Starting phenix.real_space_refine
on Mon May 12 15:13:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zmj_60249/05_2025/8zmj_60249.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zmj_60249/05_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_60249/05_2025/8zmj_60249.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zmj_60249/05_2025/8zmj_60249.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zmj_60249/05_2025/8zmj_60249.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zmj_60249/05_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.50, per 1000 atoms: 0.71
  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: 2.52
  Conformation dependent library (CDL) restraints added in 686.4 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: 3.85
  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: 3.07

  Time building geometry restraints manager: 2.95 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:             2.450
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.890
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.880
-------------------------------------------------------------------------------
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  : 0.837 
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: 0.2186
  time to fit residues: 36.2796
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  : 0.752 
-------------------------------------------------------------------------------
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 = 0.3497 r_free = 0.3497 target = 0.054981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.038558 restraints weight = 70638.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.039622 restraints weight = 44726.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.040280 restraints weight = 33128.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3030
-------------------------------------------------------------------------------
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  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9384 (mt-10) cc_final: 0.9142 (pt0)
REVERT: A  242 HIS cc_start: 0.8523 (t-170) cc_final: 0.8231 (t-170)
REVERT: B   74 HIS cc_start: 0.8474 (m170) cc_final: 0.8119 (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: 0.9528 (t0) cc_final: 0.9259 (t0)
  outliers start: 8
  outliers final: 4
  residues processed: 87
  average time/residue: 0.1882
  time to fit residues: 23.7903
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  : 0.719 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 45 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    0.2980
   chunk 66 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 81 optimal weight:   10.0000
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.3518 r_free = 0.3518 target = 0.056115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.039775 restraints weight = 71364.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.040869 restraints weight = 44044.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.041547 restraints weight = 32704.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.2442

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= 0.142
  Angle     :  0.612  11.577  13927  Z= 0.298
  Chirality :  0.034   0.159   1672
  Planarity :  0.004   0.031   1153
  Dihedral  : 23.168 176.096   3356
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 19.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 12.99 %
    Favored  : 85.39 %
  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:  1.06 (0.26), residues: 410
  sheet: -1.84 (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   0.003   0.001   HIS A  74 
 PHE   0.016   0.002   PHE B 193 
 TYR   0.015   0.002   TYR A 323 
 ARG   0.004   0.001   ARG B 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04924 (  414)
  hydrogen bonds       : angle       4.61536 ( 1057)
  covalent geometry    : bond        0.00299 ( 9718)
  covalent geometry    : angle       0.61167 (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  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9381 (mt-10) cc_final: 0.9069 (pt0)
REVERT: A   65 ASP cc_start: 0.9133 (p0) cc_final: 0.8011 (t0)
REVERT: A  242 HIS cc_start: 0.8722 (t-170) cc_final: 0.8374 (t70)
REVERT: A  243 MET cc_start: 0.8474 (mmm) cc_final: 0.8259 (mmm)
REVERT: A  294 TYR cc_start: 0.9366 (m-80) cc_final: 0.9059 (m-80)
REVERT: B   74 HIS cc_start: 0.8433 (m170) cc_final: 0.8226 (m-70)
REVERT: B   96 LYS cc_start: 0.9506 (mttm) cc_final: 0.9010 (mmmm)
REVERT: B  110 MET cc_start: 0.8774 (ptp) cc_final: 0.8427 (ptp)
REVERT: B  162 ASP cc_start: 0.9613 (t0) cc_final: 0.9405 (t0)
REVERT: B  193 PHE cc_start: 0.9770 (m-80) cc_final: 0.9315 (m-10)
  outliers start: 10
  outliers final: 4
  residues processed: 86
  average time/residue: 0.1919
  time to fit residues: 23.9211
Evaluate side-chains
  77 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 61 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 25 optimal weight:    9.9990
   chunk 36 optimal weight:    0.8980
   chunk 22 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 76 optimal weight:   10.0000
   overall best weight:    1.7384

-------------------------------------------------------------------------------
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 = 0.3500 r_free = 0.3500 target = 0.055143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.039101 restraints weight = 69170.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.040184 restraints weight = 42556.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.040823 restraints weight = 31328.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9718  Z= 0.148
  Angle     :  0.602   8.850  13927  Z= 0.293
  Chirality :  0.034   0.156   1672
  Planarity :  0.004   0.031   1153
  Dihedral  : 23.178 178.583   3356
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 20.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 17.21 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.08 (0.34), residues: 692
  helix:  1.26 (0.27), residues: 398
  sheet: -1.92 (0.62), residues: 76
  loop :  1.01 (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   0.020   0.002   TYR A 323 
 ARG   0.004   0.000   ARG B 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05004 (  414)
  hydrogen bonds       : angle       4.58011 ( 1057)
  covalent geometry    : bond        0.00311 ( 9718)
  covalent geometry    : angle       0.60229 (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
  79 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9071 (pt0)
REVERT: A   65 ASP cc_start: 0.9177 (p0) cc_final: 0.7987 (t0)
REVERT: A  157 TRP cc_start: 0.9451 (m100) cc_final: 0.9172 (m100)
REVERT: A  242 HIS cc_start: 0.8770 (t-170) cc_final: 0.8382 (t70)
REVERT: A  243 MET cc_start: 0.8612 (mmm) cc_final: 0.8328 (mmm)
REVERT: A  294 TYR cc_start: 0.9360 (m-80) cc_final: 0.9065 (m-80)
REVERT: B   96 LYS cc_start: 0.9519 (mttm) cc_final: 0.9038 (mmmm)
REVERT: B  110 MET cc_start: 0.8824 (ptp) cc_final: 0.8437 (ptp)
REVERT: B  162 ASP cc_start: 0.9666 (t0) cc_final: 0.9427 (t0)
  outliers start: 8
  outliers final: 5
  residues processed: 78
  average time/residue: 0.1687
  time to fit residues: 20.0517
Evaluate side-chains
  68 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 81 optimal weight:   10.0000
   chunk 51 optimal weight:    0.0770
   chunk 49 optimal weight:    6.9990
   chunk 47 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.6938

-------------------------------------------------------------------------------
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 = 0.3531 r_free = 0.3531 target = 0.056542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.040327 restraints weight = 69837.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.041416 restraints weight = 43418.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.042125 restraints weight = 32131.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9718  Z= 0.115
  Angle     :  0.607  10.546  13927  Z= 0.288
  Chirality :  0.034   0.162   1672
  Planarity :  0.004   0.031   1153
  Dihedral  : 23.024 179.228   3356
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 16.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 16.23 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.13 (0.34), residues: 692
  helix:  1.28 (0.26), residues: 400
  sheet: -1.85 (0.62), residues: 76
  loop :  1.07 (0.49), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  98 
 HIS   0.003   0.001   HIS A  74 
 PHE   0.024   0.002   PHE A 193 
 TYR   0.023   0.002   TYR A 323 
 ARG   0.002   0.000   ARG B 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04705 (  414)
  hydrogen bonds       : angle       4.46782 ( 1057)
  covalent geometry    : bond        0.00243 ( 9718)
  covalent geometry    : angle       0.60717 (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
  88 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9103 (pt0)
REVERT: A   65 ASP cc_start: 0.9181 (p0) cc_final: 0.7992 (t0)
REVERT: A  157 TRP cc_start: 0.9403 (m100) cc_final: 0.9082 (m100)
REVERT: A  242 HIS cc_start: 0.8806 (t-170) cc_final: 0.8388 (t70)
REVERT: A  294 TYR cc_start: 0.9319 (m-80) cc_final: 0.9116 (m-80)
REVERT: B   96 LYS cc_start: 0.9481 (mttm) cc_final: 0.8918 (mmtp)
REVERT: B  162 ASP cc_start: 0.9686 (t0) cc_final: 0.9421 (t0)
REVERT: B  197 MET cc_start: 0.9031 (mpp) cc_final: 0.8723 (mpp)
  outliers start: 9
  outliers final: 5
  residues processed: 84
  average time/residue: 0.1655
  time to fit residues: 21.2928
Evaluate side-chains
  73 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
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   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:    0.0980
   chunk 18 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 78 optimal weight:   20.0000
   chunk 32 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.055737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.039245 restraints weight = 70267.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.040303 restraints weight = 43978.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.040959 restraints weight = 32475.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.3098

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= 0.120
  Angle     :  0.599   9.817  13927  Z= 0.287
  Chirality :  0.034   0.173   1672
  Planarity :  0.004   0.033   1153
  Dihedral  : 22.947 179.191   3356
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 18.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 18.02 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.34), residues: 692
  helix:  1.29 (0.27), residues: 398
  sheet: -1.86 (0.62), residues: 76
  loop :  0.99 (0.48), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  98 
 HIS   0.002   0.001   HIS A  74 
 PHE   0.013   0.001   PHE B 193 
 TYR   0.026   0.002   TYR A 323 
 ARG   0.003   0.000   ARG B 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04703 (  414)
  hydrogen bonds       : angle       4.48850 ( 1057)
  covalent geometry    : bond        0.00255 ( 9718)
  covalent geometry    : angle       0.59902 (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
  86 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9413 (mt-10) cc_final: 0.9104 (pt0)
REVERT: A   65 ASP cc_start: 0.9187 (p0) cc_final: 0.7925 (t0)
REVERT: A  133 MET cc_start: 0.9013 (tpt) cc_final: 0.8651 (tpt)
REVERT: A  157 TRP cc_start: 0.9373 (m100) cc_final: 0.9058 (m100)
REVERT: A  214 MET cc_start: 0.8691 (mmm) cc_final: 0.8453 (mmm)
REVERT: A  242 HIS cc_start: 0.8710 (t-170) cc_final: 0.8404 (t70)
REVERT: A  243 MET cc_start: 0.8188 (mmm) cc_final: 0.7939 (mmm)
REVERT: A  294 TYR cc_start: 0.9401 (m-80) cc_final: 0.9158 (m-80)
REVERT: B   96 LYS cc_start: 0.9480 (mttm) cc_final: 0.8937 (mmtp)
REVERT: B  162 ASP cc_start: 0.9704 (t0) cc_final: 0.9409 (t0)
  outliers start: 15
  outliers final: 8
  residues processed: 82
  average time/residue: 0.1714
  time to fit residues: 21.3337
Evaluate side-chains
  79 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
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  322 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain B residue   64 TYR
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:    9.9990
   chunk 12 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 71 optimal weight:    9.9990
   chunk 61 optimal weight:    0.6980
   chunk 72 optimal weight:    9.9990
   chunk 10 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3511 r_free = 0.3511 target = 0.055774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.039616 restraints weight = 70104.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.040690 restraints weight = 43763.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.041374 restraints weight = 32408.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.3266

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     :  0.606  14.024  13927  Z= 0.289
  Chirality :  0.034   0.173   1672
  Planarity :  0.004   0.034   1153
  Dihedral  : 22.930 178.788   3356
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 19.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.86 %
    Favored  : 79.87 %
  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:  1.12 (0.34), residues: 692
  helix:  1.31 (0.27), residues: 398
  sheet: -1.85 (0.61), residues: 76
  loop :  0.97 (0.48), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  98 
 HIS   0.002   0.000   HIS A  74 
 PHE   0.017   0.002   PHE B 193 
 TYR   0.029   0.002   TYR A 323 
 ARG   0.005   0.000   ARG B 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04693 (  414)
  hydrogen bonds       : angle       4.47881 ( 1057)
  covalent geometry    : bond        0.00266 ( 9718)
  covalent geometry    : angle       0.60639 (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
  87 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9415 (mt-10) cc_final: 0.9141 (pt0)
REVERT: A   65 ASP cc_start: 0.9195 (p0) cc_final: 0.7957 (t0)
REVERT: A  133 MET cc_start: 0.8931 (tpt) cc_final: 0.8524 (tpt)
REVERT: A  242 HIS cc_start: 0.8686 (t-170) cc_final: 0.8386 (t70)
REVERT: B   95 VAL cc_start: 0.9454 (OUTLIER) cc_final: 0.9180 (p)
REVERT: B   96 LYS cc_start: 0.9505 (mttm) cc_final: 0.9012 (mmtp)
REVERT: B  162 ASP cc_start: 0.9725 (t0) cc_final: 0.9421 (t0)
  outliers start: 14
  outliers final: 11
  residues processed: 82
  average time/residue: 0.1731
  time to fit residues: 21.3666
Evaluate side-chains
  81 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
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  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
Chi-restraints excluded: chain B residue  219 VAL
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:    1.9990
   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:    5.9990
   chunk 66 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   overall best weight:    1.5384

-------------------------------------------------------------------------------
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 = 0.3504 r_free = 0.3504 target = 0.055384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.039199 restraints weight = 72548.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.040221 restraints weight = 44835.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.040873 restraints weight = 33151.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.3433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9718  Z= 0.138
  Angle     :  0.618  14.075  13927  Z= 0.294
  Chirality :  0.034   0.182   1672
  Planarity :  0.004   0.035   1153
  Dihedral  : 22.948 178.481   3356
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 20.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.02 %
    Favored  : 79.38 %
  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:  1.12 (0.34), residues: 692
  helix:  1.31 (0.26), residues: 398
  sheet: -1.81 (0.61), residues: 76
  loop :  0.96 (0.48), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  98 
 HIS   0.003   0.001   HIS A  74 
 PHE   0.018   0.002   PHE A 193 
 TYR   0.030   0.002   TYR A 323 
 ARG   0.003   0.000   ARG B 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04792 (  414)
  hydrogen bonds       : angle       4.49710 ( 1057)
  covalent geometry    : bond        0.00289 ( 9718)
  covalent geometry    : angle       0.61840 (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
  86 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9410 (mt-10) cc_final: 0.9137 (pt0)
REVERT: A   65 ASP cc_start: 0.9153 (p0) cc_final: 0.8951 (p0)
REVERT: A  133 MET cc_start: 0.8869 (tpt) cc_final: 0.8241 (tpt)
REVERT: A  242 HIS cc_start: 0.8726 (t-170) cc_final: 0.8447 (t70)
REVERT: A  243 MET cc_start: 0.8032 (mmm) cc_final: 0.7674 (mmm)
REVERT: B   95 VAL cc_start: 0.9578 (OUTLIER) cc_final: 0.9181 (p)
REVERT: B   96 LYS cc_start: 0.9532 (mttm) cc_final: 0.9048 (mmmm)
REVERT: B  162 ASP cc_start: 0.9741 (t0) cc_final: 0.9453 (t0)
  outliers start: 16
  outliers final: 14
  residues processed: 81
  average time/residue: 0.1777
  time to fit residues: 21.1787
Evaluate side-chains
  82 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
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   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
Chi-restraints excluded: chain B residue  219 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 51 optimal weight:    7.9990
   chunk 72 optimal weight:    9.9990
   chunk 45 optimal weight:    0.1980
   chunk 48 optimal weight:    0.8980
   chunk 4 optimal weight:    7.9990
   chunk 22 optimal weight:    0.2980
   chunk 3 optimal weight:    5.9990
   chunk 80 optimal weight:    7.9990
   chunk 30 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    2.0784

-------------------------------------------------------------------------------
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 = 0.3463 r_free = 0.3463 target = 0.053149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.036692 restraints weight = 72042.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.037710 restraints weight = 44793.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.038417 restraints weight = 33617.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.3785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9718  Z= 0.166
  Angle     :  0.652  13.450  13927  Z= 0.313
  Chirality :  0.035   0.200   1672
  Planarity :  0.004   0.035   1153
  Dihedral  : 23.163 179.115   3356
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 21.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.18 %
    Favored  : 79.22 %
  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:  1.04 (0.34), residues: 692
  helix:  1.25 (0.26), residues: 400
  sheet: -1.90 (0.61), residues: 76
  loop :  0.92 (0.48), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  98 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.023   0.002   PHE B 193 
 TYR   0.029   0.002   TYR A 323 
 ARG   0.004   0.000   ARG B 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05161 (  414)
  hydrogen bonds       : angle       4.57338 ( 1057)
  covalent geometry    : bond        0.00341 ( 9718)
  covalent geometry    : angle       0.65167 (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
  81 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9420 (mt-10) cc_final: 0.9132 (pt0)
REVERT: A   65 ASP cc_start: 0.9096 (p0) cc_final: 0.7913 (t0)
REVERT: A  242 HIS cc_start: 0.8910 (t-170) cc_final: 0.8568 (t70)
REVERT: A  243 MET cc_start: 0.8352 (mmm) cc_final: 0.8057 (mmm)
REVERT: A  294 TYR cc_start: 0.9378 (m-80) cc_final: 0.8969 (m-80)
REVERT: B   95 VAL cc_start: 0.9620 (OUTLIER) cc_final: 0.9269 (p)
REVERT: B   96 LYS cc_start: 0.9578 (mttm) cc_final: 0.9131 (mmmm)
REVERT: B  110 MET cc_start: 0.8797 (ptp) cc_final: 0.7976 (pmm)
REVERT: B  162 ASP cc_start: 0.9766 (t0) cc_final: 0.9483 (t0)
REVERT: B  243 MET cc_start: 0.0779 (mmt) cc_final: 0.0478 (mmt)
  outliers start: 16
  outliers final: 12
  residues processed: 76
  average time/residue: 0.1548
  time to fit residues: 17.9805
Evaluate side-chains
  78 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 80 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 68 optimal weight:   20.0000
   chunk 41 optimal weight:    5.9990
   chunk 42 optimal weight:    0.0000
   chunk 78 optimal weight:   20.0000
   chunk 70 optimal weight:    8.9990
   chunk 54 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0270
   overall best weight:    1.9446

-------------------------------------------------------------------------------
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 = 0.053430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.036763 restraints weight = 73456.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.037823 restraints weight = 45738.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.038506 restraints weight = 33922.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.3934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   9718  Z= 0.159
  Angle     :  0.652  13.767  13927  Z= 0.313
  Chirality :  0.035   0.193   1672
  Planarity :  0.004   0.035   1153
  Dihedral  : 23.201 179.033   3356
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 21.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 18.83 %
    Favored  : 79.06 %
  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:  0.89 (0.34), residues: 692
  helix:  1.23 (0.26), residues: 390
  sheet: -1.94 (0.60), residues: 76
  loop :  0.66 (0.46), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  98 
 HIS   0.003   0.001   HIS B  74 
 PHE   0.020   0.002   PHE A 193 
 TYR   0.032   0.002   TYR A 323 
 ARG   0.003   0.000   ARG B 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05043 (  414)
  hydrogen bonds       : angle       4.58733 ( 1057)
  covalent geometry    : bond        0.00336 ( 9718)
  covalent geometry    : angle       0.65168 (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
  75 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9408 (mt-10) cc_final: 0.9116 (pt0)
REVERT: A   65 ASP cc_start: 0.9107 (p0) cc_final: 0.8552 (p0)
REVERT: A  157 TRP cc_start: 0.9412 (m100) cc_final: 0.8832 (m100)
REVERT: A  242 HIS cc_start: 0.8914 (t-170) cc_final: 0.8573 (t70)
REVERT: A  294 TYR cc_start: 0.9381 (m-80) cc_final: 0.9048 (m-80)
REVERT: B   95 VAL cc_start: 0.9621 (OUTLIER) cc_final: 0.9282 (p)
REVERT: B   96 LYS cc_start: 0.9578 (mttm) cc_final: 0.9163 (mmmm)
REVERT: B  110 MET cc_start: 0.8884 (ptp) cc_final: 0.8033 (pmm)
REVERT: B  162 ASP cc_start: 0.9746 (t0) cc_final: 0.9467 (t0)
REVERT: B  179 MET cc_start: 0.8004 (mtm) cc_final: 0.7700 (mtm)
  outliers start: 13
  outliers final: 11
  residues processed: 70
  average time/residue: 0.1754
  time to fit residues: 18.6199
Evaluate side-chains
  73 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   chunk 55 optimal weight:    0.0980
   chunk 69 optimal weight:   10.0000
   chunk 31 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 11 optimal weight:    0.1980
   chunk 57 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3524 r_free = 0.3524 target = 0.056526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.040238 restraints weight = 70167.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.041318 restraints weight = 43465.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.042039 restraints weight = 32585.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.4006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9718  Z= 0.117
  Angle     :  0.649  14.181  13927  Z= 0.304
  Chirality :  0.035   0.177   1672
  Planarity :  0.003   0.037   1153
  Dihedral  : 22.860 176.800   3356
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 19.16 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.34), residues: 692
  helix:  1.18 (0.27), residues: 390
  sheet: -1.85 (0.62), residues: 76
  loop :  0.69 (0.48), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B  98 
 HIS   0.002   0.001   HIS A  74 
 PHE   0.020   0.002   PHE B 193 
 TYR   0.030   0.002   TYR A 323 
 ARG   0.002   0.000   ARG B 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04933 (  414)
  hydrogen bonds       : angle       4.42700 ( 1057)
  covalent geometry    : bond        0.00251 ( 9718)
  covalent geometry    : angle       0.64859 (13927)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3448.58 seconds
wall clock time: 61 minutes 17.29 seconds (3677.29 seconds total)