Starting phenix.real_space_refine
on Tue Mar 11 15:13:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h8f_34545/03_2025/8h8f_34545.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h8f_34545/03_2025/8h8f_34545.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h8f_34545/03_2025/8h8f_34545.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h8f_34545/03_2025/8h8f_34545.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h8f_34545/03_2025/8h8f_34545.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h8f_34545/03_2025/8h8f_34545.cif"
  }
  resolution = 3.48
  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=  -0.002 sd=   0.081
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      33      5.16       5
     C    3990      2.51       5
     N    1011      2.21       5
     O    1134      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6168
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 2056
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 12, 'TRANS': 238}
    Chain: "B"
      Number of atoms: 2056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 2056
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 12, 'TRANS': 238}
    Chain: "C"
      Number of atoms: 2056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 2056
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 12, 'TRANS': 238}
  Time building chain proxies: 4.61, per 1000 atoms: 0.75
  Number of scatterers: 6168
  At special positions: 0
  Unit cell: (84.786, 84.786, 122.831, 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      33     16.00
     O    1134      8.00
     N    1011      7.00
     C    3990      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 147 " - pdb=" SG  CYS A 169 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 147 " - pdb=" SG  CYS B 169 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 147 " - pdb=" SG  CYS C 169 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.48
  Conformation dependent library (CDL) restraints added in 888.5 milliseconds
  

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1446

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 12 sheets defined
      25.6% alpha, 35.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 97 through 117
      removed outlier: 3.924A  pdb=" N   HIS A 117 " --> pdb=" O   ASP A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 232
    Processing helix  chain 'A' and resid 236 through 247
      removed outlier: 3.678A  pdb=" N   GLN A 241 " --> pdb=" O   VAL A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 347
      removed outlier: 3.733A  pdb=" N   MET A 326 " --> pdb=" O   ASN A 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 117
      removed outlier: 3.785A  pdb=" N   HIS B 117 " --> pdb=" O   ASP B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 232
    Processing helix  chain 'B' and resid 236 through 247
      removed outlier: 3.653A  pdb=" N   GLN B 241 " --> pdb=" O   VAL B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 347
      removed outlier: 3.751A  pdb=" N   MET B 326 " --> pdb=" O   ASN B 322 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 98 through 117
      removed outlier: 3.998A  pdb=" N   HIS C 117 " --> pdb=" O   ASP C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 232
    Processing helix  chain 'C' and resid 236 through 247
      removed outlier: 3.785A  pdb=" N   GLN C 241 " --> pdb=" O   VAL C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 322 through 347
      removed outlier: 3.864A  pdb=" N   MET C 326 " --> pdb=" O   ASN C 322 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 125
      removed outlier: 4.364A  pdb=" N   ASP A 317 " --> pdb=" O   LYS A 268 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL A 304 " --> pdb=" O   THR A 258 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   SER A 146 " --> pdb=" O   GLN A 206 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   HIS A 208 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 5.515A  pdb=" N   LEU A 144 " --> pdb=" O   HIS A 208 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 125
      removed outlier: 4.364A  pdb=" N   ASP A 317 " --> pdb=" O   LYS A 268 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172
      removed outlier: 3.581A  pdb=" N   GLY A 134 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 219
      removed outlier: 3.610A  pdb=" N   ILE A 219 " --> pdb=" O   PHE A 252 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 125
      removed outlier: 3.882A  pdb=" N   GLN B 313 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ASP B 317 " --> pdb=" O   LYS B 268 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL B 304 " --> pdb=" O   THR B 258 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLN B 299 " --> pdb=" O   LEU B 209 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 143 through 144
      removed outlier: 3.532A  pdb=" N   HIS B 208 " --> pdb=" O   ARG B 143 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLN B 299 " --> pdb=" O   LEU B 209 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL B 304 " --> pdb=" O   THR B 258 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 171 through 175
      removed outlier: 3.703A  pdb=" N   ILE B 174 " --> pdb=" O   ALA B 188 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ALA B 188 " --> pdb=" O   ILE B 174 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   GLY B 134 " --> pdb=" O   PHE B 224 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 218 through 219
    Processing sheet with id=AA9, first strand: chain 'C' and resid 119 through 123
      removed outlier: 3.752A  pdb=" N   GLN C 313 " --> pdb=" O   LEU C 264 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   ASP C 317 " --> pdb=" O   LYS C 268 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   VAL C 304 " --> pdb=" O   THR C 258 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   SER C 146 " --> pdb=" O   GLN C 206 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   HIS C 208 " --> pdb=" O   LEU C 144 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   LEU C 144 " --> pdb=" O   HIS C 208 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 119 through 123
      removed outlier: 3.752A  pdb=" N   GLN C 313 " --> pdb=" O   LEU C 264 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   ASP C 317 " --> pdb=" O   LYS C 268 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 171 through 175
    Processing sheet with id=AB3, first strand: chain 'C' and resid 218 through 219

    319 hydrogen bonds defined for protein.
    882 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: 1.71

  Time building geometry restraints manager: 1.73 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1218
        1.33 -     1.45: 1612
        1.45 -     1.57: 3455
        1.57 -     1.70: 0
        1.70 -     1.82: 54
  Bond restraints: 6339
  Sorted by residual:
  bond pdb=" CE1 HIS B 154 "
       pdb=" NE2 HIS B 154 "
    ideal  model  delta    sigma   weight residual
    1.321  1.361 -0.040 1.00e-02 1.00e+04 1.62e+01
  bond pdb=" C   PRO B 156 "
       pdb=" O   PRO B 156 "
    ideal  model  delta    sigma   weight residual
    1.240  1.205  0.035 1.12e-02 7.97e+03 9.94e+00
  bond pdb=" N   ILE B 155 "
       pdb=" CA  ILE B 155 "
    ideal  model  delta    sigma   weight residual
    1.457  1.484 -0.027 9.00e-03 1.23e+04 9.11e+00
  bond pdb=" N   LEU A 144 "
       pdb=" CA  LEU A 144 "
    ideal  model  delta    sigma   weight residual
    1.455  1.493 -0.038 1.27e-02 6.20e+03 9.09e+00
  bond pdb=" N   PRO A 139 "
       pdb=" CA  PRO A 139 "
    ideal  model  delta    sigma   weight residual
    1.472  1.433  0.039 1.32e-02 5.74e+03 8.70e+00
  ... (remaining 6334 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 8243
        1.47 -     2.94: 251
        2.94 -     4.42: 55
        4.42 -     5.89: 22
        5.89 -     7.36: 12
  Bond angle restraints: 8583
  Sorted by residual:
  angle pdb=" C   HIS B 154 "
        pdb=" N   ILE B 155 "
        pdb=" CA  ILE B 155 "
      ideal   model   delta    sigma   weight residual
     123.33  117.54    5.79 8.70e-01 1.32e+00 4.43e+01
  angle pdb=" C   TYR B 152 "
        pdb=" N   ASP B 153 "
        pdb=" CA  ASP B 153 "
      ideal   model   delta    sigma   weight residual
     120.82  113.46    7.36 1.41e+00 5.03e-01 2.73e+01
  angle pdb=" N   ILE B 155 "
        pdb=" CA  ILE B 155 "
        pdb=" C   ILE B 155 "
      ideal   model   delta    sigma   weight residual
     107.61  113.28   -5.67 1.19e+00 7.06e-01 2.27e+01
  angle pdb=" C   ASP B 153 "
        pdb=" CA  ASP B 153 "
        pdb=" CB  ASP B 153 "
      ideal   model   delta    sigma   weight residual
     109.90  117.21   -7.31 1.56e+00 4.11e-01 2.20e+01
  angle pdb=" N   PRO B 157 "
        pdb=" CA  PRO B 157 "
        pdb=" C   PRO B 157 "
      ideal   model   delta    sigma   weight residual
     111.41  104.62    6.79 1.50e+00 4.44e-01 2.05e+01
  ... (remaining 8578 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 3210
       17.69 -    35.39: 431
       35.39 -    53.08: 110
       53.08 -    70.77: 19
       70.77 -    88.47: 7
  Dihedral angle restraints: 3777
    sinusoidal: 1551
      harmonic: 2226
  Sorted by residual:
  dihedral pdb=" CB  CYS B 147 "
           pdb=" SG  CYS B 147 "
           pdb=" SG  CYS B 169 "
           pdb=" CB  CYS B 169 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   19.05   73.95     1      1.00e+01 1.00e-02 6.95e+01
  dihedral pdb=" CB  CYS A 147 "
           pdb=" SG  CYS A 147 "
           pdb=" SG  CYS A 169 "
           pdb=" CB  CYS A 169 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   20.51   72.49     1      1.00e+01 1.00e-02 6.71e+01
  dihedral pdb=" CB  CYS C 147 "
           pdb=" SG  CYS C 147 "
           pdb=" SG  CYS C 169 "
           pdb=" CB  CYS C 169 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   20.65   72.35     1      1.00e+01 1.00e-02 6.69e+01
  ... (remaining 3774 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 784
       0.062 -    0.124: 120
       0.124 -    0.186: 10
       0.186 -    0.247: 2
       0.247 -    0.309: 2
  Chirality restraints: 918
  Sorted by residual:
  chirality pdb=" CA  ILE A 135 "
            pdb=" N   ILE A 135 "
            pdb=" C   ILE A 135 "
            pdb=" CB  ILE A 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.74   -0.31 2.00e-01 2.50e+01 2.39e+00
  chirality pdb=" CA  ARG A 143 "
            pdb=" N   ARG A 143 "
            pdb=" C   ARG A 143 "
            pdb=" CB  ARG A 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CA  LYS B 159 "
            pdb=" N   LYS B 159 "
            pdb=" C   LYS B 159 "
            pdb=" CB  LYS B 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 915 not shown)

  Planarity restraints: 1095
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 143 "    0.494 9.50e-02 1.11e+02   2.22e-01 3.00e+01
        pdb=" NE  ARG A 143 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 143 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 143 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 143 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 309 "    0.045 5.00e-02 4.00e+02   6.94e-02 7.71e+00
        pdb=" N   PRO A 310 "   -0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO A 310 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 310 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 133 "   -0.013 2.00e-02 2.50e+03   2.55e-02 6.49e+00
        pdb=" C   PRO A 133 "    0.044 2.00e-02 2.50e+03
        pdb=" O   PRO A 133 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLY A 134 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1092 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 131
        2.69 -     3.24: 5918
        3.24 -     3.80: 9442
        3.80 -     4.35: 11444
        4.35 -     4.90: 19636
  Nonbonded interactions: 46571
  Sorted by model distance:
  nonbonded pdb=" N   GLU C 281 "
            pdb=" OE1 GLU C 281 "
     model   vdw
     2.140 3.120
  nonbonded pdb=" OE1 GLU B 126 "
            pdb=" NH2 ARG B 198 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" O   ALA B 229 "
            pdb=" OG  SER B 233 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" NZ  LYS C 186 "
            pdb=" OE1 GLU C 244 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" OG1 THR A 181 "
            pdb=" OG1 THR A 184 "
     model   vdw
     2.284 3.040
  ... (remaining 46566 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'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.740
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6569
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6339  Z= 0.222
  Angle     :  0.692   7.362   8583  Z= 0.410
  Chirality :  0.047   0.309    918
  Planarity :  0.008   0.222   1095
  Dihedral  : 17.028  88.468   2322
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 23.00 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.30), residues: 747
  helix:  1.64 (0.39), residues: 174
  sheet:  0.36 (0.33), residues: 267
  loop : -1.68 (0.29), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 250 
 HIS   0.004   0.001   HIS B 117 
 PHE   0.013   0.002   PHE A 287 
 TYR   0.022   0.001   TYR B 176 
 ARG   0.006   0.000   ARG A 112 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A  143 ARG cc_start: 0.6143 (OUTLIER) cc_final: 0.5743 (ptt180)
  outliers start: 7
  outliers final: 3
  residues processed: 88
  average time/residue: 0.1818
  time to fit residues: 21.3518
Evaluate side-chains
  85 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  143 ARG
Chi-restraints excluded: chain B residue  154 HIS
Chi-restraints excluded: chain B residue  289 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0070
   chunk 38 optimal weight:    0.9980
   chunk 30 optimal weight:    7.9990
   chunk 58 optimal weight:    0.1980
   chunk 22 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.0400

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

Flipped N/Q/H residues before XYZ refinement:
** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 117 HIS ** 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 = 0.4752 r_free = 0.4752 target = 0.237493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4618 r_free = 0.4618 target = 0.207441 restraints weight = 9963.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.4563 rms_B_bonded: 2.00
r_work: 0.4622 rms_B_bonded: 1.42 restraints_weight: 0.5000
r_work: 0.4539 rms_B_bonded: 2.47 restraints_weight: 0.2500
r_work (final): 0.4539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6667
moved from start:          0.0913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6339  Z= 0.215
  Angle     :  0.610   6.696   8583  Z= 0.319
  Chirality :  0.045   0.152    918
  Planarity :  0.005   0.057   1095
  Dihedral  :  5.322  42.975    822
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 24.02 %
    Favored  : 73.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.30), residues: 747
  helix:  1.37 (0.39), residues: 177
  sheet:  0.59 (0.34), residues: 246
  loop : -1.78 (0.29), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 259 
 HIS   0.004   0.001   HIS B 117 
 PHE   0.018   0.002   PHE A 252 
 TYR   0.015   0.002   TYR B 176 
 ARG   0.004   0.000   ARG B 279 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.709 
Fit side-chains
  outliers start: 16
  outliers final: 8
  residues processed: 102
  average time/residue: 0.1770
  time to fit residues: 24.3972
Evaluate side-chains
  89 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  243 CYS
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain B residue  154 HIS
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain C residue  174 ILE
Chi-restraints excluded: chain C residue  177 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 5 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 208 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4761 r_free = 0.4761 target = 0.238234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.4624 r_free = 0.4624 target = 0.208086 restraints weight = 10094.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.4568 rms_B_bonded: 2.03
r_work: 0.4625 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.4542 rms_B_bonded: 2.53 restraints_weight: 0.2500
r_work (final): 0.4542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6669
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6339  Z= 0.186
  Angle     :  0.577   6.872   8583  Z= 0.300
  Chirality :  0.044   0.143    918
  Planarity :  0.005   0.051   1095
  Dihedral  :  4.837  38.581    812
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 24.89 %
    Favored  : 71.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.30), residues: 747
  helix:  1.31 (0.38), residues: 177
  sheet:  0.41 (0.33), residues: 255
  loop : -1.74 (0.30), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 259 
 HIS   0.005   0.001   HIS B 117 
 PHE   0.015   0.002   PHE C 224 
 TYR   0.030   0.002   TYR C 176 
 ARG   0.004   0.000   ARG A 257 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.724 
Fit side-chains
REVERT: A  112 ARG cc_start: 0.7915 (mmm160) cc_final: 0.7358 (mtp85)
REVERT: B  105 TYR cc_start: 0.6589 (OUTLIER) cc_final: 0.5666 (t80)
REVERT: B  144 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5400 (pp)
REVERT: C  105 TYR cc_start: 0.5215 (t80) cc_final: 0.4647 (t80)
  outliers start: 24
  outliers final: 16
  residues processed: 106
  average time/residue: 0.1654
  time to fit residues: 24.1651
Evaluate side-chains
  95 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 CYS
Chi-restraints excluded: chain A residue  243 CYS
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  154 HIS
Chi-restraints excluded: chain B residue  169 CYS
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  232 LYS
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  169 CYS
Chi-restraints excluded: chain C residue  174 ILE
Chi-restraints excluded: chain C residue  177 ILE
Chi-restraints excluded: chain C residue  282 THR
Chi-restraints excluded: chain C residue  333 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   chunk 21 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9980
   chunk 44 optimal weight:    9.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 236 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4707 r_free = 0.4707 target = 0.231629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.200498 restraints weight = 10090.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.4493 rms_B_bonded: 2.07
r_work: 0.4546 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.4463 rms_B_bonded: 2.50 restraints_weight: 0.2500
r_work (final): 0.4463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6777
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6339  Z= 0.298
  Angle     :  0.656   6.898   8583  Z= 0.345
  Chirality :  0.046   0.163    918
  Planarity :  0.005   0.064   1095
  Dihedral  :  5.180  32.555    812
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 24.16 %
    Favored  : 70.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.30), residues: 747
  helix:  1.22 (0.39), residues: 177
  sheet:  0.03 (0.31), residues: 282
  loop : -1.97 (0.31), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 259 
 HIS   0.008   0.001   HIS B 187 
 PHE   0.023   0.003   PHE C 224 
 TYR   0.026   0.002   TYR B 176 
 ARG   0.005   0.001   ARG A 257 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 84
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 ARG cc_start: 0.7872 (mmm160) cc_final: 0.7263 (mtp85)
REVERT: A  291 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.5441 (mmt90)
REVERT: A  324 TRP cc_start: 0.6893 (m100) cc_final: 0.6278 (m-90)
REVERT: B  105 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.5869 (t80)
REVERT: C  215 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.7068 (m-30)
  outliers start: 36
  outliers final: 20
  residues processed: 113
  average time/residue: 0.1691
  time to fit residues: 25.8326
Evaluate side-chains
  104 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 CYS
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  230 PHE
Chi-restraints excluded: chain A residue  243 CYS
Chi-restraints excluded: chain A residue  291 ARG
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  169 CYS
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  232 LYS
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  169 CYS
Chi-restraints excluded: chain C residue  174 ILE
Chi-restraints excluded: chain C residue  177 ILE
Chi-restraints excluded: chain C residue  215 ASP
Chi-restraints excluded: chain C residue  282 THR
Chi-restraints excluded: chain C residue  320 THR
Chi-restraints excluded: chain C residue  333 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 72 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 73 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0050
   chunk 2 optimal weight:    5.9990
   overall best weight:    2.6002

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

Flipped N/Q/H residues before XYZ refinement:
** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 236 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.225828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.193355 restraints weight = 9888.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.4451 rms_B_bonded: 1.91
r_work: 0.4503 rms_B_bonded: 1.32 restraints_weight: 0.5000
r_work: 0.4425 rms_B_bonded: 2.26 restraints_weight: 0.2500
r_work (final): 0.4425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6890
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055   6339  Z= 0.433
  Angle     :  0.769   7.873   8583  Z= 0.412
  Chirality :  0.050   0.184    918
  Planarity :  0.006   0.077   1095
  Dihedral  :  5.854  26.965    810
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  6.55 %
    Allowed  : 25.47 %
    Favored  : 67.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.30), residues: 747
  helix:  0.98 (0.39), residues: 177
  sheet: -0.58 (0.30), residues: 300
  loop : -1.98 (0.32), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C 151 
 HIS   0.008   0.002   HIS B 187 
 PHE   0.032   0.004   PHE C 224 
 TYR   0.031   0.003   TYR B 176 
 ARG   0.005   0.001   ARG A 257 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 92
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 ARG cc_start: 0.7765 (mmm160) cc_final: 0.7181 (mtp85)
REVERT: A  143 ARG cc_start: 0.6046 (OUTLIER) cc_final: 0.5620 (ptt180)
REVERT: A  291 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.5437 (mmt90)
REVERT: B  105 TYR cc_start: 0.6670 (OUTLIER) cc_final: 0.5779 (t80)
REVERT: B  200 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.5649 (ppt170)
REVERT: B  237 VAL cc_start: 0.7091 (OUTLIER) cc_final: 0.6819 (t)
REVERT: B  277 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7109 (tt0)
REVERT: C  215 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6962 (m-30)
  outliers start: 45
  outliers final: 27
  residues processed: 129
  average time/residue: 0.1956
  time to fit residues: 32.7742
Evaluate side-chains
  120 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 86
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ARG
Chi-restraints excluded: chain A residue  169 CYS
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  199 ARG
Chi-restraints excluded: chain A residue  230 PHE
Chi-restraints excluded: chain A residue  243 CYS
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  291 ARG
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  169 CYS
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  200 ARG
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  232 LYS
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  169 CYS
Chi-restraints excluded: chain C residue  174 ILE
Chi-restraints excluded: chain C residue  177 ILE
Chi-restraints excluded: chain C residue  215 ASP
Chi-restraints excluded: chain C residue  228 GLU
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  282 THR
Chi-restraints excluded: chain C residue  320 THR
Chi-restraints excluded: chain C residue  333 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 72 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 12 optimal weight:    0.2980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 117 HIS ** 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 = 0.4730 r_free = 0.4730 target = 0.234334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.203989 restraints weight = 10116.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.4537 rms_B_bonded: 1.98
r_work: 0.4593 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.4510 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work (final): 0.4510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6760
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6339  Z= 0.185
  Angle     :  0.606   6.527   8583  Z= 0.317
  Chirality :  0.044   0.137    918
  Planarity :  0.005   0.047   1095
  Dihedral  :  5.118  22.800    810
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 27.51 %
    Favored  : 67.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.29), residues: 747
  helix:  1.02 (0.39), residues: 177
  sheet: -0.32 (0.32), residues: 258
  loop : -1.87 (0.29), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 151 
 HIS   0.005   0.001   HIS B 117 
 PHE   0.019   0.002   PHE A 111 
 TYR   0.031   0.002   TYR B 176 
 ARG   0.002   0.000   ARG B 290 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 91
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 ARG cc_start: 0.7684 (mmm160) cc_final: 0.7146 (mtm180)
REVERT: A  143 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.3906 (ppt-90)
REVERT: A  291 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.5386 (mmt90)
REVERT: B  105 TYR cc_start: 0.6580 (OUTLIER) cc_final: 0.5610 (t80)
REVERT: B  277 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7166 (tt0)
REVERT: C  117 HIS cc_start: 0.7532 (p-80) cc_final: 0.7297 (p90)
REVERT: C  215 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6794 (m-30)
REVERT: C  316 GLN cc_start: 0.7806 (tt0) cc_final: 0.7579 (tt0)
  outliers start: 34
  outliers final: 20
  residues processed: 117
  average time/residue: 0.1989
  time to fit residues: 30.3833
Evaluate side-chains
  112 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ARG
Chi-restraints excluded: chain A residue  169 CYS
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  199 ARG
Chi-restraints excluded: chain A residue  230 PHE
Chi-restraints excluded: chain A residue  243 CYS
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  291 ARG
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  169 CYS
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  232 LYS
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  169 CYS
Chi-restraints excluded: chain C residue  174 ILE
Chi-restraints excluded: chain C residue  177 ILE
Chi-restraints excluded: chain C residue  215 ASP
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  320 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 59 optimal weight:    0.4980
   chunk 2 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 163 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4738 r_free = 0.4738 target = 0.234497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.204574 restraints weight = 10206.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.4527 rms_B_bonded: 1.98
r_work: 0.4583 rms_B_bonded: 1.35 restraints_weight: 0.5000
r_work: 0.4501 rms_B_bonded: 2.34 restraints_weight: 0.2500
r_work (final): 0.4501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6794
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6339  Z= 0.243
  Angle     :  0.650   8.450   8583  Z= 0.336
  Chirality :  0.045   0.150    918
  Planarity :  0.005   0.047   1095
  Dihedral  :  5.120  23.607    810
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 27.07 %
    Favored  : 67.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.29), residues: 747
  helix:  0.98 (0.38), residues: 177
  sheet: -0.37 (0.32), residues: 258
  loop : -1.85 (0.29), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 324 
 HIS   0.005   0.001   HIS B 117 
 PHE   0.020   0.002   PHE A 111 
 TYR   0.032   0.002   TYR B 176 
 ARG   0.002   0.000   ARG A 290 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 90
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 ARG cc_start: 0.7636 (mmm160) cc_final: 0.7095 (mtp85)
REVERT: A  143 ARG cc_start: 0.6333 (OUTLIER) cc_final: 0.3958 (ppt-90)
REVERT: A  291 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.5473 (mmt90)
REVERT: A  324 TRP cc_start: 0.6951 (m100) cc_final: 0.6344 (m-90)
REVERT: B  105 TYR cc_start: 0.6644 (OUTLIER) cc_final: 0.5733 (t80)
REVERT: B  277 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7120 (tt0)
REVERT: C  117 HIS cc_start: 0.7541 (p-80) cc_final: 0.7287 (p90)
REVERT: C  215 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6832 (m-30)
REVERT: C  316 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7587 (tt0)
  outliers start: 39
  outliers final: 25
  residues processed: 118
  average time/residue: 0.1854
  time to fit residues: 28.8015
Evaluate side-chains
  119 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 88
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ARG
Chi-restraints excluded: chain A residue  169 CYS
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  199 ARG
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  230 PHE
Chi-restraints excluded: chain A residue  243 CYS
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  291 ARG
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  169 CYS
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  232 LYS
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  169 CYS
Chi-restraints excluded: chain C residue  174 ILE
Chi-restraints excluded: chain C residue  177 ILE
Chi-restraints excluded: chain C residue  215 ASP
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  282 THR
Chi-restraints excluded: chain C residue  316 GLN
Chi-restraints excluded: chain C residue  320 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 28 optimal weight:    0.0470
   chunk 0 optimal weight:    8.9990
   chunk 66 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0270
   chunk 38 optimal weight:    0.1980
   chunk 15 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 163 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4750 r_free = 0.4750 target = 0.236595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4620 r_free = 0.4620 target = 0.207245 restraints weight = 10085.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.4564 rms_B_bonded: 1.99
r_work: 0.4618 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.4539 rms_B_bonded: 2.48 restraints_weight: 0.2500
r_work (final): 0.4539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6706
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6339  Z= 0.162
  Angle     :  0.615   8.009   8583  Z= 0.313
  Chirality :  0.044   0.132    918
  Planarity :  0.004   0.044   1095
  Dihedral  :  4.795  22.344    810
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 28.97 %
    Favored  : 66.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.29), residues: 747
  helix:  1.05 (0.38), residues: 177
  sheet:  0.21 (0.35), residues: 222
  loop : -1.85 (0.27), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 324 
 HIS   0.005   0.001   HIS B 117 
 PHE   0.016   0.001   PHE A 111 
 TYR   0.040   0.002   TYR B 176 
 ARG   0.004   0.000   ARG A 112 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 86
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 ARG cc_start: 0.6329 (OUTLIER) cc_final: 0.3911 (ppt-90)
REVERT: A  291 ARG cc_start: 0.6440 (OUTLIER) cc_final: 0.5495 (mmt90)
REVERT: A  324 TRP cc_start: 0.6898 (m100) cc_final: 0.6289 (m-90)
REVERT: B  105 TYR cc_start: 0.6621 (OUTLIER) cc_final: 0.5676 (t80)
REVERT: B  277 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7124 (tt0)
REVERT: C  117 HIS cc_start: 0.7508 (p-80) cc_final: 0.7286 (p90)
REVERT: C  316 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7529 (tt0)
  outliers start: 28
  outliers final: 17
  residues processed: 105
  average time/residue: 0.1912
  time to fit residues: 26.3973
Evaluate side-chains
  106 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ARG
Chi-restraints excluded: chain A residue  169 CYS
Chi-restraints excluded: chain A residue  199 ARG
Chi-restraints excluded: chain A residue  230 PHE
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  291 ARG
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  169 CYS
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain C residue  169 CYS
Chi-restraints excluded: chain C residue  174 ILE
Chi-restraints excluded: chain C residue  282 THR
Chi-restraints excluded: chain C residue  316 GLN
Chi-restraints excluded: chain C residue  320 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0050
   chunk 11 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.7394

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

Flipped N/Q/H residues before XYZ refinement:
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 187 HIS
C 163 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4743 r_free = 0.4743 target = 0.235683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.205160 restraints weight = 10126.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.4554 rms_B_bonded: 2.06
r_work: 0.4611 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.4526 rms_B_bonded: 2.57 restraints_weight: 0.2500
r_work (final): 0.4526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6731
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6339  Z= 0.184
  Angle     :  0.635   7.972   8583  Z= 0.323
  Chirality :  0.044   0.141    918
  Planarity :  0.005   0.044   1095
  Dihedral  :  4.750  22.699    810
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 29.11 %
    Favored  : 66.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.28), residues: 747
  helix:  1.03 (0.37), residues: 177
  sheet:  0.21 (0.36), residues: 210
  loop : -1.74 (0.27), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 259 
 HIS   0.005   0.001   HIS B 117 
 PHE   0.029   0.002   PHE A 111 
 TYR   0.034   0.002   TYR B 176 
 ARG   0.004   0.000   ARG A 112 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 88
  time to evaluate  : 1.068 
Fit side-chains
REVERT: A  112 ARG cc_start: 0.7760 (mmm160) cc_final: 0.7086 (mtp85)
REVERT: A  143 ARG cc_start: 0.6374 (OUTLIER) cc_final: 0.3943 (ppt-90)
REVERT: A  291 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.5523 (mmt90)
REVERT: A  324 TRP cc_start: 0.6840 (m100) cc_final: 0.6221 (m-90)
REVERT: B  105 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.5664 (t80)
REVERT: C  117 HIS cc_start: 0.7538 (p-80) cc_final: 0.7290 (p90)
REVERT: C  316 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7556 (tt0)
  outliers start: 33
  outliers final: 22
  residues processed: 113
  average time/residue: 0.2170
  time to fit residues: 32.2160
Evaluate side-chains
  113 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ARG
Chi-restraints excluded: chain A residue  169 CYS
Chi-restraints excluded: chain A residue  199 ARG
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  230 PHE
Chi-restraints excluded: chain A residue  243 CYS
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  291 ARG
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  169 CYS
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  169 CYS
Chi-restraints excluded: chain C residue  174 ILE
Chi-restraints excluded: chain C residue  215 ASP
Chi-restraints excluded: chain C residue  282 THR
Chi-restraints excluded: chain C residue  316 GLN
Chi-restraints excluded: chain C residue  320 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   chunk 37 optimal weight:    0.8980
   chunk 31 optimal weight:    8.9990
   chunk 60 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 59 optimal weight:    0.2980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 187 HIS
C 163 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4748 r_free = 0.4748 target = 0.236514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4620 r_free = 0.4620 target = 0.206256 restraints weight = 10135.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.4560 rms_B_bonded: 2.06
r_work: 0.4616 rms_B_bonded: 1.49 restraints_weight: 0.5000
r_work: 0.4531 rms_B_bonded: 2.60 restraints_weight: 0.2500
r_work (final): 0.4531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6723
moved from start:          0.2928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6339  Z= 0.182
  Angle     :  0.633   8.647   8583  Z= 0.322
  Chirality :  0.044   0.140    918
  Planarity :  0.005   0.044   1095
  Dihedral  :  4.705  22.502    810
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 28.82 %
    Favored  : 66.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.28), residues: 747
  helix:  1.07 (0.38), residues: 177
  sheet:  0.39 (0.35), residues: 222
  loop : -1.83 (0.27), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 324 
 HIS   0.009   0.001   HIS B 117 
 PHE   0.026   0.002   PHE A 111 
 TYR   0.035   0.002   TYR B 176 
 ARG   0.002   0.000   ARG A 290 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 89
  time to evaluate  : 0.734 
Fit side-chains
REVERT: A  143 ARG cc_start: 0.6399 (OUTLIER) cc_final: 0.3973 (ppt-90)
REVERT: A  291 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.5661 (mmt90)
REVERT: A  324 TRP cc_start: 0.6930 (m100) cc_final: 0.6271 (m-90)
REVERT: B  105 TYR cc_start: 0.6632 (OUTLIER) cc_final: 0.5577 (t80)
REVERT: B  117 HIS cc_start: 0.6991 (p90) cc_final: 0.6309 (p90)
REVERT: B  200 ARG cc_start: 0.6345 (OUTLIER) cc_final: 0.6134 (ppt170)
REVERT: C  117 HIS cc_start: 0.7550 (p-80) cc_final: 0.7299 (p90)
REVERT: C  316 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7558 (tt0)
  outliers start: 32
  outliers final: 23
  residues processed: 113
  average time/residue: 0.1861
  time to fit residues: 27.6035
Evaluate side-chains
  115 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 87
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ARG
Chi-restraints excluded: chain A residue  169 CYS
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  199 ARG
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  230 PHE
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  291 ARG
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  169 CYS
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  200 ARG
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain C residue  169 CYS
Chi-restraints excluded: chain C residue  174 ILE
Chi-restraints excluded: chain C residue  215 ASP
Chi-restraints excluded: chain C residue  282 THR
Chi-restraints excluded: chain C residue  316 GLN
Chi-restraints excluded: chain C residue  320 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 68 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0020
   chunk 55 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0770
   chunk 37 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0570
   overall best weight:    0.3064

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

Flipped N/Q/H residues before XYZ refinement:
B 187 HIS
C 163 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4787 r_free = 0.4787 target = 0.240751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4705 r_free = 0.4705 target = 0.215718 restraints weight = 10213.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.4637 rms_B_bonded: 2.30
r_work: 0.4652 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.4551 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.4551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6661
moved from start:          0.3048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6339  Z= 0.152
  Angle     :  0.610   7.901   8583  Z= 0.307
  Chirality :  0.043   0.130    918
  Planarity :  0.004   0.043   1095
  Dihedral  :  4.427  21.214    810
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 30.71 %
    Favored  : 66.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.28), residues: 747
  helix:  1.23 (0.37), residues: 177
  sheet:  0.62 (0.36), residues: 204
  loop : -1.69 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 151 
 HIS   0.008   0.001   HIS B 117 
 PHE   0.033   0.001   PHE A 111 
 TYR   0.025   0.001   TYR B 176 
 ARG   0.003   0.000   ARG A 112 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3510.48 seconds
wall clock time: 60 minutes 50.28 seconds (3650.28 seconds total)