Starting phenix.real_space_refine
on Wed Sep 17 17:14:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjw_39352/09_2025/8yjw_39352.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjw_39352/09_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_39352/09_2025/8yjw_39352.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjw_39352/09_2025/8yjw_39352.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjw_39352/09_2025/8yjw_39352.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjw_39352/09_2025/8yjw_39352.cif"
  }
  resolution = 3.55
  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=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.45, per 1000 atoms: 0.25
  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: 0.79
  Conformation dependent library (CDL) restraints added in 412.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 1.03
  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: 1.77

  Time building geometry restraints manager: 1.04 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:             3.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.960
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.550
-------------------------------------------------------------------------------
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  10225  Z= 0.257
  Angle     :  1.052  12.323  14063  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 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: -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
 ARG   0.018   0.001   ARG C  64 
 TYR   0.024   0.003   TYR D  40 
 PHE   0.019   0.003   PHE D  42 
 TRP   0.008   0.002   TRP A  28 
 HIS   0.008   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00561 (10223)
  covalent geometry    : angle       1.05224 (14059)
  SS BOND              : bond        0.00202 (    2)
  SS BOND              : angle       1.55866 (    4)
  hydrogen bonds       : bond        0.20503 (  455)
  hydrogen bonds       : angle       9.67495 ( 1271)

*********************** 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  : 0.348 
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: 0.0959
  time to fit residues: 22.5485
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  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
D  77 ASN
D 315 GLN
A 179 ASN
A 213 ASN
A 246 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.153305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.121028 restraints weight = 12726.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.121357 restraints weight = 10564.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.123048 restraints weight = 10515.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.123083 restraints weight = 7997.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.123610 restraints weight = 8602.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.1831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10225  Z= 0.192
  Angle     :  0.638   9.062  14063  Z= 0.345
  Chirality :  0.044   0.144   1618
  Planarity :  0.005   0.048   1595
  Dihedral  : 21.442 179.750   1923
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.91 %
    Favored  : 89.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.19 (0.23), residues: 1108
  helix: -0.87 (0.26), residues: 324
  sheet: -1.49 (0.28), residues: 308
  loop : -1.70 (0.25), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 262 
 TYR   0.011   0.002   TYR D  69 
 PHE   0.012   0.002   PHE C 169 
 TRP   0.006   0.001   TRP C  28 
 HIS   0.009   0.001   HIS C 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 (10223)
  covalent geometry    : angle       0.63771 (14059)
  SS BOND              : bond        0.00121 (    2)
  SS BOND              : angle       0.86424 (    4)
  hydrogen bonds       : bond        0.04586 (  455)
  hydrogen bonds       : angle       6.81469 ( 1271)

*********************** 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
  160 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 152
  time to evaluate  : 0.238 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8451 (m) cc_final: 0.8055 (m)
REVERT: B   84 ASN cc_start: 0.7715 (m-40) cc_final: 0.7066 (t0)
REVERT: B  207 PHE cc_start: 0.8601 (m-10) cc_final: 0.8196 (m-10)
REVERT: D  108 GLU cc_start: 0.7241 (tp30) cc_final: 0.6979 (tm-30)
REVERT: D  263 LEU cc_start: 0.6534 (tt) cc_final: 0.6142 (tp)
REVERT: A  141 SER cc_start: 0.8231 (OUTLIER) cc_final: 0.7675 (t)
REVERT: A  170 SER cc_start: 0.8591 (m) cc_final: 0.8137 (t)
  outliers start: 8
  outliers final: 4
  residues processed: 157
  average time/residue: 0.0940
  time to fit residues: 20.9094
Evaluate side-chains
  135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 130
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   37 MET
Chi-restraints excluded: chain A residue  137 VAL
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 79 optimal weight:    0.0980
   chunk 67 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0670
   chunk 64 optimal weight:    0.6980
   chunk 12 optimal weight:    4.9990
   chunk 101 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0070
   chunk 35 optimal weight:    0.4980
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.2536

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

Flipped N/Q/H residues before XYZ refinement:
C 246 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.156154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.123226 restraints weight = 12701.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.123401 restraints weight = 10296.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.125390 restraints weight = 10240.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.125807 restraints weight = 7402.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.125961 restraints weight = 7569.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10225  Z= 0.119
  Angle     :  0.548   8.406  14063  Z= 0.299
  Chirality :  0.041   0.186   1618
  Planarity :  0.004   0.040   1595
  Dihedral  : 21.235 175.006   1923
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 13.31 %
    Favored  : 85.45 %
  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: -1.49 (0.24), residues: 1108
  helix:  0.20 (0.28), residues: 323
  sheet: -1.28 (0.27), residues: 340
  loop : -1.50 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  91 
 TYR   0.008   0.001   TYR A 250 
 PHE   0.009   0.001   PHE D 126 
 TRP   0.026   0.002   TRP D 274 
 HIS   0.006   0.001   HIS C 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (10223)
  covalent geometry    : angle       0.54762 (14059)
  SS BOND              : bond        0.00129 (    2)
  SS BOND              : angle       0.55792 (    4)
  hydrogen bonds       : bond        0.03523 (  455)
  hydrogen bonds       : angle       6.01790 ( 1271)

*********************** 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
  168 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 156
  time to evaluate  : 0.295 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8379 (m) cc_final: 0.7969 (m)
REVERT: B   84 ASN cc_start: 0.7726 (m-40) cc_final: 0.6984 (t0)
REVERT: B  207 PHE cc_start: 0.8526 (m-80) cc_final: 0.8119 (m-10)
REVERT: B  244 MET cc_start: 0.7304 (ppp) cc_final: 0.7059 (ppp)
REVERT: D   64 LEU cc_start: 0.8417 (mt) cc_final: 0.8169 (mt)
REVERT: D   69 TYR cc_start: 0.6977 (m-10) cc_final: 0.6568 (m-80)
REVERT: D   73 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6621 (ttm110)
REVERT: D  108 GLU cc_start: 0.7227 (tp30) cc_final: 0.7000 (tm-30)
REVERT: D  263 LEU cc_start: 0.6660 (tt) cc_final: 0.6319 (tp)
REVERT: A   16 LEU cc_start: 0.8520 (mm) cc_final: 0.8290 (mm)
REVERT: A   25 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7458 (mt-10)
REVERT: A  141 SER cc_start: 0.8297 (OUTLIER) cc_final: 0.7724 (t)
REVERT: A  170 SER cc_start: 0.8493 (m) cc_final: 0.8055 (t)
REVERT: A  235 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7816 (pt)
  outliers start: 12
  outliers final: 4
  residues processed: 163
  average time/residue: 0.0927
  time to fit residues: 21.7540
Evaluate side-chains
  147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 140
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  222 SER
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain D residue   73 ARG
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  141 SER
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  235 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 80 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 112 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.7984

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.152619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.116990 restraints weight = 12756.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.119671 restraints weight = 10370.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.121004 restraints weight = 7023.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.121302 restraints weight = 5971.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.121730 restraints weight = 5712.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10225  Z= 0.183
  Angle     :  0.588   9.659  14063  Z= 0.316
  Chirality :  0.043   0.158   1618
  Planarity :  0.004   0.044   1595
  Dihedral  : 21.150 178.755   1923
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 14.55 %
    Favored  : 82.87 %
  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: -1.27 (0.24), residues: 1108
  helix:  0.61 (0.29), residues: 324
  sheet: -1.27 (0.28), residues: 323
  loop : -1.48 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  73 
 TYR   0.014   0.002   TYR D  83 
 PHE   0.014   0.002   PHE C 169 
 TRP   0.021   0.002   TRP D 274 
 HIS   0.003   0.001   HIS C 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (10223)
  covalent geometry    : angle       0.58788 (14059)
  SS BOND              : bond        0.00209 (    2)
  SS BOND              : angle       0.71941 (    4)
  hydrogen bonds       : bond        0.03640 (  455)
  hydrogen bonds       : angle       5.95344 ( 1271)

*********************** 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
  171 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 146
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: B   10 SER cc_start: 0.8452 (m) cc_final: 0.8174 (m)
REVERT: B   75 MET cc_start: 0.8341 (ttt) cc_final: 0.7775 (ttt)
REVERT: B   84 ASN cc_start: 0.7784 (m-40) cc_final: 0.7024 (t0)
REVERT: B  244 MET cc_start: 0.7245 (ppp) cc_final: 0.7032 (ppp)
REVERT: C  119 MET cc_start: 0.7036 (ptt) cc_final: 0.6624 (ptt)
REVERT: C  207 PHE cc_start: 0.8950 (m-80) cc_final: 0.8730 (m-80)
REVERT: D  160 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7059 (pm20)
REVERT: D  198 GLU cc_start: 0.5474 (mp0) cc_final: 0.4953 (tm-30)
REVERT: D  329 SER cc_start: 0.7414 (m) cc_final: 0.7056 (p)
REVERT: A   16 LEU cc_start: 0.8657 (mm) cc_final: 0.8377 (mm)
REVERT: A  141 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.7826 (t)
REVERT: A  170 SER cc_start: 0.8527 (m) cc_final: 0.8048 (t)
REVERT: A  235 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8001 (pt)
  outliers start: 25
  outliers final: 16
  residues processed: 160
  average time/residue: 0.0838
  time to fit residues: 19.6348
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  : 0.337 
-------------------------------------------------------------------------------
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  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 D residue  160 GLU
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  235 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0870
   chunk 75 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 44 optimal weight:    0.3980
   chunk 114 optimal weight:    5.9990
   chunk 104 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 29 optimal weight:    0.2980
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
B 184 GLN
** 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 = 0.3849 r_free = 0.3849 target = 0.154069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.119243 restraints weight = 12548.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.122695 restraints weight = 9600.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.123864 restraints weight = 6189.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.124080 restraints weight = 5320.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.124437 restraints weight = 5133.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10225  Z= 0.139
  Angle     :  0.562   9.035  14063  Z= 0.302
  Chirality :  0.042   0.172   1618
  Planarity :  0.003   0.043   1595
  Dihedral  : 21.109 177.151   1923
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.00 %
    Favored  : 81.42 %
  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: -1.04 (0.24), residues: 1108
  helix:  0.90 (0.29), residues: 324
  sheet: -1.09 (0.28), residues: 307
  loop : -1.48 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  91 
 TYR   0.011   0.001   TYR C 211 
 PHE   0.019   0.001   PHE B 207 
 TRP   0.023   0.002   TRP D 274 
 HIS   0.003   0.001   HIS C 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (10223)
  covalent geometry    : angle       0.56171 (14059)
  SS BOND              : bond        0.00115 (    2)
  SS BOND              : angle       0.62290 (    4)
  hydrogen bonds       : bond        0.03278 (  455)
  hydrogen bonds       : angle       5.79498 ( 1271)

*********************** 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
  168 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.369 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8452 (m) cc_final: 0.8121 (m)
REVERT: B   75 MET cc_start: 0.8331 (ttt) cc_final: 0.7764 (ttt)
REVERT: B   84 ASN cc_start: 0.7800 (m-40) cc_final: 0.7038 (t0)
REVERT: C  207 PHE cc_start: 0.8916 (m-80) cc_final: 0.8611 (m-80)
REVERT: D   69 TYR cc_start: 0.6839 (m-10) cc_final: 0.6338 (m-80)
REVERT: D  288 VAL cc_start: 0.7245 (OUTLIER) cc_final: 0.6972 (p)
REVERT: D  329 SER cc_start: 0.7479 (m) cc_final: 0.7140 (p)
REVERT: A   16 LEU cc_start: 0.8550 (mm) cc_final: 0.8278 (mm)
REVERT: A  141 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.7797 (t)
REVERT: A  170 SER cc_start: 0.8549 (m) cc_final: 0.8043 (t)
REVERT: A  235 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7982 (pt)
  outliers start: 25
  outliers final: 17
  residues processed: 156
  average time/residue: 0.0915
  time to fit residues: 21.0073
Evaluate side-chains
  155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
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  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  177 THR
Chi-restraints excluded: chain D residue  288 VAL
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  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 18 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 94 optimal weight:    0.0970
   chunk 115 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.6778

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.151933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.117016 restraints weight = 12652.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.119725 restraints weight = 10173.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.120983 restraints weight = 6878.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.121174 restraints weight = 5883.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.121775 restraints weight = 5638.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10225  Z= 0.166
  Angle     :  0.585   9.829  14063  Z= 0.312
  Chirality :  0.043   0.189   1618
  Planarity :  0.003   0.045   1595
  Dihedral  : 21.107 179.529   1923
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.00 %
    Favored  : 81.01 %
  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: -1.04 (0.25), residues: 1108
  helix:  0.92 (0.29), residues: 325
  sheet: -1.16 (0.29), residues: 297
  loop : -1.43 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  73 
 TYR   0.013   0.002   TYR D 268 
 PHE   0.010   0.001   PHE B 207 
 TRP   0.022   0.002   TRP D 274 
 HIS   0.003   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (10223)
  covalent geometry    : angle       0.58490 (14059)
  SS BOND              : bond        0.00174 (    2)
  SS BOND              : angle       0.54813 (    4)
  hydrogen bonds       : bond        0.03349 (  455)
  hydrogen bonds       : angle       5.79995 ( 1271)

*********************** 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
  170 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 141
  time to evaluate  : 0.298 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8492 (m) cc_final: 0.8151 (m)
REVERT: B   75 MET cc_start: 0.8384 (ttt) cc_final: 0.7807 (ttt)
REVERT: B   84 ASN cc_start: 0.7804 (m-40) cc_final: 0.7030 (t0)
REVERT: D  144 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7641 (tt)
REVERT: D  148 MET cc_start: 0.7547 (tpp) cc_final: 0.6957 (mtt)
REVERT: D  160 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7061 (pm20)
REVERT: D  288 VAL cc_start: 0.7395 (OUTLIER) cc_final: 0.7139 (p)
REVERT: D  329 SER cc_start: 0.7551 (m) cc_final: 0.7233 (p)
REVERT: A   16 LEU cc_start: 0.8622 (mm) cc_final: 0.8342 (mm)
REVERT: A  141 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.7830 (t)
  outliers start: 29
  outliers final: 20
  residues processed: 160
  average time/residue: 0.0824
  time to fit residues: 19.2355
Evaluate side-chains
  156 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
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  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  144 LEU
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   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  233 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 37 optimal weight:    0.2980
   chunk 0 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 109 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3820 r_free = 0.3820 target = 0.151555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.115721 restraints weight = 12747.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.118078 restraints weight = 10521.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.119444 restraints weight = 7269.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.119990 restraints weight = 6119.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.120294 restraints weight = 5903.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10225  Z= 0.166
  Angle     :  0.589   9.313  14063  Z= 0.313
  Chirality :  0.042   0.182   1618
  Planarity :  0.003   0.044   1595
  Dihedral  : 21.059 179.784   1923
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.92 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.98 (0.25), residues: 1108
  helix:  0.99 (0.29), residues: 323
  sheet: -1.19 (0.29), residues: 297
  loop : -1.35 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  73 
 TYR   0.013   0.002   TYR D  40 
 PHE   0.009   0.001   PHE D 207 
 TRP   0.024   0.002   TRP D 274 
 HIS   0.003   0.001   HIS C 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (10223)
  covalent geometry    : angle       0.58942 (14059)
  SS BOND              : bond        0.00173 (    2)
  SS BOND              : angle       0.63105 (    4)
  hydrogen bonds       : bond        0.03342 (  455)
  hydrogen bonds       : angle       5.77884 ( 1271)

*********************** 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
  164 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.328 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8449 (m) cc_final: 0.8202 (m)
REVERT: B   17 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7086 (mm-30)
REVERT: B   75 MET cc_start: 0.8379 (ttt) cc_final: 0.7848 (ttt)
REVERT: B   84 ASN cc_start: 0.7808 (m-40) cc_final: 0.7024 (t0)
REVERT: D  144 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8033 (tp)
REVERT: D  148 MET cc_start: 0.7590 (tpp) cc_final: 0.7111 (mtt)
REVERT: D  160 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7029 (pm20)
REVERT: D  288 VAL cc_start: 0.7461 (OUTLIER) cc_final: 0.7219 (p)
REVERT: D  329 SER cc_start: 0.7659 (m) cc_final: 0.7336 (p)
REVERT: A   16 LEU cc_start: 0.8611 (mm) cc_final: 0.8347 (mm)
REVERT: A  141 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.7914 (t)
  outliers start: 24
  outliers final: 19
  residues processed: 158
  average time/residue: 0.0876
  time to fit residues: 20.2979
Evaluate side-chains
  161 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
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  109 GLU
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  134 THR
Chi-restraints excluded: chain D residue  144 LEU
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   55 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 106 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   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 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.151371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.116350 restraints weight = 12513.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.119596 restraints weight = 9755.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.120709 restraints weight = 6358.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.120859 restraints weight = 5487.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.121370 restraints weight = 5304.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10225  Z= 0.171
  Angle     :  0.592   9.272  14063  Z= 0.314
  Chirality :  0.043   0.184   1618
  Planarity :  0.003   0.045   1595
  Dihedral  : 21.015 179.263   1923
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.34 %
    Favored  : 79.88 %
  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: -0.96 (0.25), residues: 1108
  helix:  1.01 (0.29), residues: 323
  sheet: -1.21 (0.28), residues: 305
  loop : -1.33 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  73 
 TYR   0.011   0.001   TYR C 211 
 PHE   0.009   0.001   PHE C 169 
 TRP   0.023   0.002   TRP D 274 
 HIS   0.003   0.001   HIS C 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (10223)
  covalent geometry    : angle       0.59229 (14059)
  SS BOND              : bond        0.00144 (    2)
  SS BOND              : angle       0.63054 (    4)
  hydrogen bonds       : bond        0.03318 (  455)
  hydrogen bonds       : angle       5.77506 ( 1271)

*********************** 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
  165 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 0.382 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8457 (m) cc_final: 0.8198 (m)
REVERT: B   75 MET cc_start: 0.8383 (ttt) cc_final: 0.7840 (ttt)
REVERT: B   84 ASN cc_start: 0.7820 (m-40) cc_final: 0.7050 (t0)
REVERT: D  148 MET cc_start: 0.7594 (tpp) cc_final: 0.7232 (mtt)
REVERT: D  160 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7015 (pm20)
REVERT: D  288 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.7286 (p)
REVERT: D  329 SER cc_start: 0.7767 (m) cc_final: 0.7421 (p)
REVERT: A   16 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8356 (mm)
REVERT: A  116 MET cc_start: 0.8282 (mtp) cc_final: 0.8015 (mtp)
  outliers start: 27
  outliers final: 21
  residues processed: 155
  average time/residue: 0.0933
  time to fit residues: 21.0988
Evaluate side-chains
  158 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
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  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  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   16 LEU
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  175 LEU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  233 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 103 optimal weight:    5.9990
   chunk 100 optimal weight:    0.0470
   chunk 2 optimal weight:    2.9990
   chunk 86 optimal weight:    0.6980
   chunk 75 optimal weight:    4.9990
   chunk 88 optimal weight:    0.6980
   overall best weight:    0.6280

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

Flipped N/Q/H residues before XYZ refinement:
** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3821 r_free = 0.3821 target = 0.151801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.116342 restraints weight = 12544.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.119662 restraints weight = 9799.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.120906 restraints weight = 6357.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.121113 restraints weight = 5440.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.121485 restraints weight = 5259.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.3489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10225  Z= 0.161
  Angle     :  0.591   9.026  14063  Z= 0.312
  Chirality :  0.042   0.184   1618
  Planarity :  0.003   0.046   1595
  Dihedral  : 20.943 178.573   1923
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.13 %
    Favored  : 79.98 %
  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: -0.96 (0.25), residues: 1108
  helix:  1.05 (0.29), residues: 323
  sheet: -1.24 (0.28), residues: 307
  loop : -1.31 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  73 
 TYR   0.018   0.002   TYR D  40 
 PHE   0.011   0.001   PHE C 207 
 TRP   0.027   0.002   TRP D 274 
 HIS   0.005   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (10223)
  covalent geometry    : angle       0.59057 (14059)
  SS BOND              : bond        0.00137 (    2)
  SS BOND              : angle       0.55353 (    4)
  hydrogen bonds       : bond        0.03289 (  455)
  hydrogen bonds       : angle       5.73869 ( 1271)

*********************** 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
  167 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 139
  time to evaluate  : 0.384 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8472 (m) cc_final: 0.8217 (m)
REVERT: B   84 ASN cc_start: 0.7828 (m-40) cc_final: 0.7028 (t0)
REVERT: D   86 ASP cc_start: 0.7479 (m-30) cc_final: 0.7062 (m-30)
REVERT: D  148 MET cc_start: 0.7744 (tpp) cc_final: 0.7145 (ttm)
REVERT: D  160 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6992 (pm20)
REVERT: D  288 VAL cc_start: 0.7529 (OUTLIER) cc_final: 0.7293 (p)
REVERT: D  329 SER cc_start: 0.7800 (m) cc_final: 0.7462 (p)
REVERT: A   16 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8335 (mm)
REVERT: A  116 MET cc_start: 0.8282 (mtp) cc_final: 0.8001 (mtp)
  outliers start: 28
  outliers final: 20
  residues processed: 157
  average time/residue: 0.0972
  time to fit residues: 22.2800
Evaluate side-chains
  155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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   16 LEU
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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 4 optimal weight:    0.2980
   chunk 15 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0870
   chunk 27 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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 = 0.3833 r_free = 0.3833 target = 0.152987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.118217 restraints weight = 12371.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.121406 restraints weight = 9577.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.122630 restraints weight = 6240.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.122764 restraints weight = 5328.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.123238 restraints weight = 5177.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.3501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10225  Z= 0.147
  Angle     :  0.581   8.832  14063  Z= 0.307
  Chirality :  0.042   0.183   1618
  Planarity :  0.003   0.046   1595
  Dihedral  : 20.869 177.852   1923
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 18.16 %
    Favored  : 79.57 %
  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: -0.97 (0.25), residues: 1108
  helix:  1.05 (0.29), residues: 322
  sheet: -1.47 (0.28), residues: 287
  loop : -1.19 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  73 
 TYR   0.013   0.001   TYR C 211 
 PHE   0.011   0.001   PHE C 207 
 TRP   0.028   0.002   TRP D 274 
 HIS   0.004   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (10223)
  covalent geometry    : angle       0.58096 (14059)
  SS BOND              : bond        0.00167 (    2)
  SS BOND              : angle       0.58615 (    4)
  hydrogen bonds       : bond        0.03208 (  455)
  hydrogen bonds       : angle       5.69556 ( 1271)

********************** 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
  158 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 0.440 
Fit side-chains
REVERT: B   10 SER cc_start: 0.8454 (m) cc_final: 0.8189 (m)
REVERT: B   84 ASN cc_start: 0.7817 (m-40) cc_final: 0.7015 (t0)
REVERT: C  207 PHE cc_start: 0.8928 (m-80) cc_final: 0.8534 (m-80)
REVERT: D   86 ASP cc_start: 0.7439 (m-30) cc_final: 0.6974 (m-30)
REVERT: D  148 MET cc_start: 0.7727 (tpp) cc_final: 0.7214 (ttm)
REVERT: D  288 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7260 (p)
REVERT: D  329 SER cc_start: 0.7809 (m) cc_final: 0.7452 (p)
REVERT: A   16 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8337 (mm)
REVERT: A  116 MET cc_start: 0.8280 (mtp) cc_final: 0.7998 (mtp)
  outliers start: 22
  outliers final: 17
  residues processed: 150
  average time/residue: 0.0945
  time to fit residues: 20.5099
Evaluate side-chains
  155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 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  177 THR
Chi-restraints excluded: chain D residue  288 VAL
Chi-restraints excluded: chain A residue   16 LEU
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  216 THR
Chi-restraints excluded: chain A residue  233 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 94 optimal weight:    0.0970
   chunk 86 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0970
   chunk 91 optimal weight:    1.9990
   chunk 99 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.4776

-------------------------------------------------------------------------------
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 = 0.3831 r_free = 0.3831 target = 0.152790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.118153 restraints weight = 12601.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.121639 restraints weight = 9647.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.122762 restraints weight = 6178.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.122873 restraints weight = 5323.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.123362 restraints weight = 5157.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.3563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10225  Z= 0.145
  Angle     :  0.590   8.665  14063  Z= 0.309
  Chirality :  0.042   0.183   1618
  Planarity :  0.003   0.046   1595
  Dihedral  : 20.790 176.995   1923
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 18.16 %
    Favored  : 79.57 %
  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: -0.91 (0.25), residues: 1108
  helix:  1.12 (0.29), residues: 322
  sheet: -1.47 (0.28), residues: 293
  loop : -1.13 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  53 
 TYR   0.012   0.001   TYR C 211 
 PHE   0.009   0.001   PHE C 207 
 TRP   0.027   0.002   TRP D 274 
 HIS   0.004   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (10223)
  covalent geometry    : angle       0.59008 (14059)
  SS BOND              : bond        0.00148 (    2)
  SS BOND              : angle       0.56584 (    4)
  hydrogen bonds       : bond        0.03192 (  455)
  hydrogen bonds       : angle       5.64774 ( 1271)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1585.14 seconds
wall clock time: 28 minutes 15.34 seconds (1695.34 seconds total)