Starting phenix.real_space_refine
on Fri Aug 22 16:56:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h8f_34545/08_2025/8h8f_34545.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h8f_34545/08_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_34545/08_2025/8h8f_34545.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h8f_34545/08_2025/8h8f_34545.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h8f_34545/08_2025/8h8f_34545.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h8f_34545/08_2025/8h8f_34545.cif"
  }
  resolution = 3.48
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.34, per 1000 atoms: 0.22
  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: 0.41
  Conformation dependent library (CDL) restraints added in 163.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.26
  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: 0.93

  Time building geometry restraints manager: 0.58 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: 0.01
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:             2.840
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.520
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.750
-------------------------------------------------------------------------------
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   6342  Z= 0.201
  Angle     :  0.692   7.362   8589  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.006   0.000   ARG A 112 
 TYR   0.022   0.001   TYR B 176 
 PHE   0.013   0.002   PHE A 287 
 TRP   0.004   0.001   TRP B 250 
 HIS   0.004   0.001   HIS B 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 6339)
  covalent geometry    : angle       0.69195 ( 8583)
  SS BOND              : bond        0.00371 (    3)
  SS BOND              : angle       0.85995 (    6)
  hydrogen bonds       : bond        0.19556 (  287)
  hydrogen bonds       : angle       7.71563 (  882)

*********************** 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  : 0.154 
Fit side-chains
REVERT: A  143 ARG cc_start: 0.6143 (OUTLIER) cc_final: 0.5744 (ptt180)
  outliers start: 7
  outliers final: 3
  residues processed: 88
  average time/residue: 0.0743
  time to fit residues: 8.6575
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  : 0.294 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4993 r_free = 0.4993 target = 0.265160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.4884 r_free = 0.4884 target = 0.232676 restraints weight = 10333.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.4794 rms_B_bonded: 2.07
r_work: 0.4877 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.4796 rms_B_bonded: 2.52 restraints_weight: 0.2500
r_work (final): 0.4796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6647
moved from start:          0.0878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6342  Z= 0.135
  Angle     :  0.595   6.664   8589  Z= 0.310
  Chirality :  0.044   0.142    918
  Planarity :  0.005   0.057   1095
  Dihedral  :  5.251  43.051    822
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 23.44 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.30), residues: 747
  helix:  1.40 (0.39), residues: 177
  sheet:  0.65 (0.34), residues: 246
  loop : -1.71 (0.29), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 257 
 TYR   0.015   0.001   TYR B 176 
 PHE   0.017   0.002   PHE C 252 
 TRP   0.008   0.001   TRP B 259 
 HIS   0.004   0.001   HIS B 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6339)
  covalent geometry    : angle       0.59394 ( 8583)
  SS BOND              : bond        0.00526 (    3)
  SS BOND              : angle       1.26247 (    6)
  hydrogen bonds       : bond        0.03640 (  287)
  hydrogen bonds       : angle       5.26353 (  882)

*********************** 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
  105 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.235 
Fit side-chains
REVERT: C  105 TYR cc_start: 0.5289 (t80) cc_final: 0.4628 (t80)
  outliers start: 14
  outliers final: 7
  residues processed: 102
  average time/residue: 0.0694
  time to fit residues: 9.6052
Evaluate side-chains
  88 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 63 optimal weight:    1.9990
   chunk 74 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 33 optimal weight:    0.3980
   chunk 55 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 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 = 0.238576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.208361 restraints weight = 10112.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.4570 rms_B_bonded: 2.06
r_work: 0.4627 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.4544 rms_B_bonded: 2.54 restraints_weight: 0.2500
r_work (final): 0.4544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6656
moved from start:          0.1322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6342  Z= 0.125
  Angle     :  0.577   6.454   8589  Z= 0.300
  Chirality :  0.044   0.144    918
  Planarity :  0.004   0.051   1095
  Dihedral  :  4.810  39.552    812
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 24.60 %
    Favored  : 72.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.30), residues: 747
  helix:  1.35 (0.38), residues: 177
  sheet:  0.41 (0.33), residues: 258
  loop : -1.73 (0.30), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 257 
 TYR   0.029   0.002   TYR C 176 
 PHE   0.015   0.002   PHE C 252 
 TRP   0.008   0.001   TRP C 250 
 HIS   0.005   0.001   HIS B 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6339)
  covalent geometry    : angle       0.57598 ( 8583)
  SS BOND              : bond        0.00506 (    3)
  SS BOND              : angle       1.48785 (    6)
  hydrogen bonds       : bond        0.03249 (  287)
  hydrogen bonds       : angle       4.91103 (  882)

*********************** 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: 23
    poor density    : 87
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  112 ARG cc_start: 0.7863 (mmm160) cc_final: 0.7235 (mtp85)
REVERT: B  105 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.5748 (t80)
REVERT: B  144 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5408 (pp)
REVERT: C  105 TYR cc_start: 0.5214 (t80) cc_final: 0.4671 (t80)
REVERT: C  144 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.5898 (pp)
  outliers start: 23
  outliers final: 16
  residues processed: 105
  average time/residue: 0.0640
  time to fit residues: 9.2851
Evaluate side-chains
  98 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
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  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  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 52 optimal weight:    2.9990
   chunk 44 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0060
   chunk 4 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.9800

-------------------------------------------------------------------------------
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 = 0.237780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.207894 restraints weight = 10069.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.4557 rms_B_bonded: 2.06
r_work: 0.4614 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.4529 rms_B_bonded: 2.57 restraints_weight: 0.2500
r_work (final): 0.4529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6692
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6342  Z= 0.135
  Angle     :  0.589   6.456   8589  Z= 0.304
  Chirality :  0.044   0.148    918
  Planarity :  0.004   0.048   1095
  Dihedral  :  4.834  34.973    812
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 23.73 %
    Favored  : 71.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.30), residues: 747
  helix:  1.33 (0.39), residues: 177
  sheet:  0.47 (0.36), residues: 222
  loop : -1.69 (0.29), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 257 
 TYR   0.020   0.002   TYR C 176 
 PHE   0.016   0.002   PHE B 252 
 TRP   0.007   0.001   TRP C 250 
 HIS   0.005   0.001   HIS B 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6339)
  covalent geometry    : angle       0.58729 ( 8583)
  SS BOND              : bond        0.00592 (    3)
  SS BOND              : angle       1.62133 (    6)
  hydrogen bonds       : bond        0.03073 (  287)
  hydrogen bonds       : angle       4.75421 (  882)

*********************** 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
  121 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 87
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 PHE cc_start: 0.7236 (t80) cc_final: 0.6866 (t80)
REVERT: A  112 ARG cc_start: 0.7848 (mmm160) cc_final: 0.7247 (mtp85)
REVERT: A  324 TRP cc_start: 0.6853 (m100) cc_final: 0.6240 (m-90)
REVERT: B  105 TYR cc_start: 0.6675 (OUTLIER) cc_final: 0.5727 (t80)
REVERT: B  144 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.5697 (pp)
REVERT: C  144 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.5900 (pp)
  outliers start: 34
  outliers final: 19
  residues processed: 114
  average time/residue: 0.0560
  time to fit residues: 8.7577
Evaluate side-chains
  100 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
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 60 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   chunk 29 optimal weight:    0.2980
   chunk 3 optimal weight:    0.0870
   chunk 23 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.5760

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

Flipped N/Q/H residues before XYZ refinement:
A 117 HIS
A 236 GLN
B 117 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4776 r_free = 0.4776 target = 0.240009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.210050 restraints weight = 10290.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.4583 rms_B_bonded: 2.03
r_work: 0.4640 rms_B_bonded: 1.45 restraints_weight: 0.5000
r_work: 0.4554 rms_B_bonded: 2.55 restraints_weight: 0.2500
r_work (final): 0.4554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6649
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6342  Z= 0.109
  Angle     :  0.573   6.795   8589  Z= 0.292
  Chirality :  0.043   0.137    918
  Planarity :  0.004   0.046   1095
  Dihedral  :  4.688  32.594    812
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 24.89 %
    Favored  : 71.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.29), residues: 747
  helix:  1.37 (0.38), residues: 177
  sheet:  0.62 (0.43), residues: 165
  loop : -1.60 (0.26), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 257 
 TYR   0.026   0.001   TYR B 176 
 PHE   0.015   0.002   PHE A 111 
 TRP   0.009   0.001   TRP C 250 
 HIS   0.005   0.001   HIS B 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6339)
  covalent geometry    : angle       0.57231 ( 8583)
  SS BOND              : bond        0.00418 (    3)
  SS BOND              : angle       1.18709 (    6)
  hydrogen bonds       : bond        0.02835 (  287)
  hydrogen bonds       : angle       4.57930 (  882)

*********************** 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
  115 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 88
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 ARG cc_start: 0.7779 (mmm160) cc_final: 0.7284 (mtm180)
REVERT: A  291 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.5431 (mmt90)
REVERT: A  324 TRP cc_start: 0.6847 (m100) cc_final: 0.6233 (m-90)
REVERT: B  105 TYR cc_start: 0.6662 (OUTLIER) cc_final: 0.5652 (t80)
REVERT: C  144 LEU cc_start: 0.6280 (OUTLIER) cc_final: 0.5800 (pp)
  outliers start: 27
  outliers final: 20
  residues processed: 109
  average time/residue: 0.0873
  time to fit residues: 12.7107
Evaluate side-chains
  101 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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  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  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  284 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 51 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 54 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0870
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.6558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4779 r_free = 0.4779 target = 0.240115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.210139 restraints weight = 10103.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.4583 rms_B_bonded: 2.04
r_work: 0.4643 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.4559 rms_B_bonded: 2.54 restraints_weight: 0.2500
r_work (final): 0.4559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6652
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6342  Z= 0.112
  Angle     :  0.582   7.736   8589  Z= 0.295
  Chirality :  0.043   0.138    918
  Planarity :  0.004   0.044   1095
  Dihedral  :  4.604  29.788    812
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 24.89 %
    Favored  : 70.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.29), residues: 747
  helix:  1.38 (0.38), residues: 177
  sheet:  0.67 (0.43), residues: 162
  loop : -1.58 (0.25), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 257 
 TYR   0.027   0.001   TYR B 176 
 PHE   0.015   0.002   PHE C 252 
 TRP   0.009   0.001   TRP C 324 
 HIS   0.004   0.001   HIS C 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6339)
  covalent geometry    : angle       0.58118 ( 8583)
  SS BOND              : bond        0.00431 (    3)
  SS BOND              : angle       1.22694 (    6)
  hydrogen bonds       : bond        0.02776 (  287)
  hydrogen bonds       : angle       4.45213 (  882)

*********************** 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
  114 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 84
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 ARG cc_start: 0.7781 (mmm160) cc_final: 0.7361 (mtp85)
REVERT: A  143 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.4302 (ppt-90)
REVERT: A  291 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.5612 (mmt90)
REVERT: B  105 TYR cc_start: 0.6697 (OUTLIER) cc_final: 0.5776 (t80)
  outliers start: 30
  outliers final: 22
  residues processed: 109
  average time/residue: 0.0924
  time to fit residues: 13.2530
Evaluate side-chains
  104 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 79
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
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  169 CYS
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  191 VAL
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  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  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 32 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 74 optimal weight:    8.9990
   chunk 44 optimal weight:    0.3980
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 67 optimal weight:    0.3980
   chunk 6 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
B 236 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4750 r_free = 0.4750 target = 0.236623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.206350 restraints weight = 10120.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.4559 rms_B_bonded: 2.01
r_work: 0.4612 rms_B_bonded: 1.42 restraints_weight: 0.5000
r_work: 0.4526 rms_B_bonded: 2.47 restraints_weight: 0.2500
r_work (final): 0.4526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6720
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6342  Z= 0.143
  Angle     :  0.607   7.698   8589  Z= 0.313
  Chirality :  0.044   0.152    918
  Planarity :  0.004   0.044   1095
  Dihedral  :  4.669  22.916    810
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 24.75 %
    Favored  : 70.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.29), residues: 747
  helix:  1.31 (0.38), residues: 177
  sheet:  0.39 (0.36), residues: 210
  loop : -1.65 (0.27), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 290 
 TYR   0.032   0.002   TYR B 176 
 PHE   0.018   0.002   PHE C 252 
 TRP   0.011   0.001   TRP C 324 
 HIS   0.004   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6339)
  covalent geometry    : angle       0.60548 ( 8583)
  SS BOND              : bond        0.00615 (    3)
  SS BOND              : angle       1.77834 (    6)
  hydrogen bonds       : bond        0.03068 (  287)
  hydrogen bonds       : angle       4.58871 (  882)

*********************** 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
  116 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 83
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 ARG cc_start: 0.7803 (mmm160) cc_final: 0.7366 (mtp85)
REVERT: A  143 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.4347 (ppt-90)
REVERT: A  291 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.5672 (mmt90)
REVERT: A  324 TRP cc_start: 0.6835 (m100) cc_final: 0.6272 (m-90)
REVERT: B  105 TYR cc_start: 0.6548 (OUTLIER) cc_final: 0.5659 (t80)
  outliers start: 33
  outliers final: 22
  residues processed: 110
  average time/residue: 0.0896
  time to fit residues: 12.9734
Evaluate side-chains
  105 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
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  169 CYS
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  191 VAL
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  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  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 40 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0570
   chunk 12 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 32 optimal weight:    0.1980
   chunk 3 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.7100

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4773 r_free = 0.4773 target = 0.239393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.4641 r_free = 0.4641 target = 0.209256 restraints weight = 10170.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.4577 rms_B_bonded: 2.00
r_work: 0.4628 rms_B_bonded: 1.42 restraints_weight: 0.5000
r_work: 0.4544 rms_B_bonded: 2.46 restraints_weight: 0.2500
r_work (final): 0.4544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6680
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6342  Z= 0.116
  Angle     :  0.588   7.162   8589  Z= 0.299
  Chirality :  0.044   0.141    918
  Planarity :  0.004   0.043   1095
  Dihedral  :  4.567  22.205    810
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 24.89 %
    Favored  : 70.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.29), residues: 747
  helix:  1.28 (0.38), residues: 177
  sheet:  0.45 (0.36), residues: 213
  loop : -1.62 (0.27), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 290 
 TYR   0.031   0.001   TYR B 176 
 PHE   0.016   0.002   PHE A 111 
 TRP   0.012   0.001   TRP C 324 
 HIS   0.004   0.001   HIS C 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6339)
  covalent geometry    : angle       0.58671 ( 8583)
  SS BOND              : bond        0.00469 (    3)
  SS BOND              : angle       1.32531 (    6)
  hydrogen bonds       : bond        0.02838 (  287)
  hydrogen bonds       : angle       4.46638 (  882)

*********************** 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
  112 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 83
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 ARG cc_start: 0.7730 (mmm160) cc_final: 0.7399 (mtp85)
REVERT: A  143 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.4295 (ppt-90)
REVERT: A  291 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.5648 (mmt90)
REVERT: A  324 TRP cc_start: 0.6816 (m100) cc_final: 0.6275 (m-90)
REVERT: B  105 TYR cc_start: 0.6580 (OUTLIER) cc_final: 0.5661 (t80)
  outliers start: 29
  outliers final: 23
  residues processed: 106
  average time/residue: 0.0902
  time to fit residues: 12.6191
Evaluate side-chains
  106 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 80
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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  169 CYS
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  191 VAL
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  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  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 43 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0980
   chunk 37 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.8184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4763 r_free = 0.4763 target = 0.238712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.208113 restraints weight = 10168.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.4570 rms_B_bonded: 2.00
r_work: 0.4629 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.4545 rms_B_bonded: 2.46 restraints_weight: 0.2500
r_work (final): 0.4545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6689
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6342  Z= 0.123
  Angle     :  0.596   7.040   8589  Z= 0.305
  Chirality :  0.044   0.146    918
  Planarity :  0.004   0.043   1095
  Dihedral  :  4.558  22.441    810
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 25.18 %
    Favored  : 70.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.29), residues: 747
  helix:  2.02 (0.38), residues: 159
  sheet:  0.42 (0.36), residues: 210
  loop : -1.58 (0.27), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 290 
 TYR   0.032   0.002   TYR B 176 
 PHE   0.023   0.002   PHE A 111 
 TRP   0.012   0.001   TRP C 324 
 HIS   0.004   0.001   HIS C 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6339)
  covalent geometry    : angle       0.59473 ( 8583)
  SS BOND              : bond        0.00506 (    3)
  SS BOND              : angle       1.42060 (    6)
  hydrogen bonds       : bond        0.02885 (  287)
  hydrogen bonds       : angle       4.48208 (  882)

*********************** 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
  112 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 82
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 ARG cc_start: 0.7658 (mmm160) cc_final: 0.7386 (mtm180)
REVERT: A  143 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.4327 (ppt-90)
REVERT: A  291 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.5683 (mmt90)
REVERT: A  324 TRP cc_start: 0.6842 (m100) cc_final: 0.6250 (m-90)
REVERT: B  105 TYR cc_start: 0.6643 (OUTLIER) cc_final: 0.5703 (t80)
REVERT: B  277 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7264 (tt0)
  outliers start: 30
  outliers final: 24
  residues processed: 104
  average time/residue: 0.0856
  time to fit residues: 11.6759
Evaluate side-chains
  106 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 78
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
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  169 CYS
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  177 ILE
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 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  195 ARG
Chi-restraints excluded: chain C residue  215 ASP
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 8 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0570
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.1502

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

Flipped N/Q/H residues before XYZ refinement:
B 208 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 = 0.4760 r_free = 0.4760 target = 0.237881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.206985 restraints weight = 10169.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.4553 rms_B_bonded: 2.09
r_work: 0.4608 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.4526 rms_B_bonded: 2.48 restraints_weight: 0.2500
r_work (final): 0.4526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6738
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6342  Z= 0.149
  Angle     :  0.632   7.314   8589  Z= 0.327
  Chirality :  0.045   0.159    918
  Planarity :  0.004   0.044   1095
  Dihedral  :  4.730  23.223    810
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 25.47 %
    Favored  : 70.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.29), residues: 747
  helix:  1.95 (0.38), residues: 159
  sheet:  0.41 (0.35), residues: 219
  loop : -1.70 (0.27), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 290 
 TYR   0.034   0.002   TYR B 176 
 PHE   0.023   0.002   PHE A 111 
 TRP   0.010   0.001   TRP C 324 
 HIS   0.004   0.001   HIS C 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6339)
  covalent geometry    : angle       0.63051 ( 8583)
  SS BOND              : bond        0.00665 (    3)
  SS BOND              : angle       1.82611 (    6)
  hydrogen bonds       : bond        0.03185 (  287)
  hydrogen bonds       : angle       4.62008 (  882)

********************** 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
  109 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 78
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.4003 (ppt-90)
REVERT: A  291 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.5666 (mmt90)
REVERT: A  324 TRP cc_start: 0.6876 (m100) cc_final: 0.6270 (m-90)
REVERT: B  105 TYR cc_start: 0.6645 (OUTLIER) cc_final: 0.5750 (t80)
REVERT: B  277 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7268 (tt0)
REVERT: C  111 PHE cc_start: 0.8341 (t80) cc_final: 0.8039 (t80)
  outliers start: 31
  outliers final: 25
  residues processed: 102
  average time/residue: 0.0847
  time to fit residues: 11.4233
Evaluate side-chains
  106 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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  169 CYS
Chi-restraints excluded: chain B residue  173 ASP
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 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  195 ARG
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 34 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 71 optimal weight:    0.4980
   chunk 27 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 70 optimal weight:    0.5980
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4775 r_free = 0.4775 target = 0.239726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.209464 restraints weight = 10173.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.4574 rms_B_bonded: 2.10
r_work: 0.4628 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.4542 rms_B_bonded: 2.52 restraints_weight: 0.2500
r_work (final): 0.4542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6702
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6342  Z= 0.122
  Angle     :  0.606   7.099   8589  Z= 0.310
  Chirality :  0.044   0.147    918
  Planarity :  0.004   0.043   1095
  Dihedral  :  4.602  22.278    810
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 25.76 %
    Favored  : 70.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.29), residues: 747
  helix:  1.92 (0.37), residues: 159
  sheet:  0.33 (0.36), residues: 210
  loop : -1.55 (0.28), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 290 
 TYR   0.031   0.002   TYR B 176 
 PHE   0.027   0.002   PHE A 111 
 TRP   0.011   0.001   TRP C 324 
 HIS   0.004   0.001   HIS C 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6339)
  covalent geometry    : angle       0.60517 ( 8583)
  SS BOND              : bond        0.00456 (    3)
  SS BOND              : angle       1.34124 (    6)
  hydrogen bonds       : bond        0.02927 (  287)
  hydrogen bonds       : angle       4.50236 (  882)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1690.44 seconds
wall clock time: 29 minutes 40.01 seconds (1780.01 seconds total)