Starting phenix.real_space_refine
on Sun May 11 11:56:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kh5_37237/05_2025/8kh5_37237.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kh5_37237/05_2025/8kh5_37237.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kh5_37237/05_2025/8kh5_37237.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kh5_37237/05_2025/8kh5_37237.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kh5_37237/05_2025/8kh5_37237.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kh5_37237/05_2025/8kh5_37237.cif"
  }
  resolution = 2.83
  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=   0.003 sd=   0.143
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       1      5.49       5
     S      57      5.16       5
     C    5034      2.51       5
     N    1339      2.21       5
     O    1407      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7838
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2214
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 12, 'TRANS': 268}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 122
          Unresolved non-hydrogen dihedrals: 90
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 64
    Chain: "B"
      Number of atoms: 1778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1778
          Classifications: {'peptide': 228}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 158
          Unresolved non-hydrogen dihedrals: 108
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 96
    Chain: "C"
      Number of atoms: 2467
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 338, 2460
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 141
          Unresolved non-hydrogen angles: 175
          Unresolved non-hydrogen dihedrals: 110
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 116
      Conformer: "B"
        Number of residues, atoms: 338, 2460
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 141
          Unresolved non-hydrogen angles: 175
          Unresolved non-hydrogen dihedrals: 110
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 116
          bond proxies already assigned to first conformer: 2496
    Chain: "E"
      Number of atoms: 946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 946
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "D"
      Number of atoms: 345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 345
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 43
    Chain: "A"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 88
          Unusual residues: {'CLR': 2, 'LPS': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.94, per 1000 atoms: 0.76
  Number of scatterers: 7838
  At special positions: 0
  Unit cell: (74.52, 97.2, 130.68, 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      57     16.00
     P       1     15.00
     O    1407      8.00
     N    1339      7.00
     C    5034      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  91 " - pdb=" SG  CYS A 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  99 " - pdb=" SG  CYS E 107 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.21
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1948

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      43.3% alpha, 20.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 51
      removed outlier: 4.321A  pdb=" N   VAL A  31 " --> pdb=" O   THR A  27 " (cutoff:3.500A)
      Proline residue:  A  32  - end of helix
    Processing helix  chain 'A' and resid 55 through 82
      Proline residue:  A  73  - end of helix
    Processing helix  chain 'A' and resid 87 through 122
      removed outlier: 3.630A  pdb=" N   LYS A  98 " --> pdb=" O   CYS A  94 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   TYR A  99 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 127
    Processing helix  chain 'A' and resid 133 through 149
      removed outlier: 3.526A  pdb=" N   CYS A 146 " --> pdb=" O   TRP A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 156
      removed outlier: 3.699A  pdb=" N   LEU A 154 " --> pdb=" O   VAL A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 213
      Proline residue:  A 197  - end of helix
    Processing helix  chain 'A' and resid 223 through 258
      removed outlier: 3.623A  pdb=" N   LEU A 229 " --> pdb=" O   LYS A 225 " (cutoff:3.500A)
      Proline residue:  A 245  - end of helix
      Proline residue:  A 251  - end of helix
    Processing helix  chain 'A' and resid 263 through 294
      Proline residue:  A 289  - end of helix
    Processing helix  chain 'A' and resid 296 through 303
    Processing helix  chain 'B' and resid 13 through 39
      removed outlier: 3.595A  pdb=" N   ALA B  18 " --> pdb=" O   ASN B  14 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA B  39 " --> pdb=" O   GLN B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 60
    Processing helix  chain 'B' and resid 231 through 236
    Processing helix  chain 'B' and resid 265 through 279
    Processing helix  chain 'B' and resid 293 through 304
    Processing helix  chain 'B' and resid 307 through 312
      removed outlier: 4.002A  pdb=" N   TYR B 311 " --> pdb=" O   LYS B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 318
    Processing helix  chain 'B' and resid 331 through 352
      removed outlier: 3.651A  pdb=" N   ILE B 348 " --> pdb=" O   GLU B 344 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   SER B 352 " --> pdb=" O   ILE B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 391
    Processing helix  chain 'C' and resid 4 through 26
    Processing helix  chain 'C' and resid 29 through 35
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.692A  pdb=" N   THR E  91 " --> pdb=" O   PRO E  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 9 through 25
      removed outlier: 3.836A  pdb=" N   ILE D  25 " --> pdb=" O   MET D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
    Processing helix  chain 'D' and resid 55 through 59
    Processing sheet with id=AA1, first strand: chain 'B' and resid 209 through 214
      removed outlier: 3.912A  pdb=" N   ALA B 243 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ILE B 244 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   PHE B 290 " --> pdb=" O   ILE B 244 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   PHE B 246 " --> pdb=" O   PHE B 290 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ASN B 292 " --> pdb=" O   PHE B 246 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   VAL B 248 " --> pdb=" O   ASN B 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 52
      removed outlier: 3.730A  pdb=" N   ARG C  49 " --> pdb=" O   ILE C 338 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   PHE C 335 " --> pdb=" O   SER C 331 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.818A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   ASP C  83 " --> pdb=" O   LYS C  89 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   LYS C  89 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.085A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151
      removed outlier: 3.529A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.636A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.482A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASP C 254 " --> pdb=" O   GLN C 259 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLN C 259 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.759A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   CYS C 294 " --> pdb=" O   VAL C 307 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   VAL C 307 " --> pdb=" O   CYS C 294 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   VAL C 296 " --> pdb=" O   ALA C 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.046A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 4.949A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)

    448 hydrogen bonds defined for protein.
    1290 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: 2.35

  Time building geometry restraints manager: 2.50 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1234
        1.30 -     1.43: 2168
        1.43 -     1.55: 4530
        1.55 -     1.68: 4
        1.68 -     1.81: 78
  Bond restraints: 8014
  Sorted by residual:
  bond pdb=" C   PRO A 123 "
       pdb=" O   PRO A 123 "
    ideal  model  delta    sigma   weight residual
    1.237  1.410 -0.173 1.26e-02 6.30e+03 1.88e+02
  bond pdb=" C31 LPS A 402 "
       pdb=" O32 LPS A 402 "
    ideal  model  delta    sigma   weight residual
    1.398  1.180  0.218 2.00e-02 2.50e+03 1.19e+02
  bond pdb=" CA  ALA A 140 "
       pdb=" C   ALA A 140 "
    ideal  model  delta    sigma   weight residual
    1.524  1.412  0.112 1.29e-02 6.01e+03 7.53e+01
  bond pdb=" C   ASP A  16 "
       pdb=" O   ASP A  16 "
    ideal  model  delta    sigma   weight residual
    1.235  1.314 -0.079 1.26e-02 6.30e+03 3.94e+01
  bond pdb=" C   PHE A 126 "
       pdb=" O   PHE A 126 "
    ideal  model  delta    sigma   weight residual
    1.236  1.169  0.067 1.15e-02 7.56e+03 3.44e+01
  ... (remaining 8009 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.42: 10812
        3.42 -     6.85: 92
        6.85 -    10.27: 18
       10.27 -    13.70: 4
       13.70 -    17.12: 1
  Bond angle restraints: 10927
  Sorted by residual:
  angle pdb=" N   PHE A 126 "
        pdb=" CA  PHE A 126 "
        pdb=" C   PHE A 126 "
      ideal   model   delta    sigma   weight residual
     111.07  123.34  -12.27 1.07e+00 8.73e-01 1.32e+02
  angle pdb=" N   CYS A 129 "
        pdb=" CA  CYS A 129 "
        pdb=" C   CYS A 129 "
      ideal   model   delta    sigma   weight residual
     112.92  100.41   12.51 1.23e+00 6.61e-01 1.03e+02
  angle pdb=" N   LYS A 130 "
        pdb=" CA  LYS A 130 "
        pdb=" C   LYS A 130 "
      ideal   model   delta    sigma   weight residual
     112.57  102.29   10.28 1.13e+00 7.83e-01 8.28e+01
  angle pdb=" CA  PHE A 126 "
        pdb=" C   PHE A 126 "
        pdb=" N   HIS A 127 "
      ideal   model   delta    sigma   weight residual
     117.07  126.17   -9.10 1.14e+00 7.69e-01 6.37e+01
  angle pdb=" O   PHE A 126 "
        pdb=" C   PHE A 126 "
        pdb=" N   HIS A 127 "
      ideal   model   delta    sigma   weight residual
     122.07  114.52    7.55 1.03e+00 9.43e-01 5.37e+01
  ... (remaining 10922 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.07: 4301
       15.07 -    30.14: 382
       30.14 -    45.21: 103
       45.21 -    60.29: 19
       60.29 -    75.36: 8
  Dihedral angle restraints: 4813
    sinusoidal: 1799
      harmonic: 3014
  Sorted by residual:
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  96 "
           pdb=" CB  CYS E  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  147.71  -54.71     1      1.00e+01 1.00e-02 4.05e+01
  dihedral pdb=" N   PHE A 124 "
           pdb=" C   PHE A 124 "
           pdb=" CA  PHE A 124 "
           pdb=" CB  PHE A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  110.88   11.92     0      2.50e+00 1.60e-01 2.27e+01
  dihedral pdb=" CB  CYS A  91 "
           pdb=" SG  CYS A  91 "
           pdb=" SG  CYS A 168 "
           pdb=" CB  CYS A 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  131.85  -38.85     1      1.00e+01 1.00e-02 2.12e+01
  ... (remaining 4810 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.443: 1274
       0.443 -    0.886: 1
       0.886 -    1.329: 0
       1.329 -    1.772: 0
       1.772 -    2.214: 1
  Chirality restraints: 1276
  Sorted by residual:
  chirality pdb=" C31 LPS A 402 "
            pdb=" C32 LPS A 402 "
            pdb=" O31 LPS A 402 "
            pdb=" O32 LPS A 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.18    0.04   -2.21 2.00e-01 2.50e+01 1.23e+02
  chirality pdb=" CA  PHE A 126 "
            pdb=" N   PHE A 126 "
            pdb=" C   PHE A 126 "
            pdb=" CB  PHE A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.49e+00
  chirality pdb=" C13 CLR A 401 "
            pdb=" C12 CLR A 401 "
            pdb=" C14 CLR A 401 "
            pdb=" C17 CLR A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.52   -0.41 2.00e-01 2.50e+01 4.14e+00
  ... (remaining 1273 not shown)

  Planarity restraints: 1371
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 124 "    0.025 2.00e-02 2.50e+03   4.90e-02 2.40e+01
        pdb=" C   PHE A 124 "   -0.085 2.00e-02 2.50e+03
        pdb=" O   PHE A 124 "    0.031 2.00e-02 2.50e+03
        pdb=" N   ARG A 125 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 126 "   -0.025 2.00e-02 2.50e+03   4.67e-02 2.18e+01
        pdb=" C   PHE A 126 "    0.081 2.00e-02 2.50e+03
        pdb=" O   PHE A 126 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   HIS A 127 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 122 "   -0.040 5.00e-02 4.00e+02   5.99e-02 5.74e+00
        pdb=" N   PRO A 123 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 123 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 123 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1368 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 134
        2.66 -     3.22: 7451
        3.22 -     3.78: 12640
        3.78 -     4.34: 17575
        4.34 -     4.90: 29164
  Nonbonded interactions: 66964
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E  50 "
            pdb=" OG  SER E  59 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" O   ILE C  58 "
            pdb=" OG  SER C 316 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OH  TYR A  78 "
            pdb=" OD2 ASP A 171 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" NH1 ARG B 228 "
            pdb=" OD1 ASP C 186 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" O   CYS C 149 "
            pdb=" NH1 ARG C 150 "
     model   vdw
     2.254 3.120
  ... (remaining 66959 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.45 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.340
  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:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.740
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
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      :  0.008   0.218   8017  Z= 0.523
  Angle     :  0.852  17.124  10933  Z= 0.505
  Chirality :  0.084   2.214   1276
  Planarity :  0.005   0.060   1371
  Dihedral  : 12.854  75.356   2856
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.77 %
    Favored  : 98.97 %
  Cbeta Deviations :  0.10 %
  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 (0.27), residues: 1018
  helix:  1.86 (0.27), residues: 402
  sheet:  0.40 (0.34), residues: 218
  loop : -0.56 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 142 
 HIS   0.011   0.002   HIS C 142 
 PHE   0.028   0.002   PHE A 239 
 TYR   0.031   0.002   TYR C  59 
 ARG   0.004   0.000   ARG A 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12709 (  448)
  hydrogen bonds       : angle       5.98864 ( 1290)
  SS BOND              : bond        0.00319 (    3)
  SS BOND              : angle       0.95595 (    6)
  covalent geometry    : bond        0.00783 ( 8014)
  covalent geometry    : angle       0.85188 (10927)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 204
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 TRP cc_start: 0.6917 (t-100) cc_final: 0.6332 (t60)
REVERT: A  250 PHE cc_start: 0.7690 (t80) cc_final: 0.7479 (t80)
REVERT: B  317 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7440 (mtm-85)
REVERT: B  378 ASP cc_start: 0.7929 (m-30) cc_final: 0.7619 (m-30)
REVERT: C  277 SER cc_start: 0.8496 (t) cc_final: 0.8110 (m)
  outliers start: 2
  outliers final: 2
  residues processed: 206
  average time/residue: 0.9936
  time to fit residues: 218.2838
Evaluate side-chains
  134 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 132
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 PHE
Chi-restraints excluded: chain B residue  229 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 75 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 51 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9990
   chunk 78 optimal weight:    0.0980
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 131 GLN
B 213 GLN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 387 HIS
C 119 ASN
C 156 GLN
C 175 GLN
C 176 GLN
C 220 GLN
C 259 GLN
E  31 ASN
D  44 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.160363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.126023 restraints weight = 11206.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 2.51
r_work: 0.3389 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8017  Z= 0.181
  Angle     :  0.615   6.941  10933  Z= 0.326
  Chirality :  0.045   0.161   1276
  Planarity :  0.005   0.058   1371
  Dihedral  :  7.195 105.129   1276
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 11.58 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.26), residues: 1018
  helix:  1.90 (0.26), residues: 420
  sheet:  0.49 (0.32), residues: 211
  loop : -0.54 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  82 
 HIS   0.010   0.002   HIS A 127 
 PHE   0.028   0.002   PHE A 119 
 TYR   0.019   0.002   TYR C  59 
 ARG   0.010   0.001   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04377 (  448)
  hydrogen bonds       : angle       5.03334 ( 1290)
  SS BOND              : bond        0.00513 (    3)
  SS BOND              : angle       2.56359 (    6)
  covalent geometry    : bond        0.00420 ( 8014)
  covalent geometry    : angle       0.61182 (10927)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 TRP cc_start: 0.7927 (t-100) cc_final: 0.7408 (t-100)
REVERT: A  155 LEU cc_start: 0.8353 (mm) cc_final: 0.8090 (mm)
REVERT: A  185 MET cc_start: 0.7535 (tmm) cc_final: 0.7252 (tmm)
REVERT: A  224 GLU cc_start: 0.8146 (mp0) cc_final: 0.7909 (mp0)
REVERT: A  300 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7667 (mtp180)
REVERT: B  223 ASP cc_start: 0.8586 (t0) cc_final: 0.8372 (t0)
REVERT: B  274 LYS cc_start: 0.7931 (tttt) cc_final: 0.7604 (ttpt)
REVERT: B  280 ARG cc_start: 0.8111 (ttt-90) cc_final: 0.7779 (ttt-90)
REVERT: B  310 ASP cc_start: 0.8165 (t0) cc_final: 0.7626 (m-30)
REVERT: B  317 ARG cc_start: 0.7962 (mtm-85) cc_final: 0.7751 (mtm-85)
REVERT: C  197 ARG cc_start: 0.7398 (mtp-110) cc_final: 0.6908 (mtp85)
REVERT: C  214 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6359 (mpp80)
REVERT: C  277 SER cc_start: 0.8732 (t) cc_final: 0.8352 (m)
REVERT: E   80 TYR cc_start: 0.7252 (m-80) cc_final: 0.6648 (m-80)
  outliers start: 24
  outliers final: 5
  residues processed: 157
  average time/residue: 1.3107
  time to fit residues: 216.9005
Evaluate side-chains
  133 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 126
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  214 ARG
Chi-restraints excluded: chain E residue   93 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0030
   chunk 69 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 93 optimal weight:    0.8980
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
A 284 ASN
B 213 GLN
B 227 GLN
B 292 ASN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  75 GLN
C 175 GLN
C 176 GLN
C 220 GLN
C 259 GLN
E  31 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.159663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.122746 restraints weight = 17383.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 3.01
r_work: 0.3355 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3350
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3350
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8017  Z= 0.126
  Angle     :  0.522   5.536  10933  Z= 0.280
  Chirality :  0.042   0.137   1276
  Planarity :  0.004   0.058   1371
  Dihedral  :  5.744  58.419   1272
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 14.93 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.27), residues: 1018
  helix:  2.13 (0.26), residues: 420
  sheet:  0.56 (0.32), residues: 214
  loop : -0.55 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  84 
 HIS   0.007   0.001   HIS A 127 
 PHE   0.028   0.002   PHE A 119 
 TYR   0.013   0.001   TYR A 293 
 ARG   0.005   0.001   ARG B 373 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03766 (  448)
  hydrogen bonds       : angle       4.67804 ( 1290)
  SS BOND              : bond        0.00312 (    3)
  SS BOND              : angle       1.29860 (    6)
  covalent geometry    : bond        0.00282 ( 8014)
  covalent geometry    : angle       0.52141 (10927)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A  145 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6736 (mp)
REVERT: A  185 MET cc_start: 0.7508 (tmm) cc_final: 0.7238 (tmm)
REVERT: A  224 GLU cc_start: 0.7916 (mp0) cc_final: 0.7595 (mp0)
REVERT: A  300 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7577 (mtp180)
REVERT: B  218 ASN cc_start: 0.8269 (m-40) cc_final: 0.7907 (m110)
REVERT: B  274 LYS cc_start: 0.7713 (tttt) cc_final: 0.7337 (ttpt)
REVERT: B  280 ARG cc_start: 0.7957 (ttt-90) cc_final: 0.7627 (ttt-90)
REVERT: B  317 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7273 (ptp-110)
REVERT: B  318 TYR cc_start: 0.8226 (t80) cc_final: 0.7779 (t80)
REVERT: B  330 GLU cc_start: 0.7860 (tt0) cc_final: 0.7508 (tt0)
REVERT: B  378 ASP cc_start: 0.8256 (m-30) cc_final: 0.7995 (m-30)
REVERT: C   45 MET cc_start: 0.8560 (mtt) cc_final: 0.7925 (mtt)
REVERT: C  197 ARG cc_start: 0.7399 (mtp-110) cc_final: 0.6942 (mtp85)
REVERT: C  214 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6345 (mpp80)
REVERT: E   80 TYR cc_start: 0.7236 (m-80) cc_final: 0.6644 (m-80)
REVERT: E   87 LYS cc_start: 0.6827 (mtpt) cc_final: 0.6572 (ttmm)
  outliers start: 22
  outliers final: 2
  residues processed: 151
  average time/residue: 1.1760
  time to fit residues: 187.7430
Evaluate side-chains
  125 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 120
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue  214 ARG
Chi-restraints excluded: chain E residue  105 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
B 213 GLN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  75 GLN
C 156 GLN
C 175 GLN
C 176 GLN
C 220 GLN
E  31 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.153562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.119682 restraints weight = 12961.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.57
r_work: 0.3287 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3146
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3146
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8017  Z= 0.184
  Angle     :  0.582   7.323  10933  Z= 0.310
  Chirality :  0.044   0.149   1276
  Planarity :  0.005   0.056   1371
  Dihedral  :  5.961  59.388   1272
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 16.22 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.27), residues: 1018
  helix:  2.15 (0.26), residues: 414
  sheet:  0.35 (0.32), residues: 217
  loop : -0.49 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  82 
 HIS   0.009   0.002   HIS B 357 
 PHE   0.029   0.002   PHE A 119 
 TYR   0.031   0.002   TYR C  59 
 ARG   0.011   0.001   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04231 (  448)
  hydrogen bonds       : angle       4.81162 ( 1290)
  SS BOND              : bond        0.00573 (    3)
  SS BOND              : angle       1.66458 (    6)
  covalent geometry    : bond        0.00431 ( 8014)
  covalent geometry    : angle       0.58095 (10927)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ILE cc_start: 0.7166 (mt) cc_final: 0.6941 (mt)
REVERT: A   92 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6543 (mmp)
REVERT: A  145 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7277 (mm)
REVERT: A  179 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7181 (tp)
REVERT: A  188 ILE cc_start: 0.7089 (mt) cc_final: 0.6809 (mt)
REVERT: A  296 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.7563 (p)
REVERT: A  300 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7767 (mtp180)
REVERT: B  211 LYS cc_start: 0.8609 (mttp) cc_final: 0.7741 (mttm)
REVERT: B  274 LYS cc_start: 0.7921 (tttt) cc_final: 0.7568 (ttpt)
REVERT: B  280 ARG cc_start: 0.8162 (ttt-90) cc_final: 0.7802 (ttt-90)
REVERT: B  317 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7377 (ptp-110)
REVERT: B  318 TYR cc_start: 0.8466 (t80) cc_final: 0.8116 (t80)
REVERT: B  330 GLU cc_start: 0.8101 (tt0) cc_final: 0.7873 (tt0)
REVERT: C   45 MET cc_start: 0.8800 (mtt) cc_final: 0.8212 (mtt)
REVERT: C  197 ARG cc_start: 0.7542 (mtp-110) cc_final: 0.6958 (mtp85)
REVERT: C  213 VAL cc_start: 0.6959 (m) cc_final: 0.6687 (m)
REVERT: C  214 ARG cc_start: 0.6948 (mpp80) cc_final: 0.6485 (mpp80)
REVERT: E   83 MET cc_start: 0.8241 (mtp) cc_final: 0.7910 (mtp)
  outliers start: 26
  outliers final: 8
  residues processed: 156
  average time/residue: 1.0695
  time to fit residues: 177.6194
Evaluate side-chains
  142 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain E residue   21 SER
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue  105 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    0.0370
   chunk 99 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 70 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 80 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.7660

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

Flipped N/Q/H residues before XYZ refinement:
B 213 GLN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 156 GLN
C 175 GLN
C 176 GLN
C 220 GLN
E  31 ASN
E  82 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.154614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.120913 restraints weight = 9366.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 2.18
r_work: 0.3339 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8017  Z= 0.123
  Angle     :  0.523   6.623  10933  Z= 0.278
  Chirality :  0.042   0.140   1276
  Planarity :  0.004   0.056   1371
  Dihedral  :  5.627  55.644   1272
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 17.37 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.27), residues: 1018
  helix:  2.27 (0.26), residues: 412
  sheet:  0.32 (0.32), residues: 224
  loop : -0.49 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  82 
 HIS   0.006   0.001   HIS A 127 
 PHE   0.027   0.002   PHE A 119 
 TYR   0.013   0.001   TYR B 391 
 ARG   0.009   0.001   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03701 (  448)
  hydrogen bonds       : angle       4.66108 ( 1290)
  SS BOND              : bond        0.00392 (    3)
  SS BOND              : angle       1.03617 (    6)
  covalent geometry    : bond        0.00279 ( 8014)
  covalent geometry    : angle       0.52288 (10927)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.781 
Fit side-chains
REVERT: A   27 THR cc_start: 0.7580 (m) cc_final: 0.7257 (p)
REVERT: A   92 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6841 (mmt)
REVERT: A  179 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7184 (tp)
REVERT: A  185 MET cc_start: 0.7599 (tmm) cc_final: 0.7282 (tmm)
REVERT: A  296 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7485 (p)
REVERT: A  300 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7849 (mtp180)
REVERT: B  211 LYS cc_start: 0.8520 (mttp) cc_final: 0.7615 (mttm)
REVERT: B  213 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8185 (tm-30)
REVERT: B  274 LYS cc_start: 0.7758 (tttt) cc_final: 0.7395 (ttpt)
REVERT: B  280 ARG cc_start: 0.8048 (ttt-90) cc_final: 0.7700 (ttt-90)
REVERT: B  317 ARG cc_start: 0.7960 (mtm-85) cc_final: 0.7422 (ptp-110)
REVERT: B  318 TYR cc_start: 0.8459 (t80) cc_final: 0.8087 (t80)
REVERT: C   45 MET cc_start: 0.8856 (mtt) cc_final: 0.8369 (mtt)
REVERT: C   59 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.7727 (m-80)
REVERT: C  188 MET cc_start: 0.8939 (mmm) cc_final: 0.8585 (mmm)
REVERT: C  197 ARG cc_start: 0.7464 (mtp-110) cc_final: 0.6932 (mtp85)
REVERT: C  213 VAL cc_start: 0.7019 (m) cc_final: 0.6727 (m)
REVERT: C  214 ARG cc_start: 0.6909 (mpp80) cc_final: 0.6488 (mpp80)
REVERT: E    3 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6164 (tm-30)
REVERT: E   83 MET cc_start: 0.8180 (mtp) cc_final: 0.7973 (mtp)
REVERT: E   87 LYS cc_start: 0.6901 (mtpt) cc_final: 0.6676 (ttmm)
  outliers start: 25
  outliers final: 8
  residues processed: 156
  average time/residue: 1.1063
  time to fit residues: 183.3218
Evaluate side-chains
  144 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue  105 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 92 optimal weight:    7.9990
   chunk 84 optimal weight:    5.9990
   chunk 97 optimal weight:    6.9990
   chunk 76 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 88 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   overall best weight:    1.9584

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

Flipped N/Q/H residues before XYZ refinement:
B 213 GLN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 175 GLN
C 176 GLN
C 220 GLN
E  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.151547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.116914 restraints weight = 11148.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 2.34
r_work: 0.3257 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3095
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3095 r_free = 0.3095    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3095 r_free = 0.3095    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3095
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.3952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   8017  Z= 0.200
  Angle     :  0.583   6.451  10933  Z= 0.310
  Chirality :  0.044   0.153   1276
  Planarity :  0.005   0.056   1371
  Dihedral  :  5.859  55.544   1272
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 18.28 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.27), residues: 1018
  helix:  2.17 (0.26), residues: 414
  sheet:  0.29 (0.33), residues: 224
  loop : -0.44 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  82 
 HIS   0.009   0.001   HIS B 357 
 PHE   0.029   0.002   PHE A 119 
 TYR   0.014   0.002   TYR E  95 
 ARG   0.012   0.001   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04179 (  448)
  hydrogen bonds       : angle       4.83789 ( 1290)
  SS BOND              : bond        0.00653 (    3)
  SS BOND              : angle       1.66295 (    6)
  covalent geometry    : bond        0.00474 ( 8014)
  covalent geometry    : angle       0.58234 (10927)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 TYR cc_start: 0.7742 (m-80) cc_final: 0.6514 (m-80)
REVERT: A   92 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.7083 (mmp)
REVERT: A  145 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7391 (mm)
REVERT: A  188 ILE cc_start: 0.7087 (mt) cc_final: 0.6791 (mt)
REVERT: A  276 VAL cc_start: 0.8234 (t) cc_final: 0.8018 (m)
REVERT: A  296 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.7719 (p)
REVERT: A  300 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7860 (mtp180)
REVERT: B  211 LYS cc_start: 0.8708 (mttp) cc_final: 0.7851 (mttm)
REVERT: B  274 LYS cc_start: 0.8009 (tttt) cc_final: 0.7583 (ttpt)
REVERT: B  280 ARG cc_start: 0.8294 (ttt-90) cc_final: 0.7957 (ttt-90)
REVERT: B  314 GLU cc_start: 0.7646 (pm20) cc_final: 0.7415 (pm20)
REVERT: B  317 ARG cc_start: 0.7982 (mtm-85) cc_final: 0.7463 (ptp-110)
REVERT: B  330 GLU cc_start: 0.8201 (tt0) cc_final: 0.7580 (tt0)
REVERT: C   45 MET cc_start: 0.8893 (mtt) cc_final: 0.8393 (mtt)
REVERT: C   59 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8215 (m-80)
REVERT: C  197 ARG cc_start: 0.7574 (mtp-110) cc_final: 0.7329 (ttm-80)
REVERT: E   87 LYS cc_start: 0.7235 (mtpt) cc_final: 0.6973 (ttmm)
  outliers start: 24
  outliers final: 11
  residues processed: 149
  average time/residue: 1.0750
  time to fit residues: 170.6266
Evaluate side-chains
  142 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain E residue   21 SER
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue  105 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    0.0570
   chunk 21 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 82 optimal weight:    7.9990
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
B  29 GLN
B 213 GLN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 175 GLN
C 176 GLN
C 220 GLN
E  31 ASN
E  82 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.155237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.122421 restraints weight = 12681.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.56
r_work: 0.3295 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3179
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3179
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.4073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8017  Z= 0.116
  Angle     :  0.517   7.504  10933  Z= 0.272
  Chirality :  0.041   0.138   1276
  Planarity :  0.004   0.056   1371
  Dihedral  :  5.555  55.421   1272
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.31 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.27), residues: 1018
  helix:  2.28 (0.26), residues: 414
  sheet:  0.46 (0.33), residues: 222
  loop : -0.49 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  82 
 HIS   0.006   0.001   HIS B 220 
 PHE   0.028   0.002   PHE A 119 
 TYR   0.011   0.001   TYR B 339 
 ARG   0.008   0.000   ARG C  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03576 (  448)
  hydrogen bonds       : angle       4.63761 ( 1290)
  SS BOND              : bond        0.00363 (    3)
  SS BOND              : angle       1.05476 (    6)
  covalent geometry    : bond        0.00258 ( 8014)
  covalent geometry    : angle       0.51641 (10927)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7103 (mmp)
REVERT: A  185 MET cc_start: 0.7718 (tmm) cc_final: 0.7388 (tmm)
REVERT: A  296 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.7917 (p)
REVERT: A  300 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7872 (mtp180)
REVERT: B  211 LYS cc_start: 0.8711 (mttp) cc_final: 0.7683 (mmtm)
REVERT: B  213 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8307 (tm-30)
REVERT: B  274 LYS cc_start: 0.8129 (tttt) cc_final: 0.7778 (ttpt)
REVERT: B  314 GLU cc_start: 0.7817 (pm20) cc_final: 0.7573 (pm20)
REVERT: B  317 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7629 (ptp-110)
REVERT: B  330 GLU cc_start: 0.8232 (tt0) cc_final: 0.7789 (tt0)
REVERT: C   45 MET cc_start: 0.8876 (mtt) cc_final: 0.8381 (mtt)
REVERT: C   59 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8634 (t80)
REVERT: C  188 MET cc_start: 0.8999 (mmm) cc_final: 0.8774 (mmm)
REVERT: C  197 ARG cc_start: 0.7551 (mtp-110) cc_final: 0.7158 (mtp85)
REVERT: E   83 MET cc_start: 0.8270 (mtp) cc_final: 0.8068 (mtp)
REVERT: E   87 LYS cc_start: 0.7338 (mtpt) cc_final: 0.6746 (mttm)
  outliers start: 18
  outliers final: 9
  residues processed: 145
  average time/residue: 1.0618
  time to fit residues: 164.0875
Evaluate side-chains
  142 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain E residue   93 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 89 optimal weight:    0.3980
   chunk 6 optimal weight:    3.9990
   chunk 64 optimal weight:    0.0470
   chunk 26 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 99 optimal weight:    5.9990
   chunk 59 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
B 213 GLN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 156 GLN
C 175 GLN
C 176 GLN
C 220 GLN
E  31 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.156099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.124932 restraints weight = 13081.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.50
r_work: 0.3307 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8017  Z= 0.111
  Angle     :  0.512   6.617  10933  Z= 0.271
  Chirality :  0.041   0.137   1276
  Planarity :  0.004   0.055   1371
  Dihedral  :  5.466  56.431   1272
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.82 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.27), residues: 1018
  helix:  2.29 (0.26), residues: 415
  sheet:  0.59 (0.33), residues: 218
  loop : -0.47 (0.33), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  82 
 HIS   0.005   0.001   HIS A 127 
 PHE   0.030   0.002   PHE A  77 
 TYR   0.011   0.001   TYR B 339 
 ARG   0.012   0.001   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03547 (  448)
  hydrogen bonds       : angle       4.56791 ( 1290)
  SS BOND              : bond        0.00372 (    3)
  SS BOND              : angle       1.05327 (    6)
  covalent geometry    : bond        0.00246 ( 8014)
  covalent geometry    : angle       0.51199 (10927)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A   92 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7193 (mmp)
REVERT: A  102 MET cc_start: 0.7929 (ttm) cc_final: 0.7729 (ttt)
REVERT: A  185 MET cc_start: 0.7728 (tmm) cc_final: 0.7420 (tmm)
REVERT: A  296 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.7928 (p)
REVERT: B  211 LYS cc_start: 0.8645 (mttp) cc_final: 0.7851 (mttm)
REVERT: B  213 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8216 (tm-30)
REVERT: B  218 ASN cc_start: 0.8417 (m-40) cc_final: 0.8188 (m110)
REVERT: B  274 LYS cc_start: 0.8150 (tttt) cc_final: 0.7807 (ttpt)
REVERT: B  314 GLU cc_start: 0.7858 (pm20) cc_final: 0.7590 (pm20)
REVERT: B  317 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7684 (ptp-110)
REVERT: B  330 GLU cc_start: 0.8247 (tt0) cc_final: 0.7806 (tt0)
REVERT: B  370 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7180 (mm-30)
REVERT: C   45 MET cc_start: 0.8901 (mtt) cc_final: 0.8523 (mtt)
REVERT: C  188 MET cc_start: 0.9034 (mmm) cc_final: 0.8773 (mmm)
REVERT: C  197 ARG cc_start: 0.7537 (mtp-110) cc_final: 0.7181 (mtp85)
REVERT: E   83 MET cc_start: 0.8290 (mtp) cc_final: 0.8030 (mtp)
REVERT: E   87 LYS cc_start: 0.7257 (mtpt) cc_final: 0.6674 (mttm)
  outliers start: 18
  outliers final: 10
  residues processed: 145
  average time/residue: 1.0689
  time to fit residues: 165.3527
Evaluate side-chains
  143 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue  105 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 89 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 50 optimal weight:   40.0000
   chunk 0 optimal weight:   10.0000
   chunk 93 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 213 GLN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 175 GLN
C 176 GLN
C 220 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.155974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.119778 restraints weight = 15954.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 2.85
r_work: 0.3289 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3291
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3291 r_free = 0.3291    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3291 r_free = 0.3291    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3291
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.4237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8017  Z= 0.118
  Angle     :  0.516   6.697  10933  Z= 0.273
  Chirality :  0.041   0.140   1276
  Planarity :  0.004   0.055   1371
  Dihedral  :  5.444  56.481   1272
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 20.33 %
    Favored  : 77.73 %
  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:  1.35 (0.27), residues: 1018
  helix:  2.31 (0.26), residues: 415
  sheet:  0.57 (0.33), residues: 218
  loop : -0.45 (0.33), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  82 
 HIS   0.005   0.001   HIS A 127 
 PHE   0.028   0.002   PHE A 119 
 TYR   0.012   0.001   TYR B 339 
 ARG   0.008   0.000   ARG C  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03582 (  448)
  hydrogen bonds       : angle       4.54898 ( 1290)
  SS BOND              : bond        0.00398 (    3)
  SS BOND              : angle       1.10705 (    6)
  covalent geometry    : bond        0.00267 ( 8014)
  covalent geometry    : angle       0.51585 (10927)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.800 
Fit side-chains
REVERT: A   22 TYR cc_start: 0.7643 (m-80) cc_final: 0.6635 (m-80)
REVERT: A   92 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7175 (mmp)
REVERT: A  185 MET cc_start: 0.7679 (tmm) cc_final: 0.7359 (tmm)
REVERT: A  296 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7710 (p)
REVERT: B   25 LYS cc_start: 0.8284 (ttpp) cc_final: 0.7963 (tttt)
REVERT: B  211 LYS cc_start: 0.8574 (mttp) cc_final: 0.7768 (mttm)
REVERT: B  213 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8226 (tm-30)
REVERT: B  274 LYS cc_start: 0.7948 (tttt) cc_final: 0.7576 (ttpt)
REVERT: B  314 GLU cc_start: 0.7776 (pm20) cc_final: 0.7497 (pm20)
REVERT: B  317 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7698 (ptp-110)
REVERT: B  330 GLU cc_start: 0.8215 (tt0) cc_final: 0.7775 (tt0)
REVERT: B  370 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7114 (mm-30)
REVERT: C   45 MET cc_start: 0.8872 (mtt) cc_final: 0.8518 (mtt)
REVERT: C  188 MET cc_start: 0.8949 (mmm) cc_final: 0.8686 (mmm)
REVERT: C  197 ARG cc_start: 0.7465 (mtp-110) cc_final: 0.7084 (mtp85)
REVERT: E   83 MET cc_start: 0.8191 (mtp) cc_final: 0.7946 (mtp)
REVERT: E   87 LYS cc_start: 0.7205 (mtpt) cc_final: 0.6617 (mttm)
  outliers start: 15
  outliers final: 9
  residues processed: 138
  average time/residue: 1.0954
  time to fit residues: 160.9638
Evaluate side-chains
  139 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 PHE
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain E residue   93 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 84 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 83 optimal weight:    8.9990
   chunk 55 optimal weight:    0.4980
   chunk 73 optimal weight:    3.9990
   chunk 49 optimal weight:    0.5980
   chunk 82 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 213 GLN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 156 GLN
C 175 GLN
C 176 GLN
C 220 GLN
E  31 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.155099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.121810 restraints weight = 13081.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.65
r_work: 0.3301 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.4269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8017  Z= 0.133
  Angle     :  0.530   7.046  10933  Z= 0.280
  Chirality :  0.042   0.143   1276
  Planarity :  0.004   0.058   1371
  Dihedral  :  5.482  56.117   1272
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 20.46 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.27), residues: 1018
  helix:  2.29 (0.26), residues: 415
  sheet:  0.41 (0.33), residues: 222
  loop : -0.40 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  82 
 HIS   0.006   0.001   HIS B 357 
 PHE   0.028   0.002   PHE A 119 
 TYR   0.026   0.002   TYR A  78 
 ARG   0.013   0.001   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03679 (  448)
  hydrogen bonds       : angle       4.57131 ( 1290)
  SS BOND              : bond        0.00549 (    3)
  SS BOND              : angle       1.32554 (    6)
  covalent geometry    : bond        0.00307 ( 8014)
  covalent geometry    : angle       0.52967 (10927)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 0.875 
Fit side-chains
REVERT: A   22 TYR cc_start: 0.7786 (m-80) cc_final: 0.6603 (m-80)
REVERT: A   92 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7231 (mmp)
REVERT: A  185 MET cc_start: 0.7668 (tmm) cc_final: 0.7351 (tmm)
REVERT: A  296 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.7944 (p)
REVERT: B   25 LYS cc_start: 0.8322 (ttpp) cc_final: 0.8008 (tttt)
REVERT: B  213 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8236 (tm-30)
REVERT: B  274 LYS cc_start: 0.8010 (tttt) cc_final: 0.7646 (ttpt)
REVERT: B  314 GLU cc_start: 0.7831 (pm20) cc_final: 0.7566 (pm20)
REVERT: B  317 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7738 (ptp-110)
REVERT: B  330 GLU cc_start: 0.8208 (tt0) cc_final: 0.7697 (tt0)
REVERT: B  370 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7110 (mm-30)
REVERT: C   45 MET cc_start: 0.8825 (mtt) cc_final: 0.8387 (mtt)
REVERT: C  137 ARG cc_start: 0.7168 (mtp-110) cc_final: 0.6937 (mtp85)
REVERT: C  188 MET cc_start: 0.8916 (mmm) cc_final: 0.8621 (mmm)
REVERT: C  197 ARG cc_start: 0.7452 (mtp-110) cc_final: 0.7085 (mtp85)
REVERT: E   83 MET cc_start: 0.8239 (mtp) cc_final: 0.8011 (mtp)
REVERT: E   87 LYS cc_start: 0.7343 (mtpt) cc_final: 0.6766 (mttm)
  outliers start: 15
  outliers final: 10
  residues processed: 136
  average time/residue: 1.0675
  time to fit residues: 154.7587
Evaluate side-chains
  141 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain E residue   93 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 64 optimal weight:    0.1980
   chunk 82 optimal weight:   10.0000
   chunk 7 optimal weight:    0.0270
   chunk 6 optimal weight:    2.9990
   chunk 13 optimal weight:    0.2980
   chunk 71 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 96 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
B 213 GLN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 175 GLN
C 176 GLN
C 220 GLN
E  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.157160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.120675 restraints weight = 17248.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.97
r_work: 0.3302 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3303
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3303
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.4330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8017  Z= 0.108
  Angle     :  0.510   6.520  10933  Z= 0.270
  Chirality :  0.041   0.144   1276
  Planarity :  0.004   0.055   1371
  Dihedral  :  5.366  55.153   1272
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 20.72 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.27), residues: 1018
  helix:  2.34 (0.26), residues: 415
  sheet:  0.48 (0.33), residues: 220
  loop : -0.39 (0.33), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 211 
 HIS   0.006   0.001   HIS A 127 
 PHE   0.033   0.002   PHE A  77 
 TYR   0.026   0.001   TYR A  78 
 ARG   0.013   0.000   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03529 (  448)
  hydrogen bonds       : angle       4.51072 ( 1290)
  SS BOND              : bond        0.00396 (    3)
  SS BOND              : angle       1.05558 (    6)
  covalent geometry    : bond        0.00239 ( 8014)
  covalent geometry    : angle       0.50921 (10927)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6517.66 seconds
wall clock time: 112 minutes 45.05 seconds (6765.05 seconds total)