Starting phenix.real_space_refine
on Fri Feb 14 08:26:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ahe_11784/02_2025/7ahe_11784.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ahe_11784/02_2025/7ahe_11784.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ahe_11784/02_2025/7ahe_11784.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ahe_11784/02_2025/7ahe_11784.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ahe_11784/02_2025/7ahe_11784.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ahe_11784/02_2025/7ahe_11784.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      50      5.16       5
     C    6470      2.51       5
     N    1676      2.21       5
     O    1862      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10060
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 2016
          Classifications: {'peptide': 272}
          Link IDs: {'PTRANS': 12, 'TRANS': 259}
    Chain: "B"
      Number of atoms: 2016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 2016
          Classifications: {'peptide': 272}
          Link IDs: {'PTRANS': 12, 'TRANS': 259}
    Chain: "C"
      Number of atoms: 2992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 2992
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 14, 'TRANS': 367}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 2992
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 14, 'TRANS': 367}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Classifications: {'RNA': 1}
  Time building chain proxies: 5.87, per 1000 atoms: 0.58
  Number of scatterers: 10060
  At special positions: 0
  Unit cell: (102.212, 86.02, 122.452, 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      50     16.00
     P       2     15.00
     O    1862      8.00
     N    1676      7.00
     C    6470      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.97
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2420

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 12 sheets defined
      65.5% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 24
    Processing helix  chain 'A' and resid 26 through 49
    Processing helix  chain 'A' and resid 53 through 68
    Processing helix  chain 'A' and resid 72 through 89
    Processing helix  chain 'A' and resid 91 through 122
      Proline residue:  A 114  - end of helix
    Processing helix  chain 'A' and resid 122 through 139
      removed outlier: 3.636A  pdb=" N   ALA A 126 " --> pdb=" O   SER A 122 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS A 127 " --> pdb=" O   ASP A 123 " (cutoff:3.500A)
      Proline residue:  A 131  - end of helix
      removed outlier: 3.527A  pdb=" N   MET A 139 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 152
      removed outlier: 4.396A  pdb=" N   TYR A 144 " --> pdb=" O   PRO A 140 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LEU A 145 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ILE A 146 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      Proline residue:  A 147  - end of helix
    Processing helix  chain 'A' and resid 155 through 181
      removed outlier: 4.016A  pdb=" N   GLY A 159 " --> pdb=" O   GLY A 155 " (cutoff:3.500A)
      Proline residue:  A 169  - end of helix
    Processing helix  chain 'A' and resid 183 through 193
      removed outlier: 3.555A  pdb=" N   VAL A 187 " --> pdb=" O   SER A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 204
    Processing helix  chain 'A' and resid 204 through 232
      removed outlier: 3.639A  pdb=" N   LEU A 208 " --> pdb=" O   LEU A 204 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   GLY A 211 " --> pdb=" O   PRO A 207 " (cutoff:3.500A)
      removed outlier: 5.262A  pdb=" N   THR A 212 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 250
      removed outlier: 3.944A  pdb=" N   GLY A 242 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 275
      removed outlier: 3.877A  pdb=" N   LYS A 275 " --> pdb=" O   ARG A 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 51
      removed outlier: 7.668A  pdb=" N   SER B  28 " --> pdb=" O   SER B  24 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   GLY B  29 " --> pdb=" O   THR B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 68
    Processing helix  chain 'B' and resid 72 through 89
    Processing helix  chain 'B' and resid 91 through 122
      Proline residue:  B 114  - end of helix
    Processing helix  chain 'B' and resid 122 through 139
      removed outlier: 3.636A  pdb=" N   ALA B 126 " --> pdb=" O   SER B 122 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS B 127 " --> pdb=" O   ASP B 123 " (cutoff:3.500A)
      Proline residue:  B 131  - end of helix
      removed outlier: 3.528A  pdb=" N   MET B 139 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 152
      removed outlier: 4.396A  pdb=" N   TYR B 144 " --> pdb=" O   PRO B 140 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LEU B 145 " --> pdb=" O   GLY B 141 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ILE B 146 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      Proline residue:  B 147  - end of helix
    Processing helix  chain 'B' and resid 155 through 181
      removed outlier: 4.017A  pdb=" N   GLY B 159 " --> pdb=" O   GLY B 155 " (cutoff:3.500A)
      Proline residue:  B 169  - end of helix
    Processing helix  chain 'B' and resid 183 through 193
      removed outlier: 3.556A  pdb=" N   VAL B 187 " --> pdb=" O   SER B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 204
    Processing helix  chain 'B' and resid 204 through 232
      removed outlier: 3.639A  pdb=" N   LEU B 208 " --> pdb=" O   LEU B 204 " (cutoff:3.500A)
      removed outlier: 5.809A  pdb=" N   GLY B 211 " --> pdb=" O   PRO B 207 " (cutoff:3.500A)
      removed outlier: 5.262A  pdb=" N   THR B 212 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 250
      removed outlier: 3.944A  pdb=" N   GLY B 242 " --> pdb=" O   GLY B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 275
      removed outlier: 3.876A  pdb=" N   LYS B 275 " --> pdb=" O   ARG B 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 26
      removed outlier: 3.963A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 39
    Processing helix  chain 'C' and resid 67 through 75
    Processing helix  chain 'C' and resid 96 through 107
    Processing helix  chain 'C' and resid 122 through 133
      removed outlier: 4.947A  pdb=" N   GLY C 130 " --> pdb=" O   ASN C 126 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   LEU C 131 " --> pdb=" O   THR C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 151
    Processing helix  chain 'C' and resid 152 through 153
      No H-bonds generated for 'chain 'C' and resid 152 through 153'
    Processing helix  chain 'C' and resid 154 through 158
    Processing helix  chain 'C' and resid 161 through 165
      removed outlier: 3.608A  pdb=" N   GLN C 164 " --> pdb=" O   TYR C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 180
    Processing helix  chain 'C' and resid 190 through 195
      removed outlier: 3.802A  pdb=" N   ALA C 194 " --> pdb=" O   ALA C 191 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 214
    Processing helix  chain 'C' and resid 224 through 230
    Processing helix  chain 'C' and resid 250 through 255
    Processing helix  chain 'C' and resid 260 through 265
    Processing helix  chain 'C' and resid 292 through 304
    Processing helix  chain 'C' and resid 323 through 332
    Processing helix  chain 'C' and resid 356 through 361
      removed outlier: 4.357A  pdb=" N   TYR C 361 " --> pdb=" O   LEU C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 382 through 390
      removed outlier: 3.998A  pdb=" N   LEU C 386 " --> pdb=" O   ARG C 382 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   GLU C 387 " --> pdb=" O   GLY C 383 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 17 through 26
      removed outlier: 3.964A  pdb=" N   ALA D  21 " --> pdb=" O   ARG D  17 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 39
    Processing helix  chain 'D' and resid 67 through 75
    Processing helix  chain 'D' and resid 96 through 107
    Processing helix  chain 'D' and resid 122 through 133
      removed outlier: 4.948A  pdb=" N   GLY D 130 " --> pdb=" O   ASN D 126 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   LEU D 131 " --> pdb=" O   THR D 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 137 through 151
    Processing helix  chain 'D' and resid 152 through 153
      No H-bonds generated for 'chain 'D' and resid 152 through 153'
    Processing helix  chain 'D' and resid 154 through 158
    Processing helix  chain 'D' and resid 161 through 165
      removed outlier: 3.610A  pdb=" N   GLN D 164 " --> pdb=" O   TYR D 161 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 180
    Processing helix  chain 'D' and resid 190 through 195
      removed outlier: 3.802A  pdb=" N   ALA D 194 " --> pdb=" O   ALA D 191 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 214
    Processing helix  chain 'D' and resid 224 through 230
    Processing helix  chain 'D' and resid 250 through 255
    Processing helix  chain 'D' and resid 260 through 265
    Processing helix  chain 'D' and resid 292 through 304
    Processing helix  chain 'D' and resid 323 through 332
    Processing helix  chain 'D' and resid 358 through 363
      removed outlier: 3.930A  pdb=" N   ASP D 362 " --> pdb=" O   PRO D 358 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 382 through 390
      removed outlier: 3.998A  pdb=" N   LEU D 386 " --> pdb=" O   ARG D 382 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   GLU D 387 " --> pdb=" O   GLY D 383 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 47
      removed outlier: 5.457A  pdb=" N   TYR C  45 " --> pdb=" O   LYS C  12 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   LYS C  12 " --> pdb=" O   TYR C  45 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 47
      removed outlier: 5.457A  pdb=" N   TYR C  45 " --> pdb=" O   LYS C  12 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   LYS C  12 " --> pdb=" O   TYR C  45 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   LEU C  10 " --> pdb=" O   SER C  82 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   SER C  82 " --> pdb=" O   LEU C  10 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 57 through 59
    Processing sheet with id=AA4, first strand: chain 'C' and resid 237 through 238
      removed outlier: 3.940A  pdb=" N   MET C 244 " --> pdb=" O   ILE C 237 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 307 through 311
    Processing sheet with id=AA6, first strand: chain 'C' and resid 369 through 370
      removed outlier: 3.965A  pdb=" N   GLY C 378 " --> pdb=" O   VAL C 369 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 42 through 47
      removed outlier: 5.458A  pdb=" N   TYR D  45 " --> pdb=" O   LYS D  12 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   LYS D  12 " --> pdb=" O   TYR D  45 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 42 through 47
      removed outlier: 5.458A  pdb=" N   TYR D  45 " --> pdb=" O   LYS D  12 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   LYS D  12 " --> pdb=" O   TYR D  45 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   LEU D  10 " --> pdb=" O   SER D  82 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   SER D  82 " --> pdb=" O   LEU D  10 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 57 through 59
    Processing sheet with id=AB1, first strand: chain 'D' and resid 237 through 238
      removed outlier: 3.941A  pdb=" N   MET D 244 " --> pdb=" O   ILE D 237 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 307 through 311
    Processing sheet with id=AB3, first strand: chain 'D' and resid 369 through 370
      removed outlier: 3.966A  pdb=" N   GLY D 378 " --> pdb=" O   VAL D 369 " (cutoff:3.500A)

    591 hydrogen bonds defined for protein.
    1719 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.17

  Time building geometry restraints manager: 3.33 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3207
        1.34 -     1.45: 1180
        1.45 -     1.57: 5721
        1.57 -     1.69: 4
        1.69 -     1.81: 100
  Bond restraints: 10212
  Sorted by residual:
  bond pdb=" C5' 2BA C 501 "
       pdb=" O5' 2BA C 501 "
    ideal  model  delta    sigma   weight residual
    1.433  1.357  0.076 2.00e-02 2.50e+03 1.44e+01
  bond pdb="C3'1 2BA C 501 "
       pdb="O3'1 2BA C 501 "
    ideal  model  delta    sigma   weight residual
    1.418  1.350  0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb="C5'1 2BA C 501 "
       pdb="O5'1 2BA C 501 "
    ideal  model  delta    sigma   weight residual
    1.427  1.363  0.064 2.00e-02 2.50e+03 1.03e+01
  bond pdb=" N   VAL D 353 "
       pdb=" CA  VAL D 353 "
    ideal  model  delta    sigma   weight residual
    1.462  1.497 -0.035 1.14e-02 7.69e+03 9.17e+00
  bond pdb=" N   LEU C 352 "
       pdb=" CA  LEU C 352 "
    ideal  model  delta    sigma   weight residual
    1.453  1.490 -0.037 1.22e-02 6.72e+03 9.11e+00
  ... (remaining 10207 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 13443
        2.45 -     4.89: 292
        4.89 -     7.34: 51
        7.34 -     9.79: 25
        9.79 -    12.23: 17
  Bond angle restraints: 13828
  Sorted by residual:
  angle pdb=" C   SER A  16 "
        pdb=" N   SER A  17 "
        pdb=" CA  SER A  17 "
      ideal   model   delta    sigma   weight residual
     120.54  132.77  -12.23 1.35e+00 5.49e-01 8.21e+01
  angle pdb=" C   SER B  16 "
        pdb=" N   SER B  17 "
        pdb=" CA  SER B  17 "
      ideal   model   delta    sigma   weight residual
     120.54  132.76  -12.22 1.35e+00 5.49e-01 8.19e+01
  angle pdb=" C   LEU B  40 "
        pdb=" N   MET B  41 "
        pdb=" CA  MET B  41 "
      ideal   model   delta    sigma   weight residual
     120.44  131.09  -10.65 1.30e+00 5.92e-01 6.71e+01
  angle pdb=" C   GLY A  43 "
        pdb=" N   ILE A  44 "
        pdb=" CA  ILE A  44 "
      ideal   model   delta    sigma   weight residual
     120.60  131.11  -10.51 1.29e+00 6.01e-01 6.64e+01
  angle pdb=" C   LEU A  40 "
        pdb=" N   MET A  41 "
        pdb=" CA  MET A  41 "
      ideal   model   delta    sigma   weight residual
     120.44  131.03  -10.59 1.30e+00 5.92e-01 6.64e+01
  ... (remaining 13823 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.05: 5988
       23.05 -    46.10: 223
       46.10 -    69.16: 47
       69.16 -    92.21: 6
       92.21 -   115.26: 6
  Dihedral angle restraints: 6270
    sinusoidal: 2536
      harmonic: 3734
  Sorted by residual:
  dihedral pdb=" CA  ILE D 218 "
           pdb=" C   ILE D 218 "
           pdb=" N   ILE D 219 "
           pdb=" CA  ILE D 219 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.65   20.35     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" CA  ILE C 218 "
           pdb=" C   ILE C 218 "
           pdb=" N   ILE C 219 "
           pdb=" CA  ILE C 219 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.66   20.34     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" C5' 2BA C 501 "
           pdb=" O5' 2BA C 501 "
           pdb=" P   2BA C 501 "
           pdb=" O2P 2BA C 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -34.39   80.87 -115.26     1      3.00e+01 1.11e-03 1.52e+01
  ... (remaining 6267 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.172: 1647
       0.172 -    0.345: 22
       0.345 -    0.517: 11
       0.517 -    0.690: 2
       0.690 -    0.862: 6
  Chirality restraints: 1688
  Sorted by residual:
  chirality pdb=" CG  LEU A  66 "
            pdb=" CB  LEU A  66 "
            pdb=" CD1 LEU A  66 "
            pdb=" CD2 LEU A  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.73   -0.86 2.00e-01 2.50e+01 1.86e+01
  chirality pdb=" CG  LEU B  66 "
            pdb=" CB  LEU B  66 "
            pdb=" CD1 LEU B  66 "
            pdb=" CD2 LEU B  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.73   -0.86 2.00e-01 2.50e+01 1.85e+01
  chirality pdb=" CG  LEU B 208 "
            pdb=" CB  LEU B 208 "
            pdb=" CD1 LEU B 208 "
            pdb=" CD2 LEU B 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.86   -0.73 2.00e-01 2.50e+01 1.35e+01
  ... (remaining 1685 not shown)

  Planarity restraints: 1732
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  34 "   -0.016 2.00e-02 2.50e+03   3.15e-02 9.95e+00
        pdb=" C   GLN A  34 "    0.055 2.00e-02 2.50e+03
        pdb=" O   GLN A  34 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LYS A  35 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B  34 "   -0.016 2.00e-02 2.50e+03   3.15e-02 9.95e+00
        pdb=" C   GLN B  34 "    0.055 2.00e-02 2.50e+03
        pdb=" O   GLN B  34 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LYS B  35 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  61 "   -0.009 2.00e-02 2.50e+03   1.87e-02 3.49e+00
        pdb=" C   THR A  61 "    0.032 2.00e-02 2.50e+03
        pdb=" O   THR A  61 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ILE A  62 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1729 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1305
        2.74 -     3.28: 11475
        3.28 -     3.82: 16245
        3.82 -     4.36: 19894
        4.36 -     4.90: 33884
  Nonbonded interactions: 82803
  Sorted by model distance:
  nonbonded pdb=" O   ASP B  20 "
            pdb=" OG  SER B  24 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   ASP A  20 "
            pdb=" OG  SER A  24 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   LYS D 158 "
            pdb=" OD1 ASP D 159 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   LYS C 158 "
            pdb=" OD1 ASP C 159 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" N   ASP C 371 "
            pdb=" O   PHE C 375 "
     model   vdw
     2.228 3.120
  ... (remaining 82798 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'
}
ncs_group {
  reference = (chain 'C' and resid 3 through 391)
  selection = chain 'D'
}

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:             0.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     25.430
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
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      :  0.007   0.076  10212  Z= 0.427
  Angle     :  1.010  12.232  13828  Z= 0.616
  Chirality :  0.085   0.862   1688
  Planarity :  0.004   0.034   1732
  Dihedral  : 13.736 115.258   3850
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 16.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.65 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  1.18 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.40 (0.17), residues: 1296
  helix: -2.87 (0.14), residues: 764
  sheet: -5.40 (0.25), residues: 98
  loop : -4.16 (0.23), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  21 
 HIS   0.004   0.002   HIS C 223 
 PHE   0.012   0.001   PHE D 115 
 TYR   0.005   0.001   TYR B 144 
 ARG   0.004   0.000   ARG D 104 

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  353 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 348
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 ASP cc_start: 0.7838 (m-30) cc_final: 0.7175 (m-30)
REVERT: C  284 LEU cc_start: 0.8771 (mt) cc_final: 0.8321 (mm)
REVERT: C  353 VAL cc_start: 0.7470 (OUTLIER) cc_final: 0.7192 (m)
REVERT: D   24 MET cc_start: 0.8969 (mtt) cc_final: 0.8225 (mmm)
REVERT: D  129 TYR cc_start: 0.8633 (t80) cc_final: 0.8377 (t80)
REVERT: D  160 GLN cc_start: 0.7918 (mt0) cc_final: 0.7653 (mt0)
REVERT: D  313 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8388 (tptt)
  outliers start: 5
  outliers final: 0
  residues processed: 352
  average time/residue: 0.2535
  time to fit residues: 119.5519
Evaluate side-chains
  193 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 192
  time to evaluate  : 1.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    0.0870
   chunk 98 optimal weight:    0.6980
   chunk 54 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 118 optimal weight:    0.6980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
B 181 GLN
B 248 GLN
C  96 ASN
C 126 ASN
C 160 GLN
C 226 ASN
C 255 ASN
** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 325 GLN
D  90 GLN
D  96 ASN
D 114 ASN
D 126 ASN
D 211 GLN
D 226 ASN
D 255 ASN
D 325 GLN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.093122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.082149 restraints weight = 33812.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.084295 restraints weight = 19795.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.085816 restraints weight = 13028.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  10212  Z= 0.230
  Angle     :  0.675   8.692  13828  Z= 0.343
  Chirality :  0.046   0.309   1688
  Planarity :  0.005   0.064   1732
  Dihedral  :  6.722  60.310   1426
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.52 %
    Favored  : 95.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.22), residues: 1296
  helix: -0.26 (0.18), residues: 786
  sheet: -4.39 (0.28), residues: 102
  loop : -2.66 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  91 
 HIS   0.002   0.001   HIS C 223 
 PHE   0.020   0.002   PHE D  49 
 TYR   0.008   0.001   TYR D  45 
 ARG   0.007   0.001   ARG C  17 

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 232
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.9251 (mm) cc_final: 0.8929 (tt)
REVERT: A   91 TRP cc_start: 0.8184 (t-100) cc_final: 0.7964 (t-100)
REVERT: B   93 ASP cc_start: 0.7449 (m-30) cc_final: 0.7119 (m-30)
REVERT: C   22 LEU cc_start: 0.9165 (tp) cc_final: 0.8295 (tp)
REVERT: C   26 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8278 (mt-10)
REVERT: C  190 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7196 (mm-30)
REVERT: C  234 ARG cc_start: 0.8383 (mtp-110) cc_final: 0.7989 (mtm110)
REVERT: C  308 LEU cc_start: 0.9110 (mt) cc_final: 0.8567 (mt)
REVERT: D   24 MET cc_start: 0.8825 (mtt) cc_final: 0.8363 (mmm)
REVERT: D   60 MET cc_start: 0.7313 (mtp) cc_final: 0.7099 (mtp)
REVERT: D  190 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6836 (mm-30)
REVERT: D  234 ARG cc_start: 0.8401 (mtp-110) cc_final: 0.8109 (mtm110)
REVERT: D  238 MET cc_start: 0.8091 (ttm) cc_final: 0.7624 (ttm)
REVERT: D  309 MET cc_start: 0.7769 (mmp) cc_final: 0.7561 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 233
  average time/residue: 0.2221
  time to fit residues: 73.0259
Evaluate side-chains
  165 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 69 optimal weight:    3.9990
   chunk 86 optimal weight:    0.3980
   chunk 85 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 106 optimal weight:    1.9990
   chunk 111 optimal weight:    0.9980
   chunk 101 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
A 248 GLN
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 248 GLN
C  90 GLN
C 223 HIS
** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.090098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.078959 restraints weight = 35004.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.081192 restraints weight = 19557.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.082737 restraints weight = 12530.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.4079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10212  Z= 0.229
  Angle     :  0.650  12.229  13828  Z= 0.333
  Chirality :  0.046   0.309   1688
  Planarity :  0.004   0.074   1732
  Dihedral  :  6.243  55.954   1426
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.89 %
    Favored  : 95.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.24), residues: 1296
  helix:  0.71 (0.19), residues: 784
  sheet: -3.55 (0.34), residues: 102
  loop : -2.33 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  14 
 HIS   0.001   0.001   HIS D   9 
 PHE   0.019   0.001   PHE B 166 
 TYR   0.015   0.002   TYR D 129 
 ARG   0.004   0.000   ARG C 141 

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 206
  time to evaluate  : 1.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.9265 (mm) cc_final: 0.8901 (tt)
REVERT: A  205 GLU cc_start: 0.8593 (mp0) cc_final: 0.8164 (mm-30)
REVERT: A  219 GLN cc_start: 0.8311 (mp10) cc_final: 0.7817 (mp10)
REVERT: B   14 TRP cc_start: 0.6440 (m100) cc_final: 0.6087 (m100)
REVERT: B   93 ASP cc_start: 0.7719 (m-30) cc_final: 0.7490 (m-30)
REVERT: B  133 LEU cc_start: 0.7478 (mt) cc_final: 0.7246 (tt)
REVERT: B  188 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.8001 (mt-10)
REVERT: B  200 LYS cc_start: 0.8000 (ptpp) cc_final: 0.7218 (ptpp)
REVERT: B  205 GLU cc_start: 0.8637 (mp0) cc_final: 0.7684 (mp0)
REVERT: B  219 GLN cc_start: 0.8295 (mp10) cc_final: 0.7775 (mp10)
REVERT: B  227 MET cc_start: 0.8759 (mmm) cc_final: 0.8492 (mmm)
REVERT: C   22 LEU cc_start: 0.9226 (tp) cc_final: 0.8457 (tp)
REVERT: C   24 MET cc_start: 0.8878 (mtp) cc_final: 0.8491 (mtp)
REVERT: C   26 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8424 (mt-10)
REVERT: C  234 ARG cc_start: 0.8713 (mtp-110) cc_final: 0.8155 (mtm110)
REVERT: C  308 LEU cc_start: 0.9095 (mt) cc_final: 0.8778 (mt)
REVERT: C  359 ILE cc_start: 0.8232 (mp) cc_final: 0.7682 (mm)
REVERT: D   24 MET cc_start: 0.8946 (mtt) cc_final: 0.8614 (mmm)
REVERT: D  110 MET cc_start: 0.8469 (ttm) cc_final: 0.8072 (ttm)
REVERT: D  190 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7002 (mm-30)
REVERT: D  234 ARG cc_start: 0.8569 (mtp-110) cc_final: 0.8161 (mtm110)
  outliers start: 2
  outliers final: 0
  residues processed: 207
  average time/residue: 0.2219
  time to fit residues: 64.7286
Evaluate side-chains
  165 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 164
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   chunk 63 optimal weight:    9.9990
   chunk 37 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 60 optimal weight:    0.5980
   chunk 89 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 GLN
B 248 GLN
** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 316 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.088337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.077499 restraints weight = 34749.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.079673 restraints weight = 19283.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.081163 restraints weight = 12271.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.4539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  10212  Z= 0.236
  Angle     :  0.640   9.095  13828  Z= 0.323
  Chirality :  0.045   0.296   1688
  Planarity :  0.004   0.071   1732
  Dihedral  :  6.014  51.996   1426
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.24), residues: 1296
  helix:  0.97 (0.19), residues: 780
  sheet: -3.12 (0.38), residues: 112
  loop : -2.04 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A  14 
 HIS   0.001   0.001   HIS D 223 
 PHE   0.021   0.002   PHE C 115 
 TYR   0.012   0.002   TYR C 129 
 ARG   0.006   0.000   ARG B 241 

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 1.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.9218 (mm) cc_final: 0.8802 (tt)
REVERT: A  205 GLU cc_start: 0.8620 (mp0) cc_final: 0.8307 (mm-30)
REVERT: A  219 GLN cc_start: 0.8450 (mp10) cc_final: 0.7685 (mp10)
REVERT: B   93 ASP cc_start: 0.7813 (m-30) cc_final: 0.7509 (m-30)
REVERT: B  119 MET cc_start: 0.7983 (mmm) cc_final: 0.7236 (mmm)
REVERT: B  133 LEU cc_start: 0.7754 (mt) cc_final: 0.7385 (tt)
REVERT: B  205 GLU cc_start: 0.8703 (mp0) cc_final: 0.8440 (mm-30)
REVERT: B  219 GLN cc_start: 0.8401 (mp10) cc_final: 0.8017 (mp10)
REVERT: B  227 MET cc_start: 0.8864 (mmm) cc_final: 0.8644 (mmm)
REVERT: C   22 LEU cc_start: 0.9263 (tp) cc_final: 0.8467 (tp)
REVERT: C   26 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8470 (mt-10)
REVERT: C  156 ASP cc_start: 0.7487 (p0) cc_final: 0.7076 (p0)
REVERT: C  157 PHE cc_start: 0.8287 (m-80) cc_final: 0.8035 (m-10)
REVERT: C  190 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7335 (mm-30)
REVERT: C  233 ASP cc_start: 0.8608 (m-30) cc_final: 0.7839 (t70)
REVERT: C  234 ARG cc_start: 0.8784 (mtp-110) cc_final: 0.7971 (mtm110)
REVERT: C  308 LEU cc_start: 0.9146 (mt) cc_final: 0.8938 (mt)
REVERT: D   24 MET cc_start: 0.8871 (mtt) cc_final: 0.8573 (mmm)
REVERT: D  101 LEU cc_start: 0.8828 (tp) cc_final: 0.8577 (tp)
REVERT: D  190 GLU cc_start: 0.7725 (mt-10) cc_final: 0.6825 (mm-30)
REVERT: D  234 ARG cc_start: 0.8582 (mtp-110) cc_final: 0.8128 (mtm110)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.2169
  time to fit residues: 62.1941
Evaluate side-chains
  157 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0270
   chunk 67 optimal weight:    6.9990
   chunk 96 optimal weight:    5.9990
   chunk 110 optimal weight:    0.0470
   chunk 103 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.3738

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 GLN
B 248 GLN
** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.086821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.076532 restraints weight = 34712.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.078572 restraints weight = 19672.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.080000 restraints weight = 12690.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.4996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10212  Z= 0.211
  Angle     :  0.627   7.930  13828  Z= 0.318
  Chirality :  0.045   0.288   1688
  Planarity :  0.004   0.076   1732
  Dihedral  :  5.807  48.056   1426
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.71 %
    Favored  : 97.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.24), residues: 1296
  helix:  1.10 (0.19), residues: 782
  sheet: -2.22 (0.43), residues: 116
  loop : -1.93 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A  14 
 HIS   0.001   0.000   HIS C 223 
 PHE   0.022   0.002   PHE C 115 
 TYR   0.008   0.002   TYR D 129 
 ARG   0.008   0.000   ARG B 241 

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 199
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.9243 (mm) cc_final: 0.8801 (tt)
REVERT: A  119 MET cc_start: 0.8154 (mmm) cc_final: 0.7904 (mmm)
REVERT: A  205 GLU cc_start: 0.8593 (mp0) cc_final: 0.7916 (mp0)
REVERT: A  219 GLN cc_start: 0.8358 (mp10) cc_final: 0.7979 (mp10)
REVERT: B   14 TRP cc_start: 0.7206 (m100) cc_final: 0.6882 (m100)
REVERT: B  133 LEU cc_start: 0.7888 (mt) cc_final: 0.7635 (tt)
REVERT: B  205 GLU cc_start: 0.8439 (mp0) cc_final: 0.7920 (mp0)
REVERT: B  219 GLN cc_start: 0.8503 (mp10) cc_final: 0.8024 (mp10)
REVERT: B  227 MET cc_start: 0.8907 (mmm) cc_final: 0.8474 (mmm)
REVERT: C   22 LEU cc_start: 0.9246 (tp) cc_final: 0.8377 (tp)
REVERT: C   24 MET cc_start: 0.8686 (mtp) cc_final: 0.8360 (mtp)
REVERT: C  110 MET cc_start: 0.8459 (ttm) cc_final: 0.8070 (ttm)
REVERT: C  156 ASP cc_start: 0.7469 (p0) cc_final: 0.7006 (p0)
REVERT: C  157 PHE cc_start: 0.8147 (m-80) cc_final: 0.7901 (m-10)
REVERT: C  190 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7248 (mm-30)
REVERT: C  233 ASP cc_start: 0.8588 (m-30) cc_final: 0.7825 (t70)
REVERT: C  234 ARG cc_start: 0.8728 (mtp-110) cc_final: 0.7980 (mtm110)
REVERT: C  308 LEU cc_start: 0.9148 (mt) cc_final: 0.8932 (mt)
REVERT: D   24 MET cc_start: 0.8823 (mtt) cc_final: 0.8518 (mmm)
REVERT: D  101 LEU cc_start: 0.8851 (tp) cc_final: 0.8614 (tp)
REVERT: D  190 GLU cc_start: 0.7716 (mt-10) cc_final: 0.6898 (mm-30)
REVERT: D  300 MET cc_start: 0.8757 (mmt) cc_final: 0.8521 (mmt)
REVERT: D  308 LEU cc_start: 0.8965 (mt) cc_final: 0.8477 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 199
  average time/residue: 0.2075
  time to fit residues: 59.1875
Evaluate side-chains
  153 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 90 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9990
   chunk 88 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9980
   chunk 75 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   chunk 122 optimal weight:    2.9990
   chunk 120 optimal weight:    7.9990
   chunk 31 optimal weight:    7.9990
   chunk 6 optimal weight:    0.4980
   chunk 65 optimal weight:    3.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
B 218 ASN
B 248 GLN
** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 134 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.085997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.075531 restraints weight = 34729.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.077582 restraints weight = 19359.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.079036 restraints weight = 12444.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.5360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10212  Z= 0.212
  Angle     :  0.637  10.530  13828  Z= 0.321
  Chirality :  0.045   0.291   1688
  Planarity :  0.004   0.074   1732
  Dihedral  :  5.688  44.802   1426
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.24), residues: 1296
  helix:  1.22 (0.19), residues: 780
  sheet: -1.81 (0.44), residues: 126
  loop : -1.69 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A  14 
 HIS   0.001   0.000   HIS D 223 
 PHE   0.020   0.001   PHE C 115 
 TYR   0.011   0.002   TYR D 129 
 ARG   0.008   0.000   ARG B 241 

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.9248 (mm) cc_final: 0.8830 (tt)
REVERT: A  205 GLU cc_start: 0.8674 (mp0) cc_final: 0.7827 (mp0)
REVERT: A  219 GLN cc_start: 0.8409 (mp10) cc_final: 0.7829 (mp10)
REVERT: B   14 TRP cc_start: 0.7289 (m100) cc_final: 0.6905 (m100)
REVERT: B  119 MET cc_start: 0.8346 (mmm) cc_final: 0.7668 (mmm)
REVERT: B  136 MET cc_start: 0.7865 (ptm) cc_final: 0.7571 (ptm)
REVERT: B  165 ILE cc_start: 0.9035 (tp) cc_final: 0.8790 (tt)
REVERT: B  200 LYS cc_start: 0.8178 (ptpt) cc_final: 0.7697 (ttpp)
REVERT: B  205 GLU cc_start: 0.8446 (mp0) cc_final: 0.7714 (mp0)
REVERT: B  227 MET cc_start: 0.8955 (mmm) cc_final: 0.8524 (mmm)
REVERT: B  244 LEU cc_start: 0.8942 (tt) cc_final: 0.8470 (tt)
REVERT: C  156 ASP cc_start: 0.7585 (p0) cc_final: 0.7156 (p0)
REVERT: C  157 PHE cc_start: 0.8248 (m-80) cc_final: 0.7881 (m-10)
REVERT: C  190 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7098 (mm-30)
REVERT: C  225 LEU cc_start: 0.9322 (mm) cc_final: 0.9066 (mt)
REVERT: C  234 ARG cc_start: 0.8849 (mtp-110) cc_final: 0.8111 (mtm110)
REVERT: D   24 MET cc_start: 0.8904 (mtt) cc_final: 0.8611 (mmm)
REVERT: D  101 LEU cc_start: 0.8845 (tp) cc_final: 0.8588 (tp)
REVERT: D  234 ARG cc_start: 0.8662 (mtp-110) cc_final: 0.7958 (mtm110)
REVERT: D  308 LEU cc_start: 0.9032 (mt) cc_final: 0.8532 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.2087
  time to fit residues: 55.9156
Evaluate side-chains
  151 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 115 optimal weight:    0.1980
   chunk 90 optimal weight:    0.0970
   chunk 3 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 105 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   chunk 8 optimal weight:    0.6980
   chunk 123 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 GLN
** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 211 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.087202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.076627 restraints weight = 35392.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.078762 restraints weight = 19489.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.080200 restraints weight = 12370.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.5586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10212  Z= 0.182
  Angle     :  0.631   8.295  13828  Z= 0.318
  Chirality :  0.045   0.306   1688
  Planarity :  0.004   0.075   1732
  Dihedral  :  5.610  43.302   1426
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.24), residues: 1296
  helix:  1.24 (0.19), residues: 776
  sheet: -1.04 (0.53), residues: 106
  loop : -1.69 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A  14 
 HIS   0.001   0.000   HIS D 120 
 PHE   0.017   0.001   PHE A 166 
 TYR   0.030   0.002   TYR D 129 
 ARG   0.008   0.000   ARG B 241 

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.9255 (mm) cc_final: 0.8824 (tt)
REVERT: A  119 MET cc_start: 0.8383 (mmm) cc_final: 0.8131 (mmm)
REVERT: A  136 MET cc_start: 0.7201 (ptm) cc_final: 0.6598 (ptm)
REVERT: A  205 GLU cc_start: 0.8662 (mp0) cc_final: 0.7805 (mp0)
REVERT: A  219 GLN cc_start: 0.8427 (mp10) cc_final: 0.7961 (mp10)
REVERT: A  233 MET cc_start: 0.5672 (ptp) cc_final: 0.5381 (mtm)
REVERT: B  136 MET cc_start: 0.7925 (ptm) cc_final: 0.7638 (ptm)
REVERT: B  165 ILE cc_start: 0.9114 (tp) cc_final: 0.8897 (tt)
REVERT: B  200 LYS cc_start: 0.8263 (ptpt) cc_final: 0.7677 (ttpp)
REVERT: B  205 GLU cc_start: 0.8464 (mp0) cc_final: 0.7728 (mp0)
REVERT: C   24 MET cc_start: 0.8833 (mtp) cc_final: 0.8518 (ttt)
REVERT: C  110 MET cc_start: 0.8495 (ttm) cc_final: 0.8053 (ttm)
REVERT: C  156 ASP cc_start: 0.7540 (p0) cc_final: 0.7112 (p0)
REVERT: C  157 PHE cc_start: 0.8231 (m-80) cc_final: 0.7972 (m-10)
REVERT: C  190 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6916 (mm-30)
REVERT: C  225 LEU cc_start: 0.9276 (mm) cc_final: 0.8993 (mt)
REVERT: C  233 ASP cc_start: 0.8733 (m-30) cc_final: 0.7847 (t70)
REVERT: C  234 ARG cc_start: 0.8808 (mtp-110) cc_final: 0.8089 (mtm110)
REVERT: C  300 MET cc_start: 0.9002 (mmt) cc_final: 0.8534 (mmm)
REVERT: C  308 LEU cc_start: 0.9164 (mt) cc_final: 0.8721 (mt)
REVERT: C  340 MET cc_start: 0.8509 (mtp) cc_final: 0.8033 (mtt)
REVERT: D   24 MET cc_start: 0.8923 (mtt) cc_final: 0.8649 (mmm)
REVERT: D  101 LEU cc_start: 0.8845 (tp) cc_final: 0.8548 (tp)
REVERT: D  234 ARG cc_start: 0.8682 (mtp-110) cc_final: 0.8074 (mtm110)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.2081
  time to fit residues: 55.7029
Evaluate side-chains
  150 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 88 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 105 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 107 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.086284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.075524 restraints weight = 35487.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.077683 restraints weight = 19566.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.079071 restraints weight = 12419.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.5826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10212  Z= 0.186
  Angle     :  0.633   8.448  13828  Z= 0.321
  Chirality :  0.045   0.274   1688
  Planarity :  0.004   0.074   1732
  Dihedral  :  5.477  40.963   1426
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.24), residues: 1296
  helix:  1.28 (0.19), residues: 776
  sheet: -0.77 (0.54), residues: 106
  loop : -1.56 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  91 
 HIS   0.001   0.000   HIS D 120 
 PHE   0.020   0.001   PHE D 115 
 TYR   0.033   0.002   TYR D 129 
 ARG   0.003   0.000   ARG A 173 

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 MET cc_start: 0.8275 (mmm) cc_final: 0.7431 (mmm)
REVERT: A  205 GLU cc_start: 0.8637 (mp0) cc_final: 0.7979 (mm-30)
REVERT: A  219 GLN cc_start: 0.8430 (mp10) cc_final: 0.7953 (mp10)
REVERT: A  233 MET cc_start: 0.5437 (ptp) cc_final: 0.5064 (mtm)
REVERT: B  200 LYS cc_start: 0.8298 (ptpt) cc_final: 0.7662 (ttpp)
REVERT: B  205 GLU cc_start: 0.8505 (mp0) cc_final: 0.7753 (mp0)
REVERT: B  219 GLN cc_start: 0.8423 (mp10) cc_final: 0.7939 (mp10)
REVERT: C   24 MET cc_start: 0.8849 (mtp) cc_final: 0.8593 (ttt)
REVERT: C  190 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6899 (mm-30)
REVERT: C  225 LEU cc_start: 0.9247 (mm) cc_final: 0.8926 (mt)
REVERT: C  234 ARG cc_start: 0.8813 (mtp-110) cc_final: 0.8177 (mtm110)
REVERT: C  300 MET cc_start: 0.9043 (mmt) cc_final: 0.8502 (mmm)
REVERT: C  308 LEU cc_start: 0.9146 (mt) cc_final: 0.8678 (mt)
REVERT: C  340 MET cc_start: 0.8490 (mtp) cc_final: 0.7985 (mtt)
REVERT: D   24 MET cc_start: 0.8977 (mtt) cc_final: 0.8663 (mmm)
REVERT: D  101 LEU cc_start: 0.8865 (tp) cc_final: 0.8567 (tp)
REVERT: D  225 LEU cc_start: 0.9197 (mm) cc_final: 0.8868 (mt)
REVERT: D  300 MET cc_start: 0.8946 (mmt) cc_final: 0.8375 (mmm)
REVERT: D  308 LEU cc_start: 0.8997 (mt) cc_final: 0.8745 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.2136
  time to fit residues: 56.0902
Evaluate side-chains
  149 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 85 optimal weight:    9.9990
   chunk 67 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
B 181 GLN
B 218 ASN
** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.085636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.074895 restraints weight = 35286.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.077043 restraints weight = 19240.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.078450 restraints weight = 12161.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.6068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10212  Z= 0.199
  Angle     :  0.648   7.432  13828  Z= 0.327
  Chirality :  0.045   0.276   1688
  Planarity :  0.004   0.073   1732
  Dihedral  :  5.444  39.333   1426
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.24), residues: 1296
  helix:  1.24 (0.19), residues: 782
  sheet: -0.70 (0.54), residues: 106
  loop : -1.37 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  14 
 HIS   0.001   0.000   HIS D   9 
 PHE   0.020   0.001   PHE A 166 
 TYR   0.035   0.002   TYR D 129 
 ARG   0.011   0.000   ARG B 241 

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 MET cc_start: 0.8293 (mmm) cc_final: 0.7529 (mmm)
REVERT: A  205 GLU cc_start: 0.8664 (mp0) cc_final: 0.8040 (mm-30)
REVERT: A  219 GLN cc_start: 0.8440 (mp10) cc_final: 0.7910 (mp10)
REVERT: A  233 MET cc_start: 0.5707 (ptp) cc_final: 0.5303 (mtm)
REVERT: B  200 LYS cc_start: 0.8290 (ptpt) cc_final: 0.7618 (ttpp)
REVERT: B  205 GLU cc_start: 0.8496 (mp0) cc_final: 0.7676 (mp0)
REVERT: B  219 GLN cc_start: 0.8460 (mp10) cc_final: 0.7914 (mp10)
REVERT: C   24 MET cc_start: 0.8853 (mtp) cc_final: 0.8532 (ttm)
REVERT: C  234 ARG cc_start: 0.8848 (mtp-110) cc_final: 0.8059 (mtm110)
REVERT: C  300 MET cc_start: 0.9056 (mmt) cc_final: 0.8496 (mmm)
REVERT: C  308 LEU cc_start: 0.9216 (mt) cc_final: 0.8716 (mt)
REVERT: C  312 ASP cc_start: 0.7966 (t70) cc_final: 0.7661 (m-30)
REVERT: C  340 MET cc_start: 0.8509 (mtp) cc_final: 0.7983 (mtt)
REVERT: D   24 MET cc_start: 0.9015 (mtt) cc_final: 0.8721 (mmm)
REVERT: D  101 LEU cc_start: 0.8867 (tp) cc_final: 0.8546 (tp)
REVERT: D  225 LEU cc_start: 0.9211 (mm) cc_final: 0.8898 (mt)
REVERT: D  300 MET cc_start: 0.8973 (mmt) cc_final: 0.8628 (mmm)
REVERT: D  308 LEU cc_start: 0.9171 (mt) cc_final: 0.8815 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2138
  time to fit residues: 55.6642
Evaluate side-chains
  152 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 1.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   chunk 69 optimal weight:    0.0570
   chunk 46 optimal weight:    0.5980
   chunk 9 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 118 optimal weight:    0.9990
   chunk 101 optimal weight:    6.9990
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
A 218 ASN
B 181 GLN
B 218 ASN
** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.085809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.075477 restraints weight = 35348.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.077551 restraints weight = 19791.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.078951 restraints weight = 12672.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.6272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10212  Z= 0.187
  Angle     :  0.656   7.523  13828  Z= 0.333
  Chirality :  0.045   0.264   1688
  Planarity :  0.004   0.073   1732
  Dihedral  :  5.386  37.728   1426
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.24), residues: 1296
  helix:  1.19 (0.19), residues: 794
  sheet: -0.61 (0.55), residues: 106
  loop : -1.27 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  14 
 HIS   0.001   0.000   HIS D   9 
 PHE   0.022   0.001   PHE A 166 
 TYR   0.037   0.002   TYR D 129 
 ARG   0.008   0.000   ARG B 241 

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

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

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2592 Ramachandran restraints generated.
    1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 MET cc_start: 0.8284 (mmm) cc_final: 0.7595 (mmm)
REVERT: A  136 MET cc_start: 0.8020 (ptm) cc_final: 0.7463 (ptm)
REVERT: A  205 GLU cc_start: 0.8575 (mp0) cc_final: 0.7902 (mm-30)
REVERT: A  219 GLN cc_start: 0.8458 (mp10) cc_final: 0.7937 (mp10)
REVERT: A  233 MET cc_start: 0.5584 (ptp) cc_final: 0.5197 (mtm)
REVERT: B  200 LYS cc_start: 0.8253 (ptpt) cc_final: 0.7658 (ttpp)
REVERT: B  205 GLU cc_start: 0.8404 (mp0) cc_final: 0.7705 (mp0)
REVERT: B  219 GLN cc_start: 0.8411 (mp10) cc_final: 0.7880 (mp10)
REVERT: B  244 LEU cc_start: 0.9083 (tt) cc_final: 0.8631 (tp)
REVERT: C   24 MET cc_start: 0.8752 (mtp) cc_final: 0.8469 (ttm)
REVERT: C  234 ARG cc_start: 0.8837 (mtp-110) cc_final: 0.8242 (mtm110)
REVERT: C  300 MET cc_start: 0.8981 (mmt) cc_final: 0.8423 (mmm)
REVERT: C  308 LEU cc_start: 0.9212 (mt) cc_final: 0.8764 (mt)
REVERT: C  312 ASP cc_start: 0.7887 (t70) cc_final: 0.7640 (m-30)
REVERT: C  340 MET cc_start: 0.8406 (mtp) cc_final: 0.7916 (mtt)
REVERT: D   24 MET cc_start: 0.8956 (mtt) cc_final: 0.8647 (mmm)
REVERT: D  101 LEU cc_start: 0.8820 (tp) cc_final: 0.8521 (tp)
REVERT: D  225 LEU cc_start: 0.9123 (mm) cc_final: 0.8803 (mt)
REVERT: D  300 MET cc_start: 0.8854 (mmt) cc_final: 0.8546 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2134
  time to fit residues: 55.2050
Evaluate side-chains
  149 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 88 optimal weight:   20.0000
   chunk 124 optimal weight:    2.9990
   chunk 55 optimal weight:   10.0000
   chunk 95 optimal weight:    0.9990
   chunk 9 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 77 optimal weight:   10.0000
   chunk 116 optimal weight:    0.0570
   chunk 67 optimal weight:    0.0570
   chunk 41 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
A 248 GLN
B 218 ASN
** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.086033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.075556 restraints weight = 35001.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.077666 restraints weight = 19258.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.079103 restraints weight = 12199.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.6397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10212  Z= 0.179
  Angle     :  0.650   8.040  13828  Z= 0.328
  Chirality :  0.045   0.270   1688
  Planarity :  0.004   0.072   1732
  Dihedral  :  5.346  36.376   1426
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.24), residues: 1296
  helix:  1.27 (0.19), residues: 794
  sheet: -0.55 (0.56), residues: 106
  loop : -1.19 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  14 
 HIS   0.001   0.000   HIS D 120 
 PHE   0.018   0.001   PHE A 166 
 TYR   0.033   0.002   TYR D 129 
 ARG   0.008   0.000   ARG B 241 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2718.91 seconds
wall clock time: 49 minutes 46.97 seconds (2986.97 seconds total)