Starting phenix.real_space_refine
on Tue Feb 11 15:38:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h8f_34545/02_2025/8h8f_34545.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h8f_34545/02_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_34545/02_2025/8h8f_34545.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h8f_34545/02_2025/8h8f_34545.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h8f_34545/02_2025/8h8f_34545.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h8f_34545/02_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.33, per 1000 atoms: 0.70
  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: 1.36
  Conformation dependent library (CDL) restraints added in 940.0 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: 0.62
  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: 1.57

  Time building geometry restraints manager: 1.60 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:             1.640
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.650
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.520
-------------------------------------------------------------------------------
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  : 0.660 
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: 0.1782
  time to fit residues: 20.8039
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  : 0.758 
-------------------------------------------------------------------------------
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 = 67)----------------|
| r_work = 0.4618 r_free = 0.4618 target = 0.207521 restraints weight = 9963.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.4563 rms_B_bonded: 1.99
r_work: 0.4622 rms_B_bonded: 1.42 restraints_weight: 0.5000
r_work: 0.4538 rms_B_bonded: 2.48 restraints_weight: 0.2500
r_work (final): 0.4538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6668
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  : 0.653 
Fit side-chains
  outliers start: 16
  outliers final: 8
  residues processed: 102
  average time/residue: 0.1736
  time to fit residues: 23.6948
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  : 0.670 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 5 optimal weight:    5.9990
   chunk 62 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4763 r_free = 0.4763 target = 0.238571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.208398 restraints weight = 10085.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.4572 rms_B_bonded: 2.04
r_work: 0.4631 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.4544 rms_B_bonded: 2.58 restraints_weight: 0.2500
r_work (final): 0.4544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6664
moved from start:          0.1380

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= 0.181
  Angle     :  0.573   6.998   8583  Z= 0.298
  Chirality :  0.044   0.142    918
  Planarity :  0.004   0.051   1095
  Dihedral  :  4.806  38.633    812
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 25.47 %
    Favored  : 71.47 %
  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:  1.32 (0.38), residues: 177
  sheet:  0.40 (0.33), residues: 258
  loop : -1.75 (0.31), residues: 312

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   0.014   0.002   PHE C 224 
 TYR   0.029   0.002   TYR C 176 
 ARG   0.003   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
  110 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.740 
Fit side-chains
REVERT: A  112 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7374 (mtp85)
REVERT: B  105 TYR cc_start: 0.6552 (OUTLIER) cc_final: 0.5649 (t80)
REVERT: B  144 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5437 (pp)
REVERT: C  105 TYR cc_start: 0.5142 (t80) cc_final: 0.4588 (t80)
  outliers start: 21
  outliers final: 14
  residues processed: 106
  average time/residue: 0.1675
  time to fit residues: 24.3221
Evaluate side-chains
  96 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
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  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
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:    0.0050
   chunk 25 optimal weight:    9.9990
   chunk 21 optimal weight:    5.9990
   chunk 72 optimal weight:    8.9990
   chunk 11 optimal weight:    0.2980
   chunk 39 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.9996

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4746 r_free = 0.4746 target = 0.237438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.207062 restraints weight = 10092.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.4558 rms_B_bonded: 2.04
r_work: 0.4615 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.4532 rms_B_bonded: 2.52 restraints_weight: 0.2500
r_work (final): 0.4532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6692
moved from start:          0.1633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6339  Z= 0.202
  Angle     :  0.591   7.388   8583  Z= 0.304
  Chirality :  0.044   0.147    918
  Planarity :  0.004   0.048   1095
  Dihedral  :  4.836  35.096    812
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 23.58 %
    Favored  : 71.47 %
  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: -0.44 (0.30), residues: 747
  helix:  1.33 (0.38), residues: 177
  sheet:  0.48 (0.36), residues: 219
  loop : -1.71 (0.28), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 259 
 HIS   0.005   0.001   HIS B 187 
 PHE   0.017   0.002   PHE B 252 
 TYR   0.020   0.002   TYR B 176 
 ARG   0.003   0.000   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
  119 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 85
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 ARG cc_start: 0.7899 (mmm160) cc_final: 0.7211 (mtm180)
REVERT: A  324 TRP cc_start: 0.6739 (m100) cc_final: 0.6205 (m-90)
REVERT: B  105 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.5699 (t80)
REVERT: B  144 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.6162 (tt)
REVERT: C  144 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.5869 (pp)
  outliers start: 34
  outliers final: 19
  residues processed: 113
  average time/residue: 0.1638
  time to fit residues: 25.2551
Evaluate side-chains
  99 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
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  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  173 ASP
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  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:    0.9980
   chunk 72 optimal weight:    5.9990
   chunk 53 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.4752 r_free = 0.4752 target = 0.237220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.206389 restraints weight = 10103.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.4560 rms_B_bonded: 2.09
r_work: 0.4619 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.4532 rms_B_bonded: 2.62 restraints_weight: 0.2500
r_work (final): 0.4532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6700
moved from start:          0.1886

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= 0.190
  Angle     :  0.590   6.858   8583  Z= 0.302
  Chirality :  0.044   0.145    918
  Planarity :  0.004   0.046   1095
  Dihedral  :  4.770  31.656    812
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 25.04 %
    Favored  : 70.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.29), residues: 747
  helix:  1.32 (0.38), residues: 177
  sheet:  0.64 (0.44), residues: 159
  loop : -1.66 (0.25), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 259 
 HIS   0.005   0.001   HIS B 117 
 PHE   0.015   0.002   PHE C 252 
 TYR   0.028   0.002   TYR B 176 
 ARG   0.003   0.000   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
  118 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 86
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 ARG cc_start: 0.7862 (mmm160) cc_final: 0.7298 (mtp85)
REVERT: A  143 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.4313 (ppt-90)
REVERT: A  324 TRP cc_start: 0.6802 (m100) cc_final: 0.6164 (m-90)
REVERT: B  105 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.5682 (t80)
REVERT: B  144 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6211 (tt)
  outliers start: 32
  outliers final: 24
  residues processed: 111
  average time/residue: 0.1746
  time to fit residues: 25.8739
Evaluate side-chains
  105 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 78
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
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  287 PHE
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  191 VAL
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  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  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:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 10 optimal weight:    0.1980
   chunk 65 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4733 r_free = 0.4733 target = 0.234691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.203961 restraints weight = 10046.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.4533 rms_B_bonded: 2.00
r_work: 0.4591 rms_B_bonded: 1.40 restraints_weight: 0.5000
r_work: 0.4508 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.4508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6762
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6339  Z= 0.253
  Angle     :  0.640   8.057   8583  Z= 0.332
  Chirality :  0.045   0.158    918
  Planarity :  0.005   0.055   1095
  Dihedral  :  4.918  23.878    810
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 25.18 %
    Favored  : 69.14 %
  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 (0.29), residues: 747
  helix:  1.23 (0.38), residues: 177
  sheet:  0.28 (0.36), residues: 216
  loop : -1.82 (0.26), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 324 
 HIS   0.006   0.001   HIS B 187 
 PHE   0.021   0.002   PHE C 224 
 TYR   0.034   0.002   TYR B 176 
 ARG   0.003   0.000   ARG A 257 

*********************** 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
  124 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 85
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 ARG cc_start: 0.7896 (mmm160) cc_final: 0.7362 (mtp85)
REVERT: A  143 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.3990 (ppt-90)
REVERT: A  291 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.5735 (mmt90)
REVERT: B  105 TYR cc_start: 0.6564 (OUTLIER) cc_final: 0.5607 (t80)
REVERT: B  277 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7180 (tt0)
  outliers start: 39
  outliers final: 29
  residues processed: 117
  average time/residue: 0.1936
  time to fit residues: 29.5241
Evaluate side-chains
  114 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 81
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
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  287 PHE
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  184 THR
Chi-restraints excluded: chain B residue  191 VAL
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  237 VAL
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  244 GLU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 59 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.236167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.205725 restraints weight = 10055.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.4554 rms_B_bonded: 2.04
r_work: 0.4609 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.4525 rms_B_bonded: 2.53 restraints_weight: 0.2500
r_work (final): 0.4525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6730
moved from start:          0.2322

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= 0.193
  Angle     :  0.596   7.677   8583  Z= 0.306
  Chirality :  0.044   0.145    918
  Planarity :  0.004   0.044   1095
  Dihedral  :  4.712  22.479    810
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 26.06 %
    Favored  : 68.70 %
  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: -0.55 (0.29), residues: 747
  helix:  1.25 (0.38), residues: 177
  sheet:  0.38 (0.36), residues: 216
  loop : -1.74 (0.27), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 324 
 HIS   0.004   0.001   HIS C 187 
 PHE   0.015   0.002   PHE C 252 
 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
  118 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 82
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 ARG cc_start: 0.7827 (mmm160) cc_final: 0.7421 (mtp85)
REVERT: A  143 ARG cc_start: 0.6514 (OUTLIER) cc_final: 0.3993 (ppt-90)
REVERT: A  291 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.5495 (mmt90)
REVERT: A  324 TRP cc_start: 0.6745 (m100) cc_final: 0.6185 (m-90)
REVERT: B  105 TYR cc_start: 0.6523 (OUTLIER) cc_final: 0.5581 (t80)
  outliers start: 36
  outliers final: 27
  residues processed: 111
  average time/residue: 0.1842
  time to fit residues: 27.0467
Evaluate side-chains
  109 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 79
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
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  173 ASP
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  184 THR
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  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  244 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 28 optimal weight:    0.2980
   chunk 0 optimal weight:    8.9990
   chunk 66 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.4764 r_free = 0.4764 target = 0.238059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.206561 restraints weight = 9790.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.4555 rms_B_bonded: 1.98
r_work: 0.4613 rms_B_bonded: 1.37 restraints_weight: 0.5000
r_work: 0.4530 rms_B_bonded: 2.39 restraints_weight: 0.2500
r_work (final): 0.4530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6731
moved from start:          0.2458

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= 0.207
  Angle     :  0.614   7.370   8583  Z= 0.315
  Chirality :  0.044   0.148    918
  Planarity :  0.005   0.044   1095
  Dihedral  :  4.722  23.037    810
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 26.06 %
    Favored  : 68.85 %
  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 (0.29), residues: 747
  helix:  1.94 (0.38), residues: 159
  sheet:  0.33 (0.36), residues: 219
  loop : -1.78 (0.27), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 324 
 HIS   0.004   0.001   HIS C 187 
 PHE   0.017   0.002   PHE A 111 
 TYR   0.034   0.002   TYR B 176 
 ARG   0.002   0.000   ARG A 290 

*********************** 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
  113 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 78
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 ARG cc_start: 0.7741 (mmm160) cc_final: 0.7410 (mtp85)
REVERT: A  143 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.4009 (ppt-90)
REVERT: A  291 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.5705 (mmt90)
REVERT: A  324 TRP cc_start: 0.6828 (m100) cc_final: 0.6269 (m-90)
REVERT: B  105 TYR cc_start: 0.6664 (OUTLIER) cc_final: 0.5653 (t80)
REVERT: B  277 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7276 (tt0)
  outliers start: 35
  outliers final: 28
  residues processed: 106
  average time/residue: 0.1915
  time to fit residues: 26.6530
Evaluate side-chains
  110 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 78
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
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  177 ILE
Chi-restraints excluded: chain B residue  184 THR
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  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  244 GLU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0870
   overall best weight:    0.6958

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.238194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.207934 restraints weight = 10050.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.4571 rms_B_bonded: 2.00
r_work: 0.4631 rms_B_bonded: 1.37 restraints_weight: 0.5000
r_work: 0.4546 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.4546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6691
moved from start:          0.2544

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= 0.176
  Angle     :  0.603   8.926   8583  Z= 0.307
  Chirality :  0.044   0.147    918
  Planarity :  0.004   0.043   1095
  Dihedral  :  4.615  22.330    810
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 26.64 %
    Favored  : 68.70 %
  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: -0.56 (0.29), residues: 747
  helix:  1.24 (0.37), residues: 177
  sheet:  0.95 (0.43), residues: 156
  loop : -1.72 (0.26), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 324 
 HIS   0.004   0.001   HIS C 187 
 PHE   0.021   0.002   PHE A 111 
 TYR   0.033   0.002   TYR B 176 
 ARG   0.002   0.000   ARG A 290 

*********************** 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
  114 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 82
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 ARG cc_start: 0.7653 (mmm160) cc_final: 0.7373 (mtm180)
REVERT: A  143 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.3853 (ppt-90)
REVERT: A  291 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.5787 (mmt90)
REVERT: A  324 TRP cc_start: 0.6848 (m100) cc_final: 0.6280 (m-90)
REVERT: B  105 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.5653 (t80)
REVERT: B  277 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7245 (tt0)
REVERT: C  117 HIS cc_start: 0.7467 (p-80) cc_final: 0.7256 (p90)
REVERT: C  316 GLN cc_start: 0.7803 (tt0) cc_final: 0.7523 (tp40)
  outliers start: 32
  outliers final: 26
  residues processed: 107
  average time/residue: 0.1790
  time to fit residues: 25.3324
Evaluate side-chains
  109 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 79
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
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  177 ILE
Chi-restraints excluded: chain B residue  184 THR
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 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  244 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.4740 r_free = 0.4740 target = 0.235318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.204492 restraints weight = 10185.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.4529 rms_B_bonded: 2.05
r_work: 0.4583 rms_B_bonded: 1.39 restraints_weight: 0.5000
r_work: 0.4500 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.4500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6792
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6339  Z= 0.280
  Angle     :  0.672   8.629   8583  Z= 0.348
  Chirality :  0.046   0.158    918
  Planarity :  0.005   0.053   1095
  Dihedral  :  4.976  23.869    810
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 26.78 %
    Favored  : 68.41 %
  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: -0.57 (0.29), residues: 747
  helix:  1.80 (0.38), residues: 159
  sheet:  0.23 (0.36), residues: 219
  loop : -1.83 (0.27), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 324 
 HIS   0.005   0.001   HIS B 187 
 PHE   0.023   0.003   PHE A 111 
 TYR   0.040   0.002   TYR B 176 
 ARG   0.003   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
  115 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 82
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.3871 (ppt-90)
REVERT: A  291 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.5772 (mmt90)
REVERT: A  324 TRP cc_start: 0.6876 (m100) cc_final: 0.6244 (m-90)
REVERT: B  105 TYR cc_start: 0.6617 (OUTLIER) cc_final: 0.5762 (t80)
REVERT: B  200 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.4319 (ppt170)
REVERT: B  277 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7189 (tt0)
REVERT: B  316 GLN cc_start: 0.7519 (mp10) cc_final: 0.7268 (mp10)
REVERT: C  117 HIS cc_start: 0.7584 (p-80) cc_final: 0.7328 (p90)
  outliers start: 33
  outliers final: 24
  residues processed: 108
  average time/residue: 0.1940
  time to fit residues: 27.1728
Evaluate side-chains
  111 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 82
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
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  184 THR
Chi-restraints excluded: chain B residue  200 ARG
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  277 GLU
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  244 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   chunk 68 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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**
C 163 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4745 r_free = 0.4745 target = 0.236288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4608 r_free = 0.4608 target = 0.205630 restraints weight = 10208.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.4553 rms_B_bonded: 2.02
r_work: 0.4610 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.4527 rms_B_bonded: 2.47 restraints_weight: 0.2500
r_work (final): 0.4527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
moved from start:          0.2774

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= 0.201
  Angle     :  0.632   8.489   8583  Z= 0.324
  Chirality :  0.044   0.156    918
  Planarity :  0.005   0.044   1095
  Dihedral  :  4.777  22.688    810
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 26.64 %
    Favored  : 68.27 %
  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: -0.68 (0.29), residues: 747
  helix:  1.09 (0.37), residues: 177
  sheet:  0.28 (0.35), residues: 219
  loop : -1.81 (0.28), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 324 
 HIS   0.004   0.001   HIS C 187 
 PHE   0.029   0.002   PHE A 111 
 TYR   0.041   0.002   TYR B 176 
 ARG   0.002   0.000   ARG A 290 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3472.39 seconds
wall clock time: 62 minutes 17.70 seconds (3737.70 seconds total)