Starting phenix.real_space_refine
on Mon Nov 17 15:51:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6g79_4358/11_2025/6g79_4358.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6g79_4358/11_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_4358/11_2025/6g79_4358.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6g79_4358/11_2025/6g79_4358.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6g79_4358/11_2025/6g79_4358.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6g79_4358/11_2025/6g79_4358.cif"
  }
  resolution = 3.78
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'GLU:plan': 8, 'ASP:plan': 23, 'GLN:plan1': 7, 'ARG:plan': 14, 'ASN:plan1': 7, 'PHE:plan': 1}
          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, 'ARG:plan': 2, 'GLU:plan': 5, '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: {'GLU:plan': 11, 'ARG:plan': 5, 'ASP:plan': 9, 'ASN:plan1': 6, 'GLN:plan1': 1, 'PHE:plan': 2}
          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: {'ARG:plan': 6, 'GLN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 2, 'TYR:plan': 2, 'TRP:plan': 1}
          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: 1.66, per 1000 atoms: 0.27
  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: 0.50
  Conformation dependent library (CDL) restraints added in 389.5 milliseconds
  

  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: 0.22
  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: 0.90

  Time building geometry restraints manager: 0.68 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:             0.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.700
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.320
-------------------------------------------------------------------------------
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   6188  Z= 0.537
  Angle     :  1.152   8.494   8493  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.003   0.000   ARG A 313 
 TYR   0.046   0.002   TYR A 231 
 PHE   0.015   0.002   PHE A 190 
 TRP   0.010   0.001   TRP S 149 
 HIS   0.006   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00771 ( 6187)
  covalent geometry    : angle       1.15258 ( 8491)
  SS BOND              : bond        0.00131 (    1)
  SS BOND              : angle       0.37986 (    2)
  hydrogen bonds       : bond        0.24993 (  368)
  hydrogen bonds       : angle       8.96211 ( 1080)

*********************** 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  : 0.227 
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: 0.0651
  time to fit residues: 17.1834
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  : 0.243 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    0.0980
   chunk 74 optimal weight:    0.7980
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 202 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.130971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.110906 restraints weight = 11374.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.113991 restraints weight = 6370.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.116213 restraints weight = 4408.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.117480 restraints weight = 3427.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.118632 restraints weight = 2916.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6188  Z= 0.138
  Angle     :  0.630  16.554   8493  Z= 0.316
  Chirality :  0.041   0.166   1053
  Planarity :  0.005   0.076   1051
  Dihedral  :  6.114  77.188    906
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  1.79 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 14.34 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.28), residues: 840
  helix:  1.51 (0.25), residues: 375
  sheet: -2.50 (0.32), residues: 174
  loop : -2.23 (0.34), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  15 
 TYR   0.013   0.002   TYR B 264 
 PHE   0.011   0.002   PHE S 380 
 TRP   0.013   0.002   TRP B 169 
 HIS   0.004   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6187)
  covalent geometry    : angle       0.62998 ( 8491)
  SS BOND              : bond        0.00223 (    1)
  SS BOND              : angle       0.51391 (    2)
  hydrogen bonds       : bond        0.04681 (  368)
  hydrogen bonds       : angle       4.83250 ( 1080)

*********************** 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
  152 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: B  184 THR cc_start: 0.7646 (m) cc_final: 0.7387 (m)
REVERT: B  188 MET cc_start: 0.8080 (mmm) cc_final: 0.7630 (mmm)
REVERT: B  243 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8286 (p)
REVERT: B  262 MET cc_start: 0.7735 (tpp) cc_final: 0.7417 (mmm)
REVERT: B  277 SER cc_start: 0.8447 (t) cc_final: 0.8054 (t)
REVERT: B  339 TRP cc_start: 0.8486 (m100) cc_final: 0.7980 (m100)
REVERT: G   40 TYR cc_start: 0.8489 (t80) cc_final: 0.8208 (t80)
REVERT: A   25 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7792 (tp30)
REVERT: A  244 MET cc_start: 0.8105 (tpp) cc_final: 0.7715 (mmt)
REVERT: A  305 GLN cc_start: 0.8496 (tt0) cc_final: 0.7893 (tm-30)
REVERT: A  313 ARG cc_start: 0.7905 (mtm110) cc_final: 0.7123 (ptt90)
REVERT: S   55 LEU cc_start: 0.9035 (tt) cc_final: 0.8795 (tp)
REVERT: S  367 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8413 (pt)
  outliers start: 21
  outliers final: 12
  residues processed: 147
  average time/residue: 0.0648
  time to fit residues: 13.2339
Evaluate side-chains
  125 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
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  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  364 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 7 optimal weight:    1.9990
   chunk 13 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 35 optimal weight:   20.0000
   chunk 47 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 33 optimal weight:   20.0000
   overall best weight:    1.7388

-------------------------------------------------------------------------------
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 = 0.3663 r_free = 0.3663 target = 0.127711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.107794 restraints weight = 11416.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.110909 restraints weight = 6488.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.113000 restraints weight = 4457.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.114413 restraints weight = 3469.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.114900 restraints weight = 2917.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6188  Z= 0.147
  Angle     :  0.600  16.230   8493  Z= 0.295
  Chirality :  0.040   0.153   1053
  Planarity :  0.005   0.076   1051
  Dihedral  :  5.727  77.940    906
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.62 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 17.13 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.29), residues: 840
  helix:  2.18 (0.25), residues: 376
  sheet: -1.91 (0.34), residues: 178
  loop : -1.99 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG S 238 
 TYR   0.012   0.002   TYR B 264 
 PHE   0.030   0.002   PHE B 253 
 TRP   0.019   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6187)
  covalent geometry    : angle       0.60003 ( 8491)
  SS BOND              : bond        0.00211 (    1)
  SS BOND              : angle       0.18573 (    2)
  hydrogen bonds       : bond        0.03920 (  368)
  hydrogen bonds       : angle       4.38127 ( 1080)

*********************** 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
  146 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.194 
Fit side-chains
REVERT: B  243 THR cc_start: 0.8593 (p) cc_final: 0.8309 (p)
REVERT: B  339 TRP cc_start: 0.8643 (m100) cc_final: 0.8165 (m100)
REVERT: A   25 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7815 (tp30)
REVERT: A  305 GLN cc_start: 0.8455 (tt0) cc_final: 0.7858 (tm-30)
REVERT: A  313 ARG cc_start: 0.7813 (mtm110) cc_final: 0.7112 (ptt90)
REVERT: A  341 ASP cc_start: 0.8067 (t0) cc_final: 0.7738 (t0)
  outliers start: 20
  outliers final: 13
  residues processed: 140
  average time/residue: 0.0643
  time to fit residues: 12.6698
Evaluate side-chains
  120 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain S residue   93 VAL
Chi-restraints excluded: chain S residue   98 VAL
Chi-restraints excluded: chain S residue  178 ILE
Chi-restraints excluded: chain S residue  179 SER
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 79 optimal weight:    0.9990
   chunk 23 optimal weight:   10.0000
   chunk 45 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0970
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** A 331 ASN ** 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 = 0.3680 r_free = 0.3680 target = 0.128886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.109523 restraints weight = 11584.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.112536 restraints weight = 6666.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.114605 restraints weight = 4625.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.115895 restraints weight = 3603.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.116597 restraints weight = 3062.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6188  Z= 0.120
  Angle     :  0.590  16.189   8493  Z= 0.283
  Chirality :  0.040   0.145   1053
  Planarity :  0.005   0.080   1051
  Dihedral  :  5.457  76.988    906
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.26 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 20.67 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.29), residues: 840
  helix:  2.42 (0.25), residues: 372
  sheet: -1.48 (0.35), residues: 177
  loop : -1.82 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  15 
 TYR   0.015   0.002   TYR S 148 
 PHE   0.020   0.001   PHE B 253 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6187)
  covalent geometry    : angle       0.59008 ( 8491)
  SS BOND              : bond        0.00209 (    1)
  SS BOND              : angle       0.13024 (    2)
  hydrogen bonds       : bond        0.03539 (  368)
  hydrogen bonds       : angle       4.22225 ( 1080)

*********************** 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
  132 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.231 
Fit side-chains
REVERT: B  339 TRP cc_start: 0.8708 (m100) cc_final: 0.8296 (m100)
REVERT: A   25 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7915 (tp30)
REVERT: A  305 GLN cc_start: 0.8441 (tt0) cc_final: 0.7973 (tm-30)
REVERT: A  341 ASP cc_start: 0.8149 (t0) cc_final: 0.7902 (t0)
REVERT: S   55 LEU cc_start: 0.9014 (tt) cc_final: 0.8775 (tp)
  outliers start: 14
  outliers final: 10
  residues processed: 128
  average time/residue: 0.0736
  time to fit residues: 12.9268
Evaluate side-chains
  114 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
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  234 PHE
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain S residue   93 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 6 optimal weight:    7.9990
   chunk 1 optimal weight:   50.0000
   chunk 9 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 73 optimal weight:    9.9990
   chunk 64 optimal weight:    0.0370
   chunk 42 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 57 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   overall best weight:    1.7862

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.130697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.110915 restraints weight = 11389.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.113940 restraints weight = 6545.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.115977 restraints weight = 4566.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.117284 restraints weight = 3588.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.117738 restraints weight = 3061.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.3750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6188  Z= 0.142
  Angle     :  0.575  16.074   8493  Z= 0.281
  Chirality :  0.040   0.148   1053
  Planarity :  0.005   0.089   1051
  Dihedral  :  5.322  74.978    906
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.86 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 20.86 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.30), residues: 840
  helix:  2.43 (0.25), residues: 385
  sheet: -1.21 (0.36), residues: 177
  loop : -1.53 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  15 
 TYR   0.013   0.002   TYR S 157 
 PHE   0.020   0.001   PHE B 253 
 TRP   0.014   0.002   TRP B 169 
 HIS   0.007   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6187)
  covalent geometry    : angle       0.57517 ( 8491)
  SS BOND              : bond        0.00174 (    1)
  SS BOND              : angle       0.17936 (    2)
  hydrogen bonds       : bond        0.03390 (  368)
  hydrogen bonds       : angle       4.17408 ( 1080)

*********************** 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
  129 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.180 
Fit side-chains
REVERT: B   58 ILE cc_start: 0.8677 (mt) cc_final: 0.8250 (tt)
REVERT: B  150 ARG cc_start: 0.8652 (mmt90) cc_final: 0.8387 (mmt-90)
REVERT: G   18 GLN cc_start: 0.9008 (tp40) cc_final: 0.8797 (tp-100)
REVERT: A   25 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7893 (tp30)
REVERT: A  244 MET cc_start: 0.7779 (tpp) cc_final: 0.7494 (mmt)
REVERT: A  305 GLN cc_start: 0.8313 (tt0) cc_final: 0.7854 (tm-30)
REVERT: A  341 ASP cc_start: 0.8108 (t0) cc_final: 0.7886 (t0)
REVERT: S  218 TYR cc_start: 0.7667 (m-80) cc_final: 0.7331 (m-80)
REVERT: S  316 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8338 (mp)
  outliers start: 18
  outliers final: 14
  residues processed: 122
  average time/residue: 0.0679
  time to fit residues: 11.3345
Evaluate side-chains
  121 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
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  243 THR
Chi-restraints excluded: chain B residue  300 LEU
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 S residue   93 VAL
Chi-restraints excluded: chain S residue   98 VAL
Chi-restraints excluded: chain S residue  316 LEU
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 2 optimal weight:    9.9990
   chunk 41 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 78 optimal weight:    0.8980
   chunk 7 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   chunk 73 optimal weight:    8.9990
   chunk 56 optimal weight:    0.6980
   chunk 16 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    2.4984

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.128610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.108906 restraints weight = 11292.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.111785 restraints weight = 6646.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.113728 restraints weight = 4707.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.114945 restraints weight = 3745.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.115780 restraints weight = 3222.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.3954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6188  Z= 0.169
  Angle     :  0.590  16.150   8493  Z= 0.293
  Chirality :  0.040   0.188   1053
  Planarity :  0.005   0.090   1051
  Dihedral  :  5.427  75.729    906
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.62 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 20.86 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.29), residues: 840
  helix:  2.46 (0.25), residues: 385
  sheet: -1.27 (0.37), residues: 175
  loop : -1.42 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  15 
 TYR   0.016   0.002   TYR S 148 
 PHE   0.017   0.002   PHE B 253 
 TRP   0.014   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 6187)
  covalent geometry    : angle       0.59038 ( 8491)
  SS BOND              : bond        0.00223 (    1)
  SS BOND              : angle       0.27948 (    2)
  hydrogen bonds       : bond        0.03470 (  368)
  hydrogen bonds       : angle       4.19714 ( 1080)

*********************** 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
  136 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.248 
Fit side-chains
REVERT: B   58 ILE cc_start: 0.8754 (mt) cc_final: 0.8331 (tt)
REVERT: B  253 PHE cc_start: 0.8394 (m-80) cc_final: 0.8052 (m-80)
REVERT: G   18 GLN cc_start: 0.8940 (tp40) cc_final: 0.8735 (tp-100)
REVERT: A   25 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8102 (tp30)
REVERT: A  305 GLN cc_start: 0.8296 (tt0) cc_final: 0.7633 (tm-30)
REVERT: A  313 ARG cc_start: 0.7601 (mtm-85) cc_final: 0.7089 (ptp90)
REVERT: S  316 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8362 (mp)
REVERT: S  359 TYR cc_start: 0.8743 (m-10) cc_final: 0.8453 (m-10)
  outliers start: 23
  outliers final: 16
  residues processed: 130
  average time/residue: 0.0601
  time to fit residues: 11.2018
Evaluate side-chains
  122 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
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  303 ASP
Chi-restraints excluded: chain A residue   22 ASN
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  179 SER
Chi-restraints excluded: chain S residue  181 SER
Chi-restraints excluded: chain S residue  316 LEU
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 1 optimal weight:   50.0000
   chunk 12 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 72 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 56 optimal weight:    0.0070
   chunk 22 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 61 optimal weight:    5.9990
   chunk 3 optimal weight:   20.0000
   overall best weight:    3.4006

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

Flipped N/Q/H residues before XYZ refinement:
** S 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.125943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.105978 restraints weight = 11553.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.108850 restraints weight = 6719.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.110790 restraints weight = 4769.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.111893 restraints weight = 3784.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.112919 restraints weight = 3275.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.4201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6188  Z= 0.215
  Angle     :  0.635  16.057   8493  Z= 0.318
  Chirality :  0.042   0.205   1053
  Planarity :  0.005   0.091   1051
  Dihedral  :  5.697  75.746    906
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.45 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 22.91 %
    Favored  : 73.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.29), residues: 840
  helix:  2.26 (0.25), residues: 385
  sheet: -1.31 (0.37), residues: 177
  loop : -1.36 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  15 
 TYR   0.017   0.002   TYR S 148 
 PHE   0.017   0.002   PHE B 199 
 TRP   0.020   0.002   TRP B 297 
 HIS   0.007   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 6187)
  covalent geometry    : angle       0.63513 ( 8491)
  SS BOND              : bond        0.00245 (    1)
  SS BOND              : angle       0.50683 (    2)
  hydrogen bonds       : bond        0.03699 (  368)
  hydrogen bonds       : angle       4.35298 ( 1080)

*********************** 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
  136 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.219 
Fit side-chains
REVERT: B   58 ILE cc_start: 0.8834 (mt) cc_final: 0.8425 (tt)
REVERT: B  105 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.8050 (t80)
REVERT: B  253 PHE cc_start: 0.8581 (m-80) cc_final: 0.8331 (m-80)
REVERT: G   18 GLN cc_start: 0.9001 (tp40) cc_final: 0.8790 (tp-100)
REVERT: A   25 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8133 (tp30)
REVERT: A  305 GLN cc_start: 0.8296 (tt0) cc_final: 0.7656 (tm-30)
REVERT: A  313 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7191 (ptp90)
REVERT: S  218 TYR cc_start: 0.7772 (m-80) cc_final: 0.7450 (m-80)
  outliers start: 22
  outliers final: 19
  residues processed: 127
  average time/residue: 0.0687
  time to fit residues: 12.1541
Evaluate side-chains
  127 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   95 LEU
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  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   22 ASN
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  179 SER
Chi-restraints excluded: chain S residue  181 SER
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 9 optimal weight:    0.4980
   chunk 18 optimal weight:    0.7980
   chunk 32 optimal weight:    8.9990
   chunk 66 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 42 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9990
   chunk 82 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0980
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
S 202 ASN
S 361 ASN

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 = 0.132130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.112475 restraints weight = 11085.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.115531 restraints weight = 6371.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.117579 restraints weight = 4466.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.118900 restraints weight = 3499.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.119877 restraints weight = 2973.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.4299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6188  Z= 0.105
  Angle     :  0.568  15.297   8493  Z= 0.278
  Chirality :  0.039   0.191   1053
  Planarity :  0.005   0.092   1051
  Dihedral  :  5.379  74.256    906
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.50 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 24.02 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.29), residues: 840
  helix:  2.52 (0.25), residues: 386
  sheet: -0.87 (0.38), residues: 169
  loop : -1.33 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  15 
 TYR   0.012   0.001   TYR S 148 
 PHE   0.019   0.001   PHE B 253 
 TRP   0.014   0.001   TRP S 356 
 HIS   0.006   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 6187)
  covalent geometry    : angle       0.56769 ( 8491)
  SS BOND              : bond        0.00166 (    1)
  SS BOND              : angle       0.16144 (    2)
  hydrogen bonds       : bond        0.03129 (  368)
  hydrogen bonds       : angle       4.12438 ( 1080)

*********************** 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
  134 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.237 
Fit side-chains
REVERT: B   58 ILE cc_start: 0.8730 (mt) cc_final: 0.8332 (tt)
REVERT: G   18 GLN cc_start: 0.8971 (tp40) cc_final: 0.8741 (tp-100)
REVERT: A  244 MET cc_start: 0.7681 (tmm) cc_final: 0.6872 (mmt)
REVERT: A  305 GLN cc_start: 0.8294 (tt0) cc_final: 0.7540 (tm-30)
REVERT: A  313 ARG cc_start: 0.7583 (mtm-85) cc_final: 0.7119 (ptp90)
REVERT: S  218 TYR cc_start: 0.7692 (m-80) cc_final: 0.7390 (m-80)
REVERT: S  238 ARG cc_start: 0.8637 (tpp-160) cc_final: 0.8169 (tpp-160)
REVERT: S  359 TYR cc_start: 0.8701 (m-10) cc_final: 0.8493 (m-10)
  outliers start: 17
  outliers final: 14
  residues processed: 125
  average time/residue: 0.0662
  time to fit residues: 11.4617
Evaluate side-chains
  123 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  179 THR
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   22 ASN
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain S residue  124 PHE
Chi-restraints excluded: chain S residue  179 SER
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  320 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 38 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0370
   chunk 58 optimal weight:    9.9990
   chunk 63 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 3 optimal weight:   20.0000
   chunk 6 optimal weight:    8.9990
   chunk 75 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0470
   chunk 2 optimal weight:    6.9990
   overall best weight:    0.9560

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.131796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.112163 restraints weight = 11265.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.115216 restraints weight = 6461.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.117274 restraints weight = 4509.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.118514 restraints weight = 3528.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.119594 restraints weight = 3008.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.4413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6188  Z= 0.113
  Angle     :  0.576  15.053   8493  Z= 0.281
  Chirality :  0.039   0.171   1053
  Planarity :  0.005   0.091   1051
  Dihedral  :  5.161  75.483    904
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.62 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 24.95 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.29), residues: 840
  helix:  2.61 (0.25), residues: 386
  sheet: -0.70 (0.38), residues: 167
  loop : -1.27 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  15 
 TYR   0.012   0.001   TYR S 148 
 PHE   0.016   0.001   PHE B 253 
 TRP   0.013   0.001   TRP S 356 
 HIS   0.005   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 6187)
  covalent geometry    : angle       0.57615 ( 8491)
  SS BOND              : bond        0.00110 (    1)
  SS BOND              : angle       0.22737 (    2)
  hydrogen bonds       : bond        0.03071 (  368)
  hydrogen bonds       : angle       4.06708 ( 1080)

*********************** 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
  124 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.244 
Fit side-chains
REVERT: B   58 ILE cc_start: 0.8710 (mt) cc_final: 0.8336 (tt)
REVERT: G   18 GLN cc_start: 0.8960 (tp40) cc_final: 0.8699 (tp40)
REVERT: A  244 MET cc_start: 0.7684 (tmm) cc_final: 0.7013 (tpp)
REVERT: A  305 GLN cc_start: 0.8345 (tt0) cc_final: 0.7554 (tm-30)
REVERT: A  313 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.7194 (ptp90)
REVERT: S   55 LEU cc_start: 0.9055 (tt) cc_final: 0.8833 (tp)
REVERT: S  218 TYR cc_start: 0.7693 (m-80) cc_final: 0.7367 (m-80)
REVERT: S  346 PHE cc_start: 0.5644 (OUTLIER) cc_final: 0.5315 (t80)
REVERT: S  359 TYR cc_start: 0.8721 (m-10) cc_final: 0.8497 (m-10)
  outliers start: 15
  outliers final: 12
  residues processed: 117
  average time/residue: 0.0687
  time to fit residues: 11.2226
Evaluate side-chains
  120 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  179 THR
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   22 ASN
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain S residue  124 PHE
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 25 optimal weight:    0.0070
   chunk 62 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 69 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 80 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    2.0006

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.129406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.109525 restraints weight = 11366.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.112527 restraints weight = 6621.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.114435 restraints weight = 4654.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.115842 restraints weight = 3716.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.116801 restraints weight = 3143.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.4482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6188  Z= 0.150
  Angle     :  0.590  14.884   8493  Z= 0.291
  Chirality :  0.040   0.172   1053
  Planarity :  0.005   0.093   1051
  Dihedral  :  5.280  75.699    904
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.10 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 25.33 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.30), residues: 840
  helix:  2.59 (0.26), residues: 386
  sheet: -0.86 (0.39), residues: 171
  loop : -1.19 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  15 
 TYR   0.016   0.002   TYR S 148 
 PHE   0.015   0.001   PHE B 253 
 TRP   0.018   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6187)
  covalent geometry    : angle       0.59020 ( 8491)
  SS BOND              : bond        0.00152 (    1)
  SS BOND              : angle       0.40629 (    2)
  hydrogen bonds       : bond        0.03270 (  368)
  hydrogen bonds       : angle       4.12842 ( 1080)

********************** 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
  122 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.236 
Fit side-chains
REVERT: B   58 ILE cc_start: 0.8693 (mt) cc_final: 0.8295 (tt)
REVERT: B  105 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7962 (t80)
REVERT: G   18 GLN cc_start: 0.8949 (tp40) cc_final: 0.8695 (tp40)
REVERT: A  305 GLN cc_start: 0.8349 (tt0) cc_final: 0.7553 (tm-30)
REVERT: A  313 ARG cc_start: 0.7688 (mtm-85) cc_final: 0.7227 (ptp90)
REVERT: S   55 LEU cc_start: 0.8995 (tt) cc_final: 0.8786 (tp)
REVERT: S  218 TYR cc_start: 0.7699 (m-80) cc_final: 0.7401 (m-80)
REVERT: S  359 TYR cc_start: 0.8739 (m-10) cc_final: 0.8498 (m-10)
  outliers start: 13
  outliers final: 12
  residues processed: 115
  average time/residue: 0.0721
  time to fit residues: 11.4114
Evaluate side-chains
  121 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
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  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   22 ASN
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain S residue  124 PHE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    0.2980
   chunk 77 optimal weight:    7.9990
   chunk 79 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 2 optimal weight:   20.0000
   chunk 62 optimal weight:    5.9990
   chunk 52 optimal weight:   40.0000
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.8182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.132349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.112658 restraints weight = 11299.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.115730 restraints weight = 6492.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.117819 restraints weight = 4544.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.119087 restraints weight = 3554.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.120129 restraints weight = 3034.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.4612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6188  Z= 0.107
  Angle     :  0.569  13.995   8493  Z= 0.278
  Chirality :  0.038   0.156   1053
  Planarity :  0.005   0.093   1051
  Dihedral  :  5.242  78.769    904
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.38 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 25.14 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.30), residues: 840
  helix:  2.66 (0.25), residues: 386
  sheet: -0.72 (0.39), residues: 169
  loop : -1.14 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  15 
 TYR   0.013   0.001   TYR S 148 
 PHE   0.016   0.001   PHE B 253 
 TRP   0.013   0.001   TRP B 297 
 HIS   0.005   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 6187)
  covalent geometry    : angle       0.56907 ( 8491)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       0.19515 (    2)
  hydrogen bonds       : bond        0.03020 (  368)
  hydrogen bonds       : angle       4.05722 ( 1080)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1102.35 seconds
wall clock time: 19 minutes 45.74 seconds (1185.74 seconds total)