Starting phenix.real_space_refine
on Sun May 11 02:57:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9l3y_62798/05_2025/9l3y_62798.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9l3y_62798/05_2025/9l3y_62798.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9l3y_62798/05_2025/9l3y_62798.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9l3y_62798/05_2025/9l3y_62798.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9l3y_62798/05_2025/9l3y_62798.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9l3y_62798/05_2025/9l3y_62798.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.012 sd=   0.066
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      50      5.16       5
     C    4769      2.51       5
     N    1243      2.21       5
     O    1321      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7383
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2391
          Classifications: {'peptide': 298}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 10, 'TRANS': 287}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 96
          Unresolved non-hydrogen angles: 127
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 3, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 67
    Chain: "L"
      Number of atoms: 669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 669
          Classifications: {'peptide': 103}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 183
          Unresolved non-hydrogen angles: 225
          Unresolved non-hydrogen dihedrals: 165
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 120
    Chain: "A"
      Number of atoms: 1587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1587
          Classifications: {'peptide': 211}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 2, 'TRANS': 208}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 120
          Unresolved non-hydrogen angles: 139
          Unresolved non-hydrogen dihedrals: 101
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 65
    Chain: "B"
      Number of atoms: 2408
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2408
          Classifications: {'peptide': 330}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 5, 'TRANS': 324}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 127
          Unresolved non-hydrogen angles: 155
          Unresolved non-hydrogen dihedrals: 99
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 100
    Chain: "C"
      Number of atoms: 328
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 328
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 56
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 34
  Time building chain proxies: 4.60, per 1000 atoms: 0.62
  Number of scatterers: 7383
  At special positions: 0
  Unit cell: (81.396, 95.319, 152.082, 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      50     16.00
     O    1321      8.00
     N    1243      7.00
     C    4769      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 110 " - pdb=" SG  CYS R 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  77 " - pdb=" SG  CYS L  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  98 " - pdb=" SG  CYS L 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 101 " - pdb=" SG  CYS L 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.62
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1888

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 9 sheets defined
      38.0% alpha, 17.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'R' and resid 36 through 52
      removed outlier: 4.050A  pdb=" N   VAL R  40 " --> pdb=" O   VAL R  36 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 52 through 63
    Processing helix  chain 'R' and resid 70 through 99
      removed outlier: 3.679A  pdb=" N   LEU R  74 " --> pdb=" O   THR R  70 " (cutoff:3.500A)
      Proline residue:  R  91  - end of helix
    Processing helix  chain 'R' and resid 106 through 141
    Processing helix  chain 'R' and resid 150 through 167
    Processing helix  chain 'R' and resid 202 through 215
      removed outlier: 3.803A  pdb=" N   LEU R 206 " --> pdb=" O   ARG R 202 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   THR R 207 " --> pdb=" O   HIS R 203 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 215 through 233
    Processing helix  chain 'R' and resid 234 through 236
      No H-bonds generated for 'chain 'R' and resid 234 through 236'
    Processing helix  chain 'R' and resid 240 through 268
      removed outlier: 3.833A  pdb=" N   TRP R 246 " --> pdb=" O   SER R 242 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   CYS R 258 " --> pdb=" O   ALA R 254 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   TRP R 259 " --> pdb=" O   PHE R 255 " (cutoff:3.500A)
      Proline residue:  R 261  - end of helix
    Processing helix  chain 'R' and resid 284 through 305
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'L' and resid 24 through 40
      removed outlier: 3.701A  pdb=" N   HIS L  40 " --> pdb=" O   GLU L  36 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 134 through 140
      removed outlier: 3.644A  pdb=" N   VAL L 138 " --> pdb=" O   GLN L 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 3.627A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 4.456A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 216
      No H-bonds generated for 'chain 'A' and resid 214 through 216'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.517A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 352
      removed outlier: 3.738A  pdb=" N   ASP A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 26
      removed outlier: 3.552A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.960A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   THR B  34 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 29 through 34'
    Processing helix  chain 'C' and resid 13 through 24
    Processing helix  chain 'C' and resid 29 through 45
    Processing sheet with id=AA1, first strand: chain 'R' and resid 177 through 178
    Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 190
      removed outlier: 3.825A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.233A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.045A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.005A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.439A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.831A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.042A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.268A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.616A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.596A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    343 hydrogen bonds defined for protein.
    1014 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.87

  Time building geometry restraints manager: 1.93 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2342
        1.35 -     1.47: 1974
        1.47 -     1.59: 3170
        1.59 -     1.71: 0
        1.71 -     1.83: 65
  Bond restraints: 7551
  Sorted by residual:
  bond pdb=" C   PHE L  60 "
       pdb=" N   PRO L  61 "
    ideal  model  delta    sigma   weight residual
    1.333  1.359 -0.026 1.01e-02 9.80e+03 6.61e+00
  bond pdb=" C   LYS L  83 "
       pdb=" N   LYS L  84 "
    ideal  model  delta    sigma   weight residual
    1.330  1.344 -0.014 1.47e-02 4.63e+03 9.66e-01
  bond pdb=" CA  LYS R 234 "
       pdb=" C   LYS R 234 "
    ideal  model  delta    sigma   weight residual
    1.523  1.536 -0.013 1.34e-02 5.57e+03 9.54e-01
  bond pdb=" C   GLY R 170 "
       pdb=" N   PRO R 171 "
    ideal  model  delta    sigma   weight residual
    1.334  1.354 -0.020 2.34e-02 1.83e+03 7.58e-01
  bond pdb=" CB  PRO R 171 "
       pdb=" CG  PRO R 171 "
    ideal  model  delta    sigma   weight residual
    1.492  1.451  0.041 5.00e-02 4.00e+02 6.88e-01
  ... (remaining 7546 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 10055
        1.59 -     3.18: 187
        3.18 -     4.77: 41
        4.77 -     6.36: 10
        6.36 -     7.95: 4
  Bond angle restraints: 10297
  Sorted by residual:
  angle pdb=" N   GLY R 170 "
        pdb=" CA  GLY R 170 "
        pdb=" C   GLY R 170 "
      ideal   model   delta    sigma   weight residual
     112.34  118.39   -6.05 2.04e+00 2.40e-01 8.79e+00
  angle pdb=" CA  LYS R  69 "
        pdb=" CB  LYS R  69 "
        pdb=" CG  LYS R  69 "
      ideal   model   delta    sigma   weight residual
     114.10  118.87   -4.77 2.00e+00 2.50e-01 5.69e+00
  angle pdb=" C   LYS R 232 "
        pdb=" N   VAL R 233 "
        pdb=" CA  VAL R 233 "
      ideal   model   delta    sigma   weight residual
     121.97  126.11   -4.14 1.80e+00 3.09e-01 5.29e+00
  angle pdb=" CB  LYS L 103 "
        pdb=" CG  LYS L 103 "
        pdb=" CD  LYS L 103 "
      ideal   model   delta    sigma   weight residual
     111.30  116.56   -5.26 2.30e+00 1.89e-01 5.23e+00
  angle pdb=" CA  LEU A 283 "
        pdb=" CB  LEU A 283 "
        pdb=" CG  LEU A 283 "
      ideal   model   delta    sigma   weight residual
     116.30  124.25   -7.95 3.50e+00 8.16e-02 5.16e+00
  ... (remaining 10292 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4017
       17.98 -    35.95: 287
       35.95 -    53.93: 57
       53.93 -    71.91: 9
       71.91 -    89.88: 2
  Dihedral angle restraints: 4372
    sinusoidal: 1477
      harmonic: 2895
  Sorted by residual:
  dihedral pdb=" CB  CYS B 121 "
           pdb=" SG  CYS B 121 "
           pdb=" SG  CYS B 149 "
           pdb=" CB  CYS B 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.64  -73.64     1      1.00e+01 1.00e-02 6.90e+01
  dihedral pdb=" CB  CYS L  77 "
           pdb=" SG  CYS L  77 "
           pdb=" SG  CYS L  87 "
           pdb=" CB  CYS L  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.00  -66.00     1      1.00e+01 1.00e-02 5.69e+01
  dihedral pdb=" CA  TYR R 304 "
           pdb=" C   TYR R 304 "
           pdb=" N   VAL R 305 "
           pdb=" CA  VAL R 305 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.72  -20.28     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 4369 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 779
       0.030 -    0.061: 307
       0.061 -    0.091: 92
       0.091 -    0.122: 42
       0.122 -    0.152: 6
  Chirality restraints: 1226
  Sorted by residual:
  chirality pdb=" CB  VAL R 233 "
            pdb=" CA  VAL R 233 "
            pdb=" CG1 VAL R 233 "
            pdb=" CG2 VAL R 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.80e-01
  chirality pdb=" CA  ILE B 338 "
            pdb=" N   ILE B 338 "
            pdb=" C   ILE B 338 "
            pdb=" CB  ILE B 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.20e-01
  chirality pdb=" CB  ILE R 168 "
            pdb=" CA  ILE R 168 "
            pdb=" CG1 ILE R 168 "
            pdb=" CG2 ILE R 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.52    0.13 2.00e-01 2.50e+01 4.19e-01
  ... (remaining 1223 not shown)

  Planarity restraints: 1285
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 170 "    0.054 5.00e-02 4.00e+02   8.23e-02 1.08e+01
        pdb=" N   PRO R 171 "   -0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO R 171 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO R 171 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R  62 "    0.009 2.00e-02 2.50e+03   1.71e-02 2.91e+00
        pdb=" C   PHE R  62 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   PHE R  62 "    0.011 2.00e-02 2.50e+03
        pdb=" N   THR R  63 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 181 "    0.010 2.00e-02 2.50e+03   1.21e-02 2.58e+00
        pdb=" CG  PHE R 181 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 181 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 181 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 181 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 181 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 181 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1282 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 276
        2.72 -     3.26: 7441
        3.26 -     3.81: 11907
        3.81 -     4.35: 14472
        4.35 -     4.90: 24953
  Nonbonded interactions: 59049
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 114 "
            pdb=" OXT SER L 157 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OH  TYR R 215 "
            pdb=" OG1 THR R 260 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.278 3.040
  ... (remaining 59044 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:             0.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     19.350
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6787
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      :  0.002   0.041   7556  Z= 0.114
  Angle     :  0.572   7.953  10307  Z= 0.304
  Chirality :  0.039   0.152   1226
  Planarity :  0.004   0.082   1285
  Dihedral  : 12.952  89.885   2469
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.27 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.28), residues: 963
  helix:  2.31 (0.29), residues: 353
  sheet: -0.38 (0.36), residues: 205
  loop : -1.88 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 339 
 HIS   0.006   0.001   HIS R 280 
 PHE   0.028   0.001   PHE R 181 
 TYR   0.016   0.001   TYR R 304 
 ARG   0.007   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10399 (  343)
  hydrogen bonds       : angle       6.07532 ( 1014)
  SS BOND              : bond        0.00282 (    5)
  SS BOND              : angle       0.64629 (   10)
  covalent geometry    : bond        0.00219 ( 7551)
  covalent geometry    : angle       0.57144 (10297)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.845 
Fit side-chains
REVERT: R   47 LEU cc_start: 0.7858 (mm) cc_final: 0.7605 (mp)
REVERT: A  298 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7028 (tm-30)
REVERT: B  325 MET cc_start: 0.6707 (ttm) cc_final: 0.6487 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.2039
  time to fit residues: 30.9372
Evaluate side-chains
  97 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 41 optimal weight:    7.9990
   chunk 25 optimal weight:    0.0170
   chunk 50 optimal weight:    0.5980
   chunk 39 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   chunk 29 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0980
   chunk 88 optimal weight:    4.9990
   overall best weight:    0.8820

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

Flipped N/Q/H residues before XYZ refinement:
R 244 HIS
L 134 GLN
A  22 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
B 259 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.093346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.080125 restraints weight = 21299.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.080369 restraints weight = 17495.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.081295 restraints weight = 13523.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7556  Z= 0.148
  Angle     :  0.603  10.673  10307  Z= 0.311
  Chirality :  0.041   0.144   1226
  Planarity :  0.004   0.043   1285
  Dihedral  :  4.153  30.147   1038
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.00 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  9.58 %
    Favored  : 89.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.28), residues: 963
  helix:  2.20 (0.29), residues: 361
  sheet: -0.49 (0.36), residues: 203
  loop : -1.96 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 339 
 HIS   0.006   0.001   HIS R 138 
 PHE   0.027   0.002   PHE R  62 
 TYR   0.029   0.002   TYR B 264 
 ARG   0.008   0.001   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03426 (  343)
  hydrogen bonds       : angle       4.91761 ( 1014)
  SS BOND              : bond        0.00689 (    5)
  SS BOND              : angle       1.34847 (   10)
  covalent geometry    : bond        0.00349 ( 7551)
  covalent geometry    : angle       0.60167 (10297)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.800 
Fit side-chains
REVERT: R   47 LEU cc_start: 0.7594 (mm) cc_final: 0.7374 (mp)
REVERT: R  282 MET cc_start: 0.5968 (tmm) cc_final: 0.5568 (tmm)
REVERT: B  134 ARG cc_start: 0.5355 (tpm170) cc_final: 0.5151 (tpm170)
  outliers start: 6
  outliers final: 6
  residues processed: 103
  average time/residue: 0.2131
  time to fit residues: 28.8302
Evaluate side-chains
  102 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   21 TYR
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  204 HIS
Chi-restraints excluded: chain R residue  222 MET
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   52 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 52 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
R  78 ASN
R 118 GLN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.090697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.076952 restraints weight = 21318.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.078154 restraints weight = 15566.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.078862 restraints weight = 12092.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7556  Z= 0.164
  Angle     :  0.610  10.708  10307  Z= 0.316
  Chirality :  0.042   0.144   1226
  Planarity :  0.004   0.045   1285
  Dihedral  :  4.285  28.015   1038
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.79 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 12.72 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.28), residues: 963
  helix:  2.11 (0.28), residues: 359
  sheet: -0.59 (0.35), residues: 204
  loop : -1.97 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 339 
 HIS   0.006   0.001   HIS R 135 
 PHE   0.025   0.002   PHE R  62 
 TYR   0.028   0.002   TYR B 264 
 ARG   0.006   0.001   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03742 (  343)
  hydrogen bonds       : angle       4.87559 ( 1014)
  SS BOND              : bond        0.00717 (    5)
  SS BOND              : angle       1.45679 (   10)
  covalent geometry    : bond        0.00383 ( 7551)
  covalent geometry    : angle       0.60840 (10297)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.778 
Fit side-chains
REVERT: R  180 GLU cc_start: 0.7520 (pm20) cc_final: 0.7309 (pt0)
REVERT: B  134 ARG cc_start: 0.5684 (tpm170) cc_final: 0.5389 (tpm170)
  outliers start: 11
  outliers final: 10
  residues processed: 106
  average time/residue: 0.2130
  time to fit residues: 30.7709
Evaluate side-chains
  112 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   21 TYR
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  204 HIS
Chi-restraints excluded: chain R residue  222 MET
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  299 LEU
Chi-restraints excluded: chain L residue  114 LEU
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain B residue   52 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.090459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.076669 restraints weight = 21321.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.077385 restraints weight = 16128.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.078201 restraints weight = 12606.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7556  Z= 0.137
  Angle     :  0.580  11.586  10307  Z= 0.299
  Chirality :  0.041   0.139   1226
  Planarity :  0.004   0.045   1285
  Dihedral  :  4.211  27.446   1038
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.89 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 15.60 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.28), residues: 963
  helix:  2.04 (0.28), residues: 361
  sheet: -0.66 (0.35), residues: 204
  loop : -1.96 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R  75 
 HIS   0.004   0.001   HIS R 135 
 PHE   0.020   0.001   PHE R  62 
 TYR   0.020   0.001   TYR B 264 
 ARG   0.007   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03463 (  343)
  hydrogen bonds       : angle       4.73375 ( 1014)
  SS BOND              : bond        0.00638 (    5)
  SS BOND              : angle       1.32824 (   10)
  covalent geometry    : bond        0.00318 ( 7551)
  covalent geometry    : angle       0.57861 (10297)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
REVERT: R  212 ILE cc_start: 0.8146 (tt) cc_final: 0.7876 (tt)
REVERT: R  270 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5981 (pp)
REVERT: B  134 ARG cc_start: 0.5704 (tpm170) cc_final: 0.5503 (tpm170)
REVERT: B  325 MET cc_start: 0.6906 (ttm) cc_final: 0.6618 (ttm)
  outliers start: 10
  outliers final: 8
  residues processed: 106
  average time/residue: 0.2057
  time to fit residues: 29.1158
Evaluate side-chains
  108 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   21 TYR
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  222 MET
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain R residue  299 LEU
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0570
   chunk 69 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    1.0106

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

Flipped N/Q/H residues before XYZ refinement:
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.089603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.076325 restraints weight = 21150.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.076103 restraints weight = 16202.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.076953 restraints weight = 13321.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.3071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7556  Z= 0.155
  Angle     :  0.593  11.744  10307  Z= 0.307
  Chirality :  0.041   0.145   1226
  Planarity :  0.004   0.045   1285
  Dihedral  :  4.290  26.947   1038
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.89 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.96 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.28), residues: 963
  helix:  2.04 (0.28), residues: 359
  sheet: -0.77 (0.35), residues: 205
  loop : -1.92 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  99 
 HIS   0.005   0.001   HIS R 135 
 PHE   0.017   0.001   PHE R  62 
 TYR   0.020   0.002   TYR B 264 
 ARG   0.007   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03649 (  343)
  hydrogen bonds       : angle       4.75322 ( 1014)
  SS BOND              : bond        0.00644 (    5)
  SS BOND              : angle       1.36564 (   10)
  covalent geometry    : bond        0.00364 ( 7551)
  covalent geometry    : angle       0.59148 (10297)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.752 
Fit side-chains
REVERT: R  212 ILE cc_start: 0.8071 (tt) cc_final: 0.7792 (tt)
REVERT: R  270 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.6028 (pp)
REVERT: B  127 LYS cc_start: 0.6907 (pttp) cc_final: 0.6446 (ptpt)
REVERT: B  134 ARG cc_start: 0.5789 (tpm170) cc_final: 0.5536 (tpm170)
REVERT: B  171 ILE cc_start: 0.6733 (OUTLIER) cc_final: 0.6357 (mp)
  outliers start: 15
  outliers final: 11
  residues processed: 107
  average time/residue: 0.2166
  time to fit residues: 30.9263
Evaluate side-chains
  109 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   21 TYR
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  222 MET
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain R residue  299 LEU
Chi-restraints excluded: chain L residue  114 LEU
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
C  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.089526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.075752 restraints weight = 21373.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.076205 restraints weight = 16341.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.077528 restraints weight = 12606.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
moved from start:          0.3168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7556  Z= 0.146
  Angle     :  0.584  12.004  10307  Z= 0.302
  Chirality :  0.041   0.144   1226
  Planarity :  0.004   0.045   1285
  Dihedral  :  4.295  26.484   1038
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.68 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.10 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.28), residues: 963
  helix:  2.04 (0.28), residues: 358
  sheet: -0.73 (0.36), residues: 192
  loop : -1.90 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R  75 
 HIS   0.005   0.001   HIS R 135 
 PHE   0.014   0.001   PHE A 196 
 TYR   0.017   0.002   TYR B 264 
 ARG   0.007   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03562 (  343)
  hydrogen bonds       : angle       4.71527 ( 1014)
  SS BOND              : bond        0.00648 (    5)
  SS BOND              : angle       1.35645 (   10)
  covalent geometry    : bond        0.00343 ( 7551)
  covalent geometry    : angle       0.58237 (10297)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.808 
Fit side-chains
REVERT: R  212 ILE cc_start: 0.8083 (tt) cc_final: 0.7818 (tt)
REVERT: R  270 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.6048 (pp)
REVERT: B  134 ARG cc_start: 0.5851 (tpm170) cc_final: 0.5571 (tpm170)
REVERT: B  171 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.6262 (mp)
  outliers start: 19
  outliers final: 16
  residues processed: 108
  average time/residue: 0.2016
  time to fit residues: 29.2941
Evaluate side-chains
  114 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   12 PHE
Chi-restraints excluded: chain R residue   21 TYR
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  222 MET
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain R residue  299 LEU
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  154 PHE
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 96 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   chunk 43 optimal weight:   10.0000
   chunk 13 optimal weight:    0.0370
   chunk 8 optimal weight:    0.0770
   chunk 26 optimal weight:    0.0020
   chunk 93 optimal weight:   20.0000
   overall best weight:    0.4226

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.091098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.077275 restraints weight = 21149.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.078142 restraints weight = 15411.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.079327 restraints weight = 11312.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7556  Z= 0.106
  Angle     :  0.548  11.389  10307  Z= 0.283
  Chirality :  0.040   0.143   1226
  Planarity :  0.003   0.044   1285
  Dihedral  :  4.066  25.990   1038
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.10 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.78 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.28), residues: 963
  helix:  2.14 (0.28), residues: 359
  sheet: -0.60 (0.37), residues: 192
  loop : -1.84 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R  75 
 HIS   0.003   0.001   HIS L 116 
 PHE   0.012   0.001   PHE A 196 
 TYR   0.010   0.001   TYR B 264 
 ARG   0.007   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03103 (  343)
  hydrogen bonds       : angle       4.51763 ( 1014)
  SS BOND              : bond        0.00457 (    5)
  SS BOND              : angle       1.06145 (   10)
  covalent geometry    : bond        0.00237 ( 7551)
  covalent geometry    : angle       0.54692 (10297)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.897 
Fit side-chains
REVERT: R  212 ILE cc_start: 0.8027 (tt) cc_final: 0.7756 (tt)
REVERT: R  270 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5964 (pp)
REVERT: B  134 ARG cc_start: 0.5846 (tpm170) cc_final: 0.5568 (tpm170)
REVERT: B  171 ILE cc_start: 0.6647 (OUTLIER) cc_final: 0.6276 (mp)
  outliers start: 17
  outliers final: 14
  residues processed: 111
  average time/residue: 0.2068
  time to fit residues: 30.8358
Evaluate side-chains
  112 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   12 PHE
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain R residue  299 LEU
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  154 PHE
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 18 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   chunk 93 optimal weight:   20.0000
   chunk 75 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.089468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.075290 restraints weight = 21256.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.076104 restraints weight = 15528.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.076849 restraints weight = 11569.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7556  Z= 0.155
  Angle     :  0.603  12.505  10307  Z= 0.311
  Chirality :  0.041   0.144   1226
  Planarity :  0.004   0.074   1285
  Dihedral  :  4.271  26.038   1038
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.00 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 17.51 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.28), residues: 963
  helix:  2.10 (0.28), residues: 357
  sheet: -0.67 (0.37), residues: 192
  loop : -1.79 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R  75 
 HIS   0.005   0.001   HIS R 135 
 PHE   0.013   0.001   PHE A 196 
 TYR   0.015   0.002   TYR B 264 
 ARG   0.007   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03569 (  343)
  hydrogen bonds       : angle       4.68702 ( 1014)
  SS BOND              : bond        0.00673 (    5)
  SS BOND              : angle       1.35837 (   10)
  covalent geometry    : bond        0.00367 ( 7551)
  covalent geometry    : angle       0.60193 (10297)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.871 
Fit side-chains
REVERT: R  212 ILE cc_start: 0.8096 (tt) cc_final: 0.7826 (tt)
REVERT: R  270 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.6151 (pp)
REVERT: B  134 ARG cc_start: 0.5897 (tpm170) cc_final: 0.5576 (tpm170)
REVERT: B  171 ILE cc_start: 0.6682 (OUTLIER) cc_final: 0.6286 (mp)
  outliers start: 24
  outliers final: 19
  residues processed: 110
  average time/residue: 0.2151
  time to fit residues: 32.0508
Evaluate side-chains
  119 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   12 PHE
Chi-restraints excluded: chain R residue   21 TYR
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  204 HIS
Chi-restraints excluded: chain R residue  222 MET
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain R residue  299 LEU
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  154 PHE
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   37 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 90 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0030
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
L 153 GLN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.090203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.076237 restraints weight = 21222.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.077870 restraints weight = 15513.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.078515 restraints weight = 11596.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7556  Z= 0.126
  Angle     :  0.584  12.032  10307  Z= 0.302
  Chirality :  0.040   0.140   1226
  Planarity :  0.004   0.070   1285
  Dihedral  :  4.203  25.625   1038
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.10 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.74 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.28), residues: 963
  helix:  2.10 (0.28), residues: 358
  sheet: -0.64 (0.37), residues: 192
  loop : -1.81 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R  75 
 HIS   0.004   0.001   HIS R 135 
 PHE   0.013   0.001   PHE A 196 
 TYR   0.014   0.001   TYR B 264 
 ARG   0.007   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03330 (  343)
  hydrogen bonds       : angle       4.60132 ( 1014)
  SS BOND              : bond        0.00549 (    5)
  SS BOND              : angle       1.20480 (   10)
  covalent geometry    : bond        0.00293 ( 7551)
  covalent geometry    : angle       0.58349 (10297)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.798 
Fit side-chains
REVERT: R  212 ILE cc_start: 0.8067 (tt) cc_final: 0.7811 (tt)
REVERT: R  270 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6152 (pp)
REVERT: B  134 ARG cc_start: 0.5872 (tpm170) cc_final: 0.5554 (tpm170)
REVERT: B  171 ILE cc_start: 0.6693 (OUTLIER) cc_final: 0.6307 (mp)
  outliers start: 19
  outliers final: 15
  residues processed: 110
  average time/residue: 0.2025
  time to fit residues: 29.8228
Evaluate side-chains
  113 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   12 PHE
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain R residue  299 LEU
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  154 PHE
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 80 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.089953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.075222 restraints weight = 21223.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.075445 restraints weight = 16580.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.076013 restraints weight = 13613.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.3411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7556  Z= 0.144
  Angle     :  0.605  11.932  10307  Z= 0.313
  Chirality :  0.041   0.144   1226
  Planarity :  0.004   0.066   1285
  Dihedral  :  4.301  25.660   1038
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.00 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 18.88 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.28), residues: 963
  helix:  2.00 (0.28), residues: 361
  sheet: -0.71 (0.36), residues: 192
  loop : -1.79 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R  75 
 HIS   0.005   0.001   HIS R 135 
 PHE   0.013   0.001   PHE A 196 
 TYR   0.018   0.002   TYR L 149 
 ARG   0.008   0.001   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03499 (  343)
  hydrogen bonds       : angle       4.66895 ( 1014)
  SS BOND              : bond        0.00649 (    5)
  SS BOND              : angle       1.31976 (   10)
  covalent geometry    : bond        0.00340 ( 7551)
  covalent geometry    : angle       0.60400 (10297)

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.792 
Fit side-chains
REVERT: R  212 ILE cc_start: 0.8099 (tt) cc_final: 0.7826 (tt)
REVERT: R  270 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6174 (pp)
REVERT: B  134 ARG cc_start: 0.5892 (tpm170) cc_final: 0.5551 (tpm170)
REVERT: B  171 ILE cc_start: 0.6674 (OUTLIER) cc_final: 0.6290 (mp)
  outliers start: 20
  outliers final: 17
  residues processed: 107
  average time/residue: 0.2196
  time to fit residues: 31.7382
Evaluate side-chains
  111 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   21 TYR
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  184 HIS
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  223 SER
Chi-restraints excluded: chain R residue  257 VAL
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain R residue  299 LEU
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  154 PHE
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   37 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 23 optimal weight:    0.6980
   chunk 94 optimal weight:   10.0000
   chunk 84 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
A 306 GLN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.090020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.075867 restraints weight = 21277.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.076584 restraints weight = 17126.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.077673 restraints weight = 12989.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7556  Z= 0.132
  Angle     :  0.598  11.861  10307  Z= 0.307
  Chirality :  0.041   0.141   1226
  Planarity :  0.004   0.065   1285
  Dihedral  :  4.234  25.491   1038
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.20 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 19.02 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.28), residues: 963
  helix:  2.02 (0.28), residues: 360
  sheet: -0.67 (0.36), residues: 192
  loop : -1.83 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R  75 
 HIS   0.005   0.001   HIS R 135 
 PHE   0.013   0.001   PHE A 196 
 TYR   0.014   0.001   TYR B 264 
 ARG   0.008   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03374 (  343)
  hydrogen bonds       : angle       4.61820 ( 1014)
  SS BOND              : bond        0.00590 (    5)
  SS BOND              : angle       1.26601 (   10)
  covalent geometry    : bond        0.00309 ( 7551)
  covalent geometry    : angle       0.59734 (10297)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2336.44 seconds
wall clock time: 41 minutes 53.35 seconds (2513.35 seconds total)