN E 248 " (cutoff:3.500A)
      removed outlier: 10.053A  pdb=" N   ALA E 250 " --> pdb=" O   ASP E 122 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ARG E 263 " --> pdb=" O   LEU E 247 " (cutoff:3.500A)
      removed outlier: 5.777A  pdb=" N   ALA E 226 " --> pdb=" O   ILE E 262 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   PHE E 264 " --> pdb=" O   ALA E 226 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   TYR E  58 " --> pdb=" O   THR E 227 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   VAL E 229 " --> pdb=" O   TYR E  58 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   GLU E  60 " --> pdb=" O   VAL E 229 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   VAL E 231 " --> pdb=" O   GLU E  60 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   GLN E  62 " --> pdb=" O   VAL E 231 " (cutoff:3.500A)
      removed outlier: 8.525A  pdb=" N   ARG E 233 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   LEU E  64 " --> pdb=" O   ARG E 233 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   VAL E  59 " --> pdb=" O   ARG E  80 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   ARG E  80 " --> pdb=" O   VAL E  59 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   LEU E  61 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 102 through 103
    Processing sheet with id=AA4, first strand: chain 'E' and resid 177 through 178
    Processing sheet with id=AA5, first strand: chain 'C' and resid 85 through 87
      removed outlier: 6.862A  pdb=" N   LEU C  61 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   ARG C  80 " --> pdb=" O   VAL C  59 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   VAL C  59 " --> pdb=" O   ARG C  80 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   LYS C  56 " --> pdb=" O   GLU C 225 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   THR C 227 " --> pdb=" O   LYS C  56 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   TYR C  58 " --> pdb=" O   THR C 227 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   VAL C 229 " --> pdb=" O   TYR C  58 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   GLU C  60 " --> pdb=" O   VAL C 229 " (cutoff:3.500A)
      removed outlier: 7.503A  pdb=" N   VAL C 231 " --> pdb=" O   GLU C  60 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   GLN C  62 " --> pdb=" O   VAL C 231 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   ILE C 262 " --> pdb=" O   SER C 224 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   ALA C 226 " --> pdb=" O   ILE C 262 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   PHE C 264 " --> pdb=" O   ALA C 226 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   ARG C 263 " --> pdb=" O   LEU C 247 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   GLN C 248 " --> pdb=" O   ASP C 122 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 85 through 87
      removed outlier: 6.862A  pdb=" N   LEU C  61 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   ARG C  80 " --> pdb=" O   VAL C  59 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   VAL C  59 " --> pdb=" O   ARG C  80 " (cutoff:3.500A)

    203 hydrogen bonds defined for protein.
    582 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: 0.74

  Time building geometry restraints manager: 0.51 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: 1517
        1.34 -     1.46: 832
        1.46 -     1.58: 2173
        1.58 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 4542
  Sorted by residual:
  bond pdb=" C   VAL E 336 "
       pdb=" N   PRO E 337 "
    ideal  model  delta    sigma   weight residual
    1.335  1.366 -0.032 1.28e-02 6.10e+03 6.13e+00
  bond pdb=" CB  GLN E 302 "
       pdb=" CG  GLN E 302 "
    ideal  model  delta    sigma   weight residual
    1.520  1.557 -0.037 3.00e-02 1.11e+03 1.48e+00
  bond pdb=" CB  ASN C  91 "
       pdb=" CG  ASN C  91 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.13e+00
  bond pdb=" CG  GLN E 302 "
       pdb=" CD  GLN E 302 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.39e-01
  bond pdb=" N   ASN C  91 "
       pdb=" CA  ASN C  91 "
    ideal  model  delta    sigma   weight residual
    1.458  1.474 -0.016 1.77e-02 3.19e+03 7.74e-01
  ... (remaining 4537 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 5966
        1.51 -     3.02: 161
        3.02 -     4.53: 27
        4.53 -     6.04: 7
        6.04 -     7.56: 3
  Bond angle restraints: 6164
  Sorted by residual:
  angle pdb=" C   SER E 328 "
        pdb=" N   GLU E 329 "
        pdb=" CA  GLU E 329 "
      ideal   model   delta    sigma   weight residual
     121.54  128.45   -6.91 1.91e+00 2.74e-01 1.31e+01
  angle pdb=" C   GLU C  90 "
        pdb=" N   ASN C  91 "
        pdb=" CA  ASN C  91 "
      ideal   model   delta    sigma   weight residual
     125.66  131.25   -5.59 1.85e+00 2.92e-01 9.12e+00
  angle pdb=" CB  GLN E 302 "
        pdb=" CG  GLN E 302 "
        pdb=" CD  GLN E 302 "
      ideal   model   delta    sigma   weight residual
     112.60  117.33   -4.73 1.70e+00 3.46e-01 7.73e+00
  angle pdb=" C   VAL E  82 "
        pdb=" N   GLN E  83 "
        pdb=" CA  GLN E  83 "
      ideal   model   delta    sigma   weight residual
     121.54  126.39   -4.85 1.91e+00 2.74e-01 6.45e+00
  angle pdb=" N   ASP E 277 "
        pdb=" CA  ASP E 277 "
        pdb=" C   ASP E 277 "
      ideal   model   delta    sigma   weight residual
     108.52  104.93    3.59 1.63e+00 3.76e-01 4.85e+00
  ... (remaining 6159 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.85: 2332
       16.85 -    33.71: 262
       33.71 -    50.56: 116
       50.56 -    67.42: 42
       67.42 -    84.27: 15
  Dihedral angle restraints: 2767
    sinusoidal: 1150
      harmonic: 1617
  Sorted by residual:
  dihedral pdb=" CG  ARG E 304 "
           pdb=" CD  ARG E 304 "
           pdb=" NE  ARG E 304 "
           pdb=" CZ  ARG E 304 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.41   43.59     2      1.50e+01 4.44e-03 1.01e+01
  dihedral pdb=" CA  ASP C 137 "
           pdb=" CB  ASP C 137 "
           pdb=" CG  ASP C 137 "
           pdb=" OD1 ASP C 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.50   53.50     1      2.00e+01 2.50e-03 9.72e+00
  dihedral pdb=" CB  GLU C  60 "
           pdb=" CG  GLU C  60 "
           pdb=" CD  GLU C  60 "
           pdb=" OE1 GLU C  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   84.07  -84.07     1      3.00e+01 1.11e-03 9.56e+00
  ... (remaining 2764 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 475
       0.034 -    0.068: 158
       0.068 -    0.102: 47
       0.102 -    0.136: 22
       0.136 -    0.170: 2
  Chirality restraints: 704
  Sorted by residual:
  chirality pdb=" CG  LEU E 158 "
            pdb=" CB  LEU E 158 "
            pdb=" CD1 LEU E 158 "
            pdb=" CD2 LEU E 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.21e-01
  chirality pdb=" CA  VAL E  82 "
            pdb=" N   VAL E  82 "
            pdb=" C   VAL E  82 "
            pdb=" CB  VAL E  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.19e-01
  chirality pdb=" CG  LEU E 108 "
            pdb=" CB  LEU E 108 "
            pdb=" CD1 LEU E 108 "
            pdb=" CD2 LEU E 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.41e-01
  ... (remaining 701 not shown)

  Planarity restraints: 805
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN E 302 "    0.010 2.00e-02 2.50e+03   2.05e-02 4.21e+00
        pdb=" CD  GLN E 302 "   -0.035 2.00e-02 2.50e+03
        pdb=" OE1 GLN E 302 "    0.013 2.00e-02 2.50e+03
        pdb=" NE2 GLN E 302 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E 146 "    0.023 5.00e-02 4.00e+02   3.42e-02 1.87e+00
        pdb=" N   PRO E 147 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO E 147 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO E 147 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E 340 "   -0.100 9.50e-02 1.11e+02   4.52e-02 1.59e+00
        pdb=" NE  ARG E 340 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG E 340 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG E 340 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG E 340 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 802 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 350
        2.74 -     3.28: 4143
        3.28 -     3.82: 7834
        3.82 -     4.36: 9191
        4.36 -     4.90: 15677
  Nonbonded interactions: 37195
  Sorted by model distance:
  nonbonded pdb=" OG1 THR E 179 "
            pdb=" O   ASP E 183 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OD1 ASP E 316 "
            pdb=" NE1 TRP C 105 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" OD1 ASN C 133 "
            pdb=" NH2 ARG C 150 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" O   PRO E 221 "
            pdb=" OG  SER E 224 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OE2 GLU C 109 "
            pdb=" NH1 ARG C 112 "
     model   vdw
     2.341 3.120
  ... (remaining 37190 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 'C' and (resid 54 through 203 or resid 217 through 348))
  selection = (chain 'E' and ((resid 54 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 55 or (resid 56 and (name N or name CA or name C or name O or name C \ 
B )) or resid 57 through 181 or resid 192 through 348))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.860
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.000
  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:7.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
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      :  0.003   0.037   4542  Z= 0.145
  Angle     :  0.626   7.556   6164  Z= 0.339
  Chirality :  0.041   0.170    704
  Planarity :  0.005   0.045    805
  Dihedral  : 19.396  84.270   1711
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 28.48 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.80 (0.35), residues: 548
  helix:  0.77 (0.37), residues: 211
  sheet:  1.11 (0.50), residues: 105
  loop :  0.19 (0.37), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 340 
 TYR   0.012   0.002   TYR E 278 
 PHE   0.014   0.002   PHE E 314 
 TRP   0.005   0.001   TRP C  81 
 HIS   0.003   0.001   HIS E 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4542)
  covalent geometry    : angle       0.62610 ( 6164)
  hydrogen bonds       : bond        0.14546 (  191)
  hydrogen bonds       : angle       5.69988 (  582)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.114 
Fit side-chains
REVERT: E  160 LYS cc_start: 0.8099 (mptt) cc_final: 0.7413 (mppt)
REVERT: C   74 ARG cc_start: 0.7579 (ptm160) cc_final: 0.7356 (ptp-170)
  outliers start: 7
  outliers final: 5
  residues processed: 60
  average time/residue: 0.7229
  time to fit residues: 44.5632
Evaluate side-chains
  54 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  203 GLN
Chi-restraints excluded: chain C residue  116 LYS
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  333 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    8.9990
   chunk 50 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
E  62 GLN
E 191 GLN
E 203 GLN
E 302 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.160554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.120259 restraints weight = 4740.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 2.16
r_work: 0.2930 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041   4542  Z= 0.301
  Angle     :  0.697   8.088   6164  Z= 0.354
  Chirality :  0.047   0.145    704
  Planarity :  0.005   0.039    805
  Dihedral  :  6.124  42.435    615
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  6.65 %
    Allowed  : 21.83 %
    Favored  : 71.52 %
  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:  0.64 (0.35), residues: 548
  helix:  0.64 (0.36), residues: 212
  sheet:  0.64 (0.45), residues: 126
  loop :  0.28 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E 233 
 TYR   0.018   0.004   TYR E 278 
 PHE   0.017   0.003   PHE E 294 
 TRP   0.008   0.002   TRP C  81 
 HIS   0.006   0.001   HIS C 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00708 ( 4542)
  covalent geometry    : angle       0.69685 ( 6164)
  hydrogen bonds       : bond        0.05116 (  191)
  hydrogen bonds       : angle       4.55070 (  582)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 72
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: E   56 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8054 (mttt)
REVERT: E  160 LYS cc_start: 0.8136 (mptt) cc_final: 0.7398 (mppt)
REVERT: E  306 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8358 (mt-10)
  outliers start: 32
  outliers final: 13
  residues processed: 94
  average time/residue: 0.6919
  time to fit residues: 66.9743
Evaluate side-chains
  79 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  179 THR
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  306 GLU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  116 LYS
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  260 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 41 optimal weight:    8.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
E 134 GLN
E 148 GLN
E 198 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.164887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.127107 restraints weight = 4728.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 2.60
r_work: 0.3028 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4542  Z= 0.119
  Angle     :  0.516   5.948   6164  Z= 0.264
  Chirality :  0.039   0.133    704
  Planarity :  0.004   0.030    805
  Dihedral  :  4.765  32.471    608
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 24.95 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.93 (0.36), residues: 548
  helix:  1.00 (0.37), residues: 218
  sheet:  0.87 (0.46), residues: 119
  loop :  0.23 (0.40), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 340 
 TYR   0.014   0.002   TYR E 278 
 PHE   0.013   0.001   PHE E 314 
 TRP   0.006   0.001   TRP C 105 
 HIS   0.004   0.001   HIS E 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4542)
  covalent geometry    : angle       0.51579 ( 6164)
  hydrogen bonds       : bond        0.03570 (  191)
  hydrogen bonds       : angle       4.23879 (  582)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 65
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
REVERT: E  109 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7113 (tp30)
REVERT: E  119 VAL cc_start: 0.8880 (m) cc_final: 0.8590 (t)
REVERT: E  160 LYS cc_start: 0.8154 (mptt) cc_final: 0.7424 (mppt)
REVERT: E  306 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8236 (mt-10)
REVERT: C   66 MET cc_start: 0.7235 (mtp) cc_final: 0.6550 (mtt)
REVERT: C  174 LYS cc_start: 0.6675 (OUTLIER) cc_final: 0.6382 (pttp)
  outliers start: 24
  outliers final: 8
  residues processed: 83
  average time/residue: 0.7220
  time to fit residues: 61.6068
Evaluate side-chains
  74 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  109 GLU
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  262 ILE
Chi-restraints excluded: chain E residue  306 GLU
Chi-restraints excluded: chain E residue  348 GLN
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain C residue  231 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 47 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
E 198 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.162829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.124942 restraints weight = 4656.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.39
r_work: 0.2995 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   4542  Z= 0.216
  Angle     :  0.600   7.055   6164  Z= 0.303
  Chirality :  0.043   0.132    704
  Planarity :  0.004   0.030    805
  Dihedral  :  4.874  26.256    604
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 22.87 %
    Favored  : 71.52 %
  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:  0.75 (0.35), residues: 548
  helix:  0.97 (0.37), residues: 212
  sheet:  0.53 (0.45), residues: 124
  loop :  0.18 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  74 
 TYR   0.016   0.003   TYR E 278 
 PHE   0.015   0.002   PHE E 294 
 TRP   0.007   0.001   TRP C  81 
 HIS   0.003   0.001   HIS C 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 4542)
  covalent geometry    : angle       0.60046 ( 6164)
  hydrogen bonds       : bond        0.04162 (  191)
  hydrogen bonds       : angle       4.35092 (  582)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 67
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
REVERT: E   56 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8051 (mttt)
REVERT: E   86 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8237 (mt-10)
REVERT: E  109 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7234 (tp30)
REVERT: E  119 VAL cc_start: 0.8915 (m) cc_final: 0.8599 (t)
REVERT: E  160 LYS cc_start: 0.8172 (mptt) cc_final: 0.7425 (mppt)
REVERT: E  306 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8276 (mt-10)
REVERT: C   66 MET cc_start: 0.7254 (mtp) cc_final: 0.6616 (mtt)
REVERT: C  174 LYS cc_start: 0.6794 (OUTLIER) cc_final: 0.6521 (pttp)
  outliers start: 27
  outliers final: 14
  residues processed: 82
  average time/residue: 0.6959
  time to fit residues: 58.7403
Evaluate side-chains
  82 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue   86 GLU
Chi-restraints excluded: chain E residue  109 GLU
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  262 ILE
Chi-restraints excluded: chain E residue  306 GLU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  260 VAL
Chi-restraints excluded: chain C residue  333 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 44 optimal weight:    7.9990
   chunk 9 optimal weight:    8.9990
   chunk 54 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0040
   chunk 10 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   chunk 38 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   overall best weight:    2.3796

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

Flipped N/Q/H residues before XYZ refinement:
E 198 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.162345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.123254 restraints weight = 4681.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.10
r_work: 0.2968 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4542  Z= 0.170
  Angle     :  0.555   6.377   6164  Z= 0.281
  Chirality :  0.041   0.134    704
  Planarity :  0.004   0.032    805
  Dihedral  :  4.732  25.202    604
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 23.08 %
    Favored  : 71.93 %
  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:  0.85 (0.35), residues: 548
  helix:  1.09 (0.37), residues: 212
  sheet:  0.51 (0.45), residues: 124
  loop :  0.23 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  74 
 TYR   0.015   0.002   TYR E 278 
 PHE   0.014   0.002   PHE E 294 
 TRP   0.006   0.001   TRP C 105 
 HIS   0.003   0.001   HIS E 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 4542)
  covalent geometry    : angle       0.55487 ( 6164)
  hydrogen bonds       : bond        0.03747 (  191)
  hydrogen bonds       : angle       4.27484 (  582)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 65
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
REVERT: E  119 VAL cc_start: 0.8906 (m) cc_final: 0.8638 (t)
REVERT: E  160 LYS cc_start: 0.8218 (mptt) cc_final: 0.7481 (mppt)
REVERT: E  174 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7198 (pttm)
REVERT: E  306 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8292 (mt-10)
REVERT: C   66 MET cc_start: 0.7234 (mtp) cc_final: 0.6585 (mtt)
REVERT: C  174 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6578 (pttp)
REVERT: C  299 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.6264 (t80)
  outliers start: 24
  outliers final: 9
  residues processed: 80
  average time/residue: 0.7435
  time to fit residues: 61.1947
Evaluate side-chains
  74 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  262 ILE
Chi-restraints excluded: chain E residue  306 GLU
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  260 VAL
Chi-restraints excluded: chain C residue  299 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 32 optimal weight:    8.9990
   chunk 34 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 11 optimal weight:   20.0000
   chunk 54 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    3.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.160901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.121551 restraints weight = 4775.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 2.12
r_work: 0.2938 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4542  Z= 0.224
  Angle     :  0.611   7.065   6164  Z= 0.308
  Chirality :  0.043   0.132    704
  Planarity :  0.004   0.031    805
  Dihedral  :  4.979  26.469    604
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 22.66 %
    Favored  : 71.31 %
  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:  0.72 (0.35), residues: 548
  helix:  0.97 (0.37), residues: 212
  sheet:  0.49 (0.45), residues: 124
  loop :  0.15 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  74 
 TYR   0.016   0.003   TYR E 278 
 PHE   0.015   0.002   PHE E 294 
 TRP   0.007   0.001   TRP C  81 
 HIS   0.003   0.001   HIS C 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 4542)
  covalent geometry    : angle       0.61090 ( 6164)
  hydrogen bonds       : bond        0.04136 (  191)
  hydrogen bonds       : angle       4.35492 (  582)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 64
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: E  119 VAL cc_start: 0.8960 (m) cc_final: 0.8657 (t)
REVERT: E  160 LYS cc_start: 0.8193 (mptt) cc_final: 0.7435 (mppt)
REVERT: E  174 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7270 (pttm)
REVERT: E  225 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8436 (mt-10)
REVERT: E  306 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8335 (mt-10)
REVERT: C   66 MET cc_start: 0.7300 (mtp) cc_final: 0.6679 (mtt)
REVERT: C  174 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6705 (pttp)
REVERT: C  233 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7800 (mtm180)
REVERT: C  238 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7042 (mp0)
  outliers start: 29
  outliers final: 12
  residues processed: 84
  average time/residue: 0.7458
  time to fit residues: 64.4379
Evaluate side-chains
  80 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  197 THR
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  262 ILE
Chi-restraints excluded: chain E residue  306 GLU
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 ARG
Chi-restraints excluded: chain C residue  238 GLU
Chi-restraints excluded: chain C residue  260 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 17 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0010
   chunk 30 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   overall best weight:    0.7992

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

Flipped N/Q/H residues before XYZ refinement:
E 101 HIS
E 198 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.164344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.125329 restraints weight = 4694.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 2.12
r_work: 0.2997 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4542  Z= 0.107
  Angle     :  0.510   5.951   6164  Z= 0.260
  Chirality :  0.039   0.133    704
  Planarity :  0.004   0.030    805
  Dihedral  :  4.470  23.323    604
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 24.53 %
    Favored  : 71.93 %
  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:  1.14 (0.36), residues: 548
  helix:  1.36 (0.38), residues: 212
  sheet:  0.77 (0.46), residues: 119
  loop :  0.30 (0.40), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 340 
 TYR   0.014   0.001   TYR E 278 
 PHE   0.014   0.001   PHE E 314 
 TRP   0.006   0.001   TRP C 105 
 HIS   0.003   0.001   HIS E 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 4542)
  covalent geometry    : angle       0.50993 ( 6164)
  hydrogen bonds       : bond        0.03216 (  191)
  hydrogen bonds       : angle       4.18685 (  582)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  160 LYS cc_start: 0.8208 (mptt) cc_final: 0.7464 (mppt)
REVERT: E  174 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7148 (pttm)
REVERT: E  225 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8377 (mt-10)
REVERT: E  306 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8243 (mt-10)
REVERT: E  340 ARG cc_start: 0.8073 (mmt90) cc_final: 0.7850 (ttm110)
REVERT: C   66 MET cc_start: 0.7231 (mtp) cc_final: 0.6569 (mtt)
REVERT: C  174 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6651 (pttp)
REVERT: C  233 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7786 (mtm180)
REVERT: C  299 TYR cc_start: 0.8070 (m-80) cc_final: 0.6004 (t80)
  outliers start: 17
  outliers final: 7
  residues processed: 86
  average time/residue: 0.6826
  time to fit residues: 60.3423
Evaluate side-chains
  74 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  173 VAL
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  306 GLU
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 47 optimal weight:    9.9990
   chunk 54 optimal weight:    0.9980
   chunk 16 optimal weight:    8.9990
   chunk 45 optimal weight:    0.9980
   chunk 8 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:
E 198 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.165506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.126380 restraints weight = 4689.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.12
r_work: 0.3008 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4542  Z= 0.112
  Angle     :  0.523   5.405   6164  Z= 0.262
  Chirality :  0.040   0.132    704
  Planarity :  0.004   0.029    805
  Dihedral  :  4.364  23.444    604
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 25.99 %
    Favored  : 70.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.05 (0.36), residues: 548
  helix:  1.36 (0.38), residues: 212
  sheet:  0.58 (0.49), residues: 110
  loop :  0.27 (0.39), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 340 
 TYR   0.011   0.002   TYR E 278 
 PHE   0.013   0.001   PHE E 314 
 TRP   0.006   0.001   TRP E  81 
 HIS   0.002   0.000   HIS E 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 4542)
  covalent geometry    : angle       0.52312 ( 6164)
  hydrogen bonds       : bond        0.03200 (  191)
  hydrogen bonds       : angle       4.10642 (  582)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  160 LYS cc_start: 0.8182 (mptt) cc_final: 0.7441 (mppt)
REVERT: E  174 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7164 (pttm)
REVERT: E  225 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8384 (mt-10)
REVERT: E  306 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8242 (mt-10)
REVERT: C   66 MET cc_start: 0.7253 (mtp) cc_final: 0.6587 (mtt)
REVERT: C   96 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.7530 (mtm-85)
REVERT: C  174 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6767 (pttp)
REVERT: C  233 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7836 (mtm180)
REVERT: C  299 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.5967 (t80)
  outliers start: 17
  outliers final: 6
  residues processed: 80
  average time/residue: 0.7319
  time to fit residues: 60.1236
Evaluate side-chains
  75 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  306 GLU
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 ARG
Chi-restraints excluded: chain C residue  299 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 15 optimal weight:    8.9990
   chunk 46 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 4 optimal weight:    8.9990
   overall best weight:    1.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.165164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.125824 restraints weight = 4607.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.11
r_work: 0.2994 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4542  Z= 0.138
  Angle     :  0.544   5.874   6164  Z= 0.272
  Chirality :  0.041   0.136    704
  Planarity :  0.004   0.029    805
  Dihedral  :  4.418  23.967    604
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 26.82 %
    Favored  : 69.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.18 (0.36), residues: 548
  helix:  1.45 (0.38), residues: 206
  sheet:  0.44 (0.45), residues: 124
  loop :  0.53 (0.42), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 340 
 TYR   0.013   0.002   TYR E 278 
 PHE   0.013   0.002   PHE E 314 
 TRP   0.006   0.001   TRP C  81 
 HIS   0.001   0.001   HIS C 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 4542)
  covalent geometry    : angle       0.54416 ( 6164)
  hydrogen bonds       : bond        0.03421 (  191)
  hydrogen bonds       : angle       4.15539 (  582)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  160 LYS cc_start: 0.8171 (mptt) cc_final: 0.7416 (mppt)
REVERT: E  174 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7182 (pttm)
REVERT: E  225 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8408 (mt-10)
REVERT: E  306 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8243 (mt-10)
REVERT: C   66 MET cc_start: 0.7272 (mtp) cc_final: 0.6614 (mtt)
REVERT: C   96 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7552 (mtm-85)
REVERT: C  174 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6834 (pttp)
REVERT: C  233 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7883 (mtm180)
  outliers start: 16
  outliers final: 8
  residues processed: 80
  average time/residue: 0.7166
  time to fit residues: 58.8912
Evaluate side-chains
  75 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  306 GLU
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
E 198 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.165197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.125878 restraints weight = 4622.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.12
r_work: 0.2999 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4542  Z= 0.135
  Angle     :  0.543   5.873   6164  Z= 0.273
  Chirality :  0.041   0.134    704
  Planarity :  0.004   0.029    805
  Dihedral  :  4.425  23.785    604
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 27.23 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.36), residues: 548
  helix:  1.42 (0.38), residues: 206
  sheet:  0.46 (0.45), residues: 120
  loop :  0.50 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 340 
 TYR   0.013   0.002   TYR E 278 
 PHE   0.014   0.002   PHE E 314 
 TRP   0.006   0.001   TRP C  81 
 HIS   0.001   0.001   HIS C 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4542)
  covalent geometry    : angle       0.54332 ( 6164)
  hydrogen bonds       : bond        0.03395 (  191)
  hydrogen bonds       : angle       4.12234 (  582)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: E  160 LYS cc_start: 0.8122 (mptt) cc_final: 0.7296 (mppt)
REVERT: E  174 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.7176 (pttm)
REVERT: E  225 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8412 (mt-10)
REVERT: E  272 GLU cc_start: 0.8106 (mp0) cc_final: 0.7711 (mt-10)
REVERT: E  306 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8234 (mt-10)
REVERT: C   66 MET cc_start: 0.7289 (mtp) cc_final: 0.6636 (mtt)
REVERT: C   96 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7557 (mtm-85)
REVERT: C  174 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6866 (pttp)
REVERT: C  233 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7877 (mtm180)
REVERT: C  299 TYR cc_start: 0.8039 (m-80) cc_final: 0.6116 (t80)
  outliers start: 13
  outliers final: 6
  residues processed: 73
  average time/residue: 0.7732
  time to fit residues: 57.9048
Evaluate side-chains
  70 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  306 GLU
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0470
   chunk 3 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 42 optimal weight:    7.9990
   chunk 44 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   overall best weight:    1.1482

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

Flipped N/Q/H residues before XYZ refinement:
E 198 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.165907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.128494 restraints weight = 4619.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.42
r_work: 0.3023 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4542  Z= 0.120
  Angle     :  0.537   5.929   6164  Z= 0.271
  Chirality :  0.040   0.136    704
  Planarity :  0.004   0.029    805
  Dihedral  :  4.370  23.379    604
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 27.44 %
    Favored  : 69.23 %
  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:  1.11 (0.36), residues: 548
  helix:  1.33 (0.38), residues: 211
  sheet:  0.50 (0.49), residues: 106
  loop :  0.47 (0.40), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 340 
 TYR   0.012   0.002   TYR E 278 
 PHE   0.014   0.001   PHE E 314 
 TRP   0.006   0.001   TRP C  81 
 HIS   0.001   0.000   HIS C  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4542)
  covalent geometry    : angle       0.53716 ( 6164)
  hydrogen bonds       : bond        0.03255 (  191)
  hydrogen bonds       : angle       4.10435 (  582)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1723.07 seconds
wall clock time: 29 minutes 57.98 seconds (1797.98 seconds total)