Starting phenix.real_space_refine
on Wed Feb 12 04:48:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jy7_36722/02_2025/8jy7_36722.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jy7_36722/02_2025/8jy7_36722.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jy7_36722/02_2025/8jy7_36722.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jy7_36722/02_2025/8jy7_36722.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jy7_36722/02_2025/8jy7_36722.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jy7_36722/02_2025/8jy7_36722.cif"
  }
  resolution = 3.2
  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=   0.185
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    4912      2.51       5
     N    1116      2.21       5
     O    1232      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7292
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1823
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 13, 'TRANS': 228}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 3.37, per 1000 atoms: 0.46
  Number of scatterers: 7292
  At special positions: 0
  Unit cell: (92.568, 92.568, 63.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1232      8.00
     N    1116      7.00
     C    4912      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: 1.82
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1680

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 0 sheets defined
      74.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 71 through 98
    Processing helix  chain 'A' and resid 103 through 122
      removed outlier: 3.989A  pdb=" N   VAL A 120 " --> pdb=" O   MET A 116 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   SER A 121 " --> pdb=" O   ALA A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 135
      removed outlier: 3.624A  pdb=" N   THR A 134 " --> pdb=" O   ASN A 130 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL A 135 " --> pdb=" O   SER A 131 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 130 through 135'
    Processing helix  chain 'A' and resid 136 through 139
      removed outlier: 3.689A  pdb=" N   VAL A 139 " --> pdb=" O   GLY A 136 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 136 through 139'
    Processing helix  chain 'A' and resid 144 through 146
      No H-bonds generated for 'chain 'A' and resid 144 through 146'
    Processing helix  chain 'A' and resid 147 through 170
    Processing helix  chain 'A' and resid 175 through 179
      removed outlier: 3.912A  pdb=" N   GLY A 179 " --> pdb=" O   ALA A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 195
      removed outlier: 4.251A  pdb=" N   PHE A 194 " --> pdb=" O   ILE A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 226
    Processing helix  chain 'A' and resid 236 through 253
    Processing helix  chain 'A' and resid 261 through 276
      Proline residue:  A 268  - end of helix
    Processing helix  chain 'A' and resid 277 through 281
      removed outlier: 3.811A  pdb=" N   VAL A 280 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   PHE A 281 " --> pdb=" O   GLY A 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 277 through 281'
    Processing helix  chain 'A' and resid 288 through 310
      Proline residue:  A 295  - end of helix
    Processing helix  chain 'B' and resid 72 through 98
    Processing helix  chain 'B' and resid 103 through 122
      removed outlier: 3.989A  pdb=" N   VAL B 120 " --> pdb=" O   MET B 116 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   SER B 121 " --> pdb=" O   ALA B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 135
      removed outlier: 3.624A  pdb=" N   THR B 134 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL B 135 " --> pdb=" O   SER B 131 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 130 through 135'
    Processing helix  chain 'B' and resid 136 through 139
      removed outlier: 3.690A  pdb=" N   VAL B 139 " --> pdb=" O   GLY B 136 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 136 through 139'
    Processing helix  chain 'B' and resid 144 through 146
      No H-bonds generated for 'chain 'B' and resid 144 through 146'
    Processing helix  chain 'B' and resid 147 through 170
    Processing helix  chain 'B' and resid 175 through 179
      removed outlier: 3.913A  pdb=" N   GLY B 179 " --> pdb=" O   ALA B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 195
      removed outlier: 4.251A  pdb=" N   PHE B 194 " --> pdb=" O   ILE B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 226
    Processing helix  chain 'B' and resid 236 through 253
    Processing helix  chain 'B' and resid 261 through 276
      Proline residue:  B 268  - end of helix
    Processing helix  chain 'B' and resid 277 through 281
      removed outlier: 3.810A  pdb=" N   VAL B 280 " --> pdb=" O   GLY B 277 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   PHE B 281 " --> pdb=" O   GLY B 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 277 through 281'
    Processing helix  chain 'B' and resid 288 through 310
      Proline residue:  B 295  - end of helix
    Processing helix  chain 'C' and resid 72 through 98
    Processing helix  chain 'C' and resid 103 through 122
      removed outlier: 3.989A  pdb=" N   VAL C 120 " --> pdb=" O   MET C 116 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   SER C 121 " --> pdb=" O   ALA C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 135
      removed outlier: 3.624A  pdb=" N   THR C 134 " --> pdb=" O   ASN C 130 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL C 135 " --> pdb=" O   SER C 131 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 130 through 135'
    Processing helix  chain 'C' and resid 136 through 139
      removed outlier: 3.689A  pdb=" N   VAL C 139 " --> pdb=" O   GLY C 136 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 136 through 139'
    Processing helix  chain 'C' and resid 144 through 146
      No H-bonds generated for 'chain 'C' and resid 144 through 146'
    Processing helix  chain 'C' and resid 147 through 170
    Processing helix  chain 'C' and resid 175 through 179
      removed outlier: 3.913A  pdb=" N   GLY C 179 " --> pdb=" O   ALA C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 195
      removed outlier: 4.251A  pdb=" N   PHE C 194 " --> pdb=" O   ILE C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 226
    Processing helix  chain 'C' and resid 236 through 253
    Processing helix  chain 'C' and resid 261 through 276
      Proline residue:  C 268  - end of helix
    Processing helix  chain 'C' and resid 277 through 281
      removed outlier: 3.811A  pdb=" N   VAL C 280 " --> pdb=" O   GLY C 277 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   PHE C 281 " --> pdb=" O   GLY C 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 277 through 281'
    Processing helix  chain 'C' and resid 288 through 310
      Proline residue:  C 295  - end of helix
    Processing helix  chain 'D' and resid 72 through 98
    Processing helix  chain 'D' and resid 103 through 122
      removed outlier: 3.989A  pdb=" N   VAL D 120 " --> pdb=" O   MET D 116 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   SER D 121 " --> pdb=" O   ALA D 117 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 130 through 135
      removed outlier: 3.624A  pdb=" N   THR D 134 " --> pdb=" O   ASN D 130 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL D 135 " --> pdb=" O   SER D 131 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 130 through 135'
    Processing helix  chain 'D' and resid 136 through 139
      removed outlier: 3.689A  pdb=" N   VAL D 139 " --> pdb=" O   GLY D 136 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 136 through 139'
    Processing helix  chain 'D' and resid 144 through 146
      No H-bonds generated for 'chain 'D' and resid 144 through 146'
    Processing helix  chain 'D' and resid 147 through 170
    Processing helix  chain 'D' and resid 175 through 179
      removed outlier: 3.913A  pdb=" N   GLY D 179 " --> pdb=" O   ALA D 176 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 195
      removed outlier: 4.250A  pdb=" N   PHE D 194 " --> pdb=" O   ILE D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 226
    Processing helix  chain 'D' and resid 236 through 253
    Processing helix  chain 'D' and resid 261 through 276
      Proline residue:  D 268  - end of helix
    Processing helix  chain 'D' and resid 277 through 281
      removed outlier: 3.810A  pdb=" N   VAL D 280 " --> pdb=" O   GLY D 277 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   PHE D 281 " --> pdb=" O   GLY D 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 277 through 281'
    Processing helix  chain 'D' and resid 288 through 310
      Proline residue:  D 295  - end of helix

    469 hydrogen bonds defined for protein.
    1395 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.14

  Time building geometry restraints manager: 2.11 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2185
        1.34 -     1.46: 1524
        1.46 -     1.57: 3759
        1.57 -     1.69: 0
        1.69 -     1.81: 52
  Bond restraints: 7520
  Sorted by residual:
  bond pdb=" CA  ASN B 137 "
       pdb=" CB  ASN B 137 "
    ideal  model  delta    sigma   weight residual
    1.524  1.537 -0.013 1.31e-02 5.83e+03 9.63e-01
  bond pdb=" CA  ASN A 137 "
       pdb=" CB  ASN A 137 "
    ideal  model  delta    sigma   weight residual
    1.524  1.537 -0.013 1.31e-02 5.83e+03 9.63e-01
  bond pdb=" CA  ASN D 137 "
       pdb=" CB  ASN D 137 "
    ideal  model  delta    sigma   weight residual
    1.524  1.536 -0.012 1.31e-02 5.83e+03 8.65e-01
  bond pdb=" CA  ASN C 137 "
       pdb=" CB  ASN C 137 "
    ideal  model  delta    sigma   weight residual
    1.524  1.536 -0.012 1.31e-02 5.83e+03 8.31e-01
  bond pdb=" CB  PRO C 232 "
       pdb=" CG  PRO C 232 "
    ideal  model  delta    sigma   weight residual
    1.492  1.537 -0.045 5.00e-02 4.00e+02 7.97e-01
  ... (remaining 7515 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 9740
        1.14 -     2.28: 393
        2.28 -     3.41: 82
        3.41 -     4.55: 33
        4.55 -     5.69: 16
  Bond angle restraints: 10264
  Sorted by residual:
  angle pdb=" C   VAL D 290 "
        pdb=" CA  VAL D 290 "
        pdb=" CB  VAL D 290 "
      ideal   model   delta    sigma   weight residual
     114.00  111.46    2.54 1.31e+00 5.83e-01 3.74e+00
  angle pdb=" C   VAL C 290 "
        pdb=" CA  VAL C 290 "
        pdb=" CB  VAL C 290 "
      ideal   model   delta    sigma   weight residual
     114.00  111.48    2.52 1.31e+00 5.83e-01 3.71e+00
  angle pdb=" C   VAL A 290 "
        pdb=" CA  VAL A 290 "
        pdb=" CB  VAL A 290 "
      ideal   model   delta    sigma   weight residual
     114.00  111.50    2.50 1.31e+00 5.83e-01 3.65e+00
  angle pdb=" C   VAL B 290 "
        pdb=" CA  VAL B 290 "
        pdb=" CB  VAL B 290 "
      ideal   model   delta    sigma   weight residual
     114.00  111.53    2.47 1.31e+00 5.83e-01 3.57e+00
  angle pdb=" CA  TYR A 206 "
        pdb=" C   TYR A 206 "
        pdb=" N   PRO A 207 "
      ideal   model   delta    sigma   weight residual
     118.44  121.43   -2.99 1.59e+00 3.96e-01 3.54e+00
  ... (remaining 10259 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.63: 3569
       11.63 -    23.26: 379
       23.26 -    34.89: 184
       34.89 -    46.51: 24
       46.51 -    58.14: 12
  Dihedral angle restraints: 4168
    sinusoidal: 1472
      harmonic: 2696
  Sorted by residual:
  dihedral pdb=" CB  MET B 116 "
           pdb=" CG  MET B 116 "
           pdb=" SD  MET B 116 "
           pdb=" CE  MET B 116 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  118.14  -58.14     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" CB  MET A 116 "
           pdb=" CG  MET A 116 "
           pdb=" SD  MET A 116 "
           pdb=" CE  MET A 116 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  118.12  -58.12     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" CB  MET C 116 "
           pdb=" CG  MET C 116 "
           pdb=" SD  MET C 116 "
           pdb=" CE  MET C 116 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  118.12  -58.12     3      1.50e+01 4.44e-03 9.46e+00
  ... (remaining 4165 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 626
       0.028 -    0.056: 356
       0.056 -    0.084: 126
       0.084 -    0.112: 32
       0.112 -    0.140: 8
  Chirality restraints: 1148
  Sorted by residual:
  chirality pdb=" CA  TYR A 206 "
            pdb=" N   TYR A 206 "
            pdb=" C   TYR A 206 "
            pdb=" CB  TYR A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.93e-01
  chirality pdb=" CA  TYR D 206 "
            pdb=" N   TYR D 206 "
            pdb=" C   TYR D 206 "
            pdb=" CB  TYR D 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.75e-01
  chirality pdb=" CA  TYR C 206 "
            pdb=" N   TYR C 206 "
            pdb=" C   TYR C 206 "
            pdb=" CB  TYR C 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.72e-01
  ... (remaining 1145 not shown)

  Planarity restraints: 1292
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 148 "    0.021 5.00e-02 4.00e+02   3.16e-02 1.60e+00
        pdb=" N   PRO B 149 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO B 149 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 149 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 148 "   -0.021 5.00e-02 4.00e+02   3.16e-02 1.60e+00
        pdb=" N   PRO D 149 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO D 149 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO D 149 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 148 "    0.021 5.00e-02 4.00e+02   3.16e-02 1.60e+00
        pdb=" N   PRO C 149 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO C 149 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 149 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1289 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 2543
        2.85 -     3.36: 7318
        3.36 -     3.88: 12558
        3.88 -     4.39: 13826
        4.39 -     4.90: 24561
  Nonbonded interactions: 60806
  Sorted by model distance:
  nonbonded pdb=" O   SER B 121 "
            pdb=" OG  SER B 125 "
     model   vdw
     2.340 3.040
  nonbonded pdb=" O   SER A 121 "
            pdb=" OG  SER A 125 "
     model   vdw
     2.340 3.040
  nonbonded pdb=" O   SER C 121 "
            pdb=" OG  SER C 125 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" O   SER D 121 "
            pdb=" OG  SER D 125 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" O   ASN B 251 "
            pdb=" OG1 THR C  94 "
     model   vdw
     2.366 3.040
  ... (remaining 60801 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.560
  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:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     18.580
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7520  Z= 0.174
  Angle     :  0.596   5.688  10264  Z= 0.309
  Chirality :  0.039   0.140   1148
  Planarity :  0.005   0.032   1292
  Dihedral  : 12.176  58.142   2488
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  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:  1.38 (0.27), residues: 960
  helix:  1.98 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -0.96 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 289 
 HIS   0.003   0.001   HIS B 283 
 PHE   0.014   0.001   PHE D 185 
 TYR   0.019   0.001   TYR B 206 
 ARG   0.003   0.001   ARG A 146 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 TYR cc_start: 0.6788 (t80) cc_final: 0.6427 (t80)
REVERT: B  236 TYR cc_start: 0.8098 (p90) cc_final: 0.7878 (p90)
REVERT: B  286 TYR cc_start: 0.7484 (m-80) cc_final: 0.7279 (m-10)
REVERT: B  304 PHE cc_start: 0.8251 (t80) cc_final: 0.8006 (t80)
REVERT: C  205 PHE cc_start: 0.7090 (t80) cc_final: 0.6854 (t80)
REVERT: C  236 TYR cc_start: 0.8172 (p90) cc_final: 0.7919 (p90)
REVERT: C  308 TYR cc_start: 0.6762 (t80) cc_final: 0.6413 (t80)
REVERT: D  100 ASP cc_start: 0.7110 (m-30) cc_final: 0.6887 (m-30)
REVERT: D  205 PHE cc_start: 0.7131 (t80) cc_final: 0.6885 (t80)
REVERT: D  308 TYR cc_start: 0.6787 (t80) cc_final: 0.6483 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.1431
  time to fit residues: 41.6276
Evaluate side-chains
  158 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 75 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 155 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 = 0.3566 r_free = 0.3566 target = 0.150477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.125781 restraints weight = 8863.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 1.66
r_work: 0.3103 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7520  Z= 0.231
  Angle     :  0.580   6.541  10264  Z= 0.293
  Chirality :  0.040   0.115   1148
  Planarity :  0.005   0.048   1292
  Dihedral  :  3.988  15.688   1028
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  :  9.89 %
    Favored  : 87.50 %
  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:  1.29 (0.27), residues: 960
  helix:  1.67 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -0.76 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 192 
 HIS   0.003   0.001   HIS C 128 
 PHE   0.016   0.002   PHE A 304 
 TYR   0.023   0.002   TYR A 206 
 ARG   0.004   0.001   ARG A 269 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 171
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 TYR cc_start: 0.7374 (m-10) cc_final: 0.6755 (m-80)
REVERT: B  236 TYR cc_start: 0.8419 (p90) cc_final: 0.8083 (p90)
REVERT: C  236 TYR cc_start: 0.8389 (p90) cc_final: 0.8065 (p90)
  outliers start: 19
  outliers final: 14
  residues processed: 173
  average time/residue: 0.1474
  time to fit residues: 36.9470
Evaluate side-chains
  173 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 159
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  165 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain B residue  172 ASP
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  165 CYS
Chi-restraints excluded: chain C residue  172 ASP
Chi-restraints excluded: chain D residue  135 VAL
Chi-restraints excluded: chain D residue  165 CYS
Chi-restraints excluded: chain D residue  172 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0470
   chunk 81 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0980
   chunk 52 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 87 optimal weight:    0.5980
   overall best weight:    0.3878

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

Flipped N/Q/H residues before XYZ refinement:
** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 155 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 = 0.3567 r_free = 0.3567 target = 0.149657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.125507 restraints weight = 9038.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.67
r_work: 0.3122 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7520  Z= 0.166
  Angle     :  0.516   5.724  10264  Z= 0.263
  Chirality :  0.037   0.112   1148
  Planarity :  0.005   0.047   1292
  Dihedral  :  3.908  14.890   1028
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 13.87 %
    Favored  : 84.07 %
  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 (0.27), residues: 960
  helix:  1.53 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.99 (0.33), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 289 
 HIS   0.002   0.001   HIS A 283 
 PHE   0.022   0.001   PHE B 304 
 TYR   0.016   0.001   TYR C 206 
 ARG   0.002   0.000   ARG A 269 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 157
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 TYR cc_start: 0.7395 (m-10) cc_final: 0.6907 (m-80)
REVERT: B  236 TYR cc_start: 0.8429 (p90) cc_final: 0.8027 (p90)
REVERT: C  236 TYR cc_start: 0.8420 (p90) cc_final: 0.8043 (p90)
REVERT: D  106 LEU cc_start: 0.8649 (tt) cc_final: 0.8356 (tp)
  outliers start: 15
  outliers final: 11
  residues processed: 159
  average time/residue: 0.1472
  time to fit residues: 34.0997
Evaluate side-chains
  167 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 156
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  165 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  165 CYS
Chi-restraints excluded: chain D residue  135 VAL
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  165 CYS
Chi-restraints excluded: chain D residue  196 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 93 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 155 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 = 0.3489 r_free = 0.3489 target = 0.143697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.118080 restraints weight = 9101.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 1.70
r_work: 0.3011 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2889 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7520  Z= 0.239
  Angle     :  0.575   6.104  10264  Z= 0.298
  Chirality :  0.039   0.113   1148
  Planarity :  0.005   0.049   1292
  Dihedral  :  4.240  16.339   1028
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.52 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.65 (0.27), residues: 960
  helix:  1.20 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -1.38 (0.33), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D 289 
 HIS   0.003   0.001   HIS A 128 
 PHE   0.013   0.002   PHE D 246 
 TYR   0.018   0.002   TYR A 151 
 ARG   0.003   0.001   ARG A 269 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 164
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 TYR cc_start: 0.7517 (m-10) cc_final: 0.7009 (m-80)
REVERT: B  236 TYR cc_start: 0.8484 (p90) cc_final: 0.8154 (p90)
REVERT: C  236 TYR cc_start: 0.8455 (p90) cc_final: 0.8120 (p90)
REVERT: D  106 LEU cc_start: 0.8676 (tt) cc_final: 0.8284 (tp)
  outliers start: 21
  outliers final: 16
  residues processed: 168
  average time/residue: 0.1408
  time to fit residues: 34.6079
Evaluate side-chains
  175 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  165 CYS
Chi-restraints excluded: chain A residue  196 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain B residue  196 MET
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  165 CYS
Chi-restraints excluded: chain C residue  196 MET
Chi-restraints excluded: chain D residue  135 VAL
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  165 CYS
Chi-restraints excluded: chain D residue  196 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0020
   chunk 74 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 177 HIS
** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.146213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.120911 restraints weight = 9006.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 1.70
r_work: 0.3050 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7520  Z= 0.187
  Angle     :  0.531   6.065  10264  Z= 0.273
  Chirality :  0.037   0.124   1148
  Planarity :  0.005   0.049   1292
  Dihedral  :  4.122  16.589   1028
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 17.72 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.86 (0.27), residues: 960
  helix:  1.37 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -1.34 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C 289 
 HIS   0.006   0.001   HIS A 177 
 PHE   0.010   0.001   PHE C 160 
 TYR   0.017   0.001   TYR D 206 
 ARG   0.002   0.000   ARG A 269 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 167
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 TYR cc_start: 0.7451 (m-10) cc_final: 0.6886 (m-80)
REVERT: B  236 TYR cc_start: 0.8477 (p90) cc_final: 0.8117 (p90)
REVERT: C  236 TYR cc_start: 0.8447 (p90) cc_final: 0.8099 (p90)
REVERT: D  106 LEU cc_start: 0.8700 (tt) cc_final: 0.8322 (tp)
  outliers start: 12
  outliers final: 9
  residues processed: 170
  average time/residue: 0.1406
  time to fit residues: 34.8779
Evaluate side-chains
  174 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 165
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  165 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  165 CYS
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  165 CYS
Chi-restraints excluded: chain D residue  196 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 74 optimal weight:    0.0980
   chunk 14 optimal weight:    0.9980
   chunk 60 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 155 GLN
A 177 HIS
** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 177 HIS
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 177 HIS
** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.145156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.120257 restraints weight = 9014.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 1.67
r_work: 0.3038 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7520  Z= 0.209
  Angle     :  0.549   6.340  10264  Z= 0.282
  Chirality :  0.038   0.126   1148
  Planarity :  0.005   0.049   1292
  Dihedral  :  4.207  17.355   1028
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.80 %
    Favored  : 80.91 %
  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:  0.88 (0.27), residues: 960
  helix:  1.37 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -1.28 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 289 
 HIS   0.011   0.002   HIS A 177 
 PHE   0.016   0.001   PHE A 304 
 TYR   0.016   0.001   TYR D 206 
 ARG   0.002   0.000   ARG A 269 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 169
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  237 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6504 (mp0)
REVERT: A  286 TYR cc_start: 0.7469 (m-10) cc_final: 0.6953 (m-80)
REVERT: B  236 TYR cc_start: 0.8483 (p90) cc_final: 0.8138 (p90)
REVERT: C  236 TYR cc_start: 0.8476 (p90) cc_final: 0.8143 (p90)
REVERT: C  237 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6572 (mp0)
REVERT: C  304 PHE cc_start: 0.8281 (t80) cc_final: 0.8037 (t80)
REVERT: C  308 TYR cc_start: 0.7060 (t80) cc_final: 0.6788 (t80)
REVERT: D  106 LEU cc_start: 0.8707 (tt) cc_final: 0.8324 (tp)
REVERT: D  237 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6415 (mp0)
REVERT: D  304 PHE cc_start: 0.8268 (t80) cc_final: 0.8014 (t80)
  outliers start: 24
  outliers final: 16
  residues processed: 176
  average time/residue: 0.1411
  time to fit residues: 36.2238
Evaluate side-chains
  188 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 169
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  165 CYS
Chi-restraints excluded: chain A residue  196 MET
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain B residue  196 MET
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  165 CYS
Chi-restraints excluded: chain C residue  196 MET
Chi-restraints excluded: chain C residue  237 GLU
Chi-restraints excluded: chain D residue  135 VAL
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  165 CYS
Chi-restraints excluded: chain D residue  196 MET
Chi-restraints excluded: chain D residue  237 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0870
   chunk 23 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0770
   chunk 50 optimal weight:    0.2980
   chunk 89 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.3916

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 GLN
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 155 GLN
** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 155 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.147204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.122156 restraints weight = 9025.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.68
r_work: 0.3075 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7520  Z= 0.167
  Angle     :  0.523   6.209  10264  Z= 0.269
  Chirality :  0.037   0.119   1148
  Planarity :  0.005   0.049   1292
  Dihedral  :  4.139  17.925   1028
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 16.76 %
    Favored  : 81.46 %
  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 (0.28), residues: 960
  helix:  1.55 (0.21), residues: 672
  sheet:  None (None), residues: 0
  loop : -1.17 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B 289 
 HIS   0.001   0.000   HIS A 283 
 PHE   0.027   0.001   PHE B 304 
 TYR   0.014   0.001   TYR D 206 
 ARG   0.001   0.000   ARG A 269 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 161
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 TYR cc_start: 0.7047 (m-80) cc_final: 0.6648 (m-80)
REVERT: A  237 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6495 (mp0)
REVERT: A  286 TYR cc_start: 0.7377 (m-10) cc_final: 0.6690 (m-80)
REVERT: B  236 TYR cc_start: 0.8485 (p90) cc_final: 0.8144 (p90)
REVERT: C  206 TYR cc_start: 0.7069 (m-80) cc_final: 0.6704 (m-80)
REVERT: C  236 TYR cc_start: 0.8428 (p90) cc_final: 0.8108 (p90)
REVERT: C  237 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6537 (mp0)
REVERT: D  106 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8310 (tp)
REVERT: D  206 TYR cc_start: 0.7084 (m-80) cc_final: 0.6675 (m-80)
REVERT: D  237 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6388 (mp0)
  outliers start: 13
  outliers final: 9
  residues processed: 161
  average time/residue: 0.1526
  time to fit residues: 35.4502
Evaluate side-chains
  173 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 160
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 CYS
Chi-restraints excluded: chain A residue  196 MET
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain B residue  196 MET
Chi-restraints excluded: chain C residue  165 CYS
Chi-restraints excluded: chain C residue  196 MET
Chi-restraints excluded: chain C residue  237 GLU
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  135 VAL
Chi-restraints excluded: chain D residue  165 CYS
Chi-restraints excluded: chain D residue  196 MET
Chi-restraints excluded: chain D residue  237 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   chunk 80 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0030
   chunk 76 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.145811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.120927 restraints weight = 9087.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 1.66
r_work: 0.3050 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.3137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7520  Z= 0.195
  Angle     :  0.538   6.180  10264  Z= 0.279
  Chirality :  0.037   0.116   1148
  Planarity :  0.005   0.049   1292
  Dihedral  :  4.227  18.822   1028
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.07 %
    Favored  : 81.46 %
  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 (0.28), residues: 960
  helix:  1.53 (0.21), residues: 672
  sheet:  None (None), residues: 0
  loop : -1.14 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 289 
 HIS   0.002   0.001   HIS A 283 
 PHE   0.009   0.001   PHE A 246 
 TYR   0.014   0.001   TYR D 206 
 ARG   0.002   0.000   ARG A 269 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 174
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 TYR cc_start: 0.7038 (m-80) cc_final: 0.6677 (m-80)
REVERT: A  237 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6501 (mp0)
REVERT: A  286 TYR cc_start: 0.7402 (m-10) cc_final: 0.6791 (m-80)
REVERT: B  236 TYR cc_start: 0.8503 (p90) cc_final: 0.8161 (p90)
REVERT: C  206 TYR cc_start: 0.7078 (m-80) cc_final: 0.6680 (m-80)
REVERT: C  236 TYR cc_start: 0.8442 (p90) cc_final: 0.8125 (p90)
REVERT: C  237 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6561 (mp0)
REVERT: C  304 PHE cc_start: 0.8332 (t80) cc_final: 0.8038 (t80)
REVERT: D  106 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8309 (tp)
REVERT: D  206 TYR cc_start: 0.7078 (m-80) cc_final: 0.6683 (m-80)
REVERT: D  237 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6414 (mp0)
REVERT: D  304 PHE cc_start: 0.8282 (t80) cc_final: 0.8015 (t80)
REVERT: D  308 TYR cc_start: 0.7113 (t80) cc_final: 0.6872 (t80)
  outliers start: 18
  outliers final: 13
  residues processed: 178
  average time/residue: 0.1578
  time to fit residues: 40.9492
Evaluate side-chains
  191 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 174
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  165 CYS
Chi-restraints excluded: chain A residue  196 MET
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain B residue  196 MET
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  165 CYS
Chi-restraints excluded: chain C residue  196 MET
Chi-restraints excluded: chain C residue  237 GLU
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  135 VAL
Chi-restraints excluded: chain D residue  165 CYS
Chi-restraints excluded: chain D residue  196 MET
Chi-restraints excluded: chain D residue  237 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 75 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9980
   chunk 20 optimal weight:    0.1980
   chunk 80 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.143895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.119079 restraints weight = 9242.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 1.69
r_work: 0.3042 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.3206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7520  Z= 0.208
  Angle     :  0.547   6.183  10264  Z= 0.284
  Chirality :  0.038   0.116   1148
  Planarity :  0.005   0.050   1292
  Dihedral  :  4.300  19.711   1028
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 16.35 %
    Favored  : 81.32 %
  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 (0.28), residues: 960
  helix:  1.52 (0.21), residues: 672
  sheet:  None (None), residues: 0
  loop : -1.14 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 289 
 HIS   0.002   0.001   HIS A 283 
 PHE   0.014   0.001   PHE C 205 
 TYR   0.013   0.001   TYR C 206 
 ARG   0.002   0.000   ARG A 269 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 174
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 TYR cc_start: 0.7073 (m-80) cc_final: 0.6715 (m-80)
REVERT: A  237 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6446 (mp0)
REVERT: A  286 TYR cc_start: 0.7352 (m-10) cc_final: 0.6655 (m-80)
REVERT: B  236 TYR cc_start: 0.8519 (p90) cc_final: 0.8173 (p90)
REVERT: C  206 TYR cc_start: 0.7151 (m-80) cc_final: 0.6752 (m-80)
REVERT: C  236 TYR cc_start: 0.8483 (p90) cc_final: 0.8156 (p90)
REVERT: C  237 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6488 (mp0)
REVERT: C  307 LYS cc_start: 0.6394 (mmtt) cc_final: 0.6061 (mttp)
REVERT: D  106 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8314 (tp)
REVERT: D  237 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6442 (mp0)
REVERT: D  304 PHE cc_start: 0.8314 (t80) cc_final: 0.8035 (t80)
REVERT: D  308 TYR cc_start: 0.7064 (t80) cc_final: 0.6808 (t80)
  outliers start: 17
  outliers final: 13
  residues processed: 177
  average time/residue: 0.1491
  time to fit residues: 38.1635
Evaluate side-chains
  192 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 175
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  165 CYS
Chi-restraints excluded: chain A residue  196 MET
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain B residue  196 MET
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  165 CYS
Chi-restraints excluded: chain C residue  196 MET
Chi-restraints excluded: chain C residue  237 GLU
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  135 VAL
Chi-restraints excluded: chain D residue  165 CYS
Chi-restraints excluded: chain D residue  196 MET
Chi-restraints excluded: chain D residue  237 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 88 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0970
   chunk 37 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.142575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.118452 restraints weight = 9196.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 1.58
r_work: 0.3044 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7520  Z= 0.195
  Angle     :  0.538   5.734  10264  Z= 0.281
  Chirality :  0.038   0.117   1148
  Planarity :  0.005   0.051   1292
  Dihedral  :  4.238  16.726   1028
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 17.31 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.17 (0.28), residues: 960
  helix:  1.57 (0.21), residues: 672
  sheet:  None (None), residues: 0
  loop : -1.11 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 289 
 HIS   0.002   0.001   HIS A 283 
 PHE   0.017   0.001   PHE D 205 
 TYR   0.015   0.001   TYR D 206 
 ARG   0.002   0.000   ARG A 269 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 169
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  237 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6395 (mp0)
REVERT: A  286 TYR cc_start: 0.7326 (m-10) cc_final: 0.6725 (m-80)
REVERT: B  236 TYR cc_start: 0.8488 (p90) cc_final: 0.8142 (p90)
REVERT: B  237 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6467 (mp0)
REVERT: C  206 TYR cc_start: 0.7035 (m-80) cc_final: 0.6676 (m-80)
REVERT: C  236 TYR cc_start: 0.8447 (p90) cc_final: 0.8127 (p90)
REVERT: C  237 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6488 (mp0)
REVERT: C  304 PHE cc_start: 0.8360 (t80) cc_final: 0.8052 (t80)
REVERT: C  307 LYS cc_start: 0.6397 (mmtt) cc_final: 0.6059 (mttp)
REVERT: D  106 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8320 (tp)
REVERT: D  237 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6386 (mp0)
REVERT: D  304 PHE cc_start: 0.8333 (t80) cc_final: 0.8051 (t80)
  outliers start: 15
  outliers final: 10
  residues processed: 170
  average time/residue: 0.1475
  time to fit residues: 36.1285
Evaluate side-chains
  184 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 169
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 CYS
Chi-restraints excluded: chain A residue  196 MET
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain B residue  196 MET
Chi-restraints excluded: chain B residue  237 GLU
Chi-restraints excluded: chain C residue  165 CYS
Chi-restraints excluded: chain C residue  196 MET
Chi-restraints excluded: chain C residue  237 GLU
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  135 VAL
Chi-restraints excluded: chain D residue  165 CYS
Chi-restraints excluded: chain D residue  196 MET
Chi-restraints excluded: chain D residue  237 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 0 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0000
   chunk 54 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.141758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.117743 restraints weight = 8984.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.56
r_work: 0.3034 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.3335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7520  Z= 0.217
  Angle     :  0.551   5.816  10264  Z= 0.288
  Chirality :  0.038   0.117   1148
  Planarity :  0.005   0.051   1292
  Dihedral  :  4.307  18.454   1028
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.90 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.10 (0.28), residues: 960
  helix:  1.50 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -1.10 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 289 
 HIS   0.002   0.001   HIS A 283 
 PHE   0.010   0.001   PHE A 246 
 TYR   0.014   0.001   TYR D 206 
 ARG   0.002   0.000   ARG A 269 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3463.21 seconds
wall clock time: 62 minutes 13.58 seconds (3733.58 seconds total)