Starting phenix.real_space_refine
on Thu Jan 16 21:46:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjw_39352/01_2025/8yjw_39352.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjw_39352/01_2025/8yjw_39352.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yjw_39352/01_2025/8yjw_39352.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjw_39352/01_2025/8yjw_39352.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjw_39352/01_2025/8yjw_39352.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjw_39352/01_2025/8yjw_39352.cif"
  }
  resolution = 3.55
  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=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 164 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P      63      5.49       5
     S      63      5.16       5
     C    6067      2.51       5
     N    1667      2.21       5
     O    2086      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 9946
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 1955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1955
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 7, 'TRANS': 246}
    Chain: "C"
      Number of atoms: 1972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 1972
          Classifications: {'peptide': 256}
          Link IDs: {'PTRANS': 7, 'TRANS': 248}
    Chain: "D"
      Number of atoms: 2774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2774
          Classifications: {'peptide': 352}
          Link IDs: {'PTRANS': 15, 'TRANS': 336}
    Chain: "A"
      Number of atoms: 1955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1955
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 7, 'TRANS': 246}
    Chain: "J"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 407
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "E"
      Number of atoms: 621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 621
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "H"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 60
          Classifications: {'DNA': 3}
          Link IDs: {'rna3p': 2}
    Chain: "F"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 202
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
  Time building chain proxies: 6.66, per 1000 atoms: 0.67
  Number of scatterers: 9946
  At special positions: 0
  Unit cell: (102.09, 101.26, 113.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      63     16.00
     P      63     15.00
     O    2086      8.00
     N    1667      7.00
     C    6067      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 135 " - pdb=" SG  CYS B 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 135 " - pdb=" SG  CYS C 162 " 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: 2.39
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2108

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 10 sheets defined
      29.9% alpha, 24.9% beta
      11 base pairs and 50 stacking pairs defined.
    Time for finding SS restraints: 3.66
  Creating SS restraints...
    Processing helix  chain 'B' and resid 9 through 20
      removed outlier: 3.937A  pdb=" N   LYS B  13 " --> pdb=" O   GLY B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 80
    Processing helix  chain 'B' and resid 141 through 152
    Processing helix  chain 'B' and resid 209 through 216
    Processing helix  chain 'C' and resid 8 through 23
      removed outlier: 4.088A  pdb=" N   LEU C  12 " --> pdb=" O   GLN C   8 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   ASP C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   LEU C  22 " --> pdb=" O   ALA C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 80
    Processing helix  chain 'C' and resid 141 through 152
    Processing helix  chain 'C' and resid 209 through 216
    Processing helix  chain 'C' and resid 217 through 219
      No H-bonds generated for 'chain 'C' and resid 217 through 219'
    Processing helix  chain 'D' and resid 6 through 14
    Processing helix  chain 'D' and resid 35 through 46
    Processing helix  chain 'D' and resid 61 through 77
    Processing helix  chain 'D' and resid 90 through 92
      No H-bonds generated for 'chain 'D' and resid 90 through 92'
    Processing helix  chain 'D' and resid 93 through 118
      removed outlier: 3.740A  pdb=" N   ALA D 116 " --> pdb=" O   GLN D 112 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 129
    Processing helix  chain 'D' and resid 134 through 149
      removed outlier: 3.520A  pdb=" N   ASN D 138 " --> pdb=" O   THR D 134 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLY D 149 " --> pdb=" O   LEU D 145 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 158 through 169
    Processing helix  chain 'D' and resid 181 through 186
    Processing helix  chain 'D' and resid 209 through 216
    Processing helix  chain 'D' and resid 219 through 231
      removed outlier: 3.501A  pdb=" N   PHE D 223 " --> pdb=" O   ASN D 219 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 242 through 253
      removed outlier: 3.569A  pdb=" N   ALA D 246 " --> pdb=" O   GLY D 242 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 263
      removed outlier: 3.617A  pdb=" N   ILE D 259 " --> pdb=" O   SER D 255 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 276 through 285
    Processing helix  chain 'D' and resid 303 through 311
    Processing helix  chain 'D' and resid 317 through 335
      removed outlier: 3.826A  pdb=" N   ILE D 321 " --> pdb=" O   SER D 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 8 through 23
      removed outlier: 4.269A  pdb=" N   LEU A  12 " --> pdb=" O   GLN A   8 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   ASP A  21 " --> pdb=" O   GLU A  17 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   LEU A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 82
    Processing helix  chain 'A' and resid 140 through 155
      removed outlier: 4.369A  pdb=" N   HIS A 153 " --> pdb=" O   ARG A 149 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   ILE A 154 " --> pdb=" O   ASP A 150 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLY A 155 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
    Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 61
      removed outlier: 3.558A  pdb=" N   THR B  59 " --> pdb=" O   ARG B   5 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ALA B   4 " --> pdb=" O   LEU B  90 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER B 112 " --> pdb=" O   PHE B 103 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLY A 176 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 71
      removed outlier: 4.006A  pdb=" N   MET B  68 " --> pdb=" O   TRP B  28 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   GLU B  25 " --> pdb=" O   MET B  40 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   MET B  40 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 5.716A  pdb=" N   CYS B  27 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   GLN B  38 " --> pdb=" O   CYS B  27 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   LYS B 240 " --> pdb=" O   THR B 224 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   THR B 224 " --> pdb=" O   LYS B 240 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU B 227 " --> pdb=" O   VAL B 137 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 204 through 208
      removed outlier: 5.207A  pdb=" N   ALA B 157 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   SER B 172 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   THR C  59 " --> pdb=" O   ARG C   5 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 67 through 71
      removed outlier: 5.865A  pdb=" N   CYS C  27 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   GLN C  38 " --> pdb=" O   CYS C  27 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLN C  49 " --> pdb=" O   LYS C 248 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   SER C 230 " --> pdb=" O   PRO C 234 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 122 through 123
    Processing sheet with id=AA6, first strand: chain 'C' and resid 204 through 208
      removed outlier: 5.381A  pdb=" N   ALA C 157 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   SER C 172 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   LEU A  99 " --> pdb=" O   MET A 116 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   THR A  59 " --> pdb=" O   ARG A   5 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 18 through 21
      removed outlier: 6.653A  pdb=" N   ALA D 175 " --> pdb=" O   MET D 191 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   LYS D  30 " --> pdb=" O   ALA D 174 " (cutoff:3.500A)
      removed outlier: 8.010A  pdb=" N   ALA D 176 " --> pdb=" O   LYS D  30 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ALA D  32 " --> pdb=" O   ALA D 176 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 67 through 71
      removed outlier: 3.521A  pdb=" N   MET A  68 " --> pdb=" O   TRP A  28 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   GLU A  25 " --> pdb=" O   MET A  40 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   MET A  40 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   CYS A  27 " --> pdb=" O   GLN A  38 " (cutoff:3.500A)
      removed outlier: 5.318A  pdb=" N   GLN A  38 " --> pdb=" O   CYS A  27 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLY A  34 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 138
    Processing sheet with id=AB1, first strand: chain 'A' and resid 225 through 226

    433 hydrogen bonds defined for protein.
    1227 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      22 hydrogen bonds
      44 hydrogen bond angles
      0 basepair planarities
      11 basepair parallelities
      50 stacking parallelities
  Total time for adding SS restraints: 3.64

  Time building geometry restraints manager: 2.74 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: 2601
        1.33 -     1.46: 2082
        1.46 -     1.58: 5315
        1.58 -     1.70: 123
        1.70 -     1.82: 102
  Bond restraints: 10223
  Sorted by residual:
  bond pdb=" CA  MET D 191 "
       pdb=" CB  MET D 191 "
    ideal  model  delta    sigma   weight residual
    1.526  1.456  0.070 1.53e-02 4.27e+03 2.09e+01
  bond pdb=" N   ASP C 232 "
       pdb=" CA  ASP C 232 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.29e-02 6.01e+03 9.01e+00
  bond pdb=" C3'  DA E  25 "
       pdb=" O3'  DA E  25 "
    ideal  model  delta    sigma   weight residual
    1.422  1.489 -0.067 3.00e-02 1.11e+03 4.92e+00
  bond pdb=" C   THR C 219 "
       pdb=" N   PRO C 220 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.019 9.40e-03 1.13e+04 4.16e+00
  bond pdb=" CB  GLN D 281 "
       pdb=" CG  GLN D 281 "
    ideal  model  delta    sigma   weight residual
    1.520  1.580 -0.060 3.00e-02 1.11e+03 4.01e+00
  ... (remaining 10218 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 13550
        2.46 -     4.93: 403
        4.93 -     7.39: 78
        7.39 -     9.86: 18
        9.86 -    12.32: 10
  Bond angle restraints: 14059
  Sorted by residual:
  angle pdb=" N   THR A 219 "
        pdb=" CA  THR A 219 "
        pdb=" C   THR A 219 "
      ideal   model   delta    sigma   weight residual
     109.81  121.33  -11.52 2.21e+00 2.05e-01 2.72e+01
  angle pdb=" C   ALA C 231 "
        pdb=" N   ASP C 232 "
        pdb=" CA  ASP C 232 "
      ideal   model   delta    sigma   weight residual
     121.54  131.33   -9.79 1.91e+00 2.74e-01 2.63e+01
  angle pdb=" C   LYS D 314 "
        pdb=" N   GLN D 315 "
        pdb=" CA  GLN D 315 "
      ideal   model   delta    sigma   weight residual
     122.82  129.56   -6.74 1.42e+00 4.96e-01 2.25e+01
  angle pdb=" N   MET C 244 "
        pdb=" CA  MET C 244 "
        pdb=" C   MET C 244 "
      ideal   model   delta    sigma   weight residual
     114.56  108.73    5.83 1.27e+00 6.20e-01 2.11e+01
  angle pdb=" CA  GLN D 281 "
        pdb=" CB  GLN D 281 "
        pdb=" CG  GLN D 281 "
      ideal   model   delta    sigma   weight residual
     114.10  123.25   -9.15 2.00e+00 2.50e-01 2.09e+01
  ... (remaining 14054 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.34: 5783
       35.34 -    70.67: 385
       70.67 -   106.00: 10
      106.00 -   141.34: 1
      141.34 -   176.67: 1
  Dihedral angle restraints: 6180
    sinusoidal: 2931
      harmonic: 3249
  Sorted by residual:
  dihedral pdb=" CA  GLU B 191 "
           pdb=" C   GLU B 191 "
           pdb=" N   GLU B 192 "
           pdb=" CA  GLU B 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.15   26.85     0      5.00e+00 4.00e-02 2.88e+01
  dihedral pdb=" CA  HIS D 253 "
           pdb=" C   HIS D 253 "
           pdb=" N   LYS D 254 "
           pdb=" CA  LYS D 254 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.76  -26.24     0      5.00e+00 4.00e-02 2.76e+01
  dihedral pdb=" CA  MET C 139 "
           pdb=" C   MET C 139 "
           pdb=" N   PRO C 140 "
           pdb=" CA  PRO C 140 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.60   23.40     0      5.00e+00 4.00e-02 2.19e+01
  ... (remaining 6177 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1351
       0.070 -    0.139: 223
       0.139 -    0.209: 31
       0.209 -    0.279: 10
       0.279 -    0.349: 3
  Chirality restraints: 1618
  Sorted by residual:
  chirality pdb=" CG  LEU D 144 "
            pdb=" CB  LEU D 144 "
            pdb=" CD1 LEU D 144 "
            pdb=" CD2 LEU D 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.24   -0.35 2.00e-01 2.50e+01 3.04e+00
  chirality pdb=" CB  THR A 216 "
            pdb=" CA  THR A 216 "
            pdb=" OG1 THR A 216 "
            pdb=" CG2 THR A 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.26    0.29 2.00e-01 2.50e+01 2.09e+00
  chirality pdb=" CB  VAL D  52 "
            pdb=" CA  VAL D  52 "
            pdb=" CG1 VAL D  52 "
            pdb=" CG2 VAL D  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 2.01e+00
  ... (remaining 1615 not shown)

  Planarity restraints: 1595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 219 "    0.050 5.00e-02 4.00e+02   7.48e-02 8.95e+00
        pdb=" N   PRO A 220 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO A 220 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 220 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 219 "    0.048 5.00e-02 4.00e+02   7.09e-02 8.05e+00
        pdb=" N   PRO B 220 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO B 220 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 220 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 264 "   -0.039 5.00e-02 4.00e+02   5.94e-02 5.64e+00
        pdb=" N   PRO D 265 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO D 265 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D 265 "   -0.033 5.00e-02 4.00e+02
  ... (remaining 1592 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2413
        2.81 -     3.33: 8050
        3.33 -     3.86: 17616
        3.86 -     4.38: 19708
        4.38 -     4.90: 33071
  Nonbonded interactions: 80858
  Sorted by model distance:
  nonbonded pdb=" O   MET D  67 "
            pdb=" OG1 THR D  71 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OH  TYR D  40 "
            pdb=" OP2  DT H   3 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" O   SER B  31 "
            pdb=" OH  TYR B  60 "
     model   vdw
     2.347 3.040
  nonbonded pdb=" O   ILE C 255 "
            pdb=" OG1 THR D 336 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" OG  SER D 157 "
            pdb=" O   GLU D 287 "
     model   vdw
     2.378 3.040
  ... (remaining 80853 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = (chain 'C' and resid 1 through 254)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     27.630
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.040
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
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      :  0.006   0.070  10223  Z= 0.356
  Angle     :  1.052  12.323  14059  Z= 0.553
  Chirality :  0.058   0.349   1618
  Planarity :  0.008   0.084   1595
  Dihedral  : 20.201 176.673   4066
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  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: -3.20 (0.21), residues: 1108
  helix: -2.81 (0.20), residues: 323
  sheet: -1.31 (0.27), residues: 340
  loop : -2.02 (0.24), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A  28 
 HIS   0.008   0.001   HIS C  44 
 PHE   0.019   0.003   PHE D  42 
 TYR   0.024   0.003   TYR D  40 
 ARG   0.018   0.001   ARG C  64 

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

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

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.988 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8346 (m) cc_final: 0.7806 (m)
REVERT: B   84 ASN cc_start: 0.7420 (m-40) cc_final: 0.6660 (t0)
REVERT: A   55 GLU cc_start: 0.6808 (mp0) cc_final: 0.6584 (tp30)
REVERT: A   64 ARG cc_start: 0.7419 (mtm-85) cc_final: 0.7113 (mtm110)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.2210
  time to fit residues: 51.1631
Evaluate side-chains
  138 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 90 optimal weight:    0.0670
   chunk 35 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0060
   chunk 67 optimal weight:    0.5980
   chunk 105 optimal weight:    0.0970
   overall best weight:    0.2732

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

Flipped N/Q/H residues before XYZ refinement:
** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  77 ASN
D 315 GLN
A 179 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.159424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.127226 restraints weight = 12598.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.128278 restraints weight = 9781.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.129678 restraints weight = 9209.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10223  Z= 0.180
  Angle     :  0.593   8.435  14059  Z= 0.324
  Chirality :  0.043   0.146   1618
  Planarity :  0.004   0.046   1595
  Dihedral  : 21.319 177.173   1923
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  8.98 %
    Favored  : 90.20 %
  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: -2.13 (0.23), residues: 1108
  helix: -0.91 (0.26), residues: 329
  sheet: -1.32 (0.28), residues: 318
  loop : -1.70 (0.25), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  28 
 HIS   0.010   0.001   HIS C 246 
 PHE   0.010   0.001   PHE D  27 
 TYR   0.009   0.001   TYR D  40 
 ARG   0.004   0.000   ARG D 262 

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

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

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 157
  time to evaluate  : 1.056 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8346 (m) cc_final: 0.7935 (m)
REVERT: B   84 ASN cc_start: 0.7667 (m-40) cc_final: 0.6969 (t0)
REVERT: B  207 PHE cc_start: 0.8414 (m-10) cc_final: 0.8190 (m-10)
REVERT: D  108 GLU cc_start: 0.7357 (tp30) cc_final: 0.7050 (tm-30)
REVERT: D  263 LEU cc_start: 0.6372 (tt) cc_final: 0.6009 (tp)
REVERT: A  141 SER cc_start: 0.8177 (OUTLIER) cc_final: 0.7684 (t)
REVERT: A  170 SER cc_start: 0.8519 (m) cc_final: 0.8039 (t)
  outliers start: 8
  outliers final: 1
  residues processed: 162
  average time/residue: 0.2298
  time to fit residues: 52.6387
Evaluate side-chains
  136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 134
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  222 SER
Chi-restraints excluded: chain A residue  141 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 30 optimal weight:    0.0970
   chunk 105 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 98 optimal weight:    0.0980
   chunk 71 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 65 optimal weight:    0.3980
   chunk 102 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
B 213 ASN
C 125 GLN
C 246 HIS
A 213 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.155668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.123123 restraints weight = 12773.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.123019 restraints weight = 10593.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.124688 restraints weight = 11668.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10223  Z= 0.197
  Angle     :  0.567   8.708  14059  Z= 0.308
  Chirality :  0.042   0.179   1618
  Planarity :  0.004   0.047   1595
  Dihedral  : 21.236 176.719   1923
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.80 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.24), residues: 1108
  helix:  0.20 (0.28), residues: 322
  sheet: -1.17 (0.26), residues: 350
  loop : -1.45 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D 274 
 HIS   0.007   0.001   HIS C 246 
 PHE   0.010   0.001   PHE C 169 
 TYR   0.010   0.001   TYR D  40 
 ARG   0.003   0.000   ARG C  91 

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

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

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 155
  time to evaluate  : 1.145 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8473 (m) cc_final: 0.8033 (m)
REVERT: B   84 ASN cc_start: 0.7713 (m-40) cc_final: 0.6938 (t0)
REVERT: C  207 PHE cc_start: 0.8801 (m-80) cc_final: 0.8422 (m-80)
REVERT: D   67 MET cc_start: 0.6727 (ttm) cc_final: 0.6526 (ttp)
REVERT: D   73 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6972 (ttm110)
REVERT: D  108 GLU cc_start: 0.7313 (tp30) cc_final: 0.7048 (tm-30)
REVERT: D  263 LEU cc_start: 0.6614 (tt) cc_final: 0.6284 (tp)
REVERT: A   16 LEU cc_start: 0.8540 (mm) cc_final: 0.8306 (mm)
REVERT: A   25 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7386 (mt-10)
REVERT: A  141 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.7699 (t)
REVERT: A  170 SER cc_start: 0.8489 (m) cc_final: 0.8051 (t)
  outliers start: 11
  outliers final: 6
  residues processed: 160
  average time/residue: 0.2114
  time to fit residues: 48.8856
Evaluate side-chains
  149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 SER
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   37 MET
Chi-restraints excluded: chain D residue   73 ARG
Chi-restraints excluded: chain A residue   55 GLU
Chi-restraints excluded: chain A residue  141 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 107 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  77 ASN
** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 246 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.152852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.117582 restraints weight = 12517.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.120795 restraints weight = 9772.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.121884 restraints weight = 6415.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10223  Z= 0.257
  Angle     :  0.589   9.437  14059  Z= 0.318
  Chirality :  0.043   0.160   1618
  Planarity :  0.004   0.042   1595
  Dihedral  : 21.144 178.029   1923
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 13.73 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.24), residues: 1108
  helix:  0.63 (0.29), residues: 324
  sheet: -1.25 (0.27), residues: 331
  loop : -1.44 (0.27), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 274 
 HIS   0.004   0.001   HIS C 246 
 PHE   0.015   0.002   PHE B 207 
 TYR   0.012   0.002   TYR C 211 
 ARG   0.004   0.000   ARG C 146 

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

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

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 146
  time to evaluate  : 1.052 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8518 (m) cc_final: 0.8156 (m)
REVERT: B   75 MET cc_start: 0.8334 (ttt) cc_final: 0.7791 (ttt)
REVERT: B   84 ASN cc_start: 0.7774 (m-40) cc_final: 0.7005 (t0)
REVERT: C  119 MET cc_start: 0.7147 (ptt) cc_final: 0.6880 (ptt)
REVERT: D   69 TYR cc_start: 0.7170 (m-10) cc_final: 0.6788 (m-80)
REVERT: D   73 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.7120 (ttm110)
REVERT: D  148 MET cc_start: 0.7673 (tpp) cc_final: 0.6885 (mtt)
REVERT: D  329 SER cc_start: 0.7433 (m) cc_final: 0.7085 (p)
REVERT: A   16 LEU cc_start: 0.8633 (mm) cc_final: 0.8352 (mm)
REVERT: A   25 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7492 (mt-10)
REVERT: A  141 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.7811 (t)
REVERT: A  170 SER cc_start: 0.8611 (m) cc_final: 0.8104 (t)
REVERT: A  235 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8020 (pt)
  outliers start: 26
  outliers final: 17
  residues processed: 161
  average time/residue: 0.2082
  time to fit residues: 48.3985
Evaluate side-chains
  152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   37 MET
Chi-restraints excluded: chain D residue   73 ARG
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   55 GLU
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  141 SER
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  235 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 112 optimal weight:    5.9990
   chunk 101 optimal weight:    2.9990
   chunk 99 optimal weight:    0.5980
   chunk 109 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9990
   chunk 79 optimal weight:    0.1980
   chunk 53 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
B  71 ASN
B 184 GLN
** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.152636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.117470 restraints weight = 12623.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.121007 restraints weight = 9751.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.122160 restraints weight = 6226.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10223  Z= 0.247
  Angle     :  0.592   9.146  14059  Z= 0.317
  Chirality :  0.043   0.181   1618
  Planarity :  0.003   0.043   1595
  Dihedral  : 21.147 178.254   1923
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 15.89 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.25), residues: 1108
  helix:  0.79 (0.29), residues: 322
  sheet: -1.17 (0.27), residues: 325
  loop : -1.41 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D 274 
 HIS   0.004   0.001   HIS C 246 
 PHE   0.011   0.002   PHE C 169 
 TYR   0.013   0.002   TYR C 211 
 ARG   0.003   0.000   ARG C  91 

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

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

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 154
  time to evaluate  : 1.013 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8484 (m) cc_final: 0.8139 (m)
REVERT: B   75 MET cc_start: 0.8342 (ttt) cc_final: 0.7800 (ttt)
REVERT: B   84 ASN cc_start: 0.7811 (m-40) cc_final: 0.7045 (t0)
REVERT: C  119 MET cc_start: 0.7195 (ptt) cc_final: 0.6947 (ptt)
REVERT: D   73 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6724 (ttm110)
REVERT: D  148 MET cc_start: 0.7851 (tpp) cc_final: 0.7064 (ttm)
REVERT: D  288 VAL cc_start: 0.7405 (OUTLIER) cc_final: 0.7156 (p)
REVERT: D  329 SER cc_start: 0.7563 (m) cc_final: 0.7232 (p)
REVERT: A   16 LEU cc_start: 0.8608 (mm) cc_final: 0.8343 (mm)
REVERT: A  141 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.7814 (t)
REVERT: A  170 SER cc_start: 0.8585 (m) cc_final: 0.8083 (t)
REVERT: A  235 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8125 (pt)
  outliers start: 27
  outliers final: 15
  residues processed: 167
  average time/residue: 0.2022
  time to fit residues: 48.4139
Evaluate side-chains
  162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   73 ARG
Chi-restraints excluded: chain D residue  288 VAL
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  141 SER
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  235 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   chunk 38 optimal weight:    0.3980
   chunk 78 optimal weight:    0.0060
   chunk 74 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 89 optimal weight:    0.6980
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 ASN ** 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 = 0.3838 r_free = 0.3838 target = 0.153171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.118138 restraints weight = 12540.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.121383 restraints weight = 9714.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.122521 restraints weight = 6481.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10223  Z= 0.209
  Angle     :  0.571   8.088  14059  Z= 0.306
  Chirality :  0.042   0.179   1618
  Planarity :  0.003   0.044   1595
  Dihedral  : 21.073 178.854   1923
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.03 %
    Favored  : 80.70 %
  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: -1.02 (0.25), residues: 1108
  helix:  0.92 (0.29), residues: 325
  sheet: -1.19 (0.29), residues: 297
  loop : -1.38 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D 274 
 HIS   0.005   0.001   HIS C  44 
 PHE   0.008   0.001   PHE D 207 
 TYR   0.012   0.001   TYR D  40 
 ARG   0.003   0.000   ARG C  91 

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

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

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 1.105 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8447 (m) cc_final: 0.8104 (m)
REVERT: B   84 ASN cc_start: 0.7814 (m-40) cc_final: 0.7038 (t0)
REVERT: D  148 MET cc_start: 0.7819 (tpp) cc_final: 0.7368 (ttm)
REVERT: D  268 TYR cc_start: 0.6350 (m-10) cc_final: 0.6118 (m-10)
REVERT: D  288 VAL cc_start: 0.7366 (OUTLIER) cc_final: 0.7109 (p)
REVERT: D  329 SER cc_start: 0.7528 (m) cc_final: 0.7228 (p)
REVERT: A   16 LEU cc_start: 0.8565 (mm) cc_final: 0.8325 (mm)
REVERT: A  141 SER cc_start: 0.8505 (OUTLIER) cc_final: 0.7802 (t)
REVERT: A  235 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8103 (pt)
  outliers start: 22
  outliers final: 18
  residues processed: 161
  average time/residue: 0.2137
  time to fit residues: 49.5115
Evaluate side-chains
  156 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  288 VAL
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  141 SER
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  235 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 79 optimal weight:    0.0870
   chunk 28 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 91 optimal weight:    0.6980
   chunk 90 optimal weight:    3.9990
   chunk 69 optimal weight:    0.4980
   chunk 74 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 64 optimal weight:    0.0020
   chunk 8 optimal weight:    0.5980
   chunk 113 optimal weight:    3.9990
   overall best weight:    0.3366

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

Flipped N/Q/H residues before XYZ refinement:
** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 ASN ** 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 = 0.3856 r_free = 0.3856 target = 0.154782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.119840 restraints weight = 12618.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.123653 restraints weight = 9498.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.124742 restraints weight = 5931.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10223  Z= 0.177
  Angle     :  0.561   8.192  14059  Z= 0.299
  Chirality :  0.042   0.176   1618
  Planarity :  0.003   0.044   1595
  Dihedral  : 20.978 179.479   1923
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.85 %
    Favored  : 79.46 %
  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: -0.82 (0.25), residues: 1108
  helix:  1.18 (0.29), residues: 325
  sheet: -1.10 (0.29), residues: 297
  loop : -1.32 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D 274 
 HIS   0.005   0.001   HIS C  44 
 PHE   0.008   0.001   PHE D 207 
 TYR   0.010   0.001   TYR C 211 
 ARG   0.003   0.000   ARG C  91 

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

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

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 1.063 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8417 (m) cc_final: 0.8092 (m)
REVERT: B   84 ASN cc_start: 0.7809 (m-40) cc_final: 0.7001 (t0)
REVERT: C  139 MET cc_start: 0.7983 (ptm) cc_final: 0.7583 (ptt)
REVERT: D   73 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7027 (ttm110)
REVERT: D   86 ASP cc_start: 0.7481 (m-30) cc_final: 0.7070 (m-30)
REVERT: D  148 MET cc_start: 0.7765 (tpp) cc_final: 0.7535 (ttm)
REVERT: D  160 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6963 (pm20)
REVERT: D  288 VAL cc_start: 0.7324 (OUTLIER) cc_final: 0.7055 (p)
REVERT: D  329 SER cc_start: 0.7540 (m) cc_final: 0.7230 (p)
REVERT: A   16 LEU cc_start: 0.8528 (mm) cc_final: 0.8271 (mm)
REVERT: A  235 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8093 (pt)
  outliers start: 26
  outliers final: 15
  residues processed: 164
  average time/residue: 0.2093
  time to fit residues: 49.1654
Evaluate side-chains
  153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   73 ARG
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  288 VAL
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  235 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9980
   chunk 80 optimal weight:    0.4980
   chunk 0 optimal weight:    5.9990
   chunk 112 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 107 optimal weight:    0.8980
   chunk 32 optimal weight:    0.2980
   chunk 21 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
D  21 ASN
** D 337 GLN ** 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 = 0.3827 r_free = 0.3827 target = 0.152079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.117245 restraints weight = 12616.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.120590 restraints weight = 9736.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.121673 restraints weight = 6310.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.3443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10223  Z= 0.239
  Angle     :  0.597   8.567  14059  Z= 0.315
  Chirality :  0.043   0.318   1618
  Planarity :  0.003   0.043   1595
  Dihedral  : 20.899 178.046   1923
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.27 %
    Favored  : 78.95 %
  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: -0.90 (0.25), residues: 1108
  helix:  1.05 (0.29), residues: 323
  sheet: -1.15 (0.29), residues: 305
  loop : -1.30 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D 274 
 HIS   0.003   0.001   HIS C 246 
 PHE   0.010   0.001   PHE C 169 
 TYR   0.016   0.002   TYR D  40 
 ARG   0.003   0.000   ARG C  91 

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

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

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 133
  time to evaluate  : 1.207 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8487 (m) cc_final: 0.8138 (m)
REVERT: B   75 MET cc_start: 0.8360 (ttt) cc_final: 0.7793 (ttt)
REVERT: B   84 ASN cc_start: 0.7796 (m-40) cc_final: 0.7005 (t0)
REVERT: D   73 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.7051 (ttm110)
REVERT: D  141 CYS cc_start: 0.7224 (t) cc_final: 0.6670 (t)
REVERT: D  160 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7051 (pm20)
REVERT: D  288 VAL cc_start: 0.7454 (OUTLIER) cc_final: 0.7199 (p)
REVERT: D  329 SER cc_start: 0.7644 (m) cc_final: 0.7342 (p)
REVERT: A   16 LEU cc_start: 0.8621 (mm) cc_final: 0.8328 (mm)
REVERT: A  235 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8151 (pt)
  outliers start: 27
  outliers final: 20
  residues processed: 153
  average time/residue: 0.2018
  time to fit residues: 45.1689
Evaluate side-chains
  155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  116 MET
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain D residue   73 ARG
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  288 VAL
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  235 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 43 optimal weight:    0.0170
   chunk 96 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 92 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 109 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0870
   chunk 37 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
D  21 ASN
** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 ASN ** 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 = 0.3844 r_free = 0.3844 target = 0.153678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.118801 restraints weight = 12475.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.122020 restraints weight = 9700.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.123179 restraints weight = 6372.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.3465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10223  Z= 0.191
  Angle     :  0.573   8.453  14059  Z= 0.304
  Chirality :  0.042   0.245   1618
  Planarity :  0.003   0.044   1595
  Dihedral  : 20.839 178.865   1923
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.68 %
    Favored  : 78.64 %
  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: -0.86 (0.25), residues: 1108
  helix:  1.12 (0.29), residues: 325
  sheet: -1.15 (0.29), residues: 299
  loop : -1.30 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP D 274 
 HIS   0.003   0.001   HIS C  44 
 PHE   0.011   0.001   PHE C 207 
 TYR   0.010   0.001   TYR C 211 
 ARG   0.003   0.000   ARG D  19 

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

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

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 1.070 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8463 (m) cc_final: 0.8112 (m)
REVERT: B   84 ASN cc_start: 0.7774 (m-40) cc_final: 0.6948 (t0)
REVERT: C  139 MET cc_start: 0.8122 (ptm) cc_final: 0.7605 (ptt)
REVERT: C  207 PHE cc_start: 0.8843 (m-80) cc_final: 0.8528 (m-80)
REVERT: D   73 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7096 (ttm110)
REVERT: D   86 ASP cc_start: 0.7480 (m-30) cc_final: 0.7035 (m-30)
REVERT: D  160 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6954 (pm20)
REVERT: D  288 VAL cc_start: 0.7404 (OUTLIER) cc_final: 0.7140 (p)
REVERT: D  329 SER cc_start: 0.7639 (m) cc_final: 0.7332 (p)
REVERT: A   16 LEU cc_start: 0.8565 (mm) cc_final: 0.8273 (mm)
REVERT: A  141 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.7854 (t)
REVERT: A  235 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8126 (pt)
  outliers start: 26
  outliers final: 17
  residues processed: 156
  average time/residue: 0.2084
  time to fit residues: 47.1019
Evaluate side-chains
  154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain D residue   73 ARG
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  288 VAL
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  141 SER
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  235 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 79 optimal weight:    0.0270
   chunk 58 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 88 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.6840

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

Flipped N/Q/H residues before XYZ refinement:
D  21 ASN
** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 ASN ** 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 = 0.3815 r_free = 0.3815 target = 0.151351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.116312 restraints weight = 12493.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.119549 restraints weight = 9738.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.120601 restraints weight = 6409.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.3594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10223  Z= 0.252
  Angle     :  0.611   9.172  14059  Z= 0.320
  Chirality :  0.043   0.237   1618
  Planarity :  0.003   0.042   1595
  Dihedral  : 20.786 176.872   1923
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.68 %
    Favored  : 78.84 %
  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: -0.96 (0.25), residues: 1108
  helix:  1.04 (0.29), residues: 323
  sheet: -1.41 (0.29), residues: 287
  loop : -1.21 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP D 274 
 HIS   0.004   0.001   HIS C  44 
 PHE   0.011   0.001   PHE C 207 
 TYR   0.016   0.002   TYR D  40 
 ARG   0.003   0.000   ARG C  91 

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

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

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2216 Ramachandran restraints generated.
    1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 1.062 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8559 (m) cc_final: 0.8199 (m)
REVERT: B   75 MET cc_start: 0.8371 (ttt) cc_final: 0.7836 (ttt)
REVERT: B   84 ASN cc_start: 0.7786 (m-40) cc_final: 0.6975 (t0)
REVERT: C  139 MET cc_start: 0.8305 (ptm) cc_final: 0.7789 (ptt)
REVERT: C  207 PHE cc_start: 0.8919 (m-80) cc_final: 0.8673 (m-80)
REVERT: D   73 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7054 (ttm110)
REVERT: D  141 CYS cc_start: 0.7228 (t) cc_final: 0.6692 (t)
REVERT: D  160 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7077 (pm20)
REVERT: D  288 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7222 (p)
REVERT: D  329 SER cc_start: 0.7820 (m) cc_final: 0.7157 (p)
REVERT: A   16 LEU cc_start: 0.8638 (mm) cc_final: 0.8340 (mm)
REVERT: A  141 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.7915 (t)
REVERT: A  235 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8177 (pt)
  outliers start: 24
  outliers final: 19
  residues processed: 153
  average time/residue: 0.2119
  time to fit residues: 46.5720
Evaluate side-chains
  157 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain D residue   73 ARG
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue  134 THR
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  288 VAL
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  141 SER
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  235 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 104 optimal weight:    0.7980
   chunk 111 optimal weight:    3.9990
   chunk 90 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 88 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D  21 ASN
** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 ASN ** 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 = 0.3813 r_free = 0.3813 target = 0.151212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.116139 restraints weight = 12521.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.119561 restraints weight = 9618.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.120549 restraints weight = 6201.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.3678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10223  Z= 0.255
  Angle     :  0.609   8.568  14059  Z= 0.320
  Chirality :  0.043   0.220   1618
  Planarity :  0.003   0.043   1595
  Dihedral  : 20.751 176.519   1923
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.99 %
    Favored  : 78.33 %
  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: -0.93 (0.25), residues: 1108
  helix:  1.01 (0.29), residues: 323
  sheet: -1.33 (0.29), residues: 285
  loop : -1.19 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D 274 
 HIS   0.004   0.001   HIS C  44 
 PHE   0.011   0.002   PHE C 207 
 TYR   0.012   0.002   TYR C 211 
 ARG   0.003   0.000   ARG C  91 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2925.24 seconds
wall clock time: 53 minutes 48.92 seconds (3228.92 seconds total)