Starting phenix.real_space_refine
on Wed Apr 30 01:47:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zmj_60249/04_2025/8zmj_60249.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zmj_60249/04_2025/8zmj_60249.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zmj_60249/04_2025/8zmj_60249.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zmj_60249/04_2025/8zmj_60249.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zmj_60249/04_2025/8zmj_60249.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zmj_60249/04_2025/8zmj_60249.cif"
  }
  resolution = 3.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
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: 5
    Type Number    sf(0)   Gaussians
     P     168      5.49       5
     S      40      5.16       5
     C    5166      2.51       5
     N    1589      2.21       5
     O    2221      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9184
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 348, 2795
          Classifications: {'peptide': 348}
          Link IDs: {'PTRANS': 15, 'TRANS': 332}
    Chain: "B"
      Number of atoms: 2795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 348, 2795
          Classifications: {'peptide': 348}
          Link IDs: {'PTRANS': 15, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 3594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 3594
          Classifications: {'RNA': 169}
          Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 79, 'rna3p_pyr': 74}
          Link IDs: {'rna2p': 15, 'rna3p': 153}
  Time building chain proxies: 6.29, per 1000 atoms: 0.68
  Number of scatterers: 9184
  At special positions: 0
  Unit cell: (90.2, 116.44, 136.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     P     168     15.00
     O    2221      8.00
     N    1589      7.00
     C    5166      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: 2.37
  Conformation dependent library (CDL) restraints added in 668.8 milliseconds
  

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1316

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 4 sheets defined
      64.1% alpha, 7.3% beta
      52 base pairs and 86 stacking pairs defined.
    Time for finding SS restraints: 3.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 39
      removed outlier: 4.052A  pdb=" N   PHE A  35 " --> pdb=" O   PRO A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 58
    Processing helix  chain 'A' and resid 74 through 91
      removed outlier: 3.907A  pdb=" N   LYS A  81 " --> pdb=" O   GLN A  77 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   THR A  82 " --> pdb=" O   GLY A  78 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA A  91 " --> pdb=" O   LYS A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 108
    Processing helix  chain 'A' and resid 114 through 132
    Processing helix  chain 'A' and resid 145 through 152
    Processing helix  chain 'A' and resid 152 through 167
      Proline residue:  A 158  - end of helix
    Processing helix  chain 'A' and resid 168 through 175
    Processing helix  chain 'A' and resid 188 through 205
      Proline residue:  A 195  - end of helix
      removed outlier: 3.534A  pdb=" N   ASP A 201 " --> pdb=" O   MET A 197 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ILE A 202 " --> pdb=" O   GLN A 198 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   PHE A 203 " --> pdb=" O   CYS A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 230
    Processing helix  chain 'A' and resid 268 through 279
    Processing helix  chain 'A' and resid 289 through 299
    Processing helix  chain 'A' and resid 299 through 304
    Processing helix  chain 'A' and resid 322 through 333
    Processing helix  chain 'A' and resid 336 through 362
      Proline residue:  A 342  - end of helix
      Proline residue:  A 354  - end of helix
    Processing helix  chain 'A' and resid 362 through 375
    Processing helix  chain 'B' and resid 32 through 42
      removed outlier: 3.645A  pdb=" N   VAL B  41 " --> pdb=" O   ILE B  37 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   GLY B  42 " --> pdb=" O   VAL B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 58
    Processing helix  chain 'B' and resid 74 through 92
      removed outlier: 3.563A  pdb=" N   GLY B  78 " --> pdb=" O   HIS B  74 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   LYS B  81 " --> pdb=" O   GLN B  77 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR B  82 " --> pdb=" O   GLY B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 107
    Processing helix  chain 'B' and resid 109 through 112
    Processing helix  chain 'B' and resid 113 through 132
      removed outlier: 3.545A  pdb=" N   GLY B 132 " --> pdb=" O   TRP B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
    Processing helix  chain 'B' and resid 145 through 150
    Processing helix  chain 'B' and resid 156 through 167
    Processing helix  chain 'B' and resid 168 through 175
    Processing helix  chain 'B' and resid 188 through 205
      Proline residue:  B 195  - end of helix
      removed outlier: 3.812A  pdb=" N   PHE B 203 " --> pdb=" O   CYS B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 215
      No H-bonds generated for 'chain 'B' and resid 213 through 215'
    Processing helix  chain 'B' and resid 216 through 230
    Processing helix  chain 'B' and resid 258 through 262
      removed outlier: 3.865A  pdb=" N   SER B 262 " --> pdb=" O   PRO B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 278
    Processing helix  chain 'B' and resid 289 through 299
    Processing helix  chain 'B' and resid 299 through 304
    Processing helix  chain 'B' and resid 311 through 315
      removed outlier: 3.635A  pdb=" N   GLY B 315 " --> pdb=" O   ALA B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 333
      removed outlier: 3.634A  pdb=" N   LEU B 326 " --> pdb=" O   SER B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 362
      Proline residue:  B 342  - end of helix
      Proline residue:  B 354  - end of helix
    Processing helix  chain 'B' and resid 362 through 375
    Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46
      removed outlier: 3.974A  pdb=" N   ILE A  46 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   ILE A 238 " --> pdb=" O   ILE A  46 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   CYS A 210 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   HIS A 241 " --> pdb=" O   CYS A 210 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   LEU A 212 " --> pdb=" O   HIS A 241 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   VAL A  62 " --> pdb=" O   ILE A 209 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   GLN A 211 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   TYR A  64 " --> pdb=" O   GLN A 211 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   GLY A 213 " --> pdb=" O   TYR A  64 " (cutoff:3.500A)
      removed outlier: 9.436A  pdb=" N   GLY A  66 " --> pdb=" O   GLY A 213 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   CYS A  63 " --> pdb=" O   LYS A  96 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   TRP A  98 " --> pdb=" O   CYS A  63 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   ASP A  65 " --> pdb=" O   TRP A  98 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 308
    Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 46
      removed outlier: 3.632A  pdb=" N   GLU B  44 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER B 240 " --> pdb=" O   GLU B  44 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ILE B  46 " --> pdb=" O   ILE B 238 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   ILE B 238 " --> pdb=" O   ILE B  46 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   CYS B 210 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   CYS B  63 " --> pdb=" O   LYS B  96 " (cutoff:3.500A)
      removed outlier: 7.173A  pdb=" N   TRP B  98 " --> pdb=" O   CYS B  63 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   ASP B  65 " --> pdb=" O   TRP B  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 306 through 308

    285 hydrogen bonds defined for protein.
    819 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      129 hydrogen bonds
      238 hydrogen bond angles
      0 basepair planarities
      52 basepair parallelities
      86 stacking parallelities
  Total time for adding SS restraints: 3.28

  Time building geometry restraints manager: 2.81 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1403
        1.33 -     1.45: 3291
        1.45 -     1.57: 4628
        1.57 -     1.69: 336
        1.69 -     1.81: 60
  Bond restraints: 9718
  Sorted by residual:
  bond pdb=" N   ARG B  72 "
       pdb=" CA  ARG B  72 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.035 1.23e-02 6.61e+03 8.30e+00
  bond pdb=" N   GLU B 268 "
       pdb=" CA  GLU B 268 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 1.22e-02 6.72e+03 8.26e+00
  bond pdb=" N   VAL B 372 "
       pdb=" CA  VAL B 372 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.032 1.17e-02 7.31e+03 7.65e+00
  bond pdb=" N   VAL B 263 "
       pdb=" CA  VAL B 263 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.26e-02 6.30e+03 7.12e+00
  bond pdb=" N   GLU B 266 "
       pdb=" CA  GLU B 266 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.32e-02 5.74e+03 6.79e+00
  ... (remaining 9713 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 13539
        1.95 -     3.90: 336
        3.90 -     5.84: 44
        5.84 -     7.79: 6
        7.79 -     9.74: 2
  Bond angle restraints: 13927
  Sorted by residual:
  angle pdb=" N   ILE B  75 "
        pdb=" CA  ILE B  75 "
        pdb=" C   ILE B  75 "
      ideal   model   delta    sigma   weight residual
     112.50  105.30    7.20 1.39e+00 5.18e-01 2.68e+01
  angle pdb=" C   GLY B 112 "
        pdb=" N   ASP B 113 "
        pdb=" CA  ASP B 113 "
      ideal   model   delta    sigma   weight residual
     121.50  115.11    6.39 1.43e+00 4.89e-01 1.99e+01
  angle pdb=" CB  ARG A 360 "
        pdb=" CG  ARG A 360 "
        pdb=" CD  ARG A 360 "
      ideal   model   delta    sigma   weight residual
     111.30  121.04   -9.74 2.30e+00 1.89e-01 1.79e+01
  angle pdb=" N   GLU B  68 "
        pdb=" CA  GLU B  68 "
        pdb=" C   GLU B  68 "
      ideal   model   delta    sigma   weight residual
     109.24  103.49    5.75 1.39e+00 5.18e-01 1.71e+01
  angle pdb=" CA  ALA B 100 "
        pdb=" C   ALA B 100 "
        pdb=" O   ALA B 100 "
      ideal   model   delta    sigma   weight residual
     122.63  117.56    5.07 1.29e+00 6.01e-01 1.54e+01
  ... (remaining 13922 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.13: 5485
       30.13 -    60.27: 484
       60.27 -    90.40: 159
       90.40 -   120.54: 7
      120.54 -   150.67: 3
  Dihedral angle restraints: 6138
    sinusoidal: 4106
      harmonic: 2032
  Sorted by residual:
  dihedral pdb=" O4'   U C  45 "
           pdb=" C1'   U C  45 "
           pdb=" N1    U C  45 "
           pdb=" C2    U C  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   49.33  150.67     1      1.50e+01 4.44e-03 7.99e+01
  dihedral pdb=" O4'   U C  67 "
           pdb=" C1'   U C  67 "
           pdb=" N1    U C  67 "
           pdb=" C2    U C  67 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   51.47  148.53     1      1.50e+01 4.44e-03 7.91e+01
  dihedral pdb=" O4'   C C 167 "
           pdb=" C1'   C C 167 "
           pdb=" N1    C C 167 "
           pdb=" C2    C C 167 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   57.79  142.21     1      1.50e+01 4.44e-03 7.64e+01
  ... (remaining 6135 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1480
       0.062 -    0.125: 127
       0.125 -    0.187: 45
       0.187 -    0.250: 16
       0.250 -    0.312: 4
  Chirality restraints: 1672
  Sorted by residual:
  chirality pdb=" P     G C   2 "
            pdb=" OP1   G C   2 "
            pdb=" OP2   G C   2 "
            pdb=" O5'   G C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.72   -0.31 2.00e-01 2.50e+01 2.43e+00
  chirality pdb=" CA  ILE B  99 "
            pdb=" N   ILE B  99 "
            pdb=" C   ILE B  99 "
            pdb=" CB  ILE B  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.74   -0.30 2.00e-01 2.50e+01 2.31e+00
  chirality pdb=" CA  ILE B  75 "
            pdb=" N   ILE B  75 "
            pdb=" C   ILE B  75 "
            pdb=" CB  ILE B  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.72   -0.29 2.00e-01 2.50e+01 2.04e+00
  ... (remaining 1669 not shown)

  Planarity restraints: 1153
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 128 "   -0.020 2.00e-02 2.50e+03   1.50e-02 5.62e+00
        pdb=" CG  TRP B 128 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 128 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 128 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 128 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 128 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 128 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 128 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 128 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 128 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B  67 "   -0.009 2.00e-02 2.50e+03   1.76e-02 3.11e+00
        pdb=" C   PHE B  67 "    0.030 2.00e-02 2.50e+03
        pdb=" O   PHE B  67 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLU B  68 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  68 "    0.008 2.00e-02 2.50e+03   1.66e-02 2.75e+00
        pdb=" C   GLU B  68 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   GLU B  68 "    0.010 2.00e-02 2.50e+03
        pdb=" N   PRO B  69 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1150 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 1075
        2.74 -     3.28: 9541
        3.28 -     3.82: 17719
        3.82 -     4.36: 20885
        4.36 -     4.90: 30314
  Nonbonded interactions: 79534
  Sorted by model distance:
  nonbonded pdb=" O6    G C  46 "
            pdb=" N4    C C  65 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" O4    U C  52 "
            pdb=" N6    A C 162 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" O   PRO B 282 "
            pdb=" OH  TYR B 330 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O2'   G C  96 "
            pdb=" O4'   G C  97 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OG  SER B 311 "
            pdb=" OD1 ASP B 313 "
     model   vdw
     2.241 3.040
  ... (remaining 79529 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'
}

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:             2.540
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     27.160
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6738
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9718  Z= 0.241
  Angle     :  0.682   9.739  13927  Z= 0.405
  Chirality :  0.050   0.312   1672
  Planarity :  0.004   0.039   1153
  Dihedral  : 21.614 150.671   4822
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 17.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  0.65 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.34), residues: 692
  helix:  0.84 (0.27), residues: 400
  sheet: -1.69 (0.67), residues: 68
  loop :  0.75 (0.46), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP B 128 
 HIS   0.011   0.002   HIS B 241 
 PHE   0.019   0.001   PHE A 359 
 TYR   0.017   0.002   TYR B 123 
 ARG   0.012   0.001   ARG A 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14274 (  414)
  hydrogen bonds       : angle       6.47670 ( 1057)
  covalent geometry    : bond        0.00411 ( 9718)
  covalent geometry    : angle       0.68175 (13927)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 119
  time to evaluate  : 0.755 
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: A  243 MET cc_start: 0.7767 (mmm) cc_final: 0.6852 (mmm)
  outliers start: 3
  outliers final: 0
  residues processed: 121
  average time/residue: 0.2145
  time to fit residues: 35.7843
Evaluate side-chains
  74 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 63 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 21 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   chunk 40 optimal weight:    6.9990
   chunk 49 optimal weight:    0.8980
   chunk 76 optimal weight:    9.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 242 HIS
A 358 HIS
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 248 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.054980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.038530 restraints weight = 70635.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.039599 restraints weight = 44713.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.040270 restraints weight = 33225.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9718  Z= 0.217
  Angle     :  0.649   8.837  13927  Z= 0.328
  Chirality :  0.036   0.177   1672
  Planarity :  0.005   0.040   1153
  Dihedral  : 23.228 178.331   3356
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 22.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 10.55 %
    Favored  : 88.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.34), residues: 692
  helix:  0.87 (0.26), residues: 412
  sheet: -1.88 (0.66), residues: 68
  loop :  0.98 (0.49), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 128 
 HIS   0.007   0.002   HIS B  74 
 PHE   0.021   0.002   PHE A 264 
 TYR   0.015   0.002   TYR B 123 
 ARG   0.008   0.001   ARG B 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05972 (  414)
  hydrogen bonds       : angle       4.99394 ( 1057)
  covalent geometry    : bond        0.00441 ( 9718)
  covalent geometry    : angle       0.64905 (13927)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9384 (mt-10) cc_final: 0.9143 (pt0)
REVERT: A  242 HIS cc_start: 0.8524 (t-170) cc_final: 0.8232 (t-170)
REVERT: B   74 HIS cc_start: 0.8473 (m170) cc_final: 0.8118 (m-70)
REVERT: B   96 LYS cc_start: 0.9665 (mttm) cc_final: 0.9084 (mmmm)
REVERT: B  124 LEU cc_start: 0.9884 (mt) cc_final: 0.9667 (mt)
REVERT: B  162 ASP cc_start: 0.9526 (t0) cc_final: 0.9256 (t0)
  outliers start: 8
  outliers final: 4
  residues processed: 87
  average time/residue: 0.1850
  time to fit residues: 23.4778
Evaluate side-chains
  70 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain B residue  123 TYR
Chi-restraints excluded: chain B residue  215 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 45 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 81 optimal weight:    9.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 241 HIS
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.056203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.039863 restraints weight = 71279.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.040961 restraints weight = 44015.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.041655 restraints weight = 32574.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9718  Z= 0.147
  Angle     :  0.611  11.733  13927  Z= 0.297
  Chirality :  0.034   0.159   1672
  Planarity :  0.004   0.031   1153
  Dihedral  : 23.160 176.004   3356
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 19.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.31 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.34), residues: 692
  helix:  1.05 (0.26), residues: 410
  sheet: -1.83 (0.63), residues: 76
  loop :  1.01 (0.51), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  98 
 HIS   0.004   0.001   HIS B  74 
 PHE   0.015   0.002   PHE A 264 
 TYR   0.016   0.002   TYR A 323 
 ARG   0.004   0.001   ARG B 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04906 (  414)
  hydrogen bonds       : angle       4.62050 ( 1057)
  covalent geometry    : bond        0.00305 ( 9718)
  covalent geometry    : angle       0.61146 (13927)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9382 (mt-10) cc_final: 0.9068 (pt0)
REVERT: A   65 ASP cc_start: 0.9136 (p0) cc_final: 0.8017 (t0)
REVERT: A  242 HIS cc_start: 0.8722 (t-170) cc_final: 0.8388 (t70)
REVERT: A  243 MET cc_start: 0.8499 (mmm) cc_final: 0.8276 (mmm)
REVERT: A  294 TYR cc_start: 0.9370 (m-80) cc_final: 0.9045 (m-80)
REVERT: B   96 LYS cc_start: 0.9503 (mttm) cc_final: 0.9010 (mmmm)
REVERT: B  110 MET cc_start: 0.8762 (ptp) cc_final: 0.8421 (ptp)
REVERT: B  162 ASP cc_start: 0.9612 (t0) cc_final: 0.9404 (t0)
REVERT: B  193 PHE cc_start: 0.9775 (m-80) cc_final: 0.9325 (m-10)
  outliers start: 10
  outliers final: 4
  residues processed: 86
  average time/residue: 0.1843
  time to fit residues: 23.2962
Evaluate side-chains
  78 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain B residue  123 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 25 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 28 optimal weight:    7.9990
   chunk 76 optimal weight:   10.0000
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** 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 = 0.3498 r_free = 0.3498 target = 0.055047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.038975 restraints weight = 69228.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.040071 restraints weight = 42870.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.040725 restraints weight = 31593.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.2789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9718  Z= 0.152
  Angle     :  0.598   8.724  13927  Z= 0.293
  Chirality :  0.034   0.154   1672
  Planarity :  0.004   0.032   1153
  Dihedral  : 23.182 178.719   3356
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 20.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 16.56 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.34), residues: 692
  helix:  1.25 (0.26), residues: 398
  sheet: -1.92 (0.62), residues: 76
  loop :  0.98 (0.48), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  98 
 HIS   0.003   0.001   HIS B 241 
 PHE   0.020   0.002   PHE A 306 
 TYR   0.021   0.002   TYR A 323 
 ARG   0.004   0.000   ARG B 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05043 (  414)
  hydrogen bonds       : angle       4.58216 ( 1057)
  covalent geometry    : bond        0.00314 ( 9718)
  covalent geometry    : angle       0.59806 (13927)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9416 (mt-10) cc_final: 0.9071 (pt0)
REVERT: A   65 ASP cc_start: 0.9184 (p0) cc_final: 0.7992 (t0)
REVERT: A  157 TRP cc_start: 0.9446 (m100) cc_final: 0.9212 (m100)
REVERT: A  242 HIS cc_start: 0.8771 (t-170) cc_final: 0.8380 (t70)
REVERT: A  243 MET cc_start: 0.8612 (mmm) cc_final: 0.8322 (mmm)
REVERT: A  294 TYR cc_start: 0.9356 (m-80) cc_final: 0.9060 (m-80)
REVERT: B   96 LYS cc_start: 0.9519 (mttm) cc_final: 0.9042 (mmmm)
REVERT: B  110 MET cc_start: 0.8822 (ptp) cc_final: 0.8431 (ptp)
REVERT: B  162 ASP cc_start: 0.9667 (t0) cc_final: 0.9428 (t0)
  outliers start: 8
  outliers final: 5
  residues processed: 81
  average time/residue: 0.1750
  time to fit residues: 21.0449
Evaluate side-chains
  70 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain B residue  123 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 57 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0570
   chunk 61 optimal weight:    0.5980
   chunk 81 optimal weight:   10.0000
   chunk 51 optimal weight:    0.0980
   chunk 49 optimal weight:    0.8980
   chunk 47 optimal weight:    7.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.4298

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

Flipped N/Q/H residues before XYZ refinement:
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** 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 = 0.3546 r_free = 0.3546 target = 0.056619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.040009 restraints weight = 69550.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.041093 restraints weight = 43156.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.041776 restraints weight = 31730.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.2931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   9718  Z= 0.117
  Angle     :  0.609  10.494  13927  Z= 0.290
  Chirality :  0.034   0.161   1672
  Planarity :  0.003   0.031   1153
  Dihedral  : 22.970 179.189   3356
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 16.40 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.34), residues: 692
  helix:  1.25 (0.26), residues: 398
  sheet: -1.81 (0.62), residues: 76
  loop :  0.95 (0.48), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  98 
 HIS   0.003   0.001   HIS B  74 
 PHE   0.009   0.002   PHE A 264 
 TYR   0.024   0.002   TYR A 323 
 ARG   0.002   0.000   ARG B 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04748 (  414)
  hydrogen bonds       : angle       4.43012 ( 1057)
  covalent geometry    : bond        0.00241 ( 9718)
  covalent geometry    : angle       0.60852 (13927)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9096 (pt0)
REVERT: A   65 ASP cc_start: 0.9162 (p0) cc_final: 0.7931 (t0)
REVERT: A  157 TRP cc_start: 0.9367 (m100) cc_final: 0.9047 (m100)
REVERT: A  242 HIS cc_start: 0.8769 (t-170) cc_final: 0.8341 (t70)
REVERT: B   96 LYS cc_start: 0.9463 (mttm) cc_final: 0.8917 (mmtp)
REVERT: B  162 ASP cc_start: 0.9674 (t0) cc_final: 0.9393 (t0)
REVERT: B  197 MET cc_start: 0.9046 (mpp) cc_final: 0.8717 (mpp)
  outliers start: 9
  outliers final: 4
  residues processed: 87
  average time/residue: 0.1754
  time to fit residues: 23.0441
Evaluate side-chains
  74 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue  123 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0670
   chunk 78 optimal weight:   20.0000
   chunk 32 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 31 optimal weight:    7.9990
   chunk 13 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.1922

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

Flipped N/Q/H residues before XYZ refinement:
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.056196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.039998 restraints weight = 70156.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.041083 restraints weight = 43660.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.041724 restraints weight = 32285.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9718  Z= 0.126
  Angle     :  0.611   9.683  13927  Z= 0.292
  Chirality :  0.034   0.173   1672
  Planarity :  0.004   0.033   1153
  Dihedral  : 22.934 178.820   3356
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 18.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 18.99 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.34), residues: 692
  helix:  1.29 (0.26), residues: 400
  sheet: -1.80 (0.62), residues: 76
  loop :  0.92 (0.48), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  98 
 HIS   0.002   0.001   HIS A 241 
 PHE   0.015   0.001   PHE A 193 
 TYR   0.024   0.002   TYR A 323 
 ARG   0.003   0.000   ARG B 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04832 (  414)
  hydrogen bonds       : angle       4.55357 ( 1057)
  covalent geometry    : bond        0.00268 ( 9718)
  covalent geometry    : angle       0.61061 (13927)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9422 (mt-10) cc_final: 0.9113 (pt0)
REVERT: A   65 ASP cc_start: 0.9184 (p0) cc_final: 0.7962 (t0)
REVERT: A  133 MET cc_start: 0.9048 (tpt) cc_final: 0.8749 (tpt)
REVERT: A  157 TRP cc_start: 0.9387 (m100) cc_final: 0.9079 (m100)
REVERT: A  214 MET cc_start: 0.8719 (mmm) cc_final: 0.8515 (mmm)
REVERT: A  242 HIS cc_start: 0.8724 (t-170) cc_final: 0.8421 (t70)
REVERT: B   95 VAL cc_start: 0.9420 (OUTLIER) cc_final: 0.9095 (p)
REVERT: B   96 LYS cc_start: 0.9485 (mttm) cc_final: 0.8939 (mmtp)
REVERT: B  162 ASP cc_start: 0.9700 (t0) cc_final: 0.9405 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 83
  average time/residue: 0.1841
  time to fit residues: 22.9111
Evaluate side-chains
  81 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  123 TYR
Chi-restraints excluded: chain B residue  178 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 28 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   chunk 72 optimal weight:   10.0000
   chunk 10 optimal weight:    0.3980
   chunk 16 optimal weight:    0.0010
   chunk 21 optimal weight:    5.9990
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** 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 = 0.3541 r_free = 0.3541 target = 0.056348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.039663 restraints weight = 70474.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.040772 restraints weight = 43935.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.041479 restraints weight = 32328.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9718  Z= 0.112
  Angle     :  0.613  14.142  13927  Z= 0.290
  Chirality :  0.034   0.174   1672
  Planarity :  0.003   0.035   1153
  Dihedral  : 22.818 178.102   3356
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 16.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 19.32 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.34), residues: 692
  helix:  1.28 (0.27), residues: 400
  sheet: -1.81 (0.61), residues: 76
  loop :  0.85 (0.48), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  98 
 HIS   0.002   0.000   HIS A  74 
 PHE   0.023   0.002   PHE B 193 
 TYR   0.029   0.002   TYR A 323 
 ARG   0.002   0.000   ARG B 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04704 (  414)
  hydrogen bonds       : angle       4.46361 ( 1057)
  covalent geometry    : bond        0.00236 ( 9718)
  covalent geometry    : angle       0.61296 (13927)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9410 (mt-10) cc_final: 0.9149 (pt0)
REVERT: A   65 ASP cc_start: 0.9169 (p0) cc_final: 0.7921 (t0)
REVERT: A  133 MET cc_start: 0.8897 (tpt) cc_final: 0.8411 (tpt)
REVERT: A  214 MET cc_start: 0.8794 (mmm) cc_final: 0.8521 (mmm)
REVERT: A  242 HIS cc_start: 0.8604 (t-170) cc_final: 0.8308 (t70)
REVERT: A  294 TYR cc_start: 0.9342 (m-80) cc_final: 0.8921 (m-80)
REVERT: B   95 VAL cc_start: 0.9419 (OUTLIER) cc_final: 0.9131 (p)
REVERT: B   96 LYS cc_start: 0.9478 (mttm) cc_final: 0.8939 (mmtp)
REVERT: B  162 ASP cc_start: 0.9703 (t0) cc_final: 0.9390 (t0)
  outliers start: 12
  outliers final: 11
  residues processed: 86
  average time/residue: 0.2237
  time to fit residues: 28.8340
Evaluate side-chains
  86 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  123 TYR
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  178 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 77 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 74 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 65 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 66 optimal weight:    0.4980
   chunk 18 optimal weight:    6.9990
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** 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 = 0.3468 r_free = 0.3468 target = 0.053243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.036740 restraints weight = 74744.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.037778 restraints weight = 46311.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.038464 restraints weight = 34073.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9718  Z= 0.184
  Angle     :  0.659  13.411  13927  Z= 0.319
  Chirality :  0.035   0.189   1672
  Planarity :  0.004   0.035   1153
  Dihedral  : 23.132 178.721   3356
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 23.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 18.02 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.34), residues: 692
  helix:  1.26 (0.26), residues: 400
  sheet: -1.87 (0.60), residues: 76
  loop :  0.92 (0.49), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 102 
 HIS   0.003   0.001   HIS B  74 
 PHE   0.023   0.002   PHE A 193 
 TYR   0.033   0.002   TYR A 323 
 ARG   0.003   0.000   ARG A  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05493 (  414)
  hydrogen bonds       : angle       4.63019 ( 1057)
  covalent geometry    : bond        0.00375 ( 9718)
  covalent geometry    : angle       0.65927 (13927)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9408 (mt-10) cc_final: 0.9129 (pt0)
REVERT: A   65 ASP cc_start: 0.9128 (p0) cc_final: 0.7918 (t0)
REVERT: A  214 MET cc_start: 0.8852 (mmm) cc_final: 0.8579 (mmm)
REVERT: A  242 HIS cc_start: 0.8681 (t-170) cc_final: 0.8330 (t70)
REVERT: A  294 TYR cc_start: 0.9362 (m-80) cc_final: 0.9016 (m-80)
REVERT: B   63 CYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8673 (p)
REVERT: B   95 VAL cc_start: 0.9565 (OUTLIER) cc_final: 0.9252 (p)
REVERT: B   96 LYS cc_start: 0.9596 (mttm) cc_final: 0.9156 (mmmm)
REVERT: B  110 MET cc_start: 0.8801 (ptp) cc_final: 0.7948 (pmm)
REVERT: B  162 ASP cc_start: 0.9748 (t0) cc_final: 0.9455 (t0)
  outliers start: 21
  outliers final: 14
  residues processed: 85
  average time/residue: 0.1682
  time to fit residues: 21.6977
Evaluate side-chains
  84 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain B residue   63 CYS
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  123 TYR
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain B residue  187 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 72 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 80 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** 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 = 0.3481 r_free = 0.3481 target = 0.054437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.038486 restraints weight = 71510.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.039518 restraints weight = 44187.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.040185 restraints weight = 32258.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9718  Z= 0.142
  Angle     :  0.640  14.262  13927  Z= 0.306
  Chirality :  0.035   0.186   1672
  Planarity :  0.004   0.036   1153
  Dihedral  : 23.105 178.945   3356
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 20.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 18.67 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.34), residues: 692
  helix:  1.29 (0.26), residues: 392
  sheet: -1.87 (0.59), residues: 76
  loop :  0.74 (0.48), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  98 
 HIS   0.002   0.001   HIS A  74 
 PHE   0.030   0.002   PHE A 306 
 TYR   0.026   0.002   TYR A 323 
 ARG   0.003   0.000   ARG B 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04875 (  414)
  hydrogen bonds       : angle       4.57245 ( 1057)
  covalent geometry    : bond        0.00304 ( 9718)
  covalent geometry    : angle       0.64043 (13927)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9131 (pt0)
REVERT: A   65 ASP cc_start: 0.9202 (p0) cc_final: 0.8596 (p0)
REVERT: A  214 MET cc_start: 0.8933 (mmm) cc_final: 0.8593 (mmm)
REVERT: A  242 HIS cc_start: 0.8747 (t-170) cc_final: 0.8383 (t70)
REVERT: A  294 TYR cc_start: 0.9381 (m-80) cc_final: 0.9050 (m-80)
REVERT: B   63 CYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8645 (p)
REVERT: B   95 VAL cc_start: 0.9564 (OUTLIER) cc_final: 0.9249 (p)
REVERT: B   96 LYS cc_start: 0.9594 (mttm) cc_final: 0.9154 (mmmm)
REVERT: B  110 MET cc_start: 0.8830 (ptp) cc_final: 0.8030 (pmm)
REVERT: B  162 ASP cc_start: 0.9750 (t0) cc_final: 0.9455 (t0)
  outliers start: 17
  outliers final: 14
  residues processed: 85
  average time/residue: 0.1827
  time to fit residues: 23.0899
Evaluate side-chains
  85 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain B residue   63 CYS
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  123 TYR
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain B residue  187 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 29 optimal weight:    0.3980
   chunk 80 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 68 optimal weight:   20.0000
   chunk 41 optimal weight:    5.9990
   chunk 42 optimal weight:    0.1980
   chunk 78 optimal weight:   20.0000
   chunk 70 optimal weight:    8.9990
   chunk 54 optimal weight:    5.9990
   chunk 3 optimal weight:    0.0010
   overall best weight:    1.9190

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

Flipped N/Q/H residues before XYZ refinement:
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** 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 = 0.3466 r_free = 0.3466 target = 0.053383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.036787 restraints weight = 73788.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.037829 restraints weight = 46088.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.038478 restraints weight = 34091.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.3915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9718  Z= 0.160
  Angle     :  0.661  14.164  13927  Z= 0.316
  Chirality :  0.035   0.197   1672
  Planarity :  0.004   0.036   1153
  Dihedral  : 23.154 178.435   3356
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 21.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 18.99 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.34), residues: 692
  helix:  1.12 (0.26), residues: 400
  sheet: -1.92 (0.59), residues: 76
  loop :  0.89 (0.49), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  98 
 HIS   0.002   0.000   HIS B  74 
 PHE   0.030   0.002   PHE A 306 
 TYR   0.033   0.002   TYR A 323 
 ARG   0.003   0.000   ARG B 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05083 (  414)
  hydrogen bonds       : angle       4.61779 ( 1057)
  covalent geometry    : bond        0.00339 ( 9718)
  covalent geometry    : angle       0.66126 (13927)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9157 (pt0)
REVERT: A   65 ASP cc_start: 0.9206 (p0) cc_final: 0.8644 (p0)
REVERT: A  214 MET cc_start: 0.8962 (mmm) cc_final: 0.8636 (mmm)
REVERT: A  242 HIS cc_start: 0.8762 (t-170) cc_final: 0.8385 (t70)
REVERT: A  294 TYR cc_start: 0.9388 (m-80) cc_final: 0.9097 (m-80)
REVERT: B   63 CYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8710 (p)
REVERT: B   95 VAL cc_start: 0.9583 (OUTLIER) cc_final: 0.9264 (p)
REVERT: B   96 LYS cc_start: 0.9596 (mttm) cc_final: 0.9176 (mmmm)
REVERT: B  110 MET cc_start: 0.9009 (ptp) cc_final: 0.8226 (pmm)
REVERT: B  162 ASP cc_start: 0.9765 (t0) cc_final: 0.9483 (t0)
REVERT: B  243 MET cc_start: 0.0659 (mmt) cc_final: 0.0412 (mmt)
  outliers start: 17
  outliers final: 15
  residues processed: 79
  average time/residue: 0.1765
  time to fit residues: 20.9016
Evaluate side-chains
  83 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain B residue   63 CYS
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  123 TYR
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain B residue  187 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 55 optimal weight:    9.9990
   chunk 69 optimal weight:    9.9990
   chunk 31 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 22 optimal weight:    0.3980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** 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 = 0.3493 r_free = 0.3493 target = 0.055192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.038886 restraints weight = 71601.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.039956 restraints weight = 44740.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.040656 restraints weight = 33182.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.3967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9718  Z= 0.124
  Angle     :  0.649  14.328  13927  Z= 0.306
  Chirality :  0.035   0.198   1672
  Planarity :  0.003   0.036   1153
  Dihedral  : 22.995 177.337   3356
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 18.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.32 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.34), residues: 692
  helix:  1.24 (0.26), residues: 392
  sheet: -1.87 (0.60), residues: 76
  loop :  0.68 (0.48), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  98 
 HIS   0.003   0.001   HIS B 242 
 PHE   0.030   0.002   PHE A 306 
 TYR   0.031   0.002   TYR A 323 
 ARG   0.002   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04845 (  414)
  hydrogen bonds       : angle       4.50445 ( 1057)
  covalent geometry    : bond        0.00271 ( 9718)
  covalent geometry    : angle       0.64919 (13927)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3699.95 seconds
wall clock time: 65 minutes 34.51 seconds (3934.51 seconds total)