Starting phenix.real_space_refine
on Fri May  9 16:54:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hh1_52168/05_2025/9hh1_52168.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hh1_52168/05_2025/9hh1_52168.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hh1_52168/05_2025/9hh1_52168.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hh1_52168/05_2025/9hh1_52168.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hh1_52168/05_2025/9hh1_52168.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hh1_52168/05_2025/9hh1_52168.cif"
  }
  resolution = 3.9
  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=  -0.001 sd=   0.112
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      16      5.16       5
     C    2092      2.51       5
     N     584      2.21       5
     O     608      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 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: 3300
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1650
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 194}
    Chain: "B"
      Number of atoms: 1650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1650
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 194}
  Time building chain proxies: 2.43, per 1000 atoms: 0.74
  Number of scatterers: 3300
  At special positions: 0
  Unit cell: (68.06, 74.62, 55.76, 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      16     16.00
     O     608      8.00
     N     584      7.00
     C    2092      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 429.9 milliseconds
  

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  780

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 2 sheets defined
      38.3% alpha, 20.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 102 through 109
    Processing helix  chain 'A' and resid 109 through 121
      removed outlier: 3.511A  pdb=" N   LEU A 120 " --> pdb=" O   GLU A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 179
      removed outlier: 3.922A  pdb=" N   ARG A 177 " --> pdb=" O   SER A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 190
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 3.546A  pdb=" N   ASN A 211 " --> pdb=" O   ASN A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 238
    Processing helix  chain 'A' and resid 247 through 251
    Processing helix  chain 'A' and resid 277 through 279
      No H-bonds generated for 'chain 'A' and resid 277 through 279'
    Processing helix  chain 'A' and resid 281 through 297
    Processing helix  chain 'B' and resid 102 through 109
    Processing helix  chain 'B' and resid 109 through 121
      removed outlier: 3.529A  pdb=" N   LEU B 120 " --> pdb=" O   GLU B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 179
      removed outlier: 3.956A  pdb=" N   ARG B 177 " --> pdb=" O   SER B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 190
    Processing helix  chain 'B' and resid 207 through 212
      removed outlier: 3.553A  pdb=" N   ASN B 211 " --> pdb=" O   ASN B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 238
    Processing helix  chain 'B' and resid 247 through 251
    Processing helix  chain 'B' and resid 277 through 279
      No H-bonds generated for 'chain 'B' and resid 277 through 279'
    Processing helix  chain 'B' and resid 281 through 297
    Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 164
      removed outlier: 5.301A  pdb=" N   GLN A 158 " --> pdb=" O   TYR A 274 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   TYR A 274 " --> pdb=" O   GLN A 158 " (cutoff:3.500A)
      removed outlier: 5.320A  pdb=" N   LYS A 160 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   PHE A 272 " --> pdb=" O   LYS A 160 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   PHE A 162 " --> pdb=" O   THR A 270 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ILE B 192 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
      removed outlier: 8.206A  pdb=" N   ILE B 226 " --> pdb=" O   ILE B 192 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   SER B 194 " --> pdb=" O   ILE B 226 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   CYS B 244 " --> pdb=" O   ILE B 193 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   VAL B 168 " --> pdb=" O   LEU B 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 259
      removed outlier: 4.715A  pdb=" N   VAL A 168 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   CYS A 244 " --> pdb=" O   ILE A 193 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ILE A 192 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   ILE A 226 " --> pdb=" O   ILE A 192 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   SER A 194 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   GLN A 225 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   LEU B 130 " --> pdb=" O   GLN A 225 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   PHE B 162 " --> pdb=" O   THR B 270 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   PHE B 272 " --> pdb=" O   LYS B 160 " (cutoff:3.500A)
      removed outlier: 5.311A  pdb=" N   LYS B 160 " --> pdb=" O   PHE B 272 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   TYR B 274 " --> pdb=" O   GLN B 158 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   GLN B 158 " --> pdb=" O   TYR B 274 " (cutoff:3.500A)

    132 hydrogen bonds defined for protein.
    354 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.86

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 890
        1.33 -     1.46: 626
        1.46 -     1.58: 1834
        1.58 -     1.71: 0
        1.71 -     1.83: 24
  Bond restraints: 3374
  Sorted by residual:
  bond pdb=" CZ  ARG A 147 "
       pdb=" NH2 ARG A 147 "
    ideal  model  delta    sigma   weight residual
    1.330  1.285  0.045 1.30e-02 5.92e+03 1.18e+01
  bond pdb=" CZ  ARG A 234 "
       pdb=" NH2 ARG A 234 "
    ideal  model  delta    sigma   weight residual
    1.330  1.288  0.042 1.30e-02 5.92e+03 1.03e+01
  bond pdb=" CZ  ARG B 191 "
       pdb=" NH2 ARG B 191 "
    ideal  model  delta    sigma   weight residual
    1.330  1.289  0.041 1.30e-02 5.92e+03 1.02e+01
  bond pdb=" CZ  ARG B  98 "
       pdb=" NH2 ARG B  98 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.37e+00
  bond pdb=" ND1 HIS A 167 "
       pdb=" CE1 HIS A 167 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.14e+00
  ... (remaining 3369 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 2577
        1.02 -     2.05: 1245
        2.05 -     3.07: 568
        3.07 -     4.10: 177
        4.10 -     5.12: 13
  Bond angle restraints: 4580
  Sorted by residual:
  angle pdb=" OE1 GLN B 107 "
        pdb=" CD  GLN B 107 "
        pdb=" NE2 GLN B 107 "
      ideal   model   delta    sigma   weight residual
     122.60  118.76    3.84 1.00e+00 1.00e+00 1.48e+01
  angle pdb=" OE1 GLN A 225 "
        pdb=" CD  GLN A 225 "
        pdb=" NE2 GLN A 225 "
      ideal   model   delta    sigma   weight residual
     122.60  118.84    3.76 1.00e+00 1.00e+00 1.42e+01
  angle pdb=" OE1 GLN B 119 "
        pdb=" CD  GLN B 119 "
        pdb=" NE2 GLN B 119 "
      ideal   model   delta    sigma   weight residual
     122.60  118.85    3.75 1.00e+00 1.00e+00 1.40e+01
  angle pdb=" OE1 GLN B 115 "
        pdb=" CD  GLN B 115 "
        pdb=" NE2 GLN B 115 "
      ideal   model   delta    sigma   weight residual
     122.60  118.92    3.68 1.00e+00 1.00e+00 1.35e+01
  angle pdb=" OE1 GLN A 127 "
        pdb=" CD  GLN A 127 "
        pdb=" NE2 GLN A 127 "
      ideal   model   delta    sigma   weight residual
     122.60  119.04    3.56 1.00e+00 1.00e+00 1.27e+01
  ... (remaining 4575 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.91: 1895
       13.91 -    27.81: 109
       27.81 -    41.71: 20
       41.71 -    55.62: 14
       55.62 -    69.52: 2
  Dihedral angle restraints: 2040
    sinusoidal: 836
      harmonic: 1204
  Sorted by residual:
  dihedral pdb=" CA  ALA A 145 "
           pdb=" C   ALA A 145 "
           pdb=" N   ILE A 146 "
           pdb=" CA  ILE A 146 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.84   20.16     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  ALA B 145 "
           pdb=" C   ALA B 145 "
           pdb=" N   ILE B 146 "
           pdb=" CA  ILE B 146 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.88   20.12     0      5.00e+00 4.00e-02 1.62e+01
  dihedral pdb=" CA  ILE B 126 "
           pdb=" C   ILE B 126 "
           pdb=" N   GLN B 127 "
           pdb=" CA  GLN B 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.67   19.33     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 2037 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 278
       0.062 -    0.124: 161
       0.124 -    0.186: 62
       0.186 -    0.248: 1
       0.248 -    0.310: 2
  Chirality restraints: 504
  Sorted by residual:
  chirality pdb=" CA  ASP B 205 "
            pdb=" N   ASP B 205 "
            pdb=" C   ASP B 205 "
            pdb=" CB  ASP B 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" CA  ASP A 205 "
            pdb=" N   ASP A 205 "
            pdb=" C   ASP A 205 "
            pdb=" CB  ASP A 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.22e+00
  chirality pdb=" CA  ARG A 140 "
            pdb=" N   ARG A 140 "
            pdb=" C   ARG A 140 "
            pdb=" CB  ARG A 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.33e-01
  ... (remaining 501 not shown)

  Planarity restraints: 602
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 202 "    0.066 2.00e-02 2.50e+03   3.63e-02 2.63e+01
        pdb=" CG  TYR A 202 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 202 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 202 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 202 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 202 "   -0.022 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 202 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 202 "    0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 174 "   -0.060 2.00e-02 2.50e+03   3.22e-02 2.07e+01
        pdb=" CG  TYR B 174 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 174 "    0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 174 "    0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 174 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 174 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 174 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 174 "   -0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 174 "   -0.060 2.00e-02 2.50e+03   3.17e-02 2.01e+01
        pdb=" CG  TYR A 174 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 174 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 174 "    0.025 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 174 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 174 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 174 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 174 "   -0.046 2.00e-02 2.50e+03
  ... (remaining 599 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 18
        2.49 -     3.09: 2077
        3.09 -     3.70: 4949
        3.70 -     4.30: 7687
        4.30 -     4.90: 12363
  Nonbonded interactions: 27094
  Sorted by model distance:
  nonbonded pdb=" CE2 TRP A 298 "
            pdb=" CE2 PHE A 300 "
     model   vdw
     1.889 3.560
  nonbonded pdb=" NE1 TRP A 298 "
            pdb=" CE2 PHE A 300 "
     model   vdw
     1.925 3.420
  nonbonded pdb=" CZ2 TRP A 298 "
            pdb=" CE2 PHE A 300 "
     model   vdw
     2.219 3.640
  nonbonded pdb=" OE1 GLN A 225 "
            pdb=" NZ  LYS B  96 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" NZ  LYS A  96 "
            pdb=" OE1 GLN B 225 "
     model   vdw
     2.297 3.120
  ... (remaining 27089 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: 0.02
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:             0.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.400
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  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:   15.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4610
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      :  0.015   0.456   3375  Z= 1.077
  Angle     :  1.448   5.120   4580  Z= 0.958
  Chirality :  0.080   0.310    504
  Planarity :  0.010   0.068    602
  Dihedral  : 10.772  69.520   1260
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  2.22 %
    Favored  : 97.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.27 (0.35), residues: 408
  helix: -1.72 (0.32), residues: 138
  sheet:  0.34 (0.64), residues: 56
  loop : -0.43 (0.37), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.006   TRP B 109 
 HIS   0.004   0.002   HIS B 141 
 PHE   0.027   0.006   PHE B 195 
 TYR   0.066   0.013   TYR A 202 
 ARG   0.006   0.001   ARG A 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16259 (  132)
  hydrogen bonds       : angle       6.61137 (  354)
  covalent geometry    : bond        0.01276 ( 3374)
  covalent geometry    : angle       1.44785 ( 4580)
  Misc. bond           : bond        0.45643 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 169
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 LEU cc_start: 0.6950 (tp) cc_final: 0.6704 (tp)
REVERT: A  128 LEU cc_start: 0.6873 (mt) cc_final: 0.6335 (mp)
REVERT: A  136 ASP cc_start: 0.4341 (t0) cc_final: 0.3770 (m-30)
REVERT: A  280 ASN cc_start: 0.6861 (m-40) cc_final: 0.6391 (m110)
REVERT: B  136 ASP cc_start: 0.4450 (t0) cc_final: 0.4037 (m-30)
REVERT: B  280 ASN cc_start: 0.6870 (m-40) cc_final: 0.6530 (m110)
  outliers start: 2
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1928
  time to fit residues: 37.7323
Evaluate side-chains
  111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0970
   chunk 16 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
B 141 HIS
B 158 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4911 r_free = 0.4911 target = 0.210389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.172628 restraints weight = 5923.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.180169 restraints weight = 3812.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4696 r_free = 0.4696 target = 0.185835 restraints weight = 2690.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.4648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6004
moved from start:          0.4637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3375  Z= 0.143
  Angle     :  0.661   5.692   4580  Z= 0.341
  Chirality :  0.047   0.154    504
  Planarity :  0.004   0.035    602
  Dihedral  :  5.121  19.602    450
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.28 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  1.01 (0.39), residues: 408
  helix:  0.65 (0.46), residues: 112
  sheet:  1.40 (0.49), residues: 84
  loop :  0.52 (0.41), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 109 
 HIS   0.003   0.001   HIS A 190 
 PHE   0.014   0.002   PHE B 300 
 TYR   0.017   0.003   TYR A 169 
 ARG   0.005   0.001   ARG B  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04827 (  132)
  hydrogen bonds       : angle       4.80905 (  354)
  covalent geometry    : bond        0.00318 ( 3374)
  covalent geometry    : angle       0.66121 ( 4580)
  Misc. bond           : bond        0.00037 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LYS cc_start: 0.6385 (OUTLIER) cc_final: 0.6113 (tptp)
REVERT: A  188 ASP cc_start: 0.8947 (m-30) cc_final: 0.8364 (p0)
REVERT: A  280 ASN cc_start: 0.8154 (m-40) cc_final: 0.7908 (m-40)
REVERT: B   96 LYS cc_start: 0.8629 (ptmt) cc_final: 0.8389 (ttpt)
REVERT: B  188 ASP cc_start: 0.8998 (m-30) cc_final: 0.8445 (p0)
REVERT: B  280 ASN cc_start: 0.7925 (m-40) cc_final: 0.7568 (m-40)
REVERT: B  297 ASN cc_start: 0.8729 (t0) cc_final: 0.8207 (m110)
  outliers start: 10
  outliers final: 3
  residues processed: 132
  average time/residue: 0.1849
  time to fit residues: 28.3704
Evaluate side-chains
  105 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain B residue  173 SER
Chi-restraints excluded: chain B residue  204 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   chunk 29 optimal weight:    0.3980
   chunk 39 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 32 optimal weight:    7.9990
   chunk 10 optimal weight:    0.5980
   chunk 11 optimal weight:    6.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
A 225 GLN
** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 GLN
B 225 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4844 r_free = 0.4844 target = 0.191271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.152566 restraints weight = 5526.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.160107 restraints weight = 3236.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.165872 restraints weight = 2207.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.4604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6253
moved from start:          0.6063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3375  Z= 0.141
  Angle     :  0.689   7.798   4580  Z= 0.345
  Chirality :  0.047   0.164    504
  Planarity :  0.004   0.029    602
  Dihedral  :  5.261  18.895    450
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 16.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 19.44 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.76 (0.39), residues: 408
  helix:  0.21 (0.46), residues: 112
  sheet:  1.11 (0.57), residues: 72
  loop :  0.63 (0.40), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 109 
 HIS   0.003   0.001   HIS A 141 
 PHE   0.021   0.003   PHE B 117 
 TYR   0.012   0.002   TYR B 248 
 ARG   0.003   0.000   ARG B 296 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04387 (  132)
  hydrogen bonds       : angle       4.94690 (  354)
  covalent geometry    : bond        0.00326 ( 3374)
  covalent geometry    : angle       0.68937 ( 4580)
  Misc. bond           : bond        0.00053 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 ARG cc_start: 0.7761 (mtp180) cc_final: 0.7299 (mtp180)
REVERT: B   98 ARG cc_start: 0.8056 (mtp180) cc_final: 0.7549 (mtp-110)
REVERT: B  127 GLN cc_start: 0.8132 (pm20) cc_final: 0.7923 (pm20)
REVERT: B  297 ASN cc_start: 0.8790 (t0) cc_final: 0.8261 (m110)
  outliers start: 13
  outliers final: 10
  residues processed: 121
  average time/residue: 0.1890
  time to fit residues: 26.3796
Evaluate side-chains
  106 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  227 ASN
Chi-restraints excluded: chain B residue  173 SER
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  227 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 30 optimal weight:    9.9990
   chunk 29 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 153 GLN
** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 153 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4778 r_free = 0.4778 target = 0.188172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.151676 restraints weight = 6251.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.157813 restraints weight = 4216.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.162519 restraints weight = 3096.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.4472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
moved from start:          0.7290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3375  Z= 0.170
  Angle     :  0.698   7.452   4580  Z= 0.352
  Chirality :  0.049   0.176    504
  Planarity :  0.004   0.030    602
  Dihedral  :  5.177  18.187    450
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 18.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 19.17 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.43 (0.40), residues: 408
  helix: -0.23 (0.45), residues: 122
  sheet:  1.15 (0.64), residues: 72
  loop :  0.46 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 109 
 HIS   0.002   0.001   HIS A 167 
 PHE   0.025   0.003   PHE B 117 
 TYR   0.013   0.002   TYR B 274 
 ARG   0.003   0.001   ARG B 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04748 (  132)
  hydrogen bonds       : angle       5.17979 (  354)
  covalent geometry    : bond        0.00371 ( 3374)
  covalent geometry    : angle       0.69842 ( 4580)
  Misc. bond           : bond        0.01200 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.8281 (mmm) cc_final: 0.8069 (mmm)
REVERT: B  234 ARG cc_start: 0.8823 (mtm180) cc_final: 0.8603 (mtm180)
REVERT: B  297 ASN cc_start: 0.8703 (t0) cc_final: 0.8224 (m110)
  outliers start: 18
  outliers final: 16
  residues processed: 121
  average time/residue: 0.1963
  time to fit residues: 27.4619
Evaluate side-chains
  113 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  227 ASN
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  173 SER
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  227 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 23 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.181668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.139961 restraints weight = 5906.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.146791 restraints weight = 3759.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.151982 restraints weight = 2710.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.4388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6499
moved from start:          0.7856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3375  Z= 0.118
  Angle     :  0.650   6.869   4580  Z= 0.326
  Chirality :  0.045   0.154    504
  Planarity :  0.004   0.034    602
  Dihedral  :  4.849  16.993    450
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 17.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 22.78 %
    Favored  : 72.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.55 (0.41), residues: 408
  helix: -0.23 (0.46), residues: 114
  sheet:  1.05 (0.65), residues: 72
  loop :  0.64 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 208 
 HIS   0.002   0.001   HIS B 165 
 PHE   0.024   0.003   PHE B 117 
 TYR   0.016   0.002   TYR A 121 
 ARG   0.003   0.000   ARG B 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04237 (  132)
  hydrogen bonds       : angle       5.14776 (  354)
  covalent geometry    : bond        0.00259 ( 3374)
  covalent geometry    : angle       0.65037 ( 4580)
  Misc. bond           : bond        0.00066 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7446 (mtp180)
REVERT: A  159 ARG cc_start: 0.6840 (ttm-80) cc_final: 0.6607 (ttm-80)
REVERT: A  234 ARG cc_start: 0.8689 (mmm160) cc_final: 0.8409 (ttt180)
REVERT: B   98 ARG cc_start: 0.7690 (mtp180) cc_final: 0.7245 (mtp180)
REVERT: B  234 ARG cc_start: 0.8638 (mtm180) cc_final: 0.8437 (ttt180)
  outliers start: 17
  outliers final: 15
  residues processed: 121
  average time/residue: 0.1944
  time to fit residues: 27.3816
Evaluate side-chains
  118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  227 ASN
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  224 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 20 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 25 optimal weight:    8.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 211 ASN
A 229 GLN
B 158 GLN
B 189 ASN
B 211 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.171326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.128488 restraints weight = 5936.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.134328 restraints weight = 4034.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.138806 restraints weight = 3012.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.4257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6733
moved from start:          0.9019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3375  Z= 0.169
  Angle     :  0.751   7.271   4580  Z= 0.376
  Chirality :  0.048   0.162    504
  Planarity :  0.005   0.032    602
  Dihedral  :  5.170  22.231    450
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 23.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  7.78 %
    Allowed  : 22.78 %
    Favored  : 69.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.25 (0.40), residues: 408
  helix: -0.86 (0.42), residues: 126
  sheet:  0.38 (0.62), residues: 74
  loop :  0.27 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 298 
 HIS   0.003   0.001   HIS A 167 
 PHE   0.028   0.003   PHE B 117 
 TYR   0.011   0.002   TYR B 248 
 ARG   0.006   0.001   ARG B 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04965 (  132)
  hydrogen bonds       : angle       5.52399 (  354)
  covalent geometry    : bond        0.00386 ( 3374)
  covalent geometry    : angle       0.75131 ( 4580)
  Misc. bond           : bond        0.00002 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 LEU cc_start: 0.5941 (OUTLIER) cc_final: 0.5675 (mt)
REVERT: A  234 ARG cc_start: 0.8862 (mmm160) cc_final: 0.8115 (ttt180)
REVERT: A  248 TYR cc_start: 0.8033 (p90) cc_final: 0.7801 (p90)
REVERT: A  269 ASP cc_start: 0.8460 (t0) cc_final: 0.8244 (t0)
REVERT: B  234 ARG cc_start: 0.8807 (mtm180) cc_final: 0.8561 (ttt180)
REVERT: B  297 ASN cc_start: 0.8820 (t0) cc_final: 0.8483 (m110)
  outliers start: 28
  outliers final: 22
  residues processed: 120
  average time/residue: 0.1797
  time to fit residues: 25.1362
Evaluate side-chains
  118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  247 ASP
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  169 TYR
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  189 ASN
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  247 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 31 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 ASN
** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 229 GLN
B 158 GLN
** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 189 ASN
B 225 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4683 r_free = 0.4683 target = 0.179585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.141305 restraints weight = 6231.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.146212 restraints weight = 4673.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.149800 restraints weight = 3732.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.4284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6775
moved from start:          0.9662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3375  Z= 0.172
  Angle     :  0.748   7.109   4580  Z= 0.384
  Chirality :  0.048   0.175    504
  Planarity :  0.005   0.042    602
  Dihedral  :  5.211  20.399    450
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 22.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  8.06 %
    Allowed  : 24.72 %
    Favored  : 67.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.50 (0.39), residues: 408
  helix: -1.09 (0.39), residues: 126
  sheet: -0.07 (0.56), residues: 84
  loop :  0.31 (0.43), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 208 
 HIS   0.029   0.005   HIS A 178 
 PHE   0.027   0.003   PHE B 117 
 TYR   0.010   0.002   TYR B 121 
 ARG   0.005   0.001   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04657 (  132)
  hydrogen bonds       : angle       5.81184 (  354)
  covalent geometry    : bond        0.00386 ( 3374)
  covalent geometry    : angle       0.74768 ( 4580)
  Misc. bond           : bond        0.00014 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 97
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 ARG cc_start: 0.8195 (mtp180) cc_final: 0.7983 (mtp180)
REVERT: A  166 MET cc_start: 0.7729 (mmm) cc_final: 0.6724 (mmm)
REVERT: A  204 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5628 (mt)
REVERT: B  166 MET cc_start: 0.7760 (mmm) cc_final: 0.6774 (mmm)
REVERT: B  204 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5811 (mt)
REVERT: B  234 ARG cc_start: 0.8824 (mtm180) cc_final: 0.8618 (ttt180)
REVERT: B  269 ASP cc_start: 0.8365 (t0) cc_final: 0.8069 (t0)
REVERT: B  297 ASN cc_start: 0.8854 (t0) cc_final: 0.8535 (m110)
  outliers start: 29
  outliers final: 24
  residues processed: 116
  average time/residue: 0.1975
  time to fit residues: 26.5891
Evaluate side-chains
  116 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  107 GLN
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  169 TYR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  247 ASP
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  169 TYR
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  247 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 28 optimal weight:    9.9990
   chunk 11 optimal weight:    7.9990
   chunk 6 optimal weight:    8.9990
   chunk 26 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 24 optimal weight:    8.9990
   chunk 4 optimal weight:    0.0170
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
A 153 GLN
** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 190 HIS
B 190 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.175449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.133017 restraints weight = 5944.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.138573 restraints weight = 4121.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.143014 restraints weight = 3117.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.4397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6591
moved from start:          0.9997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3375  Z= 0.131
  Angle     :  0.742   8.078   4580  Z= 0.370
  Chirality :  0.046   0.158    504
  Planarity :  0.004   0.026    602
  Dihedral  :  4.962  18.690    450
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 20.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 28.89 %
    Favored  : 66.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.45 (0.38), residues: 408
  helix: -1.13 (0.40), residues: 114
  sheet:  0.08 (0.59), residues: 72
  loop :  0.20 (0.40), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 109 
 HIS   0.021   0.003   HIS A 178 
 PHE   0.027   0.003   PHE B 117 
 TYR   0.013   0.001   TYR B 248 
 ARG   0.009   0.001   ARG A 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04327 (  132)
  hydrogen bonds       : angle       5.67986 (  354)
  covalent geometry    : bond        0.00286 ( 3374)
  covalent geometry    : angle       0.74239 ( 4580)
  Misc. bond           : bond        0.00021 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.7691 (mmm) cc_final: 0.6660 (mmm)
REVERT: A  204 LEU cc_start: 0.5779 (OUTLIER) cc_final: 0.5461 (mt)
REVERT: A  234 ARG cc_start: 0.8141 (ttt180) cc_final: 0.7714 (ttp-170)
REVERT: A  248 TYR cc_start: 0.7817 (p90) cc_final: 0.7613 (p90)
REVERT: A  269 ASP cc_start: 0.7472 (t0) cc_final: 0.6873 (t0)
REVERT: B  166 MET cc_start: 0.7718 (mmm) cc_final: 0.6701 (mmm)
REVERT: B  204 LEU cc_start: 0.5789 (OUTLIER) cc_final: 0.5477 (mt)
REVERT: B  234 ARG cc_start: 0.8200 (mmm160) cc_final: 0.7898 (mmm-85)
REVERT: B  280 ASN cc_start: 0.8135 (m-40) cc_final: 0.7700 (m-40)
  outliers start: 15
  outliers final: 13
  residues processed: 109
  average time/residue: 0.1869
  time to fit residues: 23.7554
Evaluate side-chains
  104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 GLN
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  221 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 22 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 229 GLN
B 153 GLN
B 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4722 r_free = 0.4722 target = 0.184850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.144150 restraints weight = 6290.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.149502 restraints weight = 4591.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.153783 restraints weight = 3576.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.4332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6698
moved from start:          1.0293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3375  Z= 0.133
  Angle     :  0.784   8.382   4580  Z= 0.391
  Chirality :  0.047   0.148    504
  Planarity :  0.005   0.035    602
  Dihedral  :  5.024  17.762    450
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 18.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 29.44 %
    Favored  : 66.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.40 (0.38), residues: 408
  helix: -0.94 (0.41), residues: 116
  sheet: -0.12 (0.56), residues: 82
  loop :  0.28 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 298 
 HIS   0.020   0.002   HIS A 178 
 PHE   0.028   0.003   PHE B 117 
 TYR   0.007   0.001   TYR B 169 
 ARG   0.006   0.001   ARG A 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04397 (  132)
  hydrogen bonds       : angle       5.69306 (  354)
  covalent geometry    : bond        0.00299 ( 3374)
  covalent geometry    : angle       0.78450 ( 4580)
  Misc. bond           : bond        0.00005 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.378 
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  166 MET cc_start: 0.7697 (mmm) cc_final: 0.6727 (mmm)
REVERT: A  204 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5783 (mt)
REVERT: A  234 ARG cc_start: 0.8815 (ttt180) cc_final: 0.8559 (ttp-170)
REVERT: A  248 TYR cc_start: 0.8037 (p90) cc_final: 0.7803 (p90)
REVERT: A  269 ASP cc_start: 0.8190 (t0) cc_final: 0.7572 (t0)
REVERT: A  288 ARG cc_start: 0.8147 (ptt90) cc_final: 0.7796 (ptp90)
REVERT: B  166 MET cc_start: 0.7753 (mmm) cc_final: 0.6758 (mmm)
REVERT: B  234 ARG cc_start: 0.8811 (mmm160) cc_final: 0.8587 (mmm-85)
REVERT: B  280 ASN cc_start: 0.8446 (m-40) cc_final: 0.8032 (m-40)
  outliers start: 16
  outliers final: 15
  residues processed: 102
  average time/residue: 0.1868
  time to fit residues: 22.2244
Evaluate side-chains
  105 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  107 GLN
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  224 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 25 optimal weight:    9.9990
   chunk 23 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 ASN
A 229 GLN
B 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.182623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.143457 restraints weight = 6124.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.148589 restraints weight = 4493.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.152690 restraints weight = 3538.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.4326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          1.0495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3375  Z= 0.137
  Angle     :  0.816  14.181   4580  Z= 0.396
  Chirality :  0.048   0.160    504
  Planarity :  0.004   0.026    602
  Dihedral  :  5.051  17.717    450
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 19.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 28.89 %
    Favored  : 66.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.51 (0.38), residues: 408
  helix: -1.09 (0.39), residues: 116
  sheet: -0.24 (0.55), residues: 82
  loop :  0.29 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 298 
 HIS   0.017   0.002   HIS B 178 
 PHE   0.028   0.003   PHE B 117 
 TYR   0.010   0.002   TYR B 121 
 ARG   0.008   0.001   ARG A  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04433 (  132)
  hydrogen bonds       : angle       5.85116 (  354)
  covalent geometry    : bond        0.00310 ( 3374)
  covalent geometry    : angle       0.81604 ( 4580)
  Misc. bond           : bond        0.00002 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.7743 (mmm) cc_final: 0.6771 (mmm)
REVERT: A  204 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5736 (mt)
REVERT: A  234 ARG cc_start: 0.8737 (ttt180) cc_final: 0.8442 (ttp-170)
REVERT: A  269 ASP cc_start: 0.8099 (t0) cc_final: 0.7654 (t0)
REVERT: B  166 MET cc_start: 0.7795 (mmm) cc_final: 0.6814 (mmm)
REVERT: B  280 ASN cc_start: 0.8459 (m-40) cc_final: 0.8018 (m-40)
  outliers start: 17
  outliers final: 13
  residues processed: 100
  average time/residue: 0.1765
  time to fit residues: 20.7067
Evaluate side-chains
  101 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  107 GLN
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain B residue  107 GLN
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  209 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 31 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 229 GLN
B 225 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.181596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.143822 restraints weight = 6282.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.148900 restraints weight = 4569.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.153146 restraints weight = 3555.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.4428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6653
moved from start:          1.0745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3375  Z= 0.138
  Angle     :  0.839  15.111   4580  Z= 0.408
  Chirality :  0.048   0.160    504
  Planarity :  0.004   0.028    602
  Dihedral  :  5.131  20.987    450
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 19.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 30.00 %
    Favored  : 65.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.53 (0.38), residues: 408
  helix: -1.12 (0.40), residues: 116
  sheet: -0.22 (0.55), residues: 82
  loop :  0.26 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 298 
 HIS   0.014   0.002   HIS B 178 
 PHE   0.029   0.003   PHE B 117 
 TYR   0.008   0.001   TYR B 169 
 ARG   0.010   0.001   ARG A  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04457 (  132)
  hydrogen bonds       : angle       5.77961 (  354)
  covalent geometry    : bond        0.00315 ( 3374)
  covalent geometry    : angle       0.83887 ( 4580)
  Misc. bond           : bond        0.00015 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1600.02 seconds
wall clock time: 28 minutes 35.32 seconds (1715.32 seconds total)