Starting phenix.real_space_refine
on Wed Mar 12 07:11:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5h1b_9566/03_2025/5h1b_9566.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5h1b_9566/03_2025/5h1b_9566.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5h1b_9566/03_2025/5h1b_9566.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5h1b_9566/03_2025/5h1b_9566.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5h1b_9566/03_2025/5h1b_9566.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5h1b_9566/03_2025/5h1b_9566.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 6
    Type Number    sf(0)   Gaussians
     P      18      5.49       5
     Mg      3      5.21       5
     S      39      5.16       5
     C    4557      2.51       5
     N    1287      2.21       5
     O    1455      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7359
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2361
          Classifications: {'peptide': 308}
          Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 296}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 180
          Classifications: {'DNA': 9}
          Link IDs: {'rna3p': 8}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 4.38, per 1000 atoms: 0.60
  Number of scatterers: 7359
  At special positions: 0
  Unit cell: (107.092, 69.218, 116.234, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      39     16.00
     P      18     15.00
     Mg      3     11.99
     O    1455      8.00
     N    1287      7.00
     C    4557      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.92
  Conformation dependent library (CDL) restraints added in 894.4 milliseconds
  

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1686

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 6 sheets defined
      54.1% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 28
    Processing helix  chain 'A' and resid 34 through 45
      removed outlier: 3.792A  pdb=" N   VAL A  38 " --> pdb=" O   ASN A  34 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLU A  43 " --> pdb=" O   LYS A  39 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY A  45 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 54
      removed outlier: 4.068A  pdb=" N   VAL A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 62
    Processing helix  chain 'A' and resid 67 through 82
    Processing helix  chain 'A' and resid 88 through 99
    Processing helix  chain 'A' and resid 106 through 113
    Processing helix  chain 'A' and resid 132 through 144
    Processing helix  chain 'A' and resid 145 through 146
      No H-bonds generated for 'chain 'A' and resid 145 through 146'
    Processing helix  chain 'A' and resid 147 through 151
    Processing helix  chain 'A' and resid 167 through 179
    Processing helix  chain 'A' and resid 181 through 188
      removed outlier: 3.717A  pdb=" N   ASN A 188 " --> pdb=" O   ASP A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 214
      removed outlier: 3.768A  pdb=" N   THR A 201 " --> pdb=" O   THR A 197 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLN A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLU A 213 " --> pdb=" O   ALA A 209 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER A 214 " --> pdb=" O   MET A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 232
      removed outlier: 3.974A  pdb=" N   ARG A 229 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   THR A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 260
      removed outlier: 3.602A  pdb=" N   ARG A 247 " --> pdb=" O   MET A 243 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   MET A 251 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 296
      removed outlier: 3.804A  pdb=" N   ILE A 292 " --> pdb=" O   GLY A 288 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA A 295 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 28
    Processing helix  chain 'B' and resid 34 through 45
      removed outlier: 3.792A  pdb=" N   VAL B  38 " --> pdb=" O   ASN B  34 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLU B  43 " --> pdb=" O   LYS B  39 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY B  45 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 54
      removed outlier: 4.068A  pdb=" N   VAL B  52 " --> pdb=" O   THR B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 62
    Processing helix  chain 'B' and resid 67 through 82
    Processing helix  chain 'B' and resid 89 through 99
    Processing helix  chain 'B' and resid 106 through 113
    Processing helix  chain 'B' and resid 132 through 144
    Processing helix  chain 'B' and resid 145 through 146
      No H-bonds generated for 'chain 'B' and resid 145 through 146'
    Processing helix  chain 'B' and resid 147 through 151
    Processing helix  chain 'B' and resid 167 through 179
    Processing helix  chain 'B' and resid 181 through 188
      removed outlier: 3.716A  pdb=" N   ASN B 188 " --> pdb=" O   ASP B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 214
      removed outlier: 3.768A  pdb=" N   THR B 201 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLN B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLU B 213 " --> pdb=" O   ALA B 209 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER B 214 " --> pdb=" O   MET B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 232
      removed outlier: 3.974A  pdb=" N   ARG B 229 " --> pdb=" O   THR B 225 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   THR B 230 " --> pdb=" O   ALA B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 260
      removed outlier: 3.602A  pdb=" N   ARG B 247 " --> pdb=" O   MET B 243 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   MET B 251 " --> pdb=" O   ARG B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 296
      removed outlier: 3.804A  pdb=" N   ILE B 292 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA B 295 " --> pdb=" O   ILE B 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 24 through 28
    Processing helix  chain 'C' and resid 34 through 45
      removed outlier: 3.792A  pdb=" N   VAL C  38 " --> pdb=" O   ASN C  34 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLU C  43 " --> pdb=" O   LYS C  39 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLY C  45 " --> pdb=" O   LEU C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 54
      removed outlier: 4.067A  pdb=" N   VAL C  52 " --> pdb=" O   THR C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 62
    Processing helix  chain 'C' and resid 67 through 82
    Processing helix  chain 'C' and resid 88 through 99
    Processing helix  chain 'C' and resid 106 through 113
    Processing helix  chain 'C' and resid 132 through 144
    Processing helix  chain 'C' and resid 145 through 146
      No H-bonds generated for 'chain 'C' and resid 145 through 146'
    Processing helix  chain 'C' and resid 147 through 151
    Processing helix  chain 'C' and resid 167 through 179
    Processing helix  chain 'C' and resid 181 through 188
      removed outlier: 3.716A  pdb=" N   ASN C 188 " --> pdb=" O   ASP C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 214
      removed outlier: 3.768A  pdb=" N   THR C 201 " --> pdb=" O   THR C 197 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLN C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLU C 213 " --> pdb=" O   ALA C 209 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   SER C 214 " --> pdb=" O   MET C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 225 through 232
      removed outlier: 3.973A  pdb=" N   ARG C 229 " --> pdb=" O   THR C 225 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   THR C 230 " --> pdb=" O   ALA C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 260
      removed outlier: 3.602A  pdb=" N   ARG C 247 " --> pdb=" O   MET C 243 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   MET C 251 " --> pdb=" O   ARG C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 296
      removed outlier: 3.804A  pdb=" N   ILE C 292 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA C 295 " --> pdb=" O   ILE C 291 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 324 through 327
      removed outlier: 8.173A  pdb=" N   LEU A 300 " --> pdb=" O   ILE A 122 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   GLU A 124 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU A 302 " --> pdb=" O   GLU A 124 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   PHE A 126 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   LYS A 304 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   THR A 123 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   ASN A 267 " --> pdb=" O   THR A 123 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   MET A 125 " --> pdb=" O   ASN A 267 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   LYS A 156 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU A 219 " --> pdb=" O   LYS A 156 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   MET A 158 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   VAL A 221 " --> pdb=" O   MET A 158 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   ILE A 160 " --> pdb=" O   VAL A 221 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA A 192 " --> pdb=" O   TYR A 159 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ASP A 161 " --> pdb=" O   ALA A 192 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 330
    Processing sheet with id=AA3, first strand: chain 'B' and resid 190 through 193
      removed outlier: 3.717A  pdb=" N   ALA B 192 " --> pdb=" O   TYR B 159 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ASP B 161 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   LYS B 156 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU B 219 " --> pdb=" O   LYS B 156 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   MET B 158 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   VAL B 221 " --> pdb=" O   MET B 158 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   ILE B 160 " --> pdb=" O   VAL B 221 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   THR B 123 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   ASN B 267 " --> pdb=" O   THR B 123 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   MET B 125 " --> pdb=" O   ASN B 267 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   LEU B 300 " --> pdb=" O   ILE B 122 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   GLU B 124 " --> pdb=" O   LEU B 300 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU B 302 " --> pdb=" O   GLU B 124 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   PHE B 126 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   LYS B 304 " --> pdb=" O   PHE B 126 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 329 through 330
    Processing sheet with id=AA5, first strand: chain 'C' and resid 190 through 193
      removed outlier: 3.717A  pdb=" N   ALA C 192 " --> pdb=" O   TYR C 159 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ASP C 161 " --> pdb=" O   ALA C 192 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   LYS C 156 " --> pdb=" O   ALA C 217 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU C 219 " --> pdb=" O   LYS C 156 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   MET C 158 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   VAL C 221 " --> pdb=" O   MET C 158 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   ILE C 160 " --> pdb=" O   VAL C 221 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   THR C 123 " --> pdb=" O   ILE C 265 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   ASN C 267 " --> pdb=" O   THR C 123 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   MET C 125 " --> pdb=" O   ASN C 267 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   LEU C 300 " --> pdb=" O   ILE C 122 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   GLU C 124 " --> pdb=" O   LEU C 300 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU C 302 " --> pdb=" O   GLU C 124 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   PHE C 126 " --> pdb=" O   LEU C 302 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   LYS C 304 " --> pdb=" O   PHE C 126 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 329 through 330

    334 hydrogen bonds defined for protein.
    918 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.00

  Time building geometry restraints manager: 2.17 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2372
        1.33 -     1.45: 1159
        1.45 -     1.57: 3854
        1.57 -     1.69: 33
        1.69 -     1.81: 63
  Bond restraints: 7481
  Sorted by residual:
  bond pdb=" O3A ANP A 600 "
       pdb=" PB  ANP A 600 "
    ideal  model  delta    sigma   weight residual
    1.700  1.550  0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" O3A ANP B 600 "
       pdb=" PB  ANP B 600 "
    ideal  model  delta    sigma   weight residual
    1.700  1.550  0.150 2.00e-02 2.50e+03 5.63e+01
  bond pdb=" O3A ANP C 600 "
       pdb=" PB  ANP C 600 "
    ideal  model  delta    sigma   weight residual
    1.700  1.550  0.150 2.00e-02 2.50e+03 5.60e+01
  bond pdb=" N3B ANP C 600 "
       pdb=" PG  ANP C 600 "
    ideal  model  delta    sigma   weight residual
    1.795  1.689  0.106 2.00e-02 2.50e+03 2.82e+01
  bond pdb=" N3B ANP A 600 "
       pdb=" PG  ANP A 600 "
    ideal  model  delta    sigma   weight residual
    1.795  1.689  0.106 2.00e-02 2.50e+03 2.80e+01
  ... (remaining 7476 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.75: 9923
        3.75 -     7.51: 204
        7.51 -    11.26: 15
       11.26 -    15.01: 0
       15.01 -    18.77: 3
  Bond angle restraints: 10145
  Sorted by residual:
  angle pdb=" PB  ANP C 600 "
        pdb=" N3B ANP C 600 "
        pdb=" PG  ANP C 600 "
      ideal   model   delta    sigma   weight residual
     126.95  108.18   18.77 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" PB  ANP B 600 "
        pdb=" N3B ANP B 600 "
        pdb=" PG  ANP B 600 "
      ideal   model   delta    sigma   weight residual
     126.95  108.18   18.77 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" PB  ANP A 600 "
        pdb=" N3B ANP A 600 "
        pdb=" PG  ANP A 600 "
      ideal   model   delta    sigma   weight residual
     126.95  108.20   18.75 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" N   THR A 197 "
        pdb=" CA  THR A 197 "
        pdb=" C   THR A 197 "
      ideal   model   delta    sigma   weight residual
     111.71  105.46    6.25 1.15e+00 7.56e-01 2.95e+01
  angle pdb=" N   THR B 197 "
        pdb=" CA  THR B 197 "
        pdb=" C   THR B 197 "
      ideal   model   delta    sigma   weight residual
     111.71  105.47    6.24 1.15e+00 7.56e-01 2.94e+01
  ... (remaining 10140 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.74: 4322
       23.74 -    47.48: 162
       47.48 -    71.22: 46
       71.22 -    94.96: 27
       94.96 -   118.70: 3
  Dihedral angle restraints: 4560
    sinusoidal: 1926
      harmonic: 2634
  Sorted by residual:
  dihedral pdb=" CA  CYS C 319 "
           pdb=" C   CYS C 319 "
           pdb=" N   LEU C 320 "
           pdb=" CA  LEU C 320 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.98  -23.02     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  CYS B 319 "
           pdb=" C   CYS B 319 "
           pdb=" N   LEU B 320 "
           pdb=" CA  LEU B 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.98  -23.02     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  CYS A 319 "
           pdb=" C   CYS A 319 "
           pdb=" N   LEU A 320 "
           pdb=" CA  LEU A 320 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.99  -23.01     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 4557 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 888
       0.064 -    0.129: 244
       0.129 -    0.193: 23
       0.193 -    0.257: 0
       0.257 -    0.321: 3
  Chirality restraints: 1158
  Sorted by residual:
  chirality pdb=" C3' ANP C 600 "
            pdb=" C2' ANP C 600 "
            pdb=" C4' ANP C 600 "
            pdb=" O3' ANP C 600 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.68    0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" C3' ANP B 600 "
            pdb=" C2' ANP B 600 "
            pdb=" C4' ANP B 600 "
            pdb=" O3' ANP B 600 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.68    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" C3' ANP A 600 "
            pdb=" C2' ANP A 600 "
            pdb=" C4' ANP A 600 "
            pdb=" O3' ANP A 600 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.67    0.32 2.00e-01 2.50e+01 2.50e+00
  ... (remaining 1155 not shown)

  Planarity restraints: 1272
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 246 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.15e+00
        pdb=" C   ALA A 246 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA A 246 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ARG A 247 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 246 "   -0.011 2.00e-02 2.50e+03   2.25e-02 5.06e+00
        pdb=" C   ALA B 246 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA B 246 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ARG B 247 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 246 "   -0.011 2.00e-02 2.50e+03   2.24e-02 5.00e+00
        pdb=" C   ALA C 246 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA C 246 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ARG C 247 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1269 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.18: 46
        2.18 -     2.86: 3020
        2.86 -     3.54: 11307
        3.54 -     4.22: 18610
        4.22 -     4.90: 29872
  Nonbonded interactions: 62855
  Sorted by model distance:
  nonbonded pdb=" CB  ALA A 271 "
            pdb=" OP2  DT D   4 "
     model   vdw
     1.503 3.460
  nonbonded pdb=" CA  ALA A 271 "
            pdb=" OP2  DT D   4 "
     model   vdw
     1.572 3.470
  nonbonded pdb=" N   ALA A 271 "
            pdb=" OP2  DT D   4 "
     model   vdw
     1.580 3.120
  nonbonded pdb=" OH  TYR B 159 "
            pdb=" OD2 ASP B 222 "
     model   vdw
     1.586 3.040
  nonbonded pdb=" OH  TYR A 159 "
            pdb=" OD2 ASP A 222 "
     model   vdw
     1.586 3.040
  ... (remaining 62850 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.050
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7180
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      :  0.010   0.150   7481  Z= 0.667
  Angle     :  1.411  18.767  10145  Z= 0.917
  Chirality :  0.056   0.321   1158
  Planarity :  0.005   0.034   1272
  Dihedral  : 16.126 118.695   2874
  Min Nonbonded Distance : 1.503

Molprobity Statistics.
  All-atom Clashscore : 54.25
  Ramachandran Plot:
    Outliers :  2.63 %
    Allowed  :  6.25 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  :  2.43 %
    Favored  : 91.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.27), residues: 912
  helix: -2.43 (0.18), residues: 378
  sheet: -0.80 (0.40), residues: 159
  loop :  0.92 (0.36), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS C 138 
 PHE   0.018   0.003   PHE C  86 
 TYR   0.019   0.002   TYR A 315 
 ARG   0.010   0.002   ARG C 215 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 98
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6302 (mp)
REVERT: A  265 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8424 (mm)
REVERT: B   62 ASN cc_start: 0.7700 (m-40) cc_final: 0.7444 (m110)
REVERT: B   99 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6453 (mp)
REVERT: B  170 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6648 (mpt180)
REVERT: B  265 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8012 (mm)
  outliers start: 42
  outliers final: 13
  residues processed: 132
  average time/residue: 0.3002
  time to fit residues: 48.8095
Evaluate side-chains
  72 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 54
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 68 optimal weight:    5.9990
   chunk 37 optimal weight:    9.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    8.9990
   chunk 36 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 27 optimal weight:   20.0000
   chunk 42 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  34 ASN
A 138 HIS
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 HIS
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  93 HIS
C 138 HIS
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.040395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.034850 restraints weight = 51830.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.035939 restraints weight = 28883.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.036725 restraints weight = 18397.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.4034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7481  Z= 0.287
  Angle     :  0.777   7.710  10145  Z= 0.412
  Chirality :  0.044   0.167   1158
  Planarity :  0.005   0.042   1272
  Dihedral  : 13.507 111.171   1191
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 18.10
  Ramachandran Plot:
    Outliers :  1.32 %
    Allowed  :  4.28 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  0.94 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.27), residues: 912
  helix: -0.30 (0.23), residues: 429
  sheet: -0.58 (0.40), residues: 168
  loop :  0.45 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B 294 
 PHE   0.019   0.002   PHE B 126 
 TYR   0.018   0.002   TYR B 315 
 ARG   0.007   0.001   ARG B 193 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ASN cc_start: 0.8742 (m-40) cc_final: 0.8373 (m110)
REVERT: A   99 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7838 (mt)
REVERT: A  137 CYS cc_start: 0.8984 (m) cc_final: 0.8747 (m)
REVERT: B   62 ASN cc_start: 0.8761 (m-40) cc_final: 0.8346 (m110)
REVERT: B  248 PHE cc_start: 0.9334 (t80) cc_final: 0.9023 (t80)
REVERT: B  251 MET cc_start: 0.9149 (tpt) cc_final: 0.8877 (tpt)
REVERT: C   62 ASN cc_start: 0.8748 (m-40) cc_final: 0.8361 (p0)
REVERT: C  210 MET cc_start: 0.8061 (mtt) cc_final: 0.7843 (mtt)
REVERT: C  251 MET cc_start: 0.9122 (tpt) cc_final: 0.8507 (tpt)
REVERT: C  301 TYR cc_start: 0.8912 (t80) cc_final: 0.8687 (t80)
  outliers start: 4
  outliers final: 0
  residues processed: 72
  average time/residue: 0.2136
  time to fit residues: 20.8242
Evaluate side-chains
  46 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 58 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0030
   chunk 53 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 77 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   chunk 76 optimal weight:    7.9990
   chunk 7 optimal weight:    7.9990
   chunk 74 optimal weight:    0.2980
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.6596

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 267 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.041024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.035581 restraints weight = 52072.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.036728 restraints weight = 29025.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.037557 restraints weight = 18465.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.4901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7481  Z= 0.191
  Angle     :  0.640   7.439  10145  Z= 0.338
  Chirality :  0.040   0.152   1158
  Planarity :  0.003   0.030   1272
  Dihedral  : 12.224 100.764   1191
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  1.32 %
    Allowed  :  4.06 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.21 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.27), residues: 912
  helix:  0.51 (0.23), residues: 447
  sheet: -0.52 (0.39), residues: 168
  loop :  0.14 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 294 
 PHE   0.019   0.002   PHE C 248 
 TYR   0.019   0.001   TYR C 315 
 ARG   0.005   0.001   ARG B 193 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.8835 (pttp) cc_final: 0.8548 (ptpt)
REVERT: A   62 ASN cc_start: 0.8639 (m-40) cc_final: 0.8281 (p0)
REVERT: A  137 CYS cc_start: 0.9007 (m) cc_final: 0.8729 (m)
REVERT: B   58 LYS cc_start: 0.9222 (pttp) cc_final: 0.8959 (ptpt)
REVERT: B   62 ASN cc_start: 0.8691 (m-40) cc_final: 0.8300 (m110)
REVERT: B  243 MET cc_start: 0.8587 (tmm) cc_final: 0.8348 (tmm)
REVERT: B  248 PHE cc_start: 0.9299 (t80) cc_final: 0.8894 (t80)
REVERT: B  301 TYR cc_start: 0.8367 (t80) cc_final: 0.8125 (t80)
REVERT: C   62 ASN cc_start: 0.8817 (m-40) cc_final: 0.8503 (p0)
REVERT: C  137 CYS cc_start: 0.9177 (m) cc_final: 0.8964 (m)
REVERT: C  206 GLN cc_start: 0.9083 (mt0) cc_final: 0.8799 (tt0)
REVERT: C  225 THR cc_start: 0.9072 (p) cc_final: 0.8504 (p)
REVERT: C  251 MET cc_start: 0.9042 (tpt) cc_final: 0.8734 (tpt)
  outliers start: 2
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1744
  time to fit residues: 18.7482
Evaluate side-chains
  46 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 19 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 46 optimal weight:    0.0030
   chunk 3 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 86 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   overall best weight:    3.3998

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 199 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.039341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.034036 restraints weight = 53988.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.035104 restraints weight = 30422.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.035880 restraints weight = 19524.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.5396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7481  Z= 0.247
  Angle     :  0.643   7.504  10145  Z= 0.341
  Chirality :  0.040   0.163   1158
  Planarity :  0.003   0.031   1272
  Dihedral  : 12.242 104.260   1191
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  1.32 %
    Allowed  :  4.50 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.97 %
    Favored  : 96.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.27), residues: 912
  helix:  0.86 (0.24), residues: 447
  sheet: -0.55 (0.38), residues: 168
  loop :  0.09 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 294 
 PHE   0.017   0.002   PHE B  86 
 TYR   0.017   0.001   TYR B 315 
 ARG   0.004   0.001   ARG B 193 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.8867 (pttp) cc_final: 0.8545 (ptpt)
REVERT: A   62 ASN cc_start: 0.8606 (m-40) cc_final: 0.8281 (p0)
REVERT: A  128 GLU cc_start: 0.8145 (pm20) cc_final: 0.7944 (pm20)
REVERT: A  137 CYS cc_start: 0.8981 (m) cc_final: 0.8711 (m)
REVERT: B   62 ASN cc_start: 0.8691 (m-40) cc_final: 0.8308 (m110)
REVERT: B  158 MET cc_start: 0.8051 (pmm) cc_final: 0.7412 (mpp)
REVERT: B  248 PHE cc_start: 0.9342 (t80) cc_final: 0.8848 (t80)
REVERT: C   62 ASN cc_start: 0.8808 (m-40) cc_final: 0.8521 (p0)
REVERT: C  137 CYS cc_start: 0.9155 (m) cc_final: 0.8914 (m)
REVERT: C  158 MET cc_start: 0.8361 (pmm) cc_final: 0.8147 (pmm)
REVERT: C  206 GLN cc_start: 0.9075 (mt0) cc_final: 0.8699 (tt0)
REVERT: C  251 MET cc_start: 0.8960 (tpt) cc_final: 0.8407 (tpt)
REVERT: C  326 MET cc_start: 0.8489 (tmm) cc_final: 0.8256 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1765
  time to fit residues: 15.3758
Evaluate side-chains
  46 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 5 optimal weight:    7.9990
   chunk 80 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 14 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.039894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.034633 restraints weight = 53177.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.035721 restraints weight = 30019.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.036511 restraints weight = 19172.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.5803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7481  Z= 0.205
  Angle     :  0.620   8.674  10145  Z= 0.324
  Chirality :  0.039   0.159   1158
  Planarity :  0.003   0.045   1272
  Dihedral  : 12.137 103.635   1191
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  3.62 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.27), residues: 912
  helix:  1.16 (0.24), residues: 447
  sheet: -0.60 (0.37), residues: 165
  loop :  0.10 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 294 
 PHE   0.016   0.002   PHE B 126 
 TYR   0.018   0.001   TYR B 315 
 ARG   0.004   0.000   ARG B 299 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.8793 (pttp) cc_final: 0.8291 (ptpt)
REVERT: A   62 ASN cc_start: 0.8635 (m-40) cc_final: 0.8294 (m110)
REVERT: A  128 GLU cc_start: 0.8035 (pm20) cc_final: 0.7779 (pm20)
REVERT: A  137 CYS cc_start: 0.9028 (m) cc_final: 0.8703 (m)
REVERT: A  251 MET cc_start: 0.8985 (tpt) cc_final: 0.8333 (tpt)
REVERT: B   62 ASN cc_start: 0.8639 (m-40) cc_final: 0.8297 (m110)
REVERT: B  243 MET cc_start: 0.8396 (tmm) cc_final: 0.8176 (tmm)
REVERT: B  248 PHE cc_start: 0.9307 (t80) cc_final: 0.8897 (t80)
REVERT: C   58 LYS cc_start: 0.9051 (pttp) cc_final: 0.8823 (ptpt)
REVERT: C  137 CYS cc_start: 0.9148 (m) cc_final: 0.8887 (m)
REVERT: C  206 GLN cc_start: 0.9163 (mt0) cc_final: 0.8786 (tt0)
REVERT: C  251 MET cc_start: 0.8954 (tpt) cc_final: 0.8393 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1976
  time to fit residues: 17.9527
Evaluate side-chains
  48 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 80 optimal weight:   10.0000
   chunk 54 optimal weight:    5.9990
   chunk 17 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 27 optimal weight:   10.0000
   chunk 75 optimal weight:    8.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  30 GLN
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 HIS
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 242 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.038542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.033261 restraints weight = 54549.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.034327 restraints weight = 30619.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.035098 restraints weight = 19609.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.6020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7481  Z= 0.290
  Angle     :  0.672   7.611  10145  Z= 0.349
  Chirality :  0.040   0.167   1158
  Planarity :  0.004   0.057   1272
  Dihedral  : 12.374 111.390   1191
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  5.04 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.27), residues: 912
  helix:  1.02 (0.24), residues: 438
  sheet: -0.65 (0.37), residues: 165
  loop :  0.07 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 294 
 PHE   0.014   0.002   PHE B  86 
 TYR   0.012   0.001   TYR B 191 
 ARG   0.006   0.001   ARG B  96 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 ASN cc_start: 0.8671 (m-40) cc_final: 0.8351 (m110)
REVERT: A  128 GLU cc_start: 0.8048 (pm20) cc_final: 0.7480 (pm20)
REVERT: A  137 CYS cc_start: 0.9068 (m) cc_final: 0.8768 (m)
REVERT: A  251 MET cc_start: 0.9062 (tpt) cc_final: 0.8784 (tpp)
REVERT: B   62 ASN cc_start: 0.8665 (m-40) cc_final: 0.8298 (m110)
REVERT: B  137 CYS cc_start: 0.9241 (m) cc_final: 0.8992 (m)
REVERT: B  225 THR cc_start: 0.9183 (p) cc_final: 0.8667 (p)
REVERT: B  243 MET cc_start: 0.8468 (tmm) cc_final: 0.8173 (tmm)
REVERT: C  137 CYS cc_start: 0.9142 (m) cc_final: 0.8833 (m)
REVERT: C  251 MET cc_start: 0.8992 (tpt) cc_final: 0.8561 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1700
  time to fit residues: 12.9337
Evaluate side-chains
  41 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 49 optimal weight:    7.9990
   chunk 39 optimal weight:   10.0000
   chunk 24 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 32 optimal weight:    9.9990
   chunk 52 optimal weight:    0.9990
   chunk 60 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 89 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.039345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.033987 restraints weight = 52878.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.035085 restraints weight = 29815.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.035882 restraints weight = 19166.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.6267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7481  Z= 0.206
  Angle     :  0.632   7.625  10145  Z= 0.326
  Chirality :  0.039   0.189   1158
  Planarity :  0.003   0.051   1272
  Dihedral  : 12.154 104.866   1191
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  1.10 %
    Allowed  :  3.95 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.27), residues: 912
  helix:  1.18 (0.24), residues: 447
  sheet: -0.59 (0.37), residues: 165
  loop :  0.14 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 294 
 PHE   0.012   0.002   PHE C  86 
 TYR   0.012   0.001   TYR B 191 
 ARG   0.004   0.000   ARG B  96 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.8855 (pttp) cc_final: 0.8372 (ptpt)
REVERT: A   62 ASN cc_start: 0.8638 (m-40) cc_final: 0.8299 (m110)
REVERT: A  137 CYS cc_start: 0.9170 (m) cc_final: 0.8950 (m)
REVERT: A  251 MET cc_start: 0.8977 (tpt) cc_final: 0.8373 (tpt)
REVERT: B   62 ASN cc_start: 0.8702 (m-40) cc_final: 0.8355 (m110)
REVERT: B  137 CYS cc_start: 0.9295 (m) cc_final: 0.9082 (m)
REVERT: B  243 MET cc_start: 0.8454 (tmm) cc_final: 0.8173 (tmm)
REVERT: C  137 CYS cc_start: 0.9208 (m) cc_final: 0.8939 (m)
REVERT: C  251 MET cc_start: 0.8969 (tpt) cc_final: 0.8485 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1709
  time to fit residues: 13.7366
Evaluate side-chains
  44 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 87 optimal weight:    9.9990
   chunk 59 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  47 HIS
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  47 HIS
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.037861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.032561 restraints weight = 54665.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.033636 restraints weight = 30807.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.034387 restraints weight = 19765.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.6328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   7481  Z= 0.345
  Angle     :  0.731   7.914  10145  Z= 0.374
  Chirality :  0.042   0.179   1158
  Planarity :  0.004   0.052   1272
  Dihedral  : 12.289 110.822   1191
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  4.93 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.27), residues: 912
  helix:  0.93 (0.23), residues: 444
  sheet: -0.51 (0.40), residues: 144
  loop : -0.29 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 294 
 PHE   0.019   0.002   PHE C  86 
 TYR   0.017   0.002   TYR B 191 
 ARG   0.007   0.001   ARG B  96 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A   62 ASN cc_start: 0.8646 (m-40) cc_final: 0.8332 (m110)
REVERT: A  137 CYS cc_start: 0.9150 (m) cc_final: 0.8886 (m)
REVERT: A  158 MET cc_start: 0.8061 (pmm) cc_final: 0.7695 (pmm)
REVERT: A  251 MET cc_start: 0.9039 (tpt) cc_final: 0.8780 (tpp)
REVERT: B   36 ASN cc_start: 0.9232 (m110) cc_final: 0.9027 (m110)
REVERT: B   62 ASN cc_start: 0.8780 (m-40) cc_final: 0.8505 (m110)
REVERT: B  137 CYS cc_start: 0.9248 (m) cc_final: 0.9038 (m)
REVERT: B  243 MET cc_start: 0.8597 (tmm) cc_final: 0.8357 (tmm)
REVERT: B  267 ASN cc_start: 0.8843 (p0) cc_final: 0.8556 (p0)
REVERT: C  137 CYS cc_start: 0.9214 (m) cc_final: 0.8942 (m)
REVERT: C  251 MET cc_start: 0.8950 (tpt) cc_final: 0.8444 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1677
  time to fit residues: 12.1287
Evaluate side-chains
  40 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 54 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 21 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.039083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.033642 restraints weight = 53777.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.034752 restraints weight = 30195.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.035513 restraints weight = 19295.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.6524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7481  Z= 0.234
  Angle     :  0.676   9.132  10145  Z= 0.339
  Chirality :  0.040   0.171   1158
  Planarity :  0.004   0.049   1272
  Dihedral  : 11.993 107.633   1191
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  3.84 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.27), residues: 912
  helix:  1.10 (0.24), residues: 453
  sheet: -0.45 (0.41), residues: 141
  loop : -0.36 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 138 
 PHE   0.016   0.002   PHE B  86 
 TYR   0.013   0.001   TYR B 191 
 ARG   0.005   0.000   ARG C  96 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 ASN cc_start: 0.8671 (m-40) cc_final: 0.8361 (m110)
REVERT: A  137 CYS cc_start: 0.9197 (m) cc_final: 0.8948 (m)
REVERT: A  251 MET cc_start: 0.9022 (tpt) cc_final: 0.8726 (tpp)
REVERT: B   36 ASN cc_start: 0.9235 (m110) cc_final: 0.9011 (m110)
REVERT: B   62 ASN cc_start: 0.8635 (m-40) cc_final: 0.8293 (m110)
REVERT: B  137 CYS cc_start: 0.9265 (m) cc_final: 0.9036 (m)
REVERT: B  267 ASN cc_start: 0.8797 (p0) cc_final: 0.8519 (p0)
REVERT: C  137 CYS cc_start: 0.9181 (m) cc_final: 0.8926 (m)
REVERT: C  251 MET cc_start: 0.8949 (tpt) cc_final: 0.8455 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1567
  time to fit residues: 12.7910
Evaluate side-chains
  41 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 52 optimal weight:    1.9990
   chunk 58 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   chunk 59 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 36 optimal weight:   10.0000
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 135 GLN
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.039195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.033801 restraints weight = 53540.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.034900 restraints weight = 30121.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.035684 restraints weight = 19219.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.6657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7481  Z= 0.234
  Angle     :  0.675   9.081  10145  Z= 0.340
  Chirality :  0.040   0.171   1158
  Planarity :  0.005   0.104   1272
  Dihedral  : 11.891 107.460   1191
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  4.28 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.27), residues: 912
  helix:  1.19 (0.24), residues: 447
  sheet: -0.45 (0.42), residues: 141
  loop : -0.24 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 138 
 PHE   0.019   0.002   PHE C  86 
 TYR   0.012   0.001   TYR B 191 
 ARG   0.004   0.000   ARG B  96 

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 ASN cc_start: 0.8663 (m-40) cc_final: 0.8347 (m110)
REVERT: A  137 CYS cc_start: 0.9201 (m) cc_final: 0.8951 (m)
REVERT: A  251 MET cc_start: 0.9038 (tpt) cc_final: 0.8714 (tpp)
REVERT: B   62 ASN cc_start: 0.8674 (m-40) cc_final: 0.8328 (m110)
REVERT: B  137 CYS cc_start: 0.9276 (m) cc_final: 0.9035 (m)
REVERT: B  243 MET cc_start: 0.8320 (tmm) cc_final: 0.8101 (tmm)
REVERT: B  267 ASN cc_start: 0.8778 (p0) cc_final: 0.8504 (p0)
REVERT: C  137 CYS cc_start: 0.9173 (m) cc_final: 0.8918 (m)
REVERT: C  251 MET cc_start: 0.8957 (tpt) cc_final: 0.8445 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.1624
  time to fit residues: 11.2738
Evaluate side-chains
  39 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 85 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 86 optimal weight:    3.9990
   chunk 58 optimal weight:   20.0000
   chunk 43 optimal weight:    0.9990
   chunk 7 optimal weight:    9.9990
   chunk 21 optimal weight:    0.0980
   chunk 24 optimal weight:    8.9990
   overall best weight:    2.0188

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.039813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.034402 restraints weight = 52946.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.035516 restraints weight = 30277.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.036291 restraints weight = 19550.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.6842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7481  Z= 0.184
  Angle     :  0.634   8.213  10145  Z= 0.319
  Chirality :  0.039   0.169   1158
  Planarity :  0.004   0.065   1272
  Dihedral  : 11.722 107.825   1191
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  3.62 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.28), residues: 912
  helix:  1.45 (0.24), residues: 444
  sheet: -0.43 (0.43), residues: 141
  loop : -0.23 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 244 
 PHE   0.015   0.001   PHE C  86 
 TYR   0.010   0.001   TYR B 191 
 ARG   0.003   0.000   ARG B  96 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1771.43 seconds
wall clock time: 32 minutes 8.28 seconds (1928.28 seconds total)