Starting phenix.real_space_refine
on Tue Apr 29 20:03:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ija_35483/04_2025/8ija_35483_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ija_35483/04_2025/8ija_35483.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ija_35483/04_2025/8ija_35483.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ija_35483/04_2025/8ija_35483.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ija_35483/04_2025/8ija_35483_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ija_35483/04_2025/8ija_35483_neut.cif"
  }
  resolution = 2.69
  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=   0.024
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: 4
    Type Number    sf(0)   Gaussians
     S      67      5.16       5
     C    5653      2.51       5
     N    1506      2.21       5
     O    1619      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8845
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 2357
          Classifications: {'peptide': 294}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 10, 'TRANS': 283}
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 38
    Chain: "C"
      Number of atoms: 1699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1699
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 2, 'TRANS': 213}
          Chain breaks: 2
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 28
    Chain: "B"
      Number of atoms: 2577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2577
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "G"
      Number of atoms: 431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 431
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "S"
      Number of atoms: 1772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1772
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Unusual residues: {'NIO': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.81, per 1000 atoms: 0.66
  Number of scatterers: 8845
  At special positions: 0
  Unit cell: (87.15, 119.52, 130.31, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      67     16.00
     O    1619      8.00
     N    1506      7.00
     C    5653      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  18 " - pdb=" SG  CYS A 183 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  19 " - pdb=" SG  CYS A 266 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 100 " - pdb=" SG  CYS A 177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.28
  Conformation dependent library (CDL) restraints added in 983.9 milliseconds
  

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2124

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 16 sheets defined
      36.4% alpha, 24.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 55
      removed outlier: 3.740A  pdb=" N   VAL A  27 " --> pdb=" O   ASP A  23 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A  30 " --> pdb=" O   ILE A  26 " (cutoff:3.500A)
      Proline residue:  A  31  - end of helix
      removed outlier: 3.610A  pdb=" N   LEU A  42 " --> pdb=" O   PHE A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 89
      removed outlier: 3.646A  pdb=" N   LEU A  66 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
      Proline residue:  A  81  - end of helix
      removed outlier: 3.836A  pdb=" N   ARG A  89 " --> pdb=" O   ASP A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 131
    Processing helix  chain 'A' and resid 134 through 139
      removed outlier: 3.705A  pdb=" N   ILE A 139 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 158
    Processing helix  chain 'A' and resid 159 through 163
    Processing helix  chain 'A' and resid 188 through 218
      removed outlier: 3.762A  pdb=" N   LEU A 194 " --> pdb=" O   GLU A 190 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   PHE A 197 " --> pdb=" O   PHE A 193 " (cutoff:3.500A)
      Proline residue:  A 200  - end of helix
    Processing helix  chain 'A' and resid 223 through 262
      Proline residue:  A 246  - end of helix
    Processing helix  chain 'A' and resid 265 through 269
    Processing helix  chain 'A' and resid 271 through 294
      removed outlier: 3.689A  pdb=" N   PHE A 282 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   THR A 283 " --> pdb=" O   THR A 279 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   TYR A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   SER A 287 " --> pdb=" O   THR A 283 " (cutoff:3.500A)
      Proline residue:  A 291  - end of helix
    Processing helix  chain 'C' and resid 6 through 32
      removed outlier: 3.606A  pdb=" N   ARG C  32 " --> pdb=" O   GLU C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 53
      removed outlier: 3.715A  pdb=" N   MET C  53 " --> pdb=" O   ILE C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 207 through 216
      removed outlier: 4.233A  pdb=" N   ILE C 212 " --> pdb=" O   LYS C 209 " (cutoff:3.500A)
      removed outlier: 5.756A  pdb=" N   HIS C 213 " --> pdb=" O   LYS C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 242 through 255
    Processing helix  chain 'C' and resid 270 through 281
      removed outlier: 3.507A  pdb=" N   LYS C 280 " --> pdb=" O   GLU C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 309
    Processing helix  chain 'C' and resid 330 through 352
    Processing helix  chain 'B' and resid 5 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 9 through 25
      removed outlier: 3.705A  pdb=" N   ILE G  25 " --> pdb=" O   MET G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.511A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12
    Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 170
    Processing sheet with id=AA3, first strand: chain 'C' and resid 185 through 191
      removed outlier: 6.301A  pdb=" N   VAL C  34 " --> pdb=" O   LYS C 197 " (cutoff:3.500A)
      removed outlier: 7.448A  pdb=" N   PHE C 199 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   LEU C  36 " --> pdb=" O   PHE C 199 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA C 220 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   ILE C 221 " --> pdb=" O   ILE C 265 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   PHE C 267 " --> pdb=" O   ILE C 221 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   PHE C 223 " --> pdb=" O   PHE C 267 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   ASN C 269 " --> pdb=" O   PHE C 223 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   VAL C 225 " --> pdb=" O   ASN C 269 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.552A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.560A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.687A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.981A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.138A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.726A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.738A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.687A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 4 through 7
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.758A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12
    Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.823A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.823A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   THR S 226 " --> pdb=" O   GLN S 219 " (cutoff:3.500A)

    458 hydrogen bonds defined for protein.
    1260 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: 2.62

  Time building geometry restraints manager: 2.67 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2656
        1.34 -     1.46: 2304
        1.46 -     1.59: 3981
        1.59 -     1.71: 0
        1.71 -     1.84: 97
  Bond restraints: 9038
  Sorted by residual:
  bond pdb=" ND1 HIS A   9 "
       pdb=" CE1 HIS A   9 "
    ideal  model  delta    sigma   weight residual
    1.321  1.374 -0.053 1.00e-02 1.00e+04 2.83e+01
  bond pdb=" ND1 HIS A 259 "
       pdb=" CE1 HIS A 259 "
    ideal  model  delta    sigma   weight residual
    1.321  1.374 -0.053 1.00e-02 1.00e+04 2.78e+01
  bond pdb=" CG  ASN A  17 "
       pdb=" OD1 ASN A  17 "
    ideal  model  delta    sigma   weight residual
    1.231  1.329 -0.098 1.90e-02 2.77e+03 2.65e+01
  bond pdb=" ND1 HIS A 133 "
       pdb=" CE1 HIS A 133 "
    ideal  model  delta    sigma   weight residual
    1.321  1.372 -0.051 1.00e-02 1.00e+04 2.64e+01
  bond pdb=" CD2 HIS A 133 "
       pdb=" NE2 HIS A 133 "
    ideal  model  delta    sigma   weight residual
    1.374  1.320  0.054 1.10e-02 8.26e+03 2.37e+01
  ... (remaining 9033 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.90: 12206
        6.90 -    13.80: 22
       13.80 -    20.71: 7
       20.71 -    27.61: 5
       27.61 -    34.51: 2
  Bond angle restraints: 12242
  Sorted by residual:
  angle pdb=" N   TYR A 295 "
        pdb=" CA  TYR A 295 "
        pdb=" C   TYR A 295 "
      ideal   model   delta    sigma   weight residual
     111.69  146.20  -34.51 1.23e+00 6.61e-01 7.87e+02
  angle pdb=" N   THR C 324 "
        pdb=" CA  THR C 324 "
        pdb=" C   THR C 324 "
      ideal   model   delta    sigma   weight residual
     111.24  142.05  -30.81 1.29e+00 6.01e-01 5.70e+02
  angle pdb=" N   CYS C 325 "
        pdb=" CA  CYS C 325 "
        pdb=" C   CYS C 325 "
      ideal   model   delta    sigma   weight residual
     112.86  134.01  -21.15 1.22e+00 6.72e-01 3.01e+02
  angle pdb=" C   VAL C 201 "
        pdb=" CA  VAL C 201 "
        pdb=" CB  VAL C 201 "
      ideal   model   delta    sigma   weight residual
     111.81   91.92   19.89 1.37e+00 5.33e-01 2.11e+02
  angle pdb=" N   PHE A 296 "
        pdb=" CA  PHE A 296 "
        pdb=" CB  PHE A 296 "
      ideal   model   delta    sigma   weight residual
     110.33   89.57   20.76 1.50e+00 4.44e-01 1.91e+02
  ... (remaining 12237 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 4517
       17.82 -    35.64: 590
       35.64 -    53.47: 179
       53.47 -    71.29: 33
       71.29 -    89.11: 18
  Dihedral angle restraints: 5337
    sinusoidal: 2050
      harmonic: 3287
  Sorted by residual:
  dihedral pdb=" C   VAL C 201 "
           pdb=" N   VAL C 201 "
           pdb=" CA  VAL C 201 "
           pdb=" CB  VAL C 201 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00  -90.73  -31.27     0      2.50e+00 1.60e-01 1.56e+02
  dihedral pdb=" N   PHE A 296 "
           pdb=" C   PHE A 296 "
           pdb=" CA  PHE A 296 "
           pdb=" CB  PHE A 296 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80   95.32   27.48     0      2.50e+00 1.60e-01 1.21e+02
  dihedral pdb=" C   CYS C 325 "
           pdb=" N   CYS C 325 "
           pdb=" CA  CYS C 325 "
           pdb=" CB  CYS C 325 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -143.50   20.90     0      2.50e+00 1.60e-01 6.99e+01
  ... (remaining 5334 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.260: 1375
       0.260 -    0.519: 5
       0.519 -    0.778: 2
       0.778 -    1.038: 0
       1.038 -    1.297: 4
  Chirality restraints: 1386
  Sorted by residual:
  chirality pdb=" CA  TYR A 295 "
            pdb=" N   TYR A 295 "
            pdb=" C   TYR A 295 "
            pdb=" CB  TYR A 295 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.21    1.30 2.00e-01 2.50e+01 4.21e+01
  chirality pdb=" CA  ARG A 270 "
            pdb=" N   ARG A 270 "
            pdb=" C   ARG A 270 "
            pdb=" CB  ARG A 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.38    1.13 2.00e-01 2.50e+01 3.21e+01
  chirality pdb=" CA  CYS C 325 "
            pdb=" N   CYS C 325 "
            pdb=" C   CYS C 325 "
            pdb=" CB  CYS C 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.43    1.08 2.00e-01 2.50e+01 2.94e+01
  ... (remaining 1383 not shown)

  Planarity restraints: 1548
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 284 "    0.111 2.00e-02 2.50e+03   6.51e-02 8.49e+01
        pdb=" CG  TYR A 284 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 284 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 284 "   -0.059 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 284 "   -0.053 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 284 "   -0.040 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 284 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR A 284 "    0.108 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  91 "   -0.099 2.00e-02 2.50e+03   5.25e-02 6.89e+01
        pdb=" CG  TRP A  91 "    0.004 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  91 "    0.069 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  91 "    0.025 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  91 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  91 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  91 "    0.066 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  91 "   -0.059 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  91 "    0.040 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  91 "   -0.050 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  87 "    0.062 2.00e-02 2.50e+03   3.17e-02 2.01e+01
        pdb=" CG  TYR A  87 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  87 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  87 "   -0.031 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  87 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  87 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  87 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A  87 "    0.035 2.00e-02 2.50e+03
  ... (remaining 1545 not shown)

  Histogram of nonbonded interaction distances:
        1.79 -     2.41: 51
        2.41 -     3.04: 5361
        3.04 -     3.66: 13377
        3.66 -     4.28: 21213
        4.28 -     4.90: 35863
  Nonbonded interactions: 75865
  Sorted by model distance:
  nonbonded pdb=" O   THR C 324 "
            pdb=" CG2 THR C 327 "
     model   vdw
     1.793 3.460
  nonbonded pdb=" O   ARG A 270 "
            pdb=" NH1 ARG A 270 "
     model   vdw
     1.900 3.120
  nonbonded pdb=" O   VAL C 201 "
            pdb=" CG2 VAL C 201 "
     model   vdw
     1.912 3.460
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.046 3.040
  nonbonded pdb=" OG  SER A 298 "
            pdb=" O   GLY C 352 "
     model   vdw
     2.049 3.040
  ... (remaining 75860 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=1.00 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:             26.130
  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:          0.390
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.640
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:11.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   61.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
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      :  0.005   0.098   9043  Z= 0.279
  Angle     :  1.105  34.511  12252  Z= 0.714
  Chirality :  0.084   1.297   1386
  Planarity :  0.005   0.065   1548
  Dihedral  : 18.233  89.108   3198
  Min Nonbonded Distance : 1.793

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.83 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 27.37 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.94 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.26), residues: 1118
  helix:  1.55 (0.27), residues: 376
  sheet: -0.03 (0.30), residues: 281
  loop : -1.06 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.099   0.003   TRP A  91 
 HIS   0.010   0.001   HIS A 189 
 PHE   0.023   0.002   PHE A 276 
 TYR   0.111   0.003   TYR A 284 
 ARG   0.008   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12506 (  444)
  hydrogen bonds       : angle       6.40692 ( 1260)
  SS BOND              : bond        0.00421 (    5)
  SS BOND              : angle       1.50365 (   10)
  covalent geometry    : bond        0.00466 ( 9038)
  covalent geometry    : angle       1.10463 (12242)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 141
  time to evaluate  : 1.316 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: A   38 PHE cc_start: 0.6715 (t80) cc_final: 0.6493 (t80)
REVERT: A   79 CYS cc_start: 0.7974 (m) cc_final: 0.7618 (m)
REVERT: A  156 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7274 (mm)
REVERT: A  258 LEU cc_start: 0.7171 (pp) cc_final: 0.6332 (mt)
REVERT: C  309 ASP cc_start: 0.8273 (m-30) cc_final: 0.7952 (m-30)
REVERT: B   46 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7630 (mpt180)
  outliers start: 51
  outliers final: 43
  residues processed: 185
  average time/residue: 1.3250
  time to fit residues: 261.2171
Evaluate side-chains
  172 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 128
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  140 SER
Chi-restraints excluded: chain A residue  148 SER
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  217 GLN
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  283 LEU
Chi-restraints excluded: chain C residue  325 CYS
Chi-restraints excluded: chain C residue  354 PHE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue    8 SER
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain G residue   63 GLU
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   72 ARG
Chi-restraints excluded: chain S residue   85 SER
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  138 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  144 SER
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  202 LEU
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  231 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.6980
   chunk 84 optimal weight:    6.9990
   chunk 46 optimal weight:    0.0030
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   chunk 44 optimal weight:    0.2980
   chunk 87 optimal weight:    0.3980
   chunk 33 optimal weight:    3.9990
   chunk 52 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    0.4190

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

Flipped N/Q/H residues before XYZ refinement:
A   9 HIS
A  86 ASN
C 188 HIS
G  59 ASN
S  77 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.149178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.103934 restraints weight = 10395.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.32
r_work: 0.3055 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.0963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9043  Z= 0.123
  Angle     :  0.557   6.521  12252  Z= 0.294
  Chirality :  0.042   0.183   1386
  Planarity :  0.004   0.045   1548
  Dihedral  :  7.777  59.317   1291
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 25.47 %
    Favored  : 69.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    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:  0.33 (0.26), residues: 1118
  helix:  1.81 (0.27), residues: 385
  sheet:  0.08 (0.30), residues: 286
  loop : -1.09 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.002   0.001   HIS A 259 
 PHE   0.020   0.001   PHE A  38 
 TYR   0.017   0.001   TYR S 178 
 ARG   0.006   0.000   ARG S 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03941 (  444)
  hydrogen bonds       : angle       4.76610 ( 1260)
  SS BOND              : bond        0.00343 (    5)
  SS BOND              : angle       0.77603 (   10)
  covalent geometry    : bond        0.00258 ( 9038)
  covalent geometry    : angle       0.55671 (12242)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 140
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   79 CYS cc_start: 0.7876 (m) cc_final: 0.7653 (m)
REVERT: A   80 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6827 (mm)
REVERT: A  106 MET cc_start: 0.7460 (mmm) cc_final: 0.7188 (mmm)
REVERT: A  110 ASN cc_start: 0.8013 (m-40) cc_final: 0.7205 (m-40)
REVERT: A  150 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8068 (tt)
REVERT: B   46 ARG cc_start: 0.8437 (mtp-110) cc_final: 0.7921 (mpt180)
REVERT: B  268 ASN cc_start: 0.8163 (t0) cc_final: 0.7764 (t0)
REVERT: S  135 VAL cc_start: 0.7888 (OUTLIER) cc_final: 0.7686 (m)
  outliers start: 52
  outliers final: 20
  residues processed: 177
  average time/residue: 1.2909
  time to fit residues: 243.3454
Evaluate side-chains
  148 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  269 ASN
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain C residue  295 THR
Chi-restraints excluded: chain C residue  354 PHE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  138 THR
Chi-restraints excluded: chain S residue  203 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 44 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0020
   chunk 87 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 51 optimal weight:   10.0000
   chunk 81 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0770
   chunk 70 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    1.1950

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

Flipped N/Q/H residues before XYZ refinement:
A 133 HIS
C 188 HIS
B  75 GLN
** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.146344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.100642 restraints weight = 10575.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 2.33
r_work: 0.3004 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9043  Z= 0.179
  Angle     :  0.583   6.721  12252  Z= 0.303
  Chirality :  0.044   0.168   1386
  Planarity :  0.004   0.046   1548
  Dihedral  :  6.339  56.380   1241
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 24.84 %
    Favored  : 69.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    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:  0.33 (0.26), residues: 1118
  helix:  1.83 (0.27), residues: 386
  sheet:  0.11 (0.30), residues: 287
  loop : -1.14 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.015   0.001   PHE C 189 
 TYR   0.014   0.001   TYR S 178 
 ARG   0.005   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04143 (  444)
  hydrogen bonds       : angle       4.71272 ( 1260)
  SS BOND              : bond        0.00338 (    5)
  SS BOND              : angle       0.92492 (   10)
  covalent geometry    : bond        0.00415 ( 9038)
  covalent geometry    : angle       0.58219 (12242)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 130
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.7422 (tttt) cc_final: 0.7009 (mtpm)
REVERT: A   34 LEU cc_start: 0.5551 (OUTLIER) cc_final: 0.5253 (OUTLIER)
REVERT: A   79 CYS cc_start: 0.7988 (m) cc_final: 0.7693 (m)
REVERT: A   80 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6865 (mm)
REVERT: A   97 ASP cc_start: 0.5900 (OUTLIER) cc_final: 0.5451 (t0)
REVERT: A  112 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7504 (tt0)
REVERT: A  257 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6583 (mp)
REVERT: B  227 SER cc_start: 0.9304 (t) cc_final: 0.9069 (t)
REVERT: B  268 ASN cc_start: 0.8171 (t0) cc_final: 0.7770 (t0)
REVERT: S  135 VAL cc_start: 0.7849 (OUTLIER) cc_final: 0.7644 (m)
  outliers start: 58
  outliers final: 24
  residues processed: 169
  average time/residue: 1.2186
  time to fit residues: 219.4593
Evaluate side-chains
  163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 134
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  112 GLN
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  247 MET
Chi-restraints excluded: chain C residue  269 ASN
Chi-restraints excluded: chain C residue  295 THR
Chi-restraints excluded: chain C residue  354 PHE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  203 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 104 optimal weight:    0.1980
   chunk 107 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 188 HIS
B  32 GLN
S  77 ASN
** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.146318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.100712 restraints weight = 10415.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.33
r_work: 0.3002 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.1212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9043  Z= 0.179
  Angle     :  0.584   7.497  12252  Z= 0.303
  Chirality :  0.044   0.177   1386
  Planarity :  0.004   0.042   1548
  Dihedral  :  6.041  55.513   1237
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 25.37 %
    Favored  : 68.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.26), residues: 1118
  helix:  1.83 (0.27), residues: 385
  sheet:  0.09 (0.31), residues: 287
  loop : -1.16 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.020   0.001   PHE A  38 
 TYR   0.019   0.001   TYR A 269 
 ARG   0.005   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04041 (  444)
  hydrogen bonds       : angle       4.67253 ( 1260)
  SS BOND              : bond        0.00413 (    5)
  SS BOND              : angle       1.00726 (   10)
  covalent geometry    : bond        0.00418 ( 9038)
  covalent geometry    : angle       0.58342 (12242)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 137
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.7392 (tttt) cc_final: 0.7064 (mtpm)
REVERT: A   80 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6912 (mm)
REVERT: A  112 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7563 (tt0)
REVERT: A  257 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6567 (mp)
REVERT: C  309 ASP cc_start: 0.8476 (m-30) cc_final: 0.8196 (m-30)
REVERT: B   70 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9067 (pp)
REVERT: B  227 SER cc_start: 0.9303 (t) cc_final: 0.9056 (t)
REVERT: B  268 ASN cc_start: 0.8172 (t0) cc_final: 0.7781 (t0)
REVERT: S  135 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7644 (m)
  outliers start: 55
  outliers final: 26
  residues processed: 175
  average time/residue: 1.3612
  time to fit residues: 254.5991
Evaluate side-chains
  164 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 133
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  112 GLN
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  269 ASN
Chi-restraints excluded: chain C residue  295 THR
Chi-restraints excluded: chain C residue  354 PHE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  203 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 81 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 108 optimal weight:    0.6980
   chunk 99 optimal weight:    1.9990
   chunk 85 optimal weight:    9.9990
   chunk 17 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 94 optimal weight:    0.1980
   chunk 95 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 188 HIS
B  32 GLN
** S 130 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 = 0.3740 r_free = 0.3740 target = 0.148160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.102838 restraints weight = 10519.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.34
r_work: 0.3031 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9043  Z= 0.134
  Angle     :  0.555   8.053  12252  Z= 0.287
  Chirality :  0.042   0.148   1386
  Planarity :  0.004   0.039   1548
  Dihedral  :  5.676  55.896   1235
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 26.95 %
    Favored  : 67.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.26), residues: 1118
  helix:  1.88 (0.27), residues: 385
  sheet:  0.14 (0.31), residues: 286
  loop : -1.13 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.002   0.000   HIS B 142 
 PHE   0.014   0.001   PHE C 189 
 TYR   0.015   0.001   TYR S 178 
 ARG   0.007   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03686 (  444)
  hydrogen bonds       : angle       4.52150 ( 1260)
  SS BOND              : bond        0.00283 (    5)
  SS BOND              : angle       0.87760 (   10)
  covalent geometry    : bond        0.00303 ( 9038)
  covalent geometry    : angle       0.55426 (12242)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 144
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.7403 (tttt) cc_final: 0.7095 (mtpm)
REVERT: A   34 LEU cc_start: 0.5213 (OUTLIER) cc_final: 0.4899 (OUTLIER)
REVERT: A   80 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6814 (mm)
REVERT: A  112 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7509 (tt0)
REVERT: A  257 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6514 (mp)
REVERT: A  258 LEU cc_start: 0.7010 (pp) cc_final: 0.6142 (mm)
REVERT: C  209 LYS cc_start: 0.8774 (pttm) cc_final: 0.8304 (ptpp)
REVERT: C  309 ASP cc_start: 0.8497 (m-30) cc_final: 0.8225 (m-30)
REVERT: B  268 ASN cc_start: 0.8146 (t0) cc_final: 0.7762 (t0)
REVERT: G   21 MET cc_start: 0.7567 (tpp) cc_final: 0.7301 (tpp)
REVERT: S  135 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7689 (m)
  outliers start: 50
  outliers final: 18
  residues processed: 176
  average time/residue: 1.2363
  time to fit residues: 232.0488
Evaluate side-chains
  159 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  112 GLN
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  295 THR
Chi-restraints excluded: chain C residue  354 PHE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  203 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 91 optimal weight:    0.2980
   chunk 96 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0030
   chunk 103 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
** S 130 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 = 0.3744 r_free = 0.3744 target = 0.148604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.103234 restraints weight = 10385.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.32
r_work: 0.3044 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9043  Z= 0.130
  Angle     :  0.561   9.120  12252  Z= 0.288
  Chirality :  0.042   0.143   1386
  Planarity :  0.004   0.038   1548
  Dihedral  :  5.318  56.990   1233
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 27.05 %
    Favored  : 68.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.26), residues: 1118
  helix:  1.94 (0.27), residues: 385
  sheet:  0.12 (0.31), residues: 286
  loop : -1.11 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.002   0.000   HIS S  35 
 PHE   0.020   0.001   PHE A  38 
 TYR   0.014   0.001   TYR S 178 
 ARG   0.006   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03626 (  444)
  hydrogen bonds       : angle       4.43374 ( 1260)
  SS BOND              : bond        0.00339 (    5)
  SS BOND              : angle       0.85438 (   10)
  covalent geometry    : bond        0.00295 ( 9038)
  covalent geometry    : angle       0.56054 (12242)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 139
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
REVERT: A   28 LYS cc_start: 0.7424 (tttt) cc_final: 0.7114 (mtpm)
REVERT: A   34 LEU cc_start: 0.5053 (OUTLIER) cc_final: 0.4668 (mp)
REVERT: A   80 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6764 (mm)
REVERT: A   94 LYS cc_start: 0.7078 (pptt) cc_final: 0.6009 (mmmt)
REVERT: A  112 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7511 (tt0)
REVERT: A  257 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6546 (mp)
REVERT: A  258 LEU cc_start: 0.7075 (pp) cc_final: 0.6208 (mm)
REVERT: C  209 LYS cc_start: 0.8731 (pttm) cc_final: 0.8244 (ptpp)
REVERT: C  309 ASP cc_start: 0.8476 (m-30) cc_final: 0.8217 (m-30)
REVERT: B  268 ASN cc_start: 0.8183 (t0) cc_final: 0.7777 (t0)
REVERT: G   21 MET cc_start: 0.7605 (tpp) cc_final: 0.7351 (tpp)
REVERT: S  135 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7695 (m)
  outliers start: 47
  outliers final: 23
  residues processed: 169
  average time/residue: 1.2136
  time to fit residues: 218.5950
Evaluate side-chains
  157 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 129
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  112 GLN
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  217 GLN
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  295 THR
Chi-restraints excluded: chain C residue  354 PHE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  203 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 106 optimal weight:    0.2980
   chunk 107 optimal weight:    0.6980
   chunk 80 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 188 HIS
C 269 ASN
B  32 GLN
** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.147589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.102017 restraints weight = 10445.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 2.33
r_work: 0.3022 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9043  Z= 0.155
  Angle     :  0.585   9.565  12252  Z= 0.299
  Chirality :  0.043   0.164   1386
  Planarity :  0.004   0.041   1548
  Dihedral  :  5.057  45.361   1229
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 27.47 %
    Favored  : 68.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.26), residues: 1118
  helix:  1.83 (0.27), residues: 391
  sheet:  0.07 (0.31), residues: 287
  loop : -1.13 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.015   0.001   PHE C 189 
 TYR   0.013   0.001   TYR S 178 
 ARG   0.007   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03802 (  444)
  hydrogen bonds       : angle       4.48365 ( 1260)
  SS BOND              : bond        0.00277 (    5)
  SS BOND              : angle       0.91780 (   10)
  covalent geometry    : bond        0.00361 ( 9038)
  covalent geometry    : angle       0.58460 (12242)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 136
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
REVERT: A   28 LYS cc_start: 0.7405 (tttt) cc_final: 0.7125 (mtpm)
REVERT: A   80 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6899 (mm)
REVERT: A   94 LYS cc_start: 0.7073 (pptt) cc_final: 0.6073 (mmmt)
REVERT: A  112 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7546 (tt0)
REVERT: A  232 PHE cc_start: 0.7272 (m-80) cc_final: 0.6966 (m-10)
REVERT: A  257 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6543 (mp)
REVERT: A  258 LEU cc_start: 0.6983 (pp) cc_final: 0.6113 (mm)
REVERT: C  209 LYS cc_start: 0.8708 (pttm) cc_final: 0.8226 (ptpp)
REVERT: B  268 ASN cc_start: 0.8182 (t0) cc_final: 0.7814 (t0)
REVERT: G   21 MET cc_start: 0.7605 (tpp) cc_final: 0.7367 (tpp)
REVERT: S  135 VAL cc_start: 0.7901 (OUTLIER) cc_final: 0.7697 (m)
  outliers start: 42
  outliers final: 27
  residues processed: 163
  average time/residue: 1.3043
  time to fit residues: 227.2721
Evaluate side-chains
  163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  112 GLN
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  217 GLN
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  269 ASN
Chi-restraints excluded: chain C residue  295 THR
Chi-restraints excluded: chain C residue  354 PHE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  203 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 101 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 84 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 49 optimal weight:    0.5980
   chunk 110 optimal weight:    3.9990
   chunk 93 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 188 HIS
C 269 ASN
** S 130 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 = 0.3735 r_free = 0.3735 target = 0.147744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.102187 restraints weight = 10590.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 2.35
r_work: 0.3027 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9043  Z= 0.147
  Angle     :  0.575   9.080  12252  Z= 0.295
  Chirality :  0.043   0.167   1386
  Planarity :  0.004   0.038   1548
  Dihedral  :  4.974  41.389   1229
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 27.68 %
    Favored  : 68.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.26), residues: 1118
  helix:  1.82 (0.27), residues: 390
  sheet:  0.09 (0.30), residues: 285
  loop : -1.09 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.002   0.000   HIS S  35 
 PHE   0.015   0.001   PHE C 189 
 TYR   0.014   0.001   TYR S 178 
 ARG   0.007   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03763 (  444)
  hydrogen bonds       : angle       4.46807 ( 1260)
  SS BOND              : bond        0.00356 (    5)
  SS BOND              : angle       0.93187 (   10)
  covalent geometry    : bond        0.00338 ( 9038)
  covalent geometry    : angle       0.57507 (12242)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 133
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
REVERT: A   28 LYS cc_start: 0.7375 (tttt) cc_final: 0.7125 (mtpm)
REVERT: A   34 LEU cc_start: 0.5016 (OUTLIER) cc_final: 0.4655 (mp)
REVERT: A   80 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6933 (mm)
REVERT: A   94 LYS cc_start: 0.7132 (pptt) cc_final: 0.6160 (mmmt)
REVERT: A  112 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7527 (tt0)
REVERT: A  232 PHE cc_start: 0.7227 (m-80) cc_final: 0.6912 (m-10)
REVERT: A  257 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6528 (mp)
REVERT: A  258 LEU cc_start: 0.6946 (pp) cc_final: 0.6081 (mm)
REVERT: C  209 LYS cc_start: 0.8705 (pttm) cc_final: 0.8219 (ptpp)
REVERT: B  268 ASN cc_start: 0.8184 (t0) cc_final: 0.7789 (t0)
REVERT: G   21 MET cc_start: 0.7559 (tpp) cc_final: 0.7325 (tpp)
REVERT: S  135 VAL cc_start: 0.7905 (OUTLIER) cc_final: 0.7701 (m)
  outliers start: 40
  outliers final: 24
  residues processed: 160
  average time/residue: 1.2400
  time to fit residues: 211.8634
Evaluate side-chains
  158 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  112 GLN
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  217 GLN
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  252 SER
Chi-restraints excluded: chain C residue  269 ASN
Chi-restraints excluded: chain C residue  295 THR
Chi-restraints excluded: chain C residue  354 PHE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  203 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 103 optimal weight:    0.0270
   chunk 39 optimal weight:    0.4980
   chunk 48 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 72 optimal weight:    0.6980
   chunk 84 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 43 optimal weight:    6.9990
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 188 HIS
C 269 ASN
** S 130 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 = 0.3749 r_free = 0.3749 target = 0.149059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.103690 restraints weight = 10444.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 2.34
r_work: 0.3050 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9043  Z= 0.127
  Angle     :  0.588  10.731  12252  Z= 0.297
  Chirality :  0.042   0.201   1386
  Planarity :  0.004   0.037   1548
  Dihedral  :  4.837  40.190   1229
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 28.63 %
    Favored  : 68.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.26), residues: 1118
  helix:  1.97 (0.27), residues: 384
  sheet:  0.17 (0.31), residues: 280
  loop : -1.10 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.002   0.000   HIS S  35 
 PHE   0.019   0.001   PHE A  38 
 TYR   0.016   0.001   TYR S 178 
 ARG   0.008   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03611 (  444)
  hydrogen bonds       : angle       4.40367 ( 1260)
  SS BOND              : bond        0.00312 (    5)
  SS BOND              : angle       0.88198 (   10)
  covalent geometry    : bond        0.00288 ( 9038)
  covalent geometry    : angle       0.58761 (12242)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 1.063 
Fit side-chains
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
REVERT: A   28 LYS cc_start: 0.7305 (tttt) cc_final: 0.7088 (mtpm)
REVERT: A   34 LEU cc_start: 0.4986 (OUTLIER) cc_final: 0.4607 (mp)
REVERT: A   80 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6879 (mm)
REVERT: A   94 LYS cc_start: 0.7010 (pptt) cc_final: 0.6050 (mmmt)
REVERT: A  112 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7492 (tt0)
REVERT: A  232 PHE cc_start: 0.7211 (m-80) cc_final: 0.6906 (m-10)
REVERT: A  257 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6549 (mp)
REVERT: A  258 LEU cc_start: 0.6846 (pp) cc_final: 0.6052 (mm)
REVERT: C  209 LYS cc_start: 0.8674 (pttm) cc_final: 0.8174 (ptpp)
REVERT: B  268 ASN cc_start: 0.8187 (t0) cc_final: 0.7787 (t0)
REVERT: G   21 MET cc_start: 0.7553 (tpp) cc_final: 0.7325 (tpp)
  outliers start: 30
  outliers final: 17
  residues processed: 149
  average time/residue: 1.3333
  time to fit residues: 212.0467
Evaluate side-chains
  149 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  112 GLN
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  354 PHE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain S residue   11 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 104 optimal weight:    0.0570
   chunk 61 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 108 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.7300

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

Flipped N/Q/H residues before XYZ refinement:
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 188 HIS
** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 174 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.148535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.103169 restraints weight = 10454.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 2.33
r_work: 0.3042 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.1633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9043  Z= 0.139
  Angle     :  0.607  11.113  12252  Z= 0.303
  Chirality :  0.043   0.235   1386
  Planarity :  0.004   0.038   1548
  Dihedral  :  4.729  39.861   1228
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 29.05 %
    Favored  : 67.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.26), residues: 1118
  helix:  1.89 (0.27), residues: 386
  sheet:  0.17 (0.31), residues: 280
  loop : -1.08 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.002   0.000   HIS S  35 
 PHE   0.015   0.001   PHE C 189 
 TYR   0.015   0.001   TYR S 178 
 ARG   0.007   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03668 (  444)
  hydrogen bonds       : angle       4.41931 ( 1260)
  SS BOND              : bond        0.00334 (    5)
  SS BOND              : angle       0.88492 (   10)
  covalent geometry    : bond        0.00320 ( 9038)
  covalent geometry    : angle       0.60649 (12242)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 1.007 
Fit side-chains
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
REVERT: A   34 LEU cc_start: 0.4923 (OUTLIER) cc_final: 0.4625 (mp)
REVERT: A   80 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6914 (mm)
REVERT: A   94 LYS cc_start: 0.6971 (pptt) cc_final: 0.6011 (mmmt)
REVERT: A  112 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7462 (tt0)
REVERT: A  232 PHE cc_start: 0.7153 (m-80) cc_final: 0.6856 (m-10)
REVERT: A  257 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6525 (mp)
REVERT: A  258 LEU cc_start: 0.6832 (pp) cc_final: 0.6035 (mm)
REVERT: C  209 LYS cc_start: 0.8676 (pttm) cc_final: 0.8181 (ptpp)
REVERT: B  268 ASN cc_start: 0.8186 (t0) cc_final: 0.7786 (t0)
REVERT: G   21 MET cc_start: 0.7562 (tpp) cc_final: 0.7337 (tpp)
REVERT: S  135 VAL cc_start: 0.7637 (m) cc_final: 0.7367 (p)
  outliers start: 29
  outliers final: 21
  residues processed: 148
  average time/residue: 1.2345
  time to fit residues: 194.8883
Evaluate side-chains
  154 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  112 GLN
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  252 SER
Chi-restraints excluded: chain C residue  295 THR
Chi-restraints excluded: chain C residue  354 PHE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  185 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 92 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.3188

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

Flipped N/Q/H residues before XYZ refinement:
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 188 HIS
C 269 ASN
** S 130 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 = 0.3720 r_free = 0.3720 target = 0.146395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.100667 restraints weight = 10502.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.33
r_work: 0.3003 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2863 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9043  Z= 0.195
  Angle     :  0.644  10.961  12252  Z= 0.323
  Chirality :  0.045   0.232   1386
  Planarity :  0.004   0.039   1548
  Dihedral  :  4.914  40.948   1228
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 29.26 %
    Favored  : 67.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.26), residues: 1118
  helix:  1.74 (0.27), residues: 390
  sheet:  0.05 (0.31), residues: 287
  loop : -1.10 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.016   0.001   PHE C 189 
 TYR   0.014   0.001   TYR A 284 
 ARG   0.008   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04036 (  444)
  hydrogen bonds       : angle       4.57519 ( 1260)
  SS BOND              : bond        0.00386 (    5)
  SS BOND              : angle       1.02221 (   10)
  covalent geometry    : bond        0.00461 ( 9038)
  covalent geometry    : angle       0.64381 (12242)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8687.62 seconds
wall clock time: 150 minutes 31.12 seconds (9031.12 seconds total)