Starting phenix.real_space_refine
on Fri Aug 22 21:16:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kh5_37237/08_2025/8kh5_37237.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kh5_37237/08_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_37237/08_2025/8kh5_37237.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kh5_37237/08_2025/8kh5_37237.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kh5_37237/08_2025/8kh5_37237.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kh5_37237/08_2025/8kh5_37237.cif"
  }
  resolution = 2.83
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 3, 'PHE:plan': 3, 'TYR:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, '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, 'ARG:plan': 4, 'ASN:plan1': 2, 'GLU:plan': 10, 'ASP:plan': 4, 'PHE:plan': 1}
          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: {'GLU:plan': 6, 'ASP:plan': 7, 'GLN:plan1': 5, 'ARG:plan': 7, 'ASN:plan1': 3, 'TYR:plan': 1}
          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: {'GLU:plan': 6, 'ASP:plan': 7, 'GLN:plan1': 5, 'ARG:plan': 7, 'ASN:plan1': 3, 'TYR:plan': 1}
          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: {'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 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, 'ARG:plan': 2, 'GLU:plan': 4, '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: 2.10, per 1000 atoms: 0.27
  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: 0.49
  Conformation dependent library (CDL) restraints added in 416.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.20
  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: 1.17

  Time building geometry restraints manager: 0.64 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:             0.330
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.680
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.780
-------------------------------------------------------------------------------
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 : 10.95
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (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
 ARG   0.004   0.000   ARG A 156 
 TYR   0.031   0.002   TYR C  59 
 PHE   0.028   0.002   PHE A 239 
 TRP   0.027   0.002   TRP A 142 
 HIS   0.011   0.002   HIS C 142 

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

*********************** 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  : 0.338 
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: 0.5401
  time to fit residues: 118.1666
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  : 0.370 
-------------------------------------------------------------------------------
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 49 optimal weight:    1.9990
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
A 131 GLN
B 213 GLN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN
C 156 GLN
C 175 GLN
C 176 GLN
C 220 GLN
C 259 GLN
E  31 ASN
E  35 ASN
D  44 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.158765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.121751 restraints weight = 16053.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.86
r_work: 0.3340 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3329
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3329
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8017  Z= 0.186
  Angle     :  0.632   7.813  10933  Z= 0.334
  Chirality :  0.045   0.151   1276
  Planarity :  0.005   0.058   1371
  Dihedral  :  7.263 113.710   1276
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 11.58 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.26), residues: 1018
  helix:  1.84 (0.26), residues: 420
  sheet:  0.41 (0.32), residues: 216
  loop : -0.49 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 137 
 TYR   0.019   0.002   TYR C  59 
 PHE   0.027   0.002   PHE A 119 
 TRP   0.015   0.002   TRP A  84 
 HIS   0.011   0.002   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 8014)
  covalent geometry    : angle       0.63072 (10927)
  SS BOND              : bond        0.00762 (    3)
  SS BOND              : angle       2.10643 (    6)
  hydrogen bonds       : bond        0.04371 (  448)
  hydrogen bonds       : angle       5.03274 ( 1290)

*********************** 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
  178 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 SER cc_start: 0.7819 (OUTLIER) cc_final: 0.7589 (p)
REVERT: A  145 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6682 (mp)
REVERT: A  155 LEU cc_start: 0.8298 (mm) cc_final: 0.8012 (mm)
REVERT: A  185 MET cc_start: 0.7543 (tmm) cc_final: 0.7285 (tmm)
REVERT: A  224 GLU cc_start: 0.8040 (mp0) cc_final: 0.7712 (mp0)
REVERT: A  300 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7607 (mtp180)
REVERT: A  301 ARG cc_start: 0.6976 (mtm-85) cc_final: 0.6452 (mtm-85)
REVERT: B  213 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8593 (tm-30)
REVERT: B  274 LYS cc_start: 0.7689 (tttt) cc_final: 0.7325 (ttpt)
REVERT: B  310 ASP cc_start: 0.8141 (t0) cc_final: 0.7640 (m-30)
REVERT: B  317 ARG cc_start: 0.7882 (mtm-85) cc_final: 0.7668 (mtm-85)
REVERT: B  330 GLU cc_start: 0.8090 (tt0) cc_final: 0.7846 (tt0)
REVERT: C  197 ARG cc_start: 0.7327 (mtp-110) cc_final: 0.6861 (mtp85)
REVERT: C  214 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6288 (mpp80)
REVERT: C  277 SER cc_start: 0.8666 (t) cc_final: 0.8248 (m)
REVERT: E   80 TYR cc_start: 0.7266 (m-80) cc_final: 0.6521 (m-80)
  outliers start: 27
  outliers final: 7
  residues processed: 168
  average time/residue: 0.6669
  time to fit residues: 117.9367
Evaluate side-chains
  138 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  214 ARG
Chi-restraints excluded: chain C residue  327 VAL
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 15 optimal weight:    5.9990
   chunk 43 optimal weight:    0.0870
   chunk 74 optimal weight:    7.9990
   chunk 23 optimal weight:    9.9990
   chunk 9 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 91 optimal weight:    0.6980
   chunk 96 optimal weight:    6.9990
   chunk 55 optimal weight:    0.0030
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.4368

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

Flipped N/Q/H residues before XYZ refinement:
A 284 ASN
B  23 ASN
B 292 ASN
** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 387 HIS
C  75 GLN
C  88 ASN
C 156 GLN
C 175 GLN
C 176 GLN
C 220 GLN
C 259 GLN
E  31 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.161215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.124224 restraints weight = 17239.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 3.01
r_work: 0.3375 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3372
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3372
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8017  Z= 0.112
  Angle     :  0.516   5.261  10933  Z= 0.276
  Chirality :  0.041   0.135   1276
  Planarity :  0.004   0.058   1371
  Dihedral  :  5.737  58.621   1272
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 15.83 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.27), residues: 1018
  helix:  2.15 (0.26), residues: 420
  sheet:  0.47 (0.32), residues: 218
  loop : -0.53 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  46 
 TYR   0.012   0.001   TYR B 391 
 PHE   0.028   0.002   PHE A 119 
 TRP   0.016   0.001   TRP C  82 
 HIS   0.007   0.001   HIS A 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8014)
  covalent geometry    : angle       0.51564 (10927)
  SS BOND              : bond        0.00251 (    3)
  SS BOND              : angle       1.08130 (    6)
  hydrogen bonds       : bond        0.03693 (  448)
  hydrogen bonds       : angle       4.70597 ( 1290)

*********************** 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
  160 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  185 MET cc_start: 0.7545 (tmm) cc_final: 0.7207 (tmm)
REVERT: A  296 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7099 (t)
REVERT: A  300 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7607 (mtp180)
REVERT: B  218 ASN cc_start: 0.8130 (m-40) cc_final: 0.7764 (m110)
REVERT: B  274 LYS cc_start: 0.7772 (tttt) cc_final: 0.7401 (ttpt)
REVERT: B  310 ASP cc_start: 0.8173 (t0) cc_final: 0.7724 (m-30)
REVERT: B  317 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7284 (ptp-110)
REVERT: B  318 TYR cc_start: 0.8187 (t80) cc_final: 0.7866 (t80)
REVERT: C  197 ARG cc_start: 0.7384 (mtp-110) cc_final: 0.6929 (mtp85)
REVERT: C  214 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6349 (mpp80)
REVERT: E   80 TYR cc_start: 0.7188 (m-80) cc_final: 0.6501 (m-80)
  outliers start: 20
  outliers final: 2
  residues processed: 152
  average time/residue: 0.6183
  time to fit residues: 99.3061
Evaluate side-chains
  122 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 117
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue  214 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
B  23 ASN
B 213 GLN
B 227 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: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.155299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.117785 restraints weight = 17131.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 2.97
r_work: 0.3293 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3296
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3296
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8017  Z= 0.148
  Angle     :  0.550   6.440  10933  Z= 0.293
  Chirality :  0.043   0.141   1276
  Planarity :  0.004   0.057   1371
  Dihedral  :  5.776  59.302   1272
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.50 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.27), residues: 1018
  helix:  2.24 (0.26), residues: 414
  sheet:  0.43 (0.32), residues: 220
  loop : -0.44 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 137 
 TYR   0.017   0.002   TYR C  59 
 PHE   0.027   0.002   PHE A 119 
 TRP   0.013   0.002   TRP C  82 
 HIS   0.007   0.001   HIS B 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8014)
  covalent geometry    : angle       0.54902 (10927)
  SS BOND              : bond        0.00463 (    3)
  SS BOND              : angle       1.40971 (    6)
  hydrogen bonds       : bond        0.03948 (  448)
  hydrogen bonds       : angle       4.70297 ( 1290)

*********************** 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
  158 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.6275 (mmt)
REVERT: A  185 MET cc_start: 0.7495 (tmm) cc_final: 0.7175 (tmm)
REVERT: A  296 THR cc_start: 0.8062 (m) cc_final: 0.7400 (p)
REVERT: A  300 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7684 (mtp180)
REVERT: B  211 LYS cc_start: 0.8501 (mttp) cc_final: 0.7613 (mttm)
REVERT: B  274 LYS cc_start: 0.7683 (tttt) cc_final: 0.7313 (ttpt)
REVERT: B  314 GLU cc_start: 0.7607 (pm20) cc_final: 0.7340 (pm20)
REVERT: B  317 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7319 (ptp-110)
REVERT: B  318 TYR cc_start: 0.8353 (t80) cc_final: 0.7976 (t80)
REVERT: B  330 GLU cc_start: 0.8145 (tt0) cc_final: 0.7591 (tt0)
REVERT: C  197 ARG cc_start: 0.7428 (mtp-110) cc_final: 0.6836 (mtp85)
REVERT: C  214 ARG cc_start: 0.6832 (mpp80) cc_final: 0.6374 (mpp80)
REVERT: E   83 MET cc_start: 0.8139 (mtp) cc_final: 0.7771 (mtm)
REVERT: E   87 LYS cc_start: 0.6867 (mtpt) cc_final: 0.6619 (ttmm)
  outliers start: 19
  outliers final: 6
  residues processed: 152
  average time/residue: 0.6111
  time to fit residues: 98.1877
Evaluate side-chains
  132 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  270 ILE
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   55 LEU
Chi-restraints excluded: chain E residue   21 SER
Chi-restraints excluded: chain E residue   93 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
B  23 ASN
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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.152409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.117193 restraints weight = 11549.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.43
r_work: 0.3280 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.3837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8017  Z= 0.172
  Angle     :  0.568   7.587  10933  Z= 0.301
  Chirality :  0.044   0.150   1276
  Planarity :  0.005   0.069   1371
  Dihedral  :  5.844  57.739   1272
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 18.40 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.27), residues: 1018
  helix:  2.14 (0.26), residues: 414
  sheet:  0.23 (0.32), residues: 226
  loop : -0.41 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 137 
 TYR   0.020   0.002   TYR B 391 
 PHE   0.028   0.002   PHE A 119 
 TRP   0.013   0.002   TRP C  82 
 HIS   0.009   0.001   HIS B 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 8014)
  covalent geometry    : angle       0.56724 (10927)
  SS BOND              : bond        0.00580 (    3)
  SS BOND              : angle       1.53939 (    6)
  hydrogen bonds       : bond        0.04045 (  448)
  hydrogen bonds       : angle       4.76180 ( 1290)

*********************** 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
  166 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ILE cc_start: 0.7042 (mt) cc_final: 0.6824 (mt)
REVERT: A   27 THR cc_start: 0.7805 (m) cc_final: 0.7435 (p)
REVERT: A   92 MET cc_start: 0.7247 (tpp) cc_final: 0.6858 (mmp)
REVERT: A  145 ILE cc_start: 0.7392 (OUTLIER) cc_final: 0.7176 (mm)
REVERT: A  185 MET cc_start: 0.7578 (tmm) cc_final: 0.7213 (tmm)
REVERT: A  188 ILE cc_start: 0.6907 (mt) cc_final: 0.6610 (mt)
REVERT: A  276 VAL cc_start: 0.8113 (t) cc_final: 0.7898 (m)
REVERT: A  294 PHE cc_start: 0.9162 (m-80) cc_final: 0.8958 (m-80)
REVERT: A  296 THR cc_start: 0.8184 (m) cc_final: 0.7518 (p)
REVERT: A  300 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7759 (mtp180)
REVERT: B  211 LYS cc_start: 0.8547 (mttp) cc_final: 0.7666 (mttm)
REVERT: B  274 LYS cc_start: 0.7791 (tttt) cc_final: 0.7409 (ttpt)
REVERT: B  314 GLU cc_start: 0.7620 (pm20) cc_final: 0.7339 (pm20)
REVERT: B  317 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7347 (ptp-110)
REVERT: C   55 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8363 (mt)
REVERT: C  197 ARG cc_start: 0.7498 (mtp-110) cc_final: 0.6940 (mtp85)
REVERT: C  213 VAL cc_start: 0.7046 (m) cc_final: 0.6765 (m)
REVERT: C  214 ARG cc_start: 0.6882 (mpp80) cc_final: 0.6410 (mpp80)
REVERT: E   83 MET cc_start: 0.7985 (mtp) cc_final: 0.7629 (mtp)
REVERT: E   87 LYS cc_start: 0.6883 (mtpt) cc_final: 0.6614 (ttmm)
  outliers start: 24
  outliers final: 8
  residues processed: 156
  average time/residue: 0.5539
  time to fit residues: 91.9105
Evaluate side-chains
  139 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  145 ILE
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   55 LEU
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain E residue   21 SER
Chi-restraints excluded: chain E residue   53 GLN
Chi-restraints excluded: chain E residue   93 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3788 r_free = 0.3788 target = 0.153491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.115647 restraints weight = 20383.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 3.22
r_work: 0.3253 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3235
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.3991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8017  Z= 0.138
  Angle     :  0.533   6.526  10933  Z= 0.283
  Chirality :  0.042   0.138   1276
  Planarity :  0.004   0.058   1371
  Dihedral  :  5.662  53.200   1272
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 18.92 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.27), residues: 1018
  helix:  2.26 (0.26), residues: 412
  sheet:  0.41 (0.32), residues: 222
  loop : -0.45 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 137 
 TYR   0.011   0.001   TYR A  79 
 PHE   0.028   0.002   PHE A 119 
 TRP   0.014   0.001   TRP C  82 
 HIS   0.006   0.001   HIS B 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8014)
  covalent geometry    : angle       0.53231 (10927)
  SS BOND              : bond        0.00457 (    3)
  SS BOND              : angle       1.29649 (    6)
  hydrogen bonds       : bond        0.03789 (  448)
  hydrogen bonds       : angle       4.65885 ( 1290)

*********************** 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
  165 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 TYR cc_start: 0.7483 (m-80) cc_final: 0.6366 (m-80)
REVERT: A   92 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7022 (mmp)
REVERT: A  145 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.7147 (mm)
REVERT: A  179 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7054 (tp)
REVERT: A  185 MET cc_start: 0.7536 (tmm) cc_final: 0.7147 (tmm)
REVERT: A  296 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7526 (p)
REVERT: A  300 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7739 (mtp180)
REVERT: B  211 LYS cc_start: 0.8522 (mttp) cc_final: 0.7636 (mttm)
REVERT: B  213 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8302 (tm-30)
REVERT: B  274 LYS cc_start: 0.7695 (tttt) cc_final: 0.7301 (ttpt)
REVERT: B  314 GLU cc_start: 0.7569 (pm20) cc_final: 0.7299 (pm20)
REVERT: B  317 ARG cc_start: 0.7910 (mtm-85) cc_final: 0.7428 (ptp-110)
REVERT: B  330 GLU cc_start: 0.8168 (tt0) cc_final: 0.7700 (tt0)
REVERT: C  188 MET cc_start: 0.8906 (mmm) cc_final: 0.8469 (mmm)
REVERT: C  197 ARG cc_start: 0.7465 (mtp-110) cc_final: 0.7232 (ttm-80)
REVERT: E   83 MET cc_start: 0.8098 (mtp) cc_final: 0.7768 (mtp)
REVERT: E   87 LYS cc_start: 0.6910 (mtpt) cc_final: 0.6296 (mttm)
  outliers start: 26
  outliers final: 8
  residues processed: 154
  average time/residue: 0.5599
  time to fit residues: 91.8342
Evaluate side-chains
  143 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
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  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  100 VAL
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain E residue   21 SER
Chi-restraints excluded: chain E residue   93 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 35 optimal weight:    0.4980
   chunk 19 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 63 optimal weight:    8.9990
   chunk 74 optimal weight:    7.9990
   chunk 94 optimal weight:    3.9990
   chunk 97 optimal weight:    9.9990
   chunk 40 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    1.4384

-------------------------------------------------------------------------------
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  75 GLN
C 156 GLN
C 175 GLN
C 176 GLN
C 220 GLN
E  31 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.152725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.117649 restraints weight = 11631.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 2.42
r_work: 0.3272 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3126
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3126
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.4164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8017  Z= 0.164
  Angle     :  0.551   6.822  10933  Z= 0.292
  Chirality :  0.043   0.145   1276
  Planarity :  0.004   0.056   1371
  Dihedral  :  5.749  55.191   1272
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 19.56 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.27), residues: 1018
  helix:  2.21 (0.26), residues: 412
  sheet:  0.37 (0.33), residues: 224
  loop : -0.44 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  46 
 TYR   0.013   0.002   TYR B 391 
 PHE   0.029   0.002   PHE A 119 
 TRP   0.013   0.002   TRP C  82 
 HIS   0.008   0.001   HIS B 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 8014)
  covalent geometry    : angle       0.54968 (10927)
  SS BOND              : bond        0.00544 (    3)
  SS BOND              : angle       1.48613 (    6)
  hydrogen bonds       : bond        0.03933 (  448)
  hydrogen bonds       : angle       4.73316 ( 1290)

*********************** 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
  148 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 TYR cc_start: 0.7799 (m-80) cc_final: 0.6726 (m-80)
REVERT: A   92 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7285 (mmp)
REVERT: A  145 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7386 (mm)
REVERT: A  185 MET cc_start: 0.7679 (tmm) cc_final: 0.7262 (tmm)
REVERT: A  296 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.7794 (p)
REVERT: A  300 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7797 (mtp180)
REVERT: B  211 LYS cc_start: 0.8712 (mttp) cc_final: 0.7855 (mttm)
REVERT: B  274 LYS cc_start: 0.8065 (tttt) cc_final: 0.7687 (ttpt)
REVERT: B  314 GLU cc_start: 0.7772 (pm20) cc_final: 0.7464 (pm20)
REVERT: B  317 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.7572 (ptp-110)
REVERT: B  330 GLU cc_start: 0.8240 (tt0) cc_final: 0.7753 (tt0)
REVERT: C  188 MET cc_start: 0.8985 (mmm) cc_final: 0.8611 (mmm)
REVERT: C  197 ARG cc_start: 0.7571 (mtp-110) cc_final: 0.7270 (mtp85)
REVERT: C  325 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8176 (mmp)
REVERT: E   83 MET cc_start: 0.8321 (mtp) cc_final: 0.8052 (mtp)
REVERT: E   87 LYS cc_start: 0.7239 (mtpt) cc_final: 0.6606 (mttm)
  outliers start: 22
  outliers final: 8
  residues processed: 139
  average time/residue: 0.5963
  time to fit residues: 87.8125
Evaluate side-chains
  134 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
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  173 THR
Chi-restraints excluded: chain C residue  325 MET
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0970
   chunk 91 optimal weight:    0.1980
   chunk 7 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 68 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 63 optimal weight:    4.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
B  23 ASN
B  29 GLN
B 213 GLN
B 294 GLN
C 156 GLN
C 175 GLN
C 176 GLN
C 220 GLN
E  31 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.156211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.124433 restraints weight = 13113.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 2.50
r_work: 0.3320 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    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 = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8017  Z= 0.111
  Angle     :  0.519   8.279  10933  Z= 0.271
  Chirality :  0.041   0.144   1276
  Planarity :  0.004   0.056   1371
  Dihedral  :  5.522  54.572   1272
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.27), residues: 1018
  helix:  2.18 (0.26), residues: 418
  sheet:  0.52 (0.33), residues: 222
  loop : -0.47 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 137 
 TYR   0.011   0.001   TYR B 339 
 PHE   0.030   0.002   PHE A  77 
 TRP   0.014   0.001   TRP C  82 
 HIS   0.006   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8014)
  covalent geometry    : angle       0.51812 (10927)
  SS BOND              : bond        0.00358 (    3)
  SS BOND              : angle       1.06588 (    6)
  hydrogen bonds       : bond        0.03529 (  448)
  hydrogen bonds       : angle       4.57169 ( 1290)

*********************** 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
  157 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.359 
Fit side-chains
REVERT: A   22 TYR cc_start: 0.7698 (m-80) cc_final: 0.6679 (m-80)
REVERT: A   31 VAL cc_start: 0.8387 (m) cc_final: 0.8184 (p)
REVERT: A   92 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7285 (mmp)
REVERT: A  185 MET cc_start: 0.7737 (tmm) cc_final: 0.7404 (tmm)
REVERT: A  275 SER cc_start: 0.8427 (m) cc_final: 0.8057 (m)
REVERT: A  296 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.7984 (p)
REVERT: B  211 LYS cc_start: 0.8644 (mttp) cc_final: 0.7835 (mttm)
REVERT: B  213 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8338 (tm-30)
REVERT: B  218 ASN cc_start: 0.8448 (m-40) cc_final: 0.8210 (m110)
REVERT: B  274 LYS cc_start: 0.8165 (tttt) cc_final: 0.7811 (ttpt)
REVERT: B  314 GLU cc_start: 0.7902 (pm20) cc_final: 0.7601 (pm20)
REVERT: B  317 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7810 (ptp-110)
REVERT: B  330 GLU cc_start: 0.8251 (tt0) cc_final: 0.7696 (tt0)
REVERT: C  188 MET cc_start: 0.8978 (mmm) cc_final: 0.8707 (mmm)
REVERT: C  197 ARG cc_start: 0.7553 (mtp-110) cc_final: 0.7194 (mtp85)
REVERT: C  325 MET cc_start: 0.8288 (mmp) cc_final: 0.8026 (mmp)
REVERT: E   83 MET cc_start: 0.8402 (mtp) cc_final: 0.8072 (mtp)
REVERT: E   87 LYS cc_start: 0.7364 (mtpt) cc_final: 0.6775 (mttm)
  outliers start: 15
  outliers final: 9
  residues processed: 152
  average time/residue: 0.5581
  time to fit residues: 90.6197
Evaluate side-chains
  141 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
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  173 THR
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  327 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   chunk 72 optimal weight:    8.9990
   chunk 99 optimal weight:    0.0670
   chunk 40 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    1.3920

-------------------------------------------------------------------------------
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 156 GLN
C 175 GLN
C 176 GLN
C 220 GLN
E  31 ASN
E  82 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.153408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.120176 restraints weight = 17333.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 3.06
r_work: 0.3255 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3253
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3253 r_free = 0.3253    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3253 r_free = 0.3253    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3253
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.4312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8017  Z= 0.158
  Angle     :  0.554   6.879  10933  Z= 0.292
  Chirality :  0.043   0.148   1276
  Planarity :  0.004   0.055   1371
  Dihedral  :  5.663  55.530   1272
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 19.95 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.27), residues: 1018
  helix:  2.24 (0.26), residues: 412
  sheet:  0.40 (0.33), residues: 224
  loop : -0.41 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 137 
 TYR   0.013   0.002   TYR E  95 
 PHE   0.029   0.002   PHE A 119 
 TRP   0.013   0.002   TRP A 118 
 HIS   0.007   0.001   HIS B 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 8014)
  covalent geometry    : angle       0.55268 (10927)
  SS BOND              : bond        0.00548 (    3)
  SS BOND              : angle       1.44904 (    6)
  hydrogen bonds       : bond        0.03850 (  448)
  hydrogen bonds       : angle       4.66231 ( 1290)

*********************** 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
  149 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 TYR cc_start: 0.7752 (m-80) cc_final: 0.6724 (m-80)
REVERT: A   92 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7232 (mmp)
REVERT: A  185 MET cc_start: 0.7705 (tmm) cc_final: 0.7267 (tmm)
REVERT: A  275 SER cc_start: 0.8411 (m) cc_final: 0.8023 (m)
REVERT: A  296 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.7847 (p)
REVERT: B   25 LYS cc_start: 0.8336 (ttpp) cc_final: 0.8035 (tttt)
REVERT: B  211 LYS cc_start: 0.8678 (mttp) cc_final: 0.7841 (mttm)
REVERT: B  213 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8366 (tm-30)
REVERT: B  274 LYS cc_start: 0.8052 (tttt) cc_final: 0.7682 (ttpt)
REVERT: B  314 GLU cc_start: 0.7840 (pm20) cc_final: 0.7555 (pm20)
REVERT: B  317 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7739 (ptp-110)
REVERT: B  330 GLU cc_start: 0.8224 (tt0) cc_final: 0.7790 (tt0)
REVERT: B  370 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7077 (mm-30)
REVERT: C  188 MET cc_start: 0.8954 (mmm) cc_final: 0.8622 (mmm)
REVERT: C  197 ARG cc_start: 0.7469 (mtp-110) cc_final: 0.7132 (mtp85)
REVERT: E   80 TYR cc_start: 0.8007 (m-80) cc_final: 0.7533 (m-80)
REVERT: E   87 LYS cc_start: 0.7299 (mtpt) cc_final: 0.6681 (mttm)
  outliers start: 19
  outliers final: 12
  residues processed: 142
  average time/residue: 0.5413
  time to fit residues: 81.9076
Evaluate side-chains
  139 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ILE
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  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  275 SER
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 74 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 63 optimal weight:    0.3980
   chunk 47 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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
C 156 GLN
C 175 GLN
C 176 GLN
C 220 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.154863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.121158 restraints weight = 9325.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.15
r_work: 0.3310 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.4369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8017  Z= 0.124
  Angle     :  0.546   8.565  10933  Z= 0.285
  Chirality :  0.042   0.136   1276
  Planarity :  0.004   0.064   1371
  Dihedral  :  5.594  54.106   1272
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 20.21 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.27), residues: 1018
  helix:  2.24 (0.26), residues: 414
  sheet:  0.41 (0.33), residues: 224
  loop : -0.41 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C 137 
 TYR   0.012   0.001   TYR B 339 
 PHE   0.027   0.002   PHE A 119 
 TRP   0.013   0.001   TRP A 118 
 HIS   0.006   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8014)
  covalent geometry    : angle       0.54589 (10927)
  SS BOND              : bond        0.00428 (    3)
  SS BOND              : angle       1.20241 (    6)
  hydrogen bonds       : bond        0.03658 (  448)
  hydrogen bonds       : angle       4.62626 ( 1290)

********************** 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
  143 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 TYR cc_start: 0.7686 (m-80) cc_final: 0.6697 (m-80)
REVERT: A   92 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7294 (mmp)
REVERT: A  185 MET cc_start: 0.7668 (tmm) cc_final: 0.7329 (tmm)
REVERT: A  275 SER cc_start: 0.8389 (m) cc_final: 0.8003 (m)
REVERT: A  296 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.7948 (p)
REVERT: B   25 LYS cc_start: 0.8326 (ttpp) cc_final: 0.7995 (tttt)
REVERT: B  211 LYS cc_start: 0.8698 (mttp) cc_final: 0.7845 (mttm)
REVERT: B  213 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8299 (tm-30)
REVERT: B  274 LYS cc_start: 0.8043 (tttt) cc_final: 0.7659 (ttpt)
REVERT: B  314 GLU cc_start: 0.7860 (pm20) cc_final: 0.7546 (pm20)
REVERT: B  317 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7743 (ptp-110)
REVERT: B  330 GLU cc_start: 0.8230 (tt0) cc_final: 0.7782 (tt0)
REVERT: B  370 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7083 (mm-30)
REVERT: C  188 MET cc_start: 0.8978 (mmm) cc_final: 0.8636 (mmm)
REVERT: C  197 ARG cc_start: 0.7509 (mtp-110) cc_final: 0.7158 (mtp85)
REVERT: E   80 TYR cc_start: 0.7977 (m-80) cc_final: 0.7502 (m-80)
REVERT: E   83 MET cc_start: 0.8216 (mtp) cc_final: 0.7860 (mtp)
REVERT: E   87 LYS cc_start: 0.7271 (mtpt) cc_final: 0.6701 (mttm)
  outliers start: 16
  outliers final: 11
  residues processed: 137
  average time/residue: 0.5726
  time to fit residues: 83.7336
Evaluate side-chains
  138 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
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  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  275 SER
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain E residue   21 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   chunk 73 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 92 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  29 GLN
B 213 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 = 0.3800 r_free = 0.3800 target = 0.154890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.122410 restraints weight = 15902.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.95
r_work: 0.3252 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.4409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8017  Z= 0.127
  Angle     :  0.535   6.867  10933  Z= 0.282
  Chirality :  0.042   0.147   1276
  Planarity :  0.004   0.055   1371
  Dihedral  :  5.557  54.017   1272
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 20.33 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.27), residues: 1018
  helix:  2.25 (0.26), residues: 414
  sheet:  0.38 (0.33), residues: 224
  loop : -0.38 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  46 
 TYR   0.024   0.001   TYR A  78 
 PHE   0.027   0.002   PHE A 119 
 TRP   0.013   0.001   TRP C  82 
 HIS   0.007   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8014)
  covalent geometry    : angle       0.53376 (10927)
  SS BOND              : bond        0.00455 (    3)
  SS BOND              : angle       1.43565 (    6)
  hydrogen bonds       : bond        0.03651 (  448)
  hydrogen bonds       : angle       4.60361 ( 1290)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3431.05 seconds
wall clock time: 59 minutes 24.63 seconds (3564.63 seconds total)