Starting phenix.real_space_refine
on Sat Apr 26 19:19:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hh1_52168/04_2025/9hh1_52168.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hh1_52168/04_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_52168/04_2025/9hh1_52168.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hh1_52168/04_2025/9hh1_52168.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hh1_52168/04_2025/9hh1_52168.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hh1_52168/04_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-5669/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: 2.53, per 1000 atoms: 0.77
  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: 0.82
  Conformation dependent library (CDL) restraints added in 381.2 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: 0.34
  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: 0.69

  Time building geometry restraints manager: 0.94 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: 0.01
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:             0.510
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.120
  Find NCS groups from input model:        0.050
  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:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.440
-------------------------------------------------------------------------------
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  : 0.389 
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: 0.2024
  time to fit residues: 39.3963
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  : 0.382 
-------------------------------------------------------------------------------
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 = 45)----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.172705 restraints weight = 5923.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.180331 restraints weight = 3774.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.185557 restraints weight = 2676.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.4645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6007
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  : 0.383 
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: 0.6397 (OUTLIER) cc_final: 0.6122 (tptp)
REVERT: A  188 ASP cc_start: 0.8954 (m-30) cc_final: 0.8377 (p0)
REVERT: A  280 ASN cc_start: 0.8165 (m-40) cc_final: 0.7929 (m-40)
REVERT: B   96 LYS cc_start: 0.8627 (ptmt) cc_final: 0.8387 (ttpt)
REVERT: B  188 ASP cc_start: 0.8998 (m-30) cc_final: 0.8449 (p0)
REVERT: B  280 ASN cc_start: 0.7932 (m-40) cc_final: 0.7576 (m-40)
REVERT: B  297 ASN cc_start: 0.8731 (t0) cc_final: 0.8209 (m110)
  outliers start: 10
  outliers final: 3
  residues processed: 132
  average time/residue: 0.1939
  time to fit residues: 29.6637
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  : 0.385 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 10 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7786

-------------------------------------------------------------------------------
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 = 0.4858 r_free = 0.4858 target = 0.193770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.154564 restraints weight = 5498.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.162127 restraints weight = 3276.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.167936 restraints weight = 2215.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.4617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6193
moved from start:          0.5885

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= 0.136
  Angle     :  0.668   6.836   4580  Z= 0.336
  Chirality :  0.047   0.158    504
  Planarity :  0.004   0.030    602
  Dihedral  :  5.182  18.928    450
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 16.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 19.17 %
    Favored  : 77.22 %
  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:  0.77 (0.39), residues: 408
  helix:  0.24 (0.46), residues: 112
  sheet:  1.13 (0.56), residues: 72
  loop :  0.62 (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   0.010   0.002   TYR B 248 
 ARG   0.005   0.001   ARG A  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04339 (  132)
  hydrogen bonds       : angle       4.88549 (  354)
  covalent geometry    : bond        0.00307 ( 3374)
  covalent geometry    : angle       0.66762 ( 4580)
  Misc. bond           : bond        0.00040 (    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  : 0.393 
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: A   98 ARG cc_start: 0.7935 (mtp180) cc_final: 0.7436 (mtp180)
REVERT: A  188 ASP cc_start: 0.9020 (m-30) cc_final: 0.8455 (p0)
REVERT: B   98 ARG cc_start: 0.7845 (mtp180) cc_final: 0.7388 (mtp-110)
REVERT: B  297 ASN cc_start: 0.8823 (t0) cc_final: 0.8281 (m110)
  outliers start: 13
  outliers final: 10
  residues processed: 119
  average time/residue: 0.2056
  time to fit residues: 28.2612
Evaluate side-chains
  111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 25 optimal weight:    0.2980
   chunk 15 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0770
   chunk 30 optimal weight:    0.0570
   chunk 29 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.4256

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 229 GLN
B 153 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4872 r_free = 0.4872 target = 0.200606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.162886 restraints weight = 6221.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.169858 restraints weight = 4068.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.175192 restraints weight = 2923.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.4581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6215
moved from start:          0.6468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3375  Z= 0.118
  Angle     :  0.637   6.743   4580  Z= 0.320
  Chirality :  0.044   0.143    504
  Planarity :  0.004   0.033    602
  Dihedral  :  4.886  17.931    450
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 18.06 %
    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 (0.40), residues: 408
  helix:  0.02 (0.46), residues: 112
  sheet:  1.25 (0.63), residues: 72
  loop :  0.69 (0.40), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 109 
 HIS   0.001   0.000   HIS B 165 
 PHE   0.022   0.003   PHE A 117 
 TYR   0.011   0.002   TYR A 274 
 ARG   0.003   0.000   ARG B 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04117 (  132)
  hydrogen bonds       : angle       4.78537 (  354)
  covalent geometry    : bond        0.00257 ( 3374)
  covalent geometry    : angle       0.63738 ( 4580)
  Misc. bond           : bond        0.00001 (    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
  130 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.391 
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   98 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7216 (mtp180)
REVERT: A  294 LYS cc_start: 0.7657 (mmtt) cc_final: 0.7452 (mmtm)
REVERT: B   98 ARG cc_start: 0.8074 (mtp180) cc_final: 0.7705 (mtp180)
REVERT: B  124 MET cc_start: 0.8536 (mmm) cc_final: 0.8330 (mmm)
REVERT: B  294 LYS cc_start: 0.7545 (mmtt) cc_final: 0.7296 (mmtm)
REVERT: B  297 ASN cc_start: 0.8753 (t0) cc_final: 0.8258 (m110)
  outliers start: 18
  outliers final: 16
  residues processed: 123
  average time/residue: 0.1962
  time to fit residues: 28.0179
Evaluate side-chains
  125 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 20 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 9 optimal weight:    0.3980
   chunk 27 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   overall best weight:    1.0584

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4745 r_free = 0.4745 target = 0.181995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.141507 restraints weight = 6015.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.148704 restraints weight = 3791.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.153934 restraints weight = 2672.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.4427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6443
moved from start:          0.7367

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= 0.133
  Angle     :  0.672   7.439   4580  Z= 0.332
  Chirality :  0.045   0.155    504
  Planarity :  0.004   0.033    602
  Dihedral  :  4.864  17.889    450
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 17.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 20.83 %
    Favored  : 73.89 %
  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:  0.47 (0.41), residues: 408
  helix: -0.32 (0.44), residues: 124
  sheet:  1.18 (0.64), residues: 72
  loop :  0.59 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 298 
 HIS   0.003   0.001   HIS A 141 
 PHE   0.027   0.003   PHE A 117 
 TYR   0.015   0.002   TYR A 121 
 ARG   0.002   0.000   ARG A 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04094 (  132)
  hydrogen bonds       : angle       4.96972 (  354)
  covalent geometry    : bond        0.00295 ( 3374)
  covalent geometry    : angle       0.67237 ( 4580)
  Misc. bond           : bond        0.00254 (    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
  130 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.365 
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: B   98 ARG cc_start: 0.7962 (mtp180) cc_final: 0.7574 (mtp180)
REVERT: B  297 ASN cc_start: 0.8715 (t0) cc_final: 0.8314 (m110)
  outliers start: 19
  outliers final: 15
  residues processed: 122
  average time/residue: 0.2009
  time to fit residues: 28.3739
Evaluate side-chains
  116 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
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  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  224 LEU
Chi-restraints excluded: chain B residue  227 ASN
Chi-restraints excluded: chain B residue  247 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0570
   chunk 14 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 20 optimal weight:    8.9990
   chunk 30 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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**
** B 158 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 = 0.4788 r_free = 0.4788 target = 0.193553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.156811 restraints weight = 6159.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.163202 restraints weight = 4117.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.167926 restraints weight = 3010.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.4478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6409
moved from start:          0.7890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3375  Z= 0.122
  Angle     :  0.694  10.074   4580  Z= 0.343
  Chirality :  0.044   0.147    504
  Planarity :  0.004   0.034    602
  Dihedral  :  4.807  17.425    450
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 17.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 22.78 %
    Favored  : 72.78 %
  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:  0.64 (0.41), residues: 408
  helix: -0.03 (0.47), residues: 114
  sheet:  1.05 (0.64), residues: 72
  loop :  0.64 (0.42), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 109 
 HIS   0.025   0.002   HIS A 178 
 PHE   0.024   0.003   PHE A 117 
 TYR   0.008   0.001   TYR A 169 
 ARG   0.005   0.000   ARG B 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04102 (  132)
  hydrogen bonds       : angle       5.17510 (  354)
  covalent geometry    : bond        0.00266 ( 3374)
  covalent geometry    : angle       0.69429 ( 4580)
  Misc. bond           : bond        0.00009 (    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
  122 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 MET cc_start: 0.6194 (pmm) cc_final: 0.4436 (tmm)
REVERT: A  269 ASP cc_start: 0.8206 (t0) cc_final: 0.7782 (t0)
REVERT: B   98 ARG cc_start: 0.7971 (mtp180) cc_final: 0.7414 (mtp180)
REVERT: B  166 MET cc_start: 0.6080 (mmt) cc_final: 0.5543 (mmm)
REVERT: B  269 ASP cc_start: 0.8336 (t0) cc_final: 0.8079 (t0)
REVERT: B  297 ASN cc_start: 0.8677 (t0) cc_final: 0.8332 (m-40)
  outliers start: 16
  outliers final: 14
  residues processed: 115
  average time/residue: 0.2102
  time to fit residues: 27.6997
Evaluate side-chains
  114 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  162 PHE
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  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  209 LEU
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  227 ASN
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:    6.9990
   chunk 15 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 31 optimal weight:    0.2980
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:   10.0000
   chunk 6 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0670
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 189 ASN
B 158 GLN
B 211 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4753 r_free = 0.4753 target = 0.181396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.139398 restraints weight = 5819.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.146149 restraints weight = 3697.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.151414 restraints weight = 2639.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.4520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6451
moved from start:          0.8204

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= 0.120
  Angle     :  0.710   9.173   4580  Z= 0.345
  Chirality :  0.046   0.147    504
  Planarity :  0.004   0.032    602
  Dihedral  :  4.784  16.781    450
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 17.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 23.61 %
    Favored  : 70.28 %
  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:  0.37 (0.41), residues: 408
  helix: -0.16 (0.47), residues: 114
  sheet:  0.95 (0.63), residues: 72
  loop :  0.38 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 298 
 HIS   0.020   0.002   HIS A 178 
 PHE   0.027   0.003   PHE A 117 
 TYR   0.009   0.002   TYR A 121 
 ARG   0.003   0.000   ARG B 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04073 (  132)
  hydrogen bonds       : angle       5.17178 (  354)
  covalent geometry    : bond        0.00264 ( 3374)
  covalent geometry    : angle       0.70971 ( 4580)
  Misc. bond           : bond        0.00013 (    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
  127 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.354 
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: 0.7778 (mtp180) cc_final: 0.7312 (mtp180)
REVERT: A  269 ASP cc_start: 0.8007 (t0) cc_final: 0.7532 (t0)
REVERT: B   98 ARG cc_start: 0.7766 (mtp180) cc_final: 0.7313 (mtp180)
REVERT: B  166 MET cc_start: 0.6254 (mmt) cc_final: 0.5693 (mmm)
REVERT: B  234 ARG cc_start: 0.8590 (mtm180) cc_final: 0.8098 (ttp-170)
REVERT: B  269 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.8023 (t0)
REVERT: B  297 ASN cc_start: 0.8676 (t0) cc_final: 0.8370 (m-40)
  outliers start: 22
  outliers final: 17
  residues processed: 118
  average time/residue: 0.2065
  time to fit residues: 28.0804
Evaluate side-chains
  118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  184 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  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  224 LEU
Chi-restraints excluded: chain B residue  227 ASN
Chi-restraints excluded: chain B residue  269 ASP
Chi-restraints excluded: chain B residue  278 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 38 optimal weight:   20.0000
   chunk 28 optimal weight:    9.9990
   chunk 11 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0170
   chunk 5 optimal weight:    0.0570
   chunk 24 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.5538

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.181185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.138215 restraints weight = 5789.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.145043 restraints weight = 3701.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.150509 restraints weight = 2651.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.4422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6507
moved from start:          0.8742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3375  Z= 0.125
  Angle     :  0.732   9.095   4580  Z= 0.359
  Chirality :  0.046   0.156    504
  Planarity :  0.004   0.039    602
  Dihedral  :  5.000  17.103    450
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 17.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 27.22 %
    Favored  : 68.06 %
  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: -0.21 (0.40), residues: 408
  helix: -0.49 (0.45), residues: 126
  sheet:  0.74 (0.62), residues: 72
  loop : -0.09 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 298 
 HIS   0.013   0.002   HIS A 178 
 PHE   0.026   0.002   PHE B 117 
 TYR   0.008   0.001   TYR A 169 
 ARG   0.008   0.001   ARG B 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03940 (  132)
  hydrogen bonds       : angle       5.32673 (  354)
  covalent geometry    : bond        0.00279 ( 3374)
  covalent geometry    : angle       0.73171 ( 4580)
  Misc. bond           : bond        0.00013 (    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
  124 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.387 
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: 0.8043 (mtp180) cc_final: 0.7631 (mtp180)
REVERT: A  234 ARG cc_start: 0.8688 (mtp180) cc_final: 0.8442 (ttm170)
REVERT: A  269 ASP cc_start: 0.8266 (t0) cc_final: 0.7801 (t0)
REVERT: B   98 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7422 (mtp180)
REVERT: B  166 MET cc_start: 0.6204 (mmt) cc_final: 0.5762 (mmm)
REVERT: B  269 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8214 (t0)
  outliers start: 17
  outliers final: 14
  residues processed: 117
  average time/residue: 0.2250
  time to fit residues: 30.0590
Evaluate side-chains
  115 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  173 SER
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  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  224 LEU
Chi-restraints excluded: chain B residue  269 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    0.3980
   chunk 39 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0970
   chunk 27 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0070
   chunk 38 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.3796

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.193299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.155682 restraints weight = 6195.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.161851 restraints weight = 4245.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.166696 restraints weight = 3155.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.4433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6475
moved from start:          0.9083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3375  Z= 0.125
  Angle     :  0.752   8.895   4580  Z= 0.367
  Chirality :  0.046   0.143    504
  Planarity :  0.004   0.037    602
  Dihedral  :  4.913  16.053    450
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 17.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 27.50 %
    Favored  : 68.06 %
  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: -0.33 (0.39), residues: 408
  helix: -0.66 (0.45), residues: 128
  sheet:  0.65 (0.62), residues: 72
  loop : -0.10 (0.39), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 109 
 HIS   0.010   0.001   HIS B 178 
 PHE   0.027   0.002   PHE A 117 
 TYR   0.011   0.001   TYR B 248 
 ARG   0.008   0.001   ARG B 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03788 (  132)
  hydrogen bonds       : angle       5.29586 (  354)
  covalent geometry    : bond        0.00274 ( 3374)
  covalent geometry    : angle       0.75206 ( 4580)
  Misc. bond           : bond        0.00012 (    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
  119 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.360 
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   98 ARG cc_start: 0.8310 (mtp180) cc_final: 0.7925 (mtp180)
REVERT: A  166 MET cc_start: 0.7291 (mmm) cc_final: 0.6094 (mmm)
REVERT: A  234 ARG cc_start: 0.8861 (mtp180) cc_final: 0.8629 (ttp-170)
REVERT: A  269 ASP cc_start: 0.8347 (t0) cc_final: 0.7932 (t0)
REVERT: A  294 LYS cc_start: 0.6408 (mmtm) cc_final: 0.6082 (mptt)
REVERT: B   98 ARG cc_start: 0.8275 (mtp180) cc_final: 0.7781 (mtp180)
REVERT: B  166 MET cc_start: 0.5986 (mmt) cc_final: 0.5670 (mmm)
REVERT: B  234 ARG cc_start: 0.8924 (mtm180) cc_final: 0.8456 (ttp-170)
REVERT: B  269 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8281 (t0)
  outliers start: 16
  outliers final: 15
  residues processed: 113
  average time/residue: 0.2130
  time to fit residues: 27.6886
Evaluate side-chains
  115 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  184 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  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  209 LEU
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  227 ASN
Chi-restraints excluded: chain B residue  269 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 31 optimal weight:    0.1980
   chunk 20 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0980
   chunk 23 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.0184

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4695 r_free = 0.4695 target = 0.178985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.137583 restraints weight = 5816.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.144020 restraints weight = 3766.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.148743 restraints weight = 2741.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.4342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6576
moved from start:          0.9359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3375  Z= 0.130
  Angle     :  0.757   9.165   4580  Z= 0.371
  Chirality :  0.048   0.154    504
  Planarity :  0.004   0.029    602
  Dihedral  :  5.056  18.881    450
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 18.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 26.67 %
    Favored  : 68.61 %
  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 (0.39), residues: 408
  helix: -0.71 (0.44), residues: 128
  sheet:  0.46 (0.60), residues: 72
  loop : -0.13 (0.39), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 298 
 HIS   0.008   0.001   HIS B 178 
 PHE   0.028   0.003   PHE B 117 
 TYR   0.013   0.002   TYR A 121 
 ARG   0.006   0.001   ARG A 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03880 (  132)
  hydrogen bonds       : angle       5.35119 (  354)
  covalent geometry    : bond        0.00295 ( 3374)
  covalent geometry    : angle       0.75682 ( 4580)
  Misc. bond           : bond        0.00000 (    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
  119 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.401 
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   98 ARG cc_start: 0.8019 (mtp180) cc_final: 0.7486 (mtp180)
REVERT: A  166 MET cc_start: 0.7460 (mmm) cc_final: 0.6285 (mmm)
REVERT: A  269 ASP cc_start: 0.8055 (t0) cc_final: 0.7623 (t70)
REVERT: B   98 ARG cc_start: 0.7895 (mtp180) cc_final: 0.7459 (mtp180)
REVERT: B  166 MET cc_start: 0.6259 (mmt) cc_final: 0.5879 (mmm)
REVERT: B  234 ARG cc_start: 0.8684 (mtm180) cc_final: 0.8156 (ttp-170)
REVERT: B  297 ASN cc_start: 0.8656 (t0) cc_final: 0.8406 (m110)
  outliers start: 17
  outliers final: 15
  residues processed: 112
  average time/residue: 0.1940
  time to fit residues: 25.2770
Evaluate side-chains
  112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  184 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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 21 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0670
   chunk 22 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.6118

-------------------------------------------------------------------------------
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 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.180198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.137480 restraints weight = 5838.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.144434 restraints weight = 3714.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.149461 restraints weight = 2655.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.4351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6549
moved from start:          0.9694

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= 0.129
  Angle     :  0.782   9.248   4580  Z= 0.385
  Chirality :  0.047   0.154    504
  Planarity :  0.004   0.038    602
  Dihedral  :  4.999  17.472    450
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 17.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 28.89 %
    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: -0.56 (0.38), residues: 408
  helix: -0.83 (0.44), residues: 128
  sheet:  0.36 (0.60), residues: 72
  loop : -0.19 (0.39), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 109 
 HIS   0.009   0.001   HIS B 178 
 PHE   0.027   0.002   PHE A 117 
 TYR   0.011   0.002   TYR B 248 
 ARG   0.007   0.001   ARG A 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03921 (  132)
  hydrogen bonds       : angle       5.38709 (  354)
  covalent geometry    : bond        0.00288 ( 3374)
  covalent geometry    : angle       0.78212 ( 4580)
  Misc. bond           : bond        0.00005 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1706.55 seconds
wall clock time: 30 minutes 14.43 seconds (1814.43 seconds total)