Starting phenix.real_space_refine
on Tue Mar 11 14:30:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6g79_4358/03_2025/6g79_4358.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6g79_4358/03_2025/6g79_4358.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6g79_4358/03_2025/6g79_4358.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6g79_4358/03_2025/6g79_4358.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6g79_4358/03_2025/6g79_4358.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6g79_4358/03_2025/6g79_4358.cif"
  }
  resolution = 3.78
  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=   0.002 sd=   0.016
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      34      5.16       5
     C    3922      2.51       5
     N    1021      2.21       5
     O    1076      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6053
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2270
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2270
          Classifications: {'peptide': 333}
          Incomplete info: {'truncation_to_alanine': 75}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 291
          Unresolved non-hydrogen angles: 359
          Unresolved non-hydrogen dihedrals: 225
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 7, 'ASP:plan': 23, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 14}
          Unresolved non-hydrogen planarities: 226
    Chain: "G"
      Number of atoms: 342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 342
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 103
          Unresolved non-hydrogen dihedrals: 71
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 43
    Chain: "A"
      Number of atoms: 1448
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1448
          Classifications: {'peptide': 209}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 204}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 214
          Unresolved non-hydrogen angles: 257
          Unresolved non-hydrogen dihedrals: 175
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 6, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 130
    Chain: "S"
      Number of atoms: 1963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 1963
          Classifications: {'peptide': 262}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 10, 'TRANS': 251}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 151
          Unresolved non-hydrogen angles: 188
          Unresolved non-hydrogen dihedrals: 127
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 81
    Chain: "S"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'EP5': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.50, per 1000 atoms: 0.74
  Number of scatterers: 6053
  At special positions: 0
  Unit cell: (94.34, 109.18, 97.52, 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      34     16.00
     O    1076      8.00
     N    1021      7.00
     C    3922      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 122 " - pdb=" SG  CYS S 199 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.43
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1634

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 8 sheets defined
      48.8% alpha, 16.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.600A  pdb=" N   SER A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ASP A  33 " --> pdb=" O   SER A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.819A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 214
      removed outlier: 4.325A  pdb=" N   TRP A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ILE A 213 " --> pdb=" O   ARG A 209 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 208 through 214'
    Processing helix  chain 'A' and resid 215 through 217
      No H-bonds generated for 'chain 'A' and resid 215 through 217'
    Processing helix  chain 'A' and resid 230 through 256
      removed outlier: 3.593A  pdb=" N   LEU A 248 " --> pdb=" O   MET A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 263
      removed outlier: 4.062A  pdb=" N   ASP A 262 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 3.717A  pdb=" N   GLU A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   LYS A 280 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   LYS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 311
    Processing helix  chain 'A' and resid 331 through 352
    Processing helix  chain 'S' and resid 46 through 77
    Processing helix  chain 'S' and resid 82 through 102
      removed outlier: 3.846A  pdb=" N   LEU S  87 " --> pdb=" O   PRO S  83 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ILE S  88 " --> pdb=" O   ALA S  84 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 102 through 113
      removed outlier: 3.967A  pdb=" N   MET S 108 " --> pdb=" O   PRO S 104 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 117 through 153
      removed outlier: 4.250A  pdb=" N   VAL S 121 " --> pdb=" O   LEU S 117 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   SER S 127 " --> pdb=" O   ASP S 123 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU S 140 " --> pdb=" O   SER S 136 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   CYS S 141 " --> pdb=" O   ILE S 137 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 154 through 161
      removed outlier: 4.201A  pdb=" N   ALA S 159 " --> pdb=" O   VAL S 155 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LYS S 160 " --> pdb=" O   GLU S 156 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 162 through 182
    Processing helix  chain 'S' and resid 205 through 216
    Processing helix  chain 'S' and resid 217 through 240
    Processing helix  chain 'S' and resid 306 through 337
      removed outlier: 3.808A  pdb=" N   PHE S 323 " --> pdb=" O   ILE S 319 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   CYS S 326 " --> pdb=" O   ALA S 322 " (cutoff:3.500A)
      Proline residue:  S 329  - end of helix
      removed outlier: 3.807A  pdb=" N   LEU S 335 " --> pdb=" O   PHE S 331 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 348 through 373
      removed outlier: 3.628A  pdb=" N   TRP S 356 " --> pdb=" O   ASP S 352 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   SER S 362 " --> pdb=" O   GLY S 358 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LEU S 363 " --> pdb=" O   TYR S 359 " (cutoff:3.500A)
      Proline residue:  S 366  - end of helix
      removed outlier: 4.027A  pdb=" N   ASN S 373 " --> pdb=" O   TYR S 369 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 373 through 384
      removed outlier: 3.607A  pdb=" N   HIS S 381 " --> pdb=" O   LYS S 377 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.585A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.963A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.500A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.043A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.697A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 233 through 234
      removed outlier: 3.627A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.336A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 197 through 200
      removed outlier: 3.859A  pdb=" N   ALA A 221 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)

    368 hydrogen bonds defined for protein.
    1080 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.92

  Time building geometry restraints manager: 1.68 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 943
        1.29 -     1.42: 1667
        1.42 -     1.55: 3482
        1.55 -     1.68: 53
        1.68 -     1.81: 42
  Bond restraints: 6187
  Sorted by residual:
  bond pdb=" C10 EP5 S 401 "
       pdb=" C7  EP5 S 401 "
    ideal  model  delta    sigma   weight residual
    1.421  1.284  0.137 2.00e-02 2.50e+03 4.66e+01
  bond pdb=" C15 EP5 S 401 "
       pdb=" C16 EP5 S 401 "
    ideal  model  delta    sigma   weight residual
    1.412  1.476 -0.064 2.00e-02 2.50e+03 1.04e+01
  bond pdb=" N   TYR A 231 "
       pdb=" CA  TYR A 231 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.29e-02 6.01e+03 7.64e+00
  bond pdb=" CA  PRO S 183 "
       pdb=" C   PRO S 183 "
    ideal  model  delta    sigma   weight residual
    1.517  1.542 -0.025 9.30e-03 1.16e+04 7.21e+00
  bond pdb=" C15 EP5 S 401 "
       pdb=" C20 EP5 S 401 "
    ideal  model  delta    sigma   weight residual
    1.432  1.480 -0.048 2.00e-02 2.50e+03 5.74e+00
  ... (remaining 6182 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 7410
        1.70 -     3.40: 990
        3.40 -     5.10: 73
        5.10 -     6.80: 15
        6.80 -     8.49: 3
  Bond angle restraints: 8491
  Sorted by residual:
  angle pdb=" N   TYR A 231 "
        pdb=" CA  TYR A 231 "
        pdb=" C   TYR A 231 "
      ideal   model   delta    sigma   weight residual
     112.90  119.49   -6.59 1.31e+00 5.83e-01 2.53e+01
  angle pdb=" N   PRO S 183 "
        pdb=" CA  PRO S 183 "
        pdb=" C   PRO S 183 "
      ideal   model   delta    sigma   weight residual
     110.70  116.78   -6.08 1.22e+00 6.72e-01 2.48e+01
  angle pdb=" CA  TYR A 231 "
        pdb=" CB  TYR A 231 "
        pdb=" CG  TYR A 231 "
      ideal   model   delta    sigma   weight residual
     113.90  105.57    8.33 1.80e+00 3.09e-01 2.14e+01
  angle pdb=" N   ILE A 213 "
        pdb=" CA  ILE A 213 "
        pdb=" C   ILE A 213 "
      ideal   model   delta    sigma   weight residual
     110.72  115.01   -4.29 1.01e+00 9.80e-01 1.81e+01
  angle pdb=" N   ASN A 242 "
        pdb=" CA  ASN A 242 "
        pdb=" C   ASN A 242 "
      ideal   model   delta    sigma   weight residual
     111.28  106.88    4.40 1.09e+00 8.42e-01 1.63e+01
  ... (remaining 8486 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.39: 3292
       16.39 -    32.77: 191
       32.77 -    49.15: 50
       49.15 -    65.54: 8
       65.54 -    81.92: 2
  Dihedral angle restraints: 3543
    sinusoidal: 1035
      harmonic: 2508
  Sorted by residual:
  dihedral pdb=" C   TYR A 231 "
           pdb=" N   TYR A 231 "
           pdb=" CA  TYR A 231 "
           pdb=" CB  TYR A 231 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.65    8.05     0      2.50e+00 1.60e-01 1.04e+01
  dihedral pdb=" CA  HIS S 347 "
           pdb=" C   HIS S 347 "
           pdb=" N   LEU S 348 "
           pdb=" CA  LEU S 348 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.47  -15.53     0      5.00e+00 4.00e-02 9.64e+00
  dihedral pdb=" CA  ARG S 308 "
           pdb=" CB  ARG S 308 "
           pdb=" CG  ARG S 308 "
           pdb=" CD  ARG S 308 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.25  -55.75     3      1.50e+01 4.44e-03 9.36e+00
  ... (remaining 3540 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 859
       0.075 -    0.150: 162
       0.150 -    0.225: 30
       0.225 -    0.300: 1
       0.300 -    0.375: 1
  Chirality restraints: 1053
  Sorted by residual:
  chirality pdb=" CA  TYR A 231 "
            pdb=" N   TYR A 231 "
            pdb=" C   TYR A 231 "
            pdb=" CB  TYR A 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.51e+00
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CA  ILE B 120 "
            pdb=" N   ILE B 120 "
            pdb=" C   ILE B 120 "
            pdb=" CB  ILE B 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 1050 not shown)

  Planarity restraints: 1051
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   EP5 S 401 "    0.004 2.00e-02 2.50e+03   9.37e-02 1.32e+02
        pdb=" O   EP5 S 401 "   -0.120 2.00e-02 2.50e+03
        pdb=" C1  EP5 S 401 "    0.117 2.00e-02 2.50e+03
        pdb=" C11 EP5 S 401 "   -0.007 2.00e-02 2.50e+03
        pdb=" C12 EP5 S 401 "    0.114 2.00e-02 2.50e+03
        pdb=" C2  EP5 S 401 "   -0.107 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 231 "    0.029 2.00e-02 2.50e+03   1.96e-02 7.68e+00
        pdb=" CG  TYR A 231 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 231 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 231 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 231 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 231 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 231 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 231 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE S 219 "    0.041 5.00e-02 4.00e+02   6.24e-02 6.23e+00
        pdb=" N   PRO S 220 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO S 220 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO S 220 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1048 not shown)

  Histogram of nonbonded interaction distances:
        2.44 -     2.93: 2390
        2.93 -     3.43: 6086
        3.43 -     3.92: 9935
        3.92 -     4.41: 11024
        4.41 -     4.90: 19046
  Nonbonded interactions: 48481
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 243 "
            pdb=" OG  SER A 247 "
     model   vdw
     2.442 3.040
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.553 3.040
  nonbonded pdb=" O   PRO S 366 "
            pdb=" OG1 THR S 370 "
     model   vdw
     2.559 3.040
  nonbonded pdb=" O   ASP B 195 "
            pdb=" OG1 THR B 196 "
     model   vdw
     2.561 3.040
  nonbonded pdb=" O   ILE S 130 "
            pdb=" OG1 THR S 134 "
     model   vdw
     2.564 3.040
  ... (remaining 48476 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.210
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.830
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.070
  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:3.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.137   6187  Z= 0.510
  Angle     :  1.153   8.494   8491  Z= 0.779
  Chirality :  0.060   0.375   1053
  Planarity :  0.005   0.094   1051
  Dihedral  : 12.120  81.922   1906
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 0.69
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.88 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  6.15 %
    Favored  : 93.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.95 (0.24), residues: 840
  helix: -0.61 (0.22), residues: 360
  sheet: -3.35 (0.27), residues: 164
  loop : -2.61 (0.32), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP S 149 
 HIS   0.006   0.001   HIS A 214 
 PHE   0.015   0.002   PHE A 190 
 TYR   0.046   0.002   TYR A 231 
 ARG   0.003   0.000   ARG A 313 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 189
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  188 MET cc_start: 0.7993 (mmm) cc_final: 0.7060 (mmm)
REVERT: B  323 ASP cc_start: 0.8728 (p0) cc_final: 0.8515 (p0)
REVERT: B  339 TRP cc_start: 0.8405 (m100) cc_final: 0.8087 (m100)
REVERT: G   18 GLN cc_start: 0.9014 (tp40) cc_final: 0.8552 (tp-100)
REVERT: A  244 MET cc_start: 0.8375 (tpp) cc_final: 0.7516 (mmt)
REVERT: A  305 GLN cc_start: 0.8798 (tt0) cc_final: 0.7820 (tm-30)
REVERT: A  312 ASN cc_start: 0.8860 (t0) cc_final: 0.8527 (t0)
REVERT: S  169 MET cc_start: 0.8507 (mmm) cc_final: 0.8016 (mmp)
REVERT: S  205 HIS cc_start: 0.7891 (m170) cc_final: 0.7681 (m-70)
REVERT: S  313 THR cc_start: 0.9124 (m) cc_final: 0.8916 (p)
  outliers start: 3
  outliers final: 1
  residues processed: 191
  average time/residue: 0.1444
  time to fit residues: 37.7238
Evaluate side-chains
  115 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  333 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    0.4980
   chunk 34 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   chunk 40 optimal weight:    4.9990
   chunk 49 optimal weight:    0.3980
   chunk 76 optimal weight:    5.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 230 ASN
B 295 ASN
G  18 GLN
A 307 GLN
S 202 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.127245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.107397 restraints weight = 11288.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.110447 restraints weight = 6394.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.112521 restraints weight = 4422.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6187  Z= 0.261
  Angle     :  0.652  16.367   8491  Z= 0.331
  Chirality :  0.043   0.225   1053
  Planarity :  0.005   0.075   1051
  Dihedral  :  6.215  78.696    906
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  1.79 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 14.53 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.28), residues: 840
  helix:  1.63 (0.25), residues: 369
  sheet: -2.64 (0.31), residues: 181
  loop : -2.14 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 214 
 PHE   0.012   0.002   PHE B 199 
 TYR   0.012   0.002   TYR B 264 
 ARG   0.005   0.001   ARG A  15 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 137
  time to evaluate  : 0.646 
Fit side-chains
REVERT: B  243 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8380 (p)
REVERT: B  253 PHE cc_start: 0.8184 (m-80) cc_final: 0.7952 (m-80)
REVERT: B  323 ASP cc_start: 0.8207 (p0) cc_final: 0.7970 (p0)
REVERT: B  339 TRP cc_start: 0.8649 (m100) cc_final: 0.8162 (m100)
REVERT: G   40 TYR cc_start: 0.8490 (t80) cc_final: 0.8276 (t80)
REVERT: A   25 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7770 (tp30)
REVERT: A  305 GLN cc_start: 0.8517 (tt0) cc_final: 0.7961 (tm-30)
REVERT: S   55 LEU cc_start: 0.9085 (tt) cc_final: 0.8846 (tp)
REVERT: S  367 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8468 (pt)
  outliers start: 23
  outliers final: 13
  residues processed: 153
  average time/residue: 0.1455
  time to fit residues: 30.4610
Evaluate side-chains
  129 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain S residue   93 VAL
Chi-restraints excluded: chain S residue   98 VAL
Chi-restraints excluded: chain S residue  179 SER
Chi-restraints excluded: chain S residue  209 THR
Chi-restraints excluded: chain S residue  213 THR
Chi-restraints excluded: chain S residue  231 ILE
Chi-restraints excluded: chain S residue  318 ILE
Chi-restraints excluded: chain S residue  320 LEU
Chi-restraints excluded: chain S residue  333 ILE
Chi-restraints excluded: chain S residue  367 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 78 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 59 optimal weight:    6.9990
   chunk 1 optimal weight:   50.0000
   chunk 53 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 45 optimal weight:   10.0000
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
G  18 GLN
S 202 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.127528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.108015 restraints weight = 11401.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.111072 restraints weight = 6343.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.113158 restraints weight = 4339.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6187  Z= 0.187
  Angle     :  0.590  16.255   8491  Z= 0.289
  Chirality :  0.040   0.158   1053
  Planarity :  0.005   0.076   1051
  Dihedral  :  5.767  76.856    906
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.74 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 18.44 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.29), residues: 840
  helix:  2.16 (0.25), residues: 376
  sheet: -1.91 (0.34), residues: 176
  loop : -1.94 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 214 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.013   0.002   TYR B 264 
 ARG   0.004   0.001   ARG S 238 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.621 
Fit side-chains
REVERT: B  339 TRP cc_start: 0.8723 (m100) cc_final: 0.8254 (m100)
REVERT: A  305 GLN cc_start: 0.8454 (tt0) cc_final: 0.7866 (tm-30)
REVERT: A  313 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6994 (ptt90)
REVERT: A  341 ASP cc_start: 0.8158 (t0) cc_final: 0.7897 (t0)
  outliers start: 20
  outliers final: 12
  residues processed: 135
  average time/residue: 0.1406
  time to fit residues: 26.1645
Evaluate side-chains
  115 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain S residue   93 VAL
Chi-restraints excluded: chain S residue   98 VAL
Chi-restraints excluded: chain S residue  180 ILE
Chi-restraints excluded: chain S residue  318 ILE
Chi-restraints excluded: chain S residue  320 LEU
Chi-restraints excluded: chain S residue  333 ILE
Chi-restraints excluded: chain S residue  363 LEU
Chi-restraints excluded: chain S residue  367 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 33 optimal weight:   30.0000
   chunk 42 optimal weight:    0.3980
   chunk 39 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.128958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.109202 restraints weight = 11410.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.112180 restraints weight = 6590.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.114170 restraints weight = 4616.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.3565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6187  Z= 0.249
  Angle     :  0.615  16.243   8491  Z= 0.302
  Chirality :  0.041   0.168   1053
  Planarity :  0.005   0.084   1051
  Dihedral  :  5.623  77.229    906
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.74 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 19.37 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.29), residues: 840
  helix:  2.31 (0.26), residues: 378
  sheet: -1.72 (0.34), residues: 184
  loop : -1.58 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP S 356 
 HIS   0.006   0.001   HIS A 214 
 PHE   0.030   0.002   PHE B 253 
 TYR   0.016   0.002   TYR S 148 
 ARG   0.005   0.001   ARG A  15 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.621 
Fit side-chains
REVERT: B  150 ARG cc_start: 0.8604 (mmt90) cc_final: 0.8398 (mmt-90)
REVERT: A  305 GLN cc_start: 0.8314 (tt0) cc_final: 0.7925 (tm-30)
REVERT: S   55 LEU cc_start: 0.9051 (tt) cc_final: 0.8821 (tp)
  outliers start: 24
  outliers final: 19
  residues processed: 123
  average time/residue: 0.1645
  time to fit residues: 27.2125
Evaluate side-chains
  117 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain S residue   93 VAL
Chi-restraints excluded: chain S residue   98 VAL
Chi-restraints excluded: chain S residue  180 ILE
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  318 ILE
Chi-restraints excluded: chain S residue  320 LEU
Chi-restraints excluded: chain S residue  333 ILE
Chi-restraints excluded: chain S residue  363 LEU
Chi-restraints excluded: chain S residue  367 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   chunk 35 optimal weight:   20.0000
   chunk 15 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 80 optimal weight:    0.0980
   chunk 42 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 57 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
G  18 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.131945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.112376 restraints weight = 11290.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.115421 restraints weight = 6496.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.117473 restraints weight = 4534.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.3760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6187  Z= 0.157
  Angle     :  0.565  16.109   8491  Z= 0.275
  Chirality :  0.039   0.154   1053
  Planarity :  0.005   0.085   1051
  Dihedral  :  5.388  76.045    906
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.38 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 21.04 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.29), residues: 840
  helix:  2.50 (0.25), residues: 379
  sheet: -1.28 (0.36), residues: 181
  loop : -1.53 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP S 356 
 HIS   0.006   0.001   HIS A 214 
 PHE   0.024   0.001   PHE B 253 
 TYR   0.014   0.001   TYR S 148 
 ARG   0.006   0.001   ARG A  15 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.620 
Fit side-chains
REVERT: B  120 ILE cc_start: 0.8786 (mt) cc_final: 0.8456 (tt)
REVERT: B  150 ARG cc_start: 0.8617 (mmt90) cc_final: 0.8381 (mmt-90)
REVERT: A  305 GLN cc_start: 0.8352 (tt0) cc_final: 0.7629 (tm-30)
REVERT: A  313 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6985 (ptp90)
REVERT: S  218 TYR cc_start: 0.7664 (m-80) cc_final: 0.7316 (m-80)
REVERT: S  359 TYR cc_start: 0.8726 (m-10) cc_final: 0.8381 (m-10)
  outliers start: 16
  outliers final: 12
  residues processed: 120
  average time/residue: 0.1477
  time to fit residues: 24.2279
Evaluate side-chains
  117 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain S residue  180 ILE
Chi-restraints excluded: chain S residue  318 ILE
Chi-restraints excluded: chain S residue  320 LEU
Chi-restraints excluded: chain S residue  333 ILE
Chi-restraints excluded: chain S residue  363 LEU
Chi-restraints excluded: chain S residue  367 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 81 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 74 optimal weight:    7.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
G  18 GLN
S 202 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.128127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.108575 restraints weight = 11192.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.111481 restraints weight = 6516.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.113435 restraints weight = 4603.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6187  Z= 0.264
  Angle     :  0.596  16.202   8491  Z= 0.296
  Chirality :  0.040   0.181   1053
  Planarity :  0.005   0.089   1051
  Dihedral  :  5.462  75.340    906
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.98 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 20.11 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.29), residues: 840
  helix:  2.35 (0.25), residues: 385
  sheet: -1.33 (0.37), residues: 171
  loop : -1.44 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 214 
 PHE   0.020   0.002   PHE B 253 
 TYR   0.014   0.002   TYR S 148 
 ARG   0.003   0.000   ARG A  15 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.643 
Fit side-chains
REVERT: B  120 ILE cc_start: 0.8819 (mt) cc_final: 0.8523 (tt)
REVERT: B  253 PHE cc_start: 0.8372 (m-80) cc_final: 0.8130 (m-80)
REVERT: A  305 GLN cc_start: 0.8323 (tt0) cc_final: 0.7648 (tm-30)
REVERT: A  313 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7055 (ptp90)
  outliers start: 24
  outliers final: 16
  residues processed: 125
  average time/residue: 0.1358
  time to fit residues: 24.1070
Evaluate side-chains
  117 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain S residue   93 VAL
Chi-restraints excluded: chain S residue  124 PHE
Chi-restraints excluded: chain S residue  180 ILE
Chi-restraints excluded: chain S residue  318 ILE
Chi-restraints excluded: chain S residue  320 LEU
Chi-restraints excluded: chain S residue  333 ILE
Chi-restraints excluded: chain S residue  363 LEU
Chi-restraints excluded: chain S residue  367 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 0 optimal weight:   50.0000
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
G  18 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.129099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.109443 restraints weight = 11191.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.112425 restraints weight = 6491.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.114403 restraints weight = 4553.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.4109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6187  Z= 0.214
  Angle     :  0.582  15.936   8491  Z= 0.287
  Chirality :  0.040   0.169   1053
  Planarity :  0.005   0.089   1051
  Dihedral  :  5.453  74.842    906
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.10 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 22.91 %
    Favored  : 74.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.29), residues: 840
  helix:  2.50 (0.25), residues: 380
  sheet: -1.15 (0.38), residues: 170
  loop : -1.36 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP S 356 
 HIS   0.006   0.001   HIS A 214 
 PHE   0.020   0.001   PHE B 253 
 TYR   0.015   0.001   TYR S 148 
 ARG   0.004   0.000   ARG A  15 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.625 
Fit side-chains
REVERT: B   58 ILE cc_start: 0.8740 (mt) cc_final: 0.8315 (tt)
REVERT: B  120 ILE cc_start: 0.8786 (mt) cc_final: 0.8506 (tt)
REVERT: B  253 PHE cc_start: 0.8382 (m-80) cc_final: 0.8135 (m-80)
REVERT: A  305 GLN cc_start: 0.8278 (tt0) cc_final: 0.7593 (tm-30)
REVERT: A  313 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7045 (ptp90)
REVERT: S  218 TYR cc_start: 0.7689 (m-80) cc_final: 0.7396 (m-80)
REVERT: S  238 ARG cc_start: 0.8381 (tpp-160) cc_final: 0.8063 (tpp-160)
REVERT: S  359 TYR cc_start: 0.8709 (m-10) cc_final: 0.8443 (m-10)
  outliers start: 16
  outliers final: 15
  residues processed: 121
  average time/residue: 0.1423
  time to fit residues: 23.9326
Evaluate side-chains
  119 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain S residue   93 VAL
Chi-restraints excluded: chain S residue   98 VAL
Chi-restraints excluded: chain S residue  124 PHE
Chi-restraints excluded: chain S residue  180 ILE
Chi-restraints excluded: chain S residue  318 ILE
Chi-restraints excluded: chain S residue  320 LEU
Chi-restraints excluded: chain S residue  333 ILE
Chi-restraints excluded: chain S residue  363 LEU
Chi-restraints excluded: chain S residue  367 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 31 optimal weight:    0.4980
   chunk 32 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 64 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 125 ASN
S 202 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.131845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.112421 restraints weight = 11080.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.115471 restraints weight = 6427.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.117502 restraints weight = 4469.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.4237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6187  Z= 0.150
  Angle     :  0.546  15.422   8491  Z= 0.269
  Chirality :  0.039   0.177   1053
  Planarity :  0.005   0.092   1051
  Dihedral  :  5.293  74.690    906
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.50 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 22.91 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.29), residues: 840
  helix:  2.67 (0.25), residues: 380
  sheet: -0.91 (0.38), residues: 169
  loop : -1.32 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP S 356 
 HIS   0.005   0.001   HIS A 214 
 PHE   0.019   0.001   PHE B 253 
 TYR   0.012   0.001   TYR S 157 
 ARG   0.005   0.000   ARG A  15 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.634 
Fit side-chains
REVERT: B   58 ILE cc_start: 0.8742 (mt) cc_final: 0.8368 (tt)
REVERT: B  105 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7867 (t80)
REVERT: B  120 ILE cc_start: 0.8735 (mt) cc_final: 0.8457 (tt)
REVERT: A  244 MET cc_start: 0.7416 (tpp) cc_final: 0.7046 (tmm)
REVERT: A  248 LEU cc_start: 0.8673 (mm) cc_final: 0.8130 (mm)
REVERT: A  305 GLN cc_start: 0.8299 (tt0) cc_final: 0.7554 (tm-30)
REVERT: A  313 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7051 (ptp90)
REVERT: S  218 TYR cc_start: 0.7620 (m-80) cc_final: 0.7318 (m-80)
REVERT: S  238 ARG cc_start: 0.8355 (tpp-160) cc_final: 0.8032 (tpp-160)
REVERT: S  359 TYR cc_start: 0.8673 (m-10) cc_final: 0.8445 (m-10)
  outliers start: 19
  outliers final: 14
  residues processed: 122
  average time/residue: 0.1511
  time to fit residues: 25.1031
Evaluate side-chains
  120 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain S residue   93 VAL
Chi-restraints excluded: chain S residue  124 PHE
Chi-restraints excluded: chain S residue  180 ILE
Chi-restraints excluded: chain S residue  318 ILE
Chi-restraints excluded: chain S residue  320 LEU
Chi-restraints excluded: chain S residue  363 LEU
Chi-restraints excluded: chain S residue  367 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 10 optimal weight:    7.9990
   chunk 70 optimal weight:    0.9990
   chunk 77 optimal weight:    8.9990
   chunk 83 optimal weight:    7.9990
   chunk 3 optimal weight:   20.0000
   chunk 76 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
G  18 GLN
S 202 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.130844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.111487 restraints weight = 11197.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.114513 restraints weight = 6443.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.116440 restraints weight = 4478.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.4350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6187  Z= 0.183
  Angle     :  0.573  15.200   8491  Z= 0.282
  Chirality :  0.039   0.194   1053
  Planarity :  0.005   0.091   1051
  Dihedral  :  5.138  75.217    904
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.74 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 23.46 %
    Favored  : 73.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.30), residues: 840
  helix:  2.69 (0.25), residues: 380
  sheet: -0.86 (0.39), residues: 171
  loop : -1.24 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 297 
 HIS   0.006   0.001   HIS A 214 
 PHE   0.019   0.001   PHE A 275 
 TYR   0.016   0.002   TYR B 289 
 ARG   0.006   0.001   ARG A  15 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.654 
Fit side-chains
REVERT: B   58 ILE cc_start: 0.8763 (mt) cc_final: 0.8385 (tt)
REVERT: B  105 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7886 (t80)
REVERT: B  120 ILE cc_start: 0.8752 (mt) cc_final: 0.8465 (tt)
REVERT: A  244 MET cc_start: 0.7336 (tpp) cc_final: 0.7015 (tmm)
REVERT: A  248 LEU cc_start: 0.8668 (mm) cc_final: 0.8109 (mm)
REVERT: A  305 GLN cc_start: 0.8320 (tt0) cc_final: 0.7535 (tm-30)
REVERT: A  313 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7042 (ptp90)
REVERT: S   55 LEU cc_start: 0.9095 (tt) cc_final: 0.8846 (tp)
REVERT: S  218 TYR cc_start: 0.7632 (m-80) cc_final: 0.7316 (m-80)
REVERT: S  346 PHE cc_start: 0.5811 (OUTLIER) cc_final: 0.5470 (t80)
REVERT: S  359 TYR cc_start: 0.8687 (m-10) cc_final: 0.8450 (m-10)
  outliers start: 18
  outliers final: 14
  residues processed: 119
  average time/residue: 0.1557
  time to fit residues: 25.3080
Evaluate side-chains
  124 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain S residue   93 VAL
Chi-restraints excluded: chain S residue  124 PHE
Chi-restraints excluded: chain S residue  180 ILE
Chi-restraints excluded: chain S residue  320 LEU
Chi-restraints excluded: chain S residue  346 PHE
Chi-restraints excluded: chain S residue  363 LEU
Chi-restraints excluded: chain S residue  367 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 3 optimal weight:   20.0000
   chunk 65 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0010
   chunk 35 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    2.5592

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 266 HIS
S 202 ASN
S 365 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.127310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.107869 restraints weight = 11259.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.110796 restraints weight = 6503.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.112638 restraints weight = 4557.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.4438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6187  Z= 0.266
  Angle     :  0.603  15.007   8491  Z= 0.302
  Chirality :  0.041   0.204   1053
  Planarity :  0.005   0.091   1051
  Dihedral  :  5.410  79.389    904
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.33 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 22.91 %
    Favored  : 73.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.29), residues: 840
  helix:  2.52 (0.25), residues: 386
  sheet: -0.80 (0.40), residues: 169
  loop : -1.27 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 297 
 HIS   0.007   0.001   HIS A 214 
 PHE   0.020   0.002   PHE A 275 
 TYR   0.016   0.002   TYR S 148 
 ARG   0.005   0.001   ARG A  15 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.620 
Fit side-chains
REVERT: B   58 ILE cc_start: 0.8782 (mt) cc_final: 0.8421 (tt)
REVERT: B  105 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.7914 (t80)
REVERT: B  120 ILE cc_start: 0.8812 (mt) cc_final: 0.8520 (tt)
REVERT: B  253 PHE cc_start: 0.8413 (m-80) cc_final: 0.8182 (m-80)
REVERT: A  244 MET cc_start: 0.7294 (tpp) cc_final: 0.6858 (tmm)
REVERT: A  248 LEU cc_start: 0.8719 (mm) cc_final: 0.8188 (mm)
REVERT: A  305 GLN cc_start: 0.8352 (tt0) cc_final: 0.7553 (tm-30)
REVERT: A  313 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7137 (ptp90)
REVERT: S   55 LEU cc_start: 0.9005 (tt) cc_final: 0.8784 (tp)
REVERT: S   75 TYR cc_start: 0.8298 (t80) cc_final: 0.8020 (t80)
REVERT: S  218 TYR cc_start: 0.7644 (m-80) cc_final: 0.7342 (m-80)
REVERT: S  238 ARG cc_start: 0.8661 (tpp-160) cc_final: 0.8089 (tpp-160)
REVERT: S  346 PHE cc_start: 0.5650 (OUTLIER) cc_final: 0.5262 (t80)
REVERT: S  359 TYR cc_start: 0.8708 (m-10) cc_final: 0.8440 (m-10)
  outliers start: 20
  outliers final: 15
  residues processed: 123
  average time/residue: 0.1493
  time to fit residues: 25.0681
Evaluate side-chains
  127 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain S residue   93 VAL
Chi-restraints excluded: chain S residue  124 PHE
Chi-restraints excluded: chain S residue  180 ILE
Chi-restraints excluded: chain S residue  333 ILE
Chi-restraints excluded: chain S residue  346 PHE
Chi-restraints excluded: chain S residue  355 THR
Chi-restraints excluded: chain S residue  363 LEU
Chi-restraints excluded: chain S residue  367 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 8 optimal weight:    0.1980
   chunk 33 optimal weight:   30.0000
   chunk 72 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 68 optimal weight:    0.8980
   chunk 1 optimal weight:   50.0000
   chunk 51 optimal weight:    9.9990
   chunk 70 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    2.1784

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

Flipped N/Q/H residues before XYZ refinement:
G  18 GLN
S 202 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.127939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.108490 restraints weight = 11451.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.111405 restraints weight = 6667.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.113286 restraints weight = 4695.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.4520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6187  Z= 0.236
  Angle     :  0.595  14.474   8491  Z= 0.297
  Chirality :  0.040   0.205   1053
  Planarity :  0.005   0.089   1051
  Dihedral  :  5.424  77.292    904
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.21 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 23.28 %
    Favored  : 73.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.29), residues: 840
  helix:  2.59 (0.25), residues: 380
  sheet: -0.87 (0.40), residues: 169
  loop : -1.26 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 297 
 HIS   0.007   0.001   HIS A 214 
 PHE   0.019   0.002   PHE A 275 
 TYR   0.014   0.002   TYR S 157 
 ARG   0.006   0.001   ARG A  15 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1895.03 seconds
wall clock time: 33 minutes 39.23 seconds (2019.23 seconds total)