Starting phenix.real_space_refine
on Fri Jun  6 04:47:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t6t_25727/06_2025/7t6t_25727_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t6t_25727/06_2025/7t6t_25727.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7t6t_25727/06_2025/7t6t_25727.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t6t_25727/06_2025/7t6t_25727.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t6t_25727/06_2025/7t6t_25727_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t6t_25727/06_2025/7t6t_25727_neut.cif"
  }
  resolution = 3.2
  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=   0.005 sd=   0.052
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      53      5.16       5
     C    4593      2.51       5
     N    1216      2.21       5
     O    1302      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7164
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1753
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2584
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "C"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "L"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 46
          Classifications: {'peptide': 5}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 4}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 2327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 296, 2327
          Classifications: {'peptide': 296}
          Link IDs: {'PTRANS': 12, 'TRANS': 283}
    Chain: "R"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 36
          Unusual residues: {'PLM': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.80, per 1000 atoms: 0.67
  Number of scatterers: 7164
  At special positions: 0
  Unit cell: (87.78, 104.5, 123.31, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    1302      8.00
     N    1216      7.00
     C    4593      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  98 " - pdb=" SG  CYS R 176 " 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: 1.80
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1706

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      47.4% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 33
      removed outlier: 3.879A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 52
      removed outlier: 3.979A  pdb=" N   LYS A  46 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
      removed outlier: 5.818A  pdb=" N   THR A  48 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.030A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.727A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.728A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 327 through 351
    Processing helix  chain 'B' and resid 6 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 10 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'R' and resid 23 through 53
      removed outlier: 3.701A  pdb=" N   ILE R  27 " --> pdb=" O   LEU R  23 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE R  28 " --> pdb=" O   PHE R  24 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   THR R  29 " --> pdb=" O   LEU R  25 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 58 through 87
      removed outlier: 3.717A  pdb=" N   PHE R  74 " --> pdb=" O   ALA R  70 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   THR R  75 " --> pdb=" O   ASP R  71 " (cutoff:3.500A)
      Proline residue:  R  79  - end of helix
    Processing helix  chain 'R' and resid 95 through 129
      removed outlier: 4.291A  pdb=" N   ILE R 116 " --> pdb=" O   SER R 112 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   VAL R 127 " --> pdb=" O   ARG R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 129 through 136
    Processing helix  chain 'R' and resid 138 through 146
    Processing helix  chain 'R' and resid 146 through 156
      removed outlier: 3.992A  pdb=" N   TRP R 150 " --> pdb=" O   ILE R 146 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 157 through 164
    Processing helix  chain 'R' and resid 186 through 208
    Processing helix  chain 'R' and resid 210 through 231
    Processing helix  chain 'R' and resid 237 through 266
      removed outlier: 3.838A  pdb=" N   ALA R 249 " --> pdb=" O   PHE R 245 " (cutoff:3.500A)
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 267 through 272
    Processing helix  chain 'R' and resid 276 through 302
      removed outlier: 3.917A  pdb=" N   GLY R 280 " --> pdb=" O   TYR R 276 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ILE R 281 " --> pdb=" O   LYS R 277 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASN R 293 " --> pdb=" O   LEU R 289 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   SER R 294 " --> pdb=" O   ALA R 290 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   CYS R 295 " --> pdb=" O   PHE R 291 " (cutoff:3.500A)
      Proline residue:  R 298  - end of helix
      removed outlier: 3.723A  pdb=" N   VAL R 302 " --> pdb=" O   PRO R 298 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 305 through 316
      removed outlier: 3.609A  pdb=" N   LEU R 316 " --> pdb=" O   LEU R 312 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.736A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 226
      removed outlier: 6.394A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52
      removed outlier: 6.585A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 5.895A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.701A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.022A  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: 5.854A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.004A  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: 3.706A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.792A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.490A  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: 3.658A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.807A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'R' and resid 167 through 168

    388 hydrogen bonds defined for protein.
    1116 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.04

  Time building geometry restraints manager: 2.11 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1375
        1.32 -     1.45: 1754
        1.45 -     1.57: 4101
        1.57 -     1.69: 0
        1.69 -     1.82: 77
  Bond restraints: 7307
  Sorted by residual:
  bond pdb=" C   LYS C  20 "
       pdb=" O   LYS C  20 "
    ideal  model  delta    sigma   weight residual
    1.236  1.291 -0.055 1.19e-02 7.06e+03 2.11e+01
  bond pdb=" CA  SER R 255 "
       pdb=" CB  SER R 255 "
    ideal  model  delta    sigma   weight residual
    1.531  1.474  0.057 1.33e-02 5.65e+03 1.85e+01
  bond pdb=" N   SER R 181 "
       pdb=" CA  SER R 181 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 7.40e-03 1.83e+04 1.47e+01
  bond pdb=" N   VAL R 127 "
       pdb=" CA  VAL R 127 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 9.00e-03 1.23e+04 1.28e+01
  bond pdb=" N   VAL R 174 "
       pdb=" CA  VAL R 174 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.15e-02 7.56e+03 1.27e+01
  ... (remaining 7302 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 7649
        1.89 -     3.77: 2059
        3.77 -     5.66: 148
        5.66 -     7.54: 22
        7.54 -     9.43: 5
  Bond angle restraints: 9883
  Sorted by residual:
  angle pdb=" N   PRO R 182 "
        pdb=" CA  PRO R 182 "
        pdb=" C   PRO R 182 "
      ideal   model   delta    sigma   weight residual
     113.84  104.41    9.43 1.30e+00 5.92e-01 5.26e+01
  angle pdb=" N   ASP B 291 "
        pdb=" CA  ASP B 291 "
        pdb=" C   ASP B 291 "
      ideal   model   delta    sigma   weight residual
     112.93  106.05    6.88 1.12e+00 7.97e-01 3.78e+01
  angle pdb=" N   LEU R 300 "
        pdb=" CA  LEU R 300 "
        pdb=" CB  LEU R 300 "
      ideal   model   delta    sigma   weight residual
     110.88  102.71    8.17 1.38e+00 5.25e-01 3.51e+01
  angle pdb=" N   VAL R 266 "
        pdb=" CA  VAL R 266 "
        pdb=" C   VAL R 266 "
      ideal   model   delta    sigma   weight residual
     112.83  107.05    5.78 9.90e-01 1.02e+00 3.41e+01
  angle pdb=" N   MET R 304 "
        pdb=" CA  MET R 304 "
        pdb=" C   MET R 304 "
      ideal   model   delta    sigma   weight residual
     112.92  105.86    7.06 1.23e+00 6.61e-01 3.29e+01
  ... (remaining 9878 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 3909
       16.92 -    33.85: 333
       33.85 -    50.77: 80
       50.77 -    67.69: 13
       67.69 -    84.62: 3
  Dihedral angle restraints: 4338
    sinusoidal: 1709
      harmonic: 2629
  Sorted by residual:
  dihedral pdb=" CB  CYS R  98 "
           pdb=" SG  CYS R  98 "
           pdb=" SG  CYS R 176 "
           pdb=" CB  CYS R 176 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  177.62  -84.62     1      1.00e+01 1.00e-02 8.70e+01
  dihedral pdb=" C   PHE R 178 "
           pdb=" N   PHE R 178 "
           pdb=" CA  PHE R 178 "
           pdb=" CB  PHE R 178 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.55  -10.05     0      2.50e+00 1.60e-01 1.62e+01
  dihedral pdb=" C   GLU R 189 "
           pdb=" N   GLU R 189 "
           pdb=" CA  GLU R 189 "
           pdb=" CB  GLU R 189 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.08    9.48     0      2.50e+00 1.60e-01 1.44e+01
  ... (remaining 4335 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 532
       0.070 -    0.140: 398
       0.140 -    0.211: 169
       0.211 -    0.281: 34
       0.281 -    0.351: 4
  Chirality restraints: 1137
  Sorted by residual:
  chirality pdb=" CA  PHE B 235 "
            pdb=" N   PHE B 235 "
            pdb=" C   PHE B 235 "
            pdb=" CB  PHE B 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.08e+00
  chirality pdb=" CA  LEU B  79 "
            pdb=" N   LEU B  79 "
            pdb=" C   LEU B  79 "
            pdb=" CB  LEU B  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.91e+00
  chirality pdb=" CA  PHE R 178 "
            pdb=" N   PHE R 178 "
            pdb=" C   PHE R 178 "
            pdb=" CB  PHE R 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.54e+00
  ... (remaining 1134 not shown)

  Planarity restraints: 1241
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   FME L   1 "    0.057 2.00e-02 2.50e+03   7.27e-02 5.28e+01
        pdb=" CA  FME L   1 "   -0.064 2.00e-02 2.50e+03
        pdb=" CN  FME L   1 "    0.086 2.00e-02 2.50e+03
        pdb=" O1  FME L   1 "   -0.080 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C  24 "   -0.023 2.00e-02 2.50e+03   4.56e-02 2.08e+01
        pdb=" C   ASN C  24 "    0.079 2.00e-02 2.50e+03
        pdb=" O   ASN C  24 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   ILE C  25 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C  19 "    0.022 2.00e-02 2.50e+03   4.26e-02 1.81e+01
        pdb=" C   LEU C  19 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   LEU C  19 "    0.027 2.00e-02 2.50e+03
        pdb=" N   LYS C  20 "    0.025 2.00e-02 2.50e+03
  ... (remaining 1238 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 968
        2.76 -     3.29: 7499
        3.29 -     3.83: 11775
        3.83 -     4.36: 15301
        4.36 -     4.90: 25450
  Nonbonded interactions: 60993
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 313 "
            pdb=" N   ARG B 314 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OG1 THR B  34 "
            pdb=" O   LEU B 300 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.350 3.040
  ... (remaining 60988 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.320
  Find NCS groups from input model:        0.070
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
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      :  0.011   0.075   7308  Z= 0.835
  Angle     :  1.551   9.431   9885  Z= 1.170
  Chirality :  0.105   0.351   1137
  Planarity :  0.008   0.073   1241
  Dihedral  : 13.221  78.320   2629
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  5.68 %
    Favored  : 93.15 %
  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 (0.27), residues: 893
  helix:  1.10 (0.25), residues: 395
  sheet: -0.77 (0.38), residues: 178
  loop : -0.42 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP R 132 
 HIS   0.012   0.002   HIS B  54 
 PHE   0.013   0.002   PHE R 110 
 TYR   0.013   0.002   TYR C  40 
 ARG   0.005   0.001   ARG R 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18182 (  388)
  hydrogen bonds       : angle       7.59724 ( 1116)
  SS BOND              : bond        0.01070 (    1)
  SS BOND              : angle       3.49872 (    2)
  covalent geometry    : bond        0.01148 ( 7307)
  covalent geometry    : angle       1.55025 ( 9883)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 293
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.8017 (p0) cc_final: 0.7781 (p0)
REVERT: A   38 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8012 (tt)
REVERT: A  251 ASP cc_start: 0.7989 (t0) cc_final: 0.7697 (t0)
REVERT: A  252 SER cc_start: 0.8868 (t) cc_final: 0.8664 (t)
REVERT: A  262 THR cc_start: 0.9096 (m) cc_final: 0.8782 (p)
REVERT: A  276 GLU cc_start: 0.7594 (mp0) cc_final: 0.6575 (mp0)
REVERT: A  280 LYS cc_start: 0.8507 (mptt) cc_final: 0.8092 (mptt)
REVERT: A  296 TYR cc_start: 0.8746 (t80) cc_final: 0.8131 (t80)
REVERT: A  312 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8329 (mmmt)
REVERT: A  321 THR cc_start: 0.8481 (m) cc_final: 0.8196 (p)
REVERT: B   13 GLN cc_start: 0.8188 (tt0) cc_final: 0.7962 (tt0)
REVERT: B   19 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7693 (ttp80)
REVERT: B   50 THR cc_start: 0.8206 (m) cc_final: 0.8006 (t)
REVERT: B  175 GLN cc_start: 0.7949 (pp30) cc_final: 0.7548 (pp30)
REVERT: B  176 GLN cc_start: 0.8405 (mt0) cc_final: 0.7794 (mt0)
REVERT: B  189 SER cc_start: 0.8737 (p) cc_final: 0.8491 (p)
REVERT: B  212 ASP cc_start: 0.7385 (m-30) cc_final: 0.7167 (t0)
REVERT: B  225 HIS cc_start: 0.8517 (m-70) cc_final: 0.8283 (m-70)
REVERT: B  243 THR cc_start: 0.8572 (m) cc_final: 0.8211 (p)
REVERT: B  247 ASP cc_start: 0.8079 (p0) cc_final: 0.7822 (p0)
REVERT: B  258 ASP cc_start: 0.7620 (t0) cc_final: 0.7114 (t0)
REVERT: B  333 ASP cc_start: 0.7086 (p0) cc_final: 0.6852 (p0)
REVERT: C   18 GLN cc_start: 0.8152 (tp-100) cc_final: 0.7705 (tp40)
REVERT: R   63 SER cc_start: 0.8003 (m) cc_final: 0.7765 (p)
REVERT: R   80 PHE cc_start: 0.8520 (m-80) cc_final: 0.8246 (m-80)
REVERT: R  190 ARG cc_start: 0.8510 (ttp80) cc_final: 0.8236 (ttp-170)
REVERT: R  207 ILE cc_start: 0.8840 (pt) cc_final: 0.8514 (mm)
REVERT: R  265 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8106 (p)
REVERT: R  277 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8548 (mmmt)
REVERT: R  294 SER cc_start: 0.8550 (m) cc_final: 0.8279 (t)
REVERT: R  302 VAL cc_start: 0.8408 (m) cc_final: 0.8039 (t)
  outliers start: 9
  outliers final: 1
  residues processed: 295
  average time/residue: 0.2289
  time to fit residues: 85.5031
Evaluate side-chains
  257 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 254
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain R residue  265 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 66 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
B 311 HIS
R  57 HIS
R 231 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.105977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.093515 restraints weight = 12726.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.60
r_work: 0.3207 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7308  Z= 0.164
  Angle     :  0.614   6.789   9885  Z= 0.335
  Chirality :  0.046   0.183   1137
  Planarity :  0.005   0.050   1241
  Dihedral  :  5.852  48.962   1006
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 16.15 %
    Favored  : 80.49 %
  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 (0.27), residues: 893
  helix:  0.83 (0.25), residues: 402
  sheet: -0.49 (0.38), residues: 171
  loop : -0.94 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.019   0.002   PHE R 178 
 TYR   0.016   0.002   TYR B 124 
 ARG   0.005   0.001   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05087 (  388)
  hydrogen bonds       : angle       5.34848 ( 1116)
  SS BOND              : bond        0.00350 (    1)
  SS BOND              : angle       1.11805 (    2)
  covalent geometry    : bond        0.00349 ( 7307)
  covalent geometry    : angle       0.61396 ( 9883)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 269
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8081 (t0) cc_final: 0.7717 (m-30)
REVERT: A  209 LYS cc_start: 0.8527 (ttmt) cc_final: 0.8118 (ttpp)
REVERT: A  251 ASP cc_start: 0.8337 (t0) cc_final: 0.8027 (t0)
REVERT: A  252 SER cc_start: 0.8787 (t) cc_final: 0.8560 (t)
REVERT: A  262 THR cc_start: 0.9255 (m) cc_final: 0.8653 (p)
REVERT: A  271 LYS cc_start: 0.8421 (pttp) cc_final: 0.7983 (pttm)
REVERT: A  279 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8367 (mtpp)
REVERT: A  280 LYS cc_start: 0.8756 (mptt) cc_final: 0.7838 (mptt)
REVERT: A  296 TYR cc_start: 0.8818 (t80) cc_final: 0.8158 (t80)
REVERT: A  312 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8454 (mmmt)
REVERT: A  321 THR cc_start: 0.8798 (m) cc_final: 0.8423 (p)
REVERT: A  332 VAL cc_start: 0.8735 (t) cc_final: 0.8455 (p)
REVERT: B   16 ASN cc_start: 0.8647 (m-40) cc_final: 0.8302 (m-40)
REVERT: B   19 ARG cc_start: 0.8347 (ttp-110) cc_final: 0.7874 (ttp80)
REVERT: B   29 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7956 (t)
REVERT: B   50 THR cc_start: 0.8719 (m) cc_final: 0.8447 (t)
REVERT: B  130 GLU cc_start: 0.5486 (tp30) cc_final: 0.4931 (tp30)
REVERT: B  176 GLN cc_start: 0.8784 (mt0) cc_final: 0.8437 (mt0)
REVERT: B  186 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7200 (p0)
REVERT: B  189 SER cc_start: 0.8859 (p) cc_final: 0.8611 (p)
REVERT: B  225 HIS cc_start: 0.8695 (m-70) cc_final: 0.8238 (m-70)
REVERT: B  226 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8165 (mm-30)
REVERT: B  228 ASP cc_start: 0.7588 (m-30) cc_final: 0.6888 (m-30)
REVERT: B  243 THR cc_start: 0.8748 (m) cc_final: 0.8423 (t)
REVERT: B  258 ASP cc_start: 0.8079 (t0) cc_final: 0.7190 (t0)
REVERT: B  262 MET cc_start: 0.8368 (tpp) cc_final: 0.8074 (tpp)
REVERT: B  292 PHE cc_start: 0.8483 (m-10) cc_final: 0.7978 (m-80)
REVERT: B  312 ASP cc_start: 0.8315 (t0) cc_final: 0.7944 (t0)
REVERT: B  333 ASP cc_start: 0.7669 (p0) cc_final: 0.7429 (p0)
REVERT: C   21 MET cc_start: 0.8460 (mmm) cc_final: 0.7709 (mmm)
REVERT: R   53 PHE cc_start: 0.7990 (m-10) cc_final: 0.7761 (m-10)
REVERT: R  133 THR cc_start: 0.8851 (t) cc_final: 0.8473 (p)
REVERT: R  152 MET cc_start: 0.8282 (mmm) cc_final: 0.8045 (mmm)
REVERT: R  197 MET cc_start: 0.8376 (mmp) cc_final: 0.8063 (mmt)
REVERT: R  207 ILE cc_start: 0.8834 (pt) cc_final: 0.8545 (mm)
REVERT: R  215 SER cc_start: 0.8545 (t) cc_final: 0.8287 (p)
REVERT: R  230 LYS cc_start: 0.8534 (ttpp) cc_final: 0.8149 (ttpp)
REVERT: R  231 GLN cc_start: 0.7906 (mm110) cc_final: 0.7580 (mm110)
REVERT: R  277 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8615 (mmmt)
REVERT: R  294 SER cc_start: 0.8603 (m) cc_final: 0.8180 (t)
  outliers start: 26
  outliers final: 11
  residues processed: 279
  average time/residue: 0.2227
  time to fit residues: 79.0223
Evaluate side-chains
  278 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 264
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue  173 THR
Chi-restraints excluded: chain R residue  195 VAL
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain R residue  296 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   chunk 56 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9980
   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 213 HIS
A 241 ASN
A 269 ASN
B 119 ASN
B 220 GLN
R  57 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.105045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.091979 restraints weight = 12755.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.57
r_work: 0.3181 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7308  Z= 0.151
  Angle     :  0.564   6.958   9885  Z= 0.304
  Chirality :  0.044   0.168   1137
  Planarity :  0.004   0.048   1241
  Dihedral  :  5.561  47.477   1003
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 19.90 %
    Favored  : 76.49 %
  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 (0.27), residues: 893
  helix:  0.86 (0.26), residues: 402
  sheet: -0.41 (0.40), residues: 159
  loop : -1.13 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 169 
 HIS   0.002   0.001   HIS B 183 
 PHE   0.025   0.002   PHE R 180 
 TYR   0.015   0.001   TYR B 124 
 ARG   0.006   0.001   ARG R 267 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04441 (  388)
  hydrogen bonds       : angle       5.07135 ( 1116)
  SS BOND              : bond        0.00249 (    1)
  SS BOND              : angle       1.81241 (    2)
  covalent geometry    : bond        0.00336 ( 7307)
  covalent geometry    : angle       0.56382 ( 9883)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 274
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8133 (mtpp)
REVERT: A  198 MET cc_start: 0.8339 (ttm) cc_final: 0.8139 (ttm)
REVERT: A  251 ASP cc_start: 0.8319 (t0) cc_final: 0.8035 (t0)
REVERT: A  257 LYS cc_start: 0.9053 (ptmm) cc_final: 0.8680 (ptmm)
REVERT: A  262 THR cc_start: 0.9244 (m) cc_final: 0.8680 (p)
REVERT: A  279 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8568 (mtmt)
REVERT: A  280 LYS cc_start: 0.8793 (mptt) cc_final: 0.8161 (mptt)
REVERT: A  285 ILE cc_start: 0.9279 (mm) cc_final: 0.9073 (tt)
REVERT: A  296 TYR cc_start: 0.8906 (t80) cc_final: 0.8331 (t80)
REVERT: A  312 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8507 (mmmt)
REVERT: A  321 THR cc_start: 0.8876 (m) cc_final: 0.8442 (p)
REVERT: A  341 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7943 (t0)
REVERT: B   10 GLU cc_start: 0.8924 (tp30) cc_final: 0.8637 (tp30)
REVERT: B   19 ARG cc_start: 0.8370 (ttp-110) cc_final: 0.8035 (ttp80)
REVERT: B   29 THR cc_start: 0.8205 (p) cc_final: 0.7957 (t)
REVERT: B  176 GLN cc_start: 0.8710 (mt0) cc_final: 0.8401 (mt0)
REVERT: B  186 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.7176 (p0)
REVERT: B  189 SER cc_start: 0.8861 (p) cc_final: 0.8610 (p)
REVERT: B  217 MET cc_start: 0.8475 (ppp) cc_final: 0.7948 (ppp)
REVERT: B  225 HIS cc_start: 0.8674 (m-70) cc_final: 0.8288 (m-70)
REVERT: B  226 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8150 (mm-30)
REVERT: B  243 THR cc_start: 0.8730 (m) cc_final: 0.8413 (t)
REVERT: B  258 ASP cc_start: 0.7957 (t0) cc_final: 0.7069 (t0)
REVERT: B  262 MET cc_start: 0.8242 (tpp) cc_final: 0.7812 (tpp)
REVERT: B  292 PHE cc_start: 0.8474 (m-10) cc_final: 0.7913 (m-80)
REVERT: B  301 LYS cc_start: 0.9018 (mtpp) cc_final: 0.8766 (mmmt)
REVERT: B  311 HIS cc_start: 0.7720 (m-70) cc_final: 0.7327 (m-70)
REVERT: B  312 ASP cc_start: 0.8315 (t0) cc_final: 0.7833 (t0)
REVERT: B  333 ASP cc_start: 0.7782 (p0) cc_final: 0.7491 (p0)
REVERT: C   17 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8296 (mm-30)
REVERT: C   21 MET cc_start: 0.8230 (mmm) cc_final: 0.7853 (mmm)
REVERT: R  152 MET cc_start: 0.8325 (mmm) cc_final: 0.8031 (mmm)
REVERT: R  161 ILE cc_start: 0.8547 (tt) cc_final: 0.8335 (pt)
REVERT: R  190 ARG cc_start: 0.8336 (tmm160) cc_final: 0.8105 (tmm160)
REVERT: R  197 MET cc_start: 0.8150 (mmp) cc_final: 0.7804 (mmt)
REVERT: R  220 SER cc_start: 0.8187 (m) cc_final: 0.7820 (p)
REVERT: R  277 LYS cc_start: 0.8852 (mmmt) cc_final: 0.8551 (mmmt)
REVERT: R  294 SER cc_start: 0.8624 (m) cc_final: 0.8206 (t)
REVERT: R  309 ARG cc_start: 0.8591 (ttm110) cc_final: 0.7934 (mtm110)
  outliers start: 28
  outliers final: 17
  residues processed: 285
  average time/residue: 0.2376
  time to fit residues: 85.4011
Evaluate side-chains
  280 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 260
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue   31 LEU
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  173 THR
Chi-restraints excluded: chain R residue  189 GLU
Chi-restraints excluded: chain R residue  195 VAL
Chi-restraints excluded: chain R residue  199 THR
Chi-restraints excluded: chain R residue  226 THR
Chi-restraints excluded: chain R residue  265 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 83 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 54 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 8 optimal weight:    0.5980
   chunk 51 optimal weight:    8.9990
   chunk 87 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 213 HIS
B 230 ASN
C  18 GLN
R  57 HIS
R 297 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.102305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.089383 restraints weight = 12891.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 2.56
r_work: 0.3143 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   7308  Z= 0.235
  Angle     :  0.591   6.534   9885  Z= 0.320
  Chirality :  0.045   0.202   1137
  Planarity :  0.005   0.048   1241
  Dihedral  :  5.738  45.277   1003
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 22.48 %
    Favored  : 73.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.27), residues: 893
  helix:  0.79 (0.26), residues: 400
  sheet: -0.54 (0.39), residues: 173
  loop : -1.19 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 169 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.029   0.002   PHE B 199 
 TYR   0.014   0.002   TYR B  59 
 ARG   0.009   0.001   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04440 (  388)
  hydrogen bonds       : angle       5.03646 ( 1116)
  SS BOND              : bond        0.00381 (    1)
  SS BOND              : angle       2.61777 (    2)
  covalent geometry    : bond        0.00521 ( 7307)
  covalent geometry    : angle       0.58985 ( 9883)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 268
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8295 (mtpp)
REVERT: A  205 ARG cc_start: 0.8058 (mmt180) cc_final: 0.7706 (mmt-90)
REVERT: A  251 ASP cc_start: 0.8477 (t0) cc_final: 0.8244 (t0)
REVERT: A  257 LYS cc_start: 0.9106 (ptmm) cc_final: 0.8727 (ptmm)
REVERT: A  276 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7004 (mp0)
REVERT: A  279 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8584 (mtmt)
REVERT: A  280 LYS cc_start: 0.8856 (mptt) cc_final: 0.8254 (mptt)
REVERT: A  296 TYR cc_start: 0.9008 (t80) cc_final: 0.8530 (t80)
REVERT: A  312 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8638 (mmmt)
REVERT: A  321 THR cc_start: 0.8992 (m) cc_final: 0.8571 (p)
REVERT: B   10 GLU cc_start: 0.8928 (tp30) cc_final: 0.8627 (tp30)
REVERT: B   19 ARG cc_start: 0.8583 (ttp-110) cc_final: 0.8211 (ttp80)
REVERT: B  145 TYR cc_start: 0.9039 (p90) cc_final: 0.8518 (p90)
REVERT: B  156 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8129 (mm110)
REVERT: B  176 GLN cc_start: 0.8795 (mt0) cc_final: 0.8550 (mt0)
REVERT: B  186 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7334 (p0)
REVERT: B  188 MET cc_start: 0.8282 (mmm) cc_final: 0.7748 (mmm)
REVERT: B  189 SER cc_start: 0.8953 (p) cc_final: 0.8663 (p)
REVERT: B  217 MET cc_start: 0.8732 (ppp) cc_final: 0.8165 (ppp)
REVERT: B  225 HIS cc_start: 0.8743 (m-70) cc_final: 0.8389 (m-70)
REVERT: B  228 ASP cc_start: 0.7886 (m-30) cc_final: 0.7310 (t0)
REVERT: B  243 THR cc_start: 0.8839 (m) cc_final: 0.8495 (t)
REVERT: B  258 ASP cc_start: 0.8248 (t0) cc_final: 0.7402 (t0)
REVERT: B  292 PHE cc_start: 0.8596 (m-10) cc_final: 0.7973 (m-80)
REVERT: B  301 LYS cc_start: 0.9125 (mtpp) cc_final: 0.8790 (mmmt)
REVERT: B  312 ASP cc_start: 0.8525 (t0) cc_final: 0.7949 (t0)
REVERT: C   18 GLN cc_start: 0.8279 (tp40) cc_final: 0.8064 (tp40)
REVERT: C   20 LYS cc_start: 0.8869 (ttpp) cc_final: 0.8024 (pttm)
REVERT: C   21 MET cc_start: 0.8578 (mmm) cc_final: 0.8303 (mmm)
REVERT: R   25 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8364 (mp)
REVERT: R  133 THR cc_start: 0.8915 (t) cc_final: 0.8680 (p)
REVERT: R  152 MET cc_start: 0.8539 (mmm) cc_final: 0.8238 (mmm)
REVERT: R  161 ILE cc_start: 0.8558 (tt) cc_final: 0.8303 (pt)
REVERT: R  163 ARG cc_start: 0.8824 (mmp80) cc_final: 0.8588 (mmm160)
REVERT: R  195 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8979 (p)
REVERT: R  197 MET cc_start: 0.8400 (mmp) cc_final: 0.8049 (mmt)
REVERT: R  215 SER cc_start: 0.8872 (t) cc_final: 0.8518 (p)
REVERT: R  230 LYS cc_start: 0.8645 (ttpp) cc_final: 0.8259 (ttpp)
REVERT: R  231 GLN cc_start: 0.8149 (mm110) cc_final: 0.7833 (mm110)
REVERT: R  243 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8208 (mm)
REVERT: R  270 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8201 (mt-10)
REVERT: R  273 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.7688 (mp10)
REVERT: R  277 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8742 (mmmt)
REVERT: R  287 SER cc_start: 0.8239 (p) cc_final: 0.7872 (p)
REVERT: R  294 SER cc_start: 0.8766 (m) cc_final: 0.8355 (t)
  outliers start: 35
  outliers final: 23
  residues processed: 283
  average time/residue: 0.2339
  time to fit residues: 83.5130
Evaluate side-chains
  290 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 260
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue   31 LEU
Chi-restraints excluded: chain R residue   69 VAL
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  173 THR
Chi-restraints excluded: chain R residue  195 VAL
Chi-restraints excluded: chain R residue  199 THR
Chi-restraints excluded: chain R residue  208 ILE
Chi-restraints excluded: chain R residue  226 THR
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  252 LEU
Chi-restraints excluded: chain R residue  265 THR
Chi-restraints excluded: chain R residue  273 GLN
Chi-restraints excluded: chain R residue  296 LEU
Chi-restraints excluded: chain R residue  302 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 12 optimal weight:    0.4980
   chunk 39 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN
R  57 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.103249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.090230 restraints weight = 12693.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 2.57
r_work: 0.3160 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7308  Z= 0.174
  Angle     :  0.574   8.164   9885  Z= 0.305
  Chirality :  0.044   0.163   1137
  Planarity :  0.004   0.046   1241
  Dihedral  :  5.672  44.654   1003
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 23.39 %
    Favored  : 71.96 %
  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: 893
  helix:  0.87 (0.26), residues: 403
  sheet: -0.25 (0.41), residues: 159
  loop : -1.24 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.024   0.002   PHE B 199 
 TYR   0.013   0.001   TYR B 124 
 ARG   0.011   0.001   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04170 (  388)
  hydrogen bonds       : angle       4.94311 ( 1116)
  SS BOND              : bond        0.00849 (    1)
  SS BOND              : angle       4.61126 (    2)
  covalent geometry    : bond        0.00387 ( 7307)
  covalent geometry    : angle       0.57006 ( 9883)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 261
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 ARG cc_start: 0.7848 (mmt180) cc_final: 0.7475 (mmt-90)
REVERT: A  257 LYS cc_start: 0.9104 (ptmm) cc_final: 0.8732 (ptmm)
REVERT: A  279 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8481 (mtmt)
REVERT: A  280 LYS cc_start: 0.8903 (mptt) cc_final: 0.8362 (mptt)
REVERT: A  296 TYR cc_start: 0.8997 (t80) cc_final: 0.8599 (t80)
REVERT: A  312 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8615 (mmmt)
REVERT: A  321 THR cc_start: 0.8916 (m) cc_final: 0.8472 (p)
REVERT: A  341 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7938 (t0)
REVERT: B   16 ASN cc_start: 0.8681 (m-40) cc_final: 0.8455 (m-40)
REVERT: B   19 ARG cc_start: 0.8403 (ttp-110) cc_final: 0.8078 (ttp80)
REVERT: B  145 TYR cc_start: 0.8951 (p90) cc_final: 0.8476 (p90)
REVERT: B  186 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7215 (p0)
REVERT: B  189 SER cc_start: 0.8895 (p) cc_final: 0.8661 (p)
REVERT: B  225 HIS cc_start: 0.8687 (m-70) cc_final: 0.8323 (m-70)
REVERT: B  228 ASP cc_start: 0.7635 (m-30) cc_final: 0.7157 (t0)
REVERT: B  243 THR cc_start: 0.8722 (m) cc_final: 0.8064 (p)
REVERT: B  258 ASP cc_start: 0.8063 (t0) cc_final: 0.7165 (t0)
REVERT: B  262 MET cc_start: 0.8253 (tpp) cc_final: 0.7992 (tpp)
REVERT: B  292 PHE cc_start: 0.8511 (m-10) cc_final: 0.7910 (m-80)
REVERT: B  312 ASP cc_start: 0.8153 (t0) cc_final: 0.7685 (t0)
REVERT: C   17 GLU cc_start: 0.8742 (mm-30) cc_final: 0.7411 (mm-30)
REVERT: C   20 LYS cc_start: 0.8797 (ttpp) cc_final: 0.7691 (pttm)
REVERT: C   21 MET cc_start: 0.8313 (mmm) cc_final: 0.8076 (mmm)
REVERT: R   82 MET cc_start: 0.7891 (mpp) cc_final: 0.7687 (mpp)
REVERT: R  133 THR cc_start: 0.8778 (t) cc_final: 0.8500 (p)
REVERT: R  152 MET cc_start: 0.8308 (mmm) cc_final: 0.7973 (mmm)
REVERT: R  163 ARG cc_start: 0.8687 (mmp80) cc_final: 0.8467 (mmm160)
REVERT: R  195 VAL cc_start: 0.9092 (OUTLIER) cc_final: 0.8888 (p)
REVERT: R  197 MET cc_start: 0.8097 (mmp) cc_final: 0.7793 (mmt)
REVERT: R  215 SER cc_start: 0.8753 (t) cc_final: 0.8438 (p)
REVERT: R  220 SER cc_start: 0.8165 (m) cc_final: 0.7874 (p)
REVERT: R  231 GLN cc_start: 0.7937 (mm110) cc_final: 0.7645 (mm110)
REVERT: R  243 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8088 (mm)
REVERT: R  244 SER cc_start: 0.8371 (m) cc_final: 0.8152 (m)
REVERT: R  270 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7948 (mt-10)
REVERT: R  273 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7711 (mp10)
REVERT: R  277 LYS cc_start: 0.8958 (mmmt) cc_final: 0.8626 (mmmt)
REVERT: R  287 SER cc_start: 0.8165 (p) cc_final: 0.7792 (p)
REVERT: R  294 SER cc_start: 0.8782 (m) cc_final: 0.8354 (t)
REVERT: R  309 ARG cc_start: 0.8546 (ttm110) cc_final: 0.8114 (mtm110)
  outliers start: 36
  outliers final: 22
  residues processed: 275
  average time/residue: 0.2369
  time to fit residues: 82.1421
Evaluate side-chains
  287 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 259
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue   31 LEU
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  173 THR
Chi-restraints excluded: chain R residue  195 VAL
Chi-restraints excluded: chain R residue  199 THR
Chi-restraints excluded: chain R residue  208 ILE
Chi-restraints excluded: chain R residue  226 THR
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  252 LEU
Chi-restraints excluded: chain R residue  273 GLN
Chi-restraints excluded: chain R residue  302 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0570
   chunk 50 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
R  57 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.104509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.091610 restraints weight = 12776.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.51
r_work: 0.3180 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7308  Z= 0.132
  Angle     :  0.562  10.235   9885  Z= 0.298
  Chirality :  0.044   0.177   1137
  Planarity :  0.004   0.041   1241
  Dihedral  :  5.469  43.512   1003
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 24.29 %
    Favored  : 70.80 %
  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: -0.12 (0.28), residues: 893
  helix:  0.90 (0.26), residues: 403
  sheet: -0.13 (0.41), residues: 159
  loop : -1.21 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.002   0.000   HIS B 183 
 PHE   0.023   0.001   PHE R 180 
 TYR   0.011   0.001   TYR B 124 
 ARG   0.008   0.001   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03978 (  388)
  hydrogen bonds       : angle       4.80438 ( 1116)
  SS BOND              : bond        0.01040 (    1)
  SS BOND              : angle       3.35733 (    2)
  covalent geometry    : bond        0.00296 ( 7307)
  covalent geometry    : angle       0.56036 ( 9883)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 278
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 LYS cc_start: 0.9119 (ptmm) cc_final: 0.8775 (ptmm)
REVERT: A  279 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8522 (mtmt)
REVERT: A  280 LYS cc_start: 0.8937 (mptt) cc_final: 0.8464 (mptt)
REVERT: A  296 TYR cc_start: 0.9001 (t80) cc_final: 0.8588 (t80)
REVERT: A  312 LYS cc_start: 0.9014 (mmmt) cc_final: 0.8632 (mmmt)
REVERT: A  321 THR cc_start: 0.9015 (m) cc_final: 0.8584 (p)
REVERT: A  341 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8196 (t0)
REVERT: B   16 ASN cc_start: 0.8744 (m-40) cc_final: 0.8511 (m-40)
REVERT: B   19 ARG cc_start: 0.8573 (ttp-110) cc_final: 0.8248 (ttp80)
REVERT: B  145 TYR cc_start: 0.9015 (p90) cc_final: 0.8566 (p90)
REVERT: B  212 ASP cc_start: 0.8329 (t0) cc_final: 0.8048 (t0)
REVERT: B  237 ASN cc_start: 0.9066 (t0) cc_final: 0.8832 (t0)
REVERT: B  243 THR cc_start: 0.8744 (m) cc_final: 0.8028 (p)
REVERT: B  258 ASP cc_start: 0.8302 (t0) cc_final: 0.7441 (t0)
REVERT: B  262 MET cc_start: 0.8518 (tpp) cc_final: 0.8278 (tpp)
REVERT: B  292 PHE cc_start: 0.8574 (m-10) cc_final: 0.7968 (m-80)
REVERT: B  312 ASP cc_start: 0.8395 (t0) cc_final: 0.7941 (t0)
REVERT: C   17 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8383 (mm-30)
REVERT: C   21 MET cc_start: 0.8617 (mmm) cc_final: 0.8239 (mmm)
REVERT: R   25 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8389 (mp)
REVERT: R  106 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7785 (t0)
REVERT: R  133 THR cc_start: 0.8871 (t) cc_final: 0.8583 (p)
REVERT: R  152 MET cc_start: 0.8427 (mmm) cc_final: 0.8101 (mmm)
REVERT: R  195 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8917 (p)
REVERT: R  197 MET cc_start: 0.8338 (mmp) cc_final: 0.8021 (mmt)
REVERT: R  215 SER cc_start: 0.8830 (t) cc_final: 0.8582 (p)
REVERT: R  220 SER cc_start: 0.8224 (m) cc_final: 0.7974 (p)
REVERT: R  244 SER cc_start: 0.8458 (m) cc_final: 0.8256 (m)
REVERT: R  270 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8241 (mt-10)
REVERT: R  273 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7757 (mp10)
REVERT: R  277 LYS cc_start: 0.9039 (mmmt) cc_final: 0.8816 (mmmt)
REVERT: R  294 SER cc_start: 0.8835 (m) cc_final: 0.8412 (t)
REVERT: R  309 ARG cc_start: 0.8620 (ttm110) cc_final: 0.8173 (mtm110)
  outliers start: 38
  outliers final: 20
  residues processed: 292
  average time/residue: 0.2365
  time to fit residues: 87.4004
Evaluate side-chains
  289 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 263
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue   69 VAL
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  106 ASP
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  112 SER
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  195 VAL
Chi-restraints excluded: chain R residue  199 THR
Chi-restraints excluded: chain R residue  208 ILE
Chi-restraints excluded: chain R residue  273 GLN
Chi-restraints excluded: chain R residue  302 VAL
Chi-restraints excluded: chain R residue  304 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 30 optimal weight:    0.0980
   chunk 74 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 269 ASN
** B  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  57 HIS
R  90 HIS
** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.104667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.091899 restraints weight = 12770.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 2.50
r_work: 0.3185 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.3694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7308  Z= 0.135
  Angle     :  0.579  11.596   9885  Z= 0.301
  Chirality :  0.044   0.178   1137
  Planarity :  0.004   0.039   1241
  Dihedral  :  5.430  46.333   1003
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 26.74 %
    Favored  : 68.99 %
  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: 893
  helix:  0.94 (0.26), residues: 404
  sheet: -0.04 (0.41), residues: 157
  loop : -1.20 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.019   0.001   PHE B 199 
 TYR   0.010   0.001   TYR B 124 
 ARG   0.006   0.001   ARG R 267 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03836 (  388)
  hydrogen bonds       : angle       4.70918 ( 1116)
  SS BOND              : bond        0.00120 (    1)
  SS BOND              : angle       2.86073 (    2)
  covalent geometry    : bond        0.00307 ( 7307)
  covalent geometry    : angle       0.57761 ( 9883)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 261
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6657 (pt0)
REVERT: A  198 MET cc_start: 0.8598 (ttm) cc_final: 0.8361 (ttm)
REVERT: A  204 GLN cc_start: 0.8658 (tp-100) cc_final: 0.8180 (tp40)
REVERT: A  257 LYS cc_start: 0.9093 (ptmm) cc_final: 0.8750 (ptmm)
REVERT: A  279 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8554 (mtmt)
REVERT: A  280 LYS cc_start: 0.8940 (mptt) cc_final: 0.8466 (mptt)
REVERT: A  296 TYR cc_start: 0.8980 (t80) cc_final: 0.8558 (t80)
REVERT: A  309 ASP cc_start: 0.7999 (m-30) cc_final: 0.7583 (m-30)
REVERT: A  312 LYS cc_start: 0.8997 (mmmt) cc_final: 0.8607 (mmmt)
REVERT: A  321 THR cc_start: 0.8930 (m) cc_final: 0.8467 (p)
REVERT: A  341 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8062 (t0)
REVERT: B   16 ASN cc_start: 0.8654 (m-40) cc_final: 0.8435 (m-40)
REVERT: B   19 ARG cc_start: 0.8310 (ttp-110) cc_final: 0.7990 (ttp80)
REVERT: B   45 MET cc_start: 0.8877 (mtt) cc_final: 0.8590 (mtp)
REVERT: B   50 THR cc_start: 0.8751 (m) cc_final: 0.8447 (t)
REVERT: B  145 TYR cc_start: 0.8922 (p90) cc_final: 0.8578 (p90)
REVERT: B  212 ASP cc_start: 0.8116 (t0) cc_final: 0.7872 (t0)
REVERT: B  217 MET cc_start: 0.8525 (ptm) cc_final: 0.7731 (ppp)
REVERT: B  237 ASN cc_start: 0.8901 (t0) cc_final: 0.8677 (t0)
REVERT: B  243 THR cc_start: 0.8683 (m) cc_final: 0.7953 (p)
REVERT: B  258 ASP cc_start: 0.8072 (t0) cc_final: 0.7167 (t0)
REVERT: B  262 MET cc_start: 0.8251 (tpp) cc_final: 0.8039 (mmm)
REVERT: B  292 PHE cc_start: 0.8476 (m-10) cc_final: 0.7897 (m-80)
REVERT: B  312 ASP cc_start: 0.8082 (t0) cc_final: 0.7673 (t0)
REVERT: C   17 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8394 (mm-30)
REVERT: C   21 MET cc_start: 0.8307 (mmm) cc_final: 0.7931 (mmm)
REVERT: C   52 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.8071 (p)
REVERT: R  100 PHE cc_start: 0.8348 (t80) cc_final: 0.7991 (t80)
REVERT: R  106 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7479 (t0)
REVERT: R  133 THR cc_start: 0.8783 (t) cc_final: 0.8478 (p)
REVERT: R  152 MET cc_start: 0.8234 (mmm) cc_final: 0.7893 (mmm)
REVERT: R  195 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8838 (p)
REVERT: R  197 MET cc_start: 0.8005 (mmp) cc_final: 0.7756 (mmt)
REVERT: R  270 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7917 (mt-10)
REVERT: R  273 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7754 (mp10)
REVERT: R  277 LYS cc_start: 0.8978 (mmmt) cc_final: 0.8606 (mmmt)
REVERT: R  287 SER cc_start: 0.8082 (p) cc_final: 0.7716 (p)
REVERT: R  294 SER cc_start: 0.8742 (m) cc_final: 0.8307 (t)
REVERT: R  306 GLN cc_start: 0.8600 (tt0) cc_final: 0.8396 (tp40)
REVERT: R  309 ARG cc_start: 0.8543 (ttm110) cc_final: 0.8095 (mtm110)
  outliers start: 33
  outliers final: 20
  residues processed: 275
  average time/residue: 0.2350
  time to fit residues: 81.3264
Evaluate side-chains
  278 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 252
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  106 ASP
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  129 HIS
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  195 VAL
Chi-restraints excluded: chain R residue  199 THR
Chi-restraints excluded: chain R residue  208 ILE
Chi-restraints excluded: chain R residue  252 LEU
Chi-restraints excluded: chain R residue  273 GLN
Chi-restraints excluded: chain R residue  302 VAL
Chi-restraints excluded: chain R residue  304 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 51 optimal weight:    8.9990
   chunk 50 optimal weight:    0.6980
   chunk 78 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
R  57 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.104617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.091757 restraints weight = 12914.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.54
r_work: 0.3185 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7308  Z= 0.139
  Angle     :  0.588  12.122   9885  Z= 0.307
  Chirality :  0.044   0.182   1137
  Planarity :  0.004   0.039   1241
  Dihedral  :  5.299  43.966   1003
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 27.13 %
    Favored  : 69.25 %
  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: -0.06 (0.28), residues: 893
  helix:  0.99 (0.26), residues: 404
  sheet: -0.09 (0.40), residues: 157
  loop : -1.25 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.002   0.001   HIS A 213 
 PHE   0.022   0.001   PHE R 180 
 TYR   0.011   0.001   TYR B 124 
 ARG   0.007   0.001   ARG R 267 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03851 (  388)
  hydrogen bonds       : angle       4.66983 ( 1116)
  SS BOND              : bond        0.00254 (    1)
  SS BOND              : angle       2.73151 (    2)
  covalent geometry    : bond        0.00314 ( 7307)
  covalent geometry    : angle       0.58658 ( 9883)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 256
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6699 (pt0)
REVERT: A   33 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8018 (tt0)
REVERT: A  197 LYS cc_start: 0.8618 (mtpp) cc_final: 0.8161 (ttmm)
REVERT: A  257 LYS cc_start: 0.9102 (ptmm) cc_final: 0.8765 (ptmm)
REVERT: A  279 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8535 (mtmt)
REVERT: A  280 LYS cc_start: 0.8947 (mptt) cc_final: 0.8449 (mptt)
REVERT: A  296 TYR cc_start: 0.8984 (t80) cc_final: 0.8552 (t80)
REVERT: A  309 ASP cc_start: 0.8120 (m-30) cc_final: 0.7805 (m-30)
REVERT: A  312 LYS cc_start: 0.9018 (mmmt) cc_final: 0.8614 (mmmt)
REVERT: A  321 THR cc_start: 0.9062 (m) cc_final: 0.8620 (p)
REVERT: B   19 ARG cc_start: 0.8517 (ttp-110) cc_final: 0.8221 (ttp80)
REVERT: B   45 MET cc_start: 0.9105 (mtt) cc_final: 0.8817 (mtp)
REVERT: B  101 MET cc_start: 0.9015 (mtp) cc_final: 0.8766 (mtp)
REVERT: B  145 TYR cc_start: 0.8990 (p90) cc_final: 0.8540 (p90)
REVERT: B  212 ASP cc_start: 0.8345 (t0) cc_final: 0.8048 (t0)
REVERT: B  237 ASN cc_start: 0.9044 (t0) cc_final: 0.8794 (t0)
REVERT: B  243 THR cc_start: 0.8801 (m) cc_final: 0.8083 (p)
REVERT: B  258 ASP cc_start: 0.8305 (t0) cc_final: 0.7462 (t0)
REVERT: B  292 PHE cc_start: 0.8564 (m-10) cc_final: 0.7960 (m-80)
REVERT: B  312 ASP cc_start: 0.8356 (t0) cc_final: 0.7899 (t0)
REVERT: C   17 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8488 (mm-30)
REVERT: C   21 MET cc_start: 0.8609 (mmm) cc_final: 0.8184 (mmm)
REVERT: R  100 PHE cc_start: 0.8310 (t80) cc_final: 0.7961 (t80)
REVERT: R  106 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7781 (t0)
REVERT: R  133 THR cc_start: 0.8915 (t) cc_final: 0.8616 (p)
REVERT: R  152 MET cc_start: 0.8377 (mmm) cc_final: 0.8046 (mmm)
REVERT: R  195 VAL cc_start: 0.9109 (p) cc_final: 0.8888 (p)
REVERT: R  197 MET cc_start: 0.8301 (mmp) cc_final: 0.8029 (mmt)
REVERT: R  270 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8231 (mt-10)
REVERT: R  273 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7761 (mp10)
REVERT: R  277 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8679 (mmmt)
REVERT: R  287 SER cc_start: 0.8136 (p) cc_final: 0.7774 (p)
REVERT: R  294 SER cc_start: 0.8812 (m) cc_final: 0.8374 (t)
REVERT: R  309 ARG cc_start: 0.8639 (ttm110) cc_final: 0.8174 (mtm110)
  outliers start: 28
  outliers final: 20
  residues processed: 268
  average time/residue: 0.2534
  time to fit residues: 85.2543
Evaluate side-chains
  275 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 252
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   69 VAL
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  106 ASP
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  129 HIS
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  199 THR
Chi-restraints excluded: chain R residue  273 GLN
Chi-restraints excluded: chain R residue  302 VAL
Chi-restraints excluded: chain R residue  304 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 47 optimal weight:    0.0980
   chunk 20 optimal weight:    1.9990
   chunk 46 optimal weight:    0.1980
   chunk 70 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 77 optimal weight:    0.1980
   chunk 75 optimal weight:    0.0010
   overall best weight:    0.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.106704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.093899 restraints weight = 12948.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 2.55
r_work: 0.3221 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.4026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7308  Z= 0.117
  Angle     :  0.588  12.578   9885  Z= 0.303
  Chirality :  0.043   0.192   1137
  Planarity :  0.004   0.039   1241
  Dihedral  :  5.103  45.563   1003
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 27.39 %
    Favored  : 69.38 %
  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:  0.09 (0.28), residues: 893
  helix:  1.07 (0.27), residues: 404
  sheet:  0.02 (0.40), residues: 158
  loop : -1.14 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.000   HIS A 213 
 PHE   0.021   0.001   PHE R 180 
 TYR   0.010   0.001   TYR B 124 
 ARG   0.007   0.001   ARG R 267 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03716 (  388)
  hydrogen bonds       : angle       4.57013 ( 1116)
  SS BOND              : bond        0.00223 (    1)
  SS BOND              : angle       2.00445 (    2)
  covalent geometry    : bond        0.00255 ( 7307)
  covalent geometry    : angle       0.58763 ( 9883)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 250
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 LYS cc_start: 0.8438 (ttmt) cc_final: 0.8137 (ttpp)
REVERT: A  252 SER cc_start: 0.8861 (t) cc_final: 0.8266 (p)
REVERT: A  269 ASN cc_start: 0.8515 (m110) cc_final: 0.8272 (m110)
REVERT: A  271 LYS cc_start: 0.8571 (pttp) cc_final: 0.8247 (ptmm)
REVERT: A  279 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8683 (mtmm)
REVERT: A  296 TYR cc_start: 0.8970 (t80) cc_final: 0.8341 (t80)
REVERT: A  309 ASP cc_start: 0.7910 (m-30) cc_final: 0.7636 (m-30)
REVERT: A  312 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8587 (mmmt)
REVERT: A  321 THR cc_start: 0.9007 (m) cc_final: 0.8528 (p)
REVERT: A  324 THR cc_start: 0.6203 (p) cc_final: 0.5970 (t)
REVERT: A  345 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8114 (mptt)
REVERT: B    8 ARG cc_start: 0.7270 (mpt180) cc_final: 0.6345 (mpp-170)
REVERT: B   19 ARG cc_start: 0.8303 (ttp-110) cc_final: 0.8031 (ttp80)
REVERT: B   45 MET cc_start: 0.8895 (mtt) cc_final: 0.8631 (mtp)
REVERT: B  101 MET cc_start: 0.8812 (mtp) cc_final: 0.8570 (mtp)
REVERT: B  145 TYR cc_start: 0.8916 (p90) cc_final: 0.8498 (p90)
REVERT: B  212 ASP cc_start: 0.8073 (t0) cc_final: 0.7849 (t0)
REVERT: B  243 THR cc_start: 0.8699 (m) cc_final: 0.7999 (p)
REVERT: B  258 ASP cc_start: 0.8131 (t0) cc_final: 0.7230 (t0)
REVERT: B  292 PHE cc_start: 0.8437 (m-10) cc_final: 0.7877 (m-80)
REVERT: B  312 ASP cc_start: 0.8045 (t0) cc_final: 0.7656 (t0)
REVERT: C   17 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8408 (mm-30)
REVERT: C   21 MET cc_start: 0.8258 (mmm) cc_final: 0.7901 (mmm)
REVERT: R  100 PHE cc_start: 0.8285 (t80) cc_final: 0.7918 (t80)
REVERT: R  106 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7517 (t0)
REVERT: R  152 MET cc_start: 0.8109 (mmm) cc_final: 0.7839 (tpp)
REVERT: R  197 MET cc_start: 0.7930 (mmp) cc_final: 0.7694 (mmt)
REVERT: R  270 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7772 (mt-10)
REVERT: R  273 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7727 (mp10)
REVERT: R  277 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8555 (mmmt)
REVERT: R  287 SER cc_start: 0.8165 (p) cc_final: 0.7764 (p)
REVERT: R  294 SER cc_start: 0.8727 (m) cc_final: 0.8322 (t)
REVERT: R  309 ARG cc_start: 0.8555 (ttm110) cc_final: 0.8102 (mtm110)
  outliers start: 25
  outliers final: 20
  residues processed: 260
  average time/residue: 0.2563
  time to fit residues: 84.9393
Evaluate side-chains
  266 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 243
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  106 ASP
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  112 SER
Chi-restraints excluded: chain R residue  129 HIS
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  199 THR
Chi-restraints excluded: chain R residue  273 GLN
Chi-restraints excluded: chain R residue  302 VAL
Chi-restraints excluded: chain R residue  304 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 72 optimal weight:    0.4980
   chunk 85 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 48 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.103794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.090576 restraints weight = 13107.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.58
r_work: 0.3153 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.3962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7308  Z= 0.177
  Angle     :  0.629  13.246   9885  Z= 0.326
  Chirality :  0.045   0.175   1137
  Planarity :  0.004   0.038   1241
  Dihedral  :  5.337  45.669   1003
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 28.17 %
    Favored  : 68.48 %
  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: -0.00 (0.28), residues: 893
  helix:  1.10 (0.27), residues: 399
  sheet: -0.14 (0.40), residues: 163
  loop : -1.25 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.033   0.002   PHE R  74 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.007   0.001   ARG R 267 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03844 (  388)
  hydrogen bonds       : angle       4.64259 ( 1116)
  SS BOND              : bond        0.00311 (    1)
  SS BOND              : angle       3.00338 (    2)
  covalent geometry    : bond        0.00403 ( 7307)
  covalent geometry    : angle       0.62774 ( 9883)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 246
  time to evaluate  : 1.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.7485 (tm-30) cc_final: 0.6679 (pt0)
REVERT: A  209 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8221 (ttpp)
REVERT: A  252 SER cc_start: 0.8875 (t) cc_final: 0.8355 (p)
REVERT: A  271 LYS cc_start: 0.8558 (pttp) cc_final: 0.8280 (ptmm)
REVERT: A  279 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8594 (mtmm)
REVERT: A  280 LYS cc_start: 0.8937 (mptt) cc_final: 0.8390 (mptt)
REVERT: A  296 TYR cc_start: 0.8955 (t80) cc_final: 0.8308 (t80)
REVERT: A  309 ASP cc_start: 0.7972 (m-30) cc_final: 0.7739 (m-30)
REVERT: A  312 LYS cc_start: 0.8983 (mmmt) cc_final: 0.8564 (mmmt)
REVERT: A  321 THR cc_start: 0.8956 (m) cc_final: 0.8502 (p)
REVERT: A  345 LYS cc_start: 0.8474 (ttmm) cc_final: 0.8094 (mptt)
REVERT: B    8 ARG cc_start: 0.7364 (mpt180) cc_final: 0.6647 (mtm-85)
REVERT: B   19 ARG cc_start: 0.8311 (ttp-110) cc_final: 0.8051 (ttp80)
REVERT: B   25 CYS cc_start: 0.8527 (m) cc_final: 0.8230 (p)
REVERT: B   45 MET cc_start: 0.8894 (mtt) cc_final: 0.8616 (mtp)
REVERT: B  137 ARG cc_start: 0.8261 (tpp-160) cc_final: 0.7981 (tpp-160)
REVERT: B  145 TYR cc_start: 0.8961 (p90) cc_final: 0.8527 (p90)
REVERT: B  212 ASP cc_start: 0.8133 (t0) cc_final: 0.7878 (t0)
REVERT: B  217 MET cc_start: 0.8736 (ptm) cc_final: 0.8499 (ptm)
REVERT: B  243 THR cc_start: 0.8695 (m) cc_final: 0.7997 (p)
REVERT: B  258 ASP cc_start: 0.8201 (t0) cc_final: 0.7269 (t0)
REVERT: B  262 MET cc_start: 0.8236 (tpp) cc_final: 0.7750 (mmt)
REVERT: B  292 PHE cc_start: 0.8527 (m-10) cc_final: 0.7932 (m-80)
REVERT: B  312 ASP cc_start: 0.8046 (t0) cc_final: 0.7607 (t0)
REVERT: C   17 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8428 (mm-30)
REVERT: C   21 MET cc_start: 0.8351 (mmm) cc_final: 0.7956 (mmm)
REVERT: C   32 LYS cc_start: 0.9141 (ttpt) cc_final: 0.8778 (ttpp)
REVERT: R   25 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8337 (mp)
REVERT: R  100 PHE cc_start: 0.8253 (t80) cc_final: 0.7923 (t80)
REVERT: R  152 MET cc_start: 0.8180 (mmm) cc_final: 0.7837 (mmm)
REVERT: R  197 MET cc_start: 0.8077 (mmp) cc_final: 0.7853 (mmt)
REVERT: R  220 SER cc_start: 0.8063 (m) cc_final: 0.7817 (p)
REVERT: R  270 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7863 (mt-10)
REVERT: R  273 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7707 (mp10)
REVERT: R  277 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8558 (mmmt)
REVERT: R  287 SER cc_start: 0.8229 (p) cc_final: 0.7782 (p)
REVERT: R  294 SER cc_start: 0.8717 (m) cc_final: 0.8341 (t)
REVERT: R  309 ARG cc_start: 0.8580 (ttm110) cc_final: 0.8137 (mtm110)
  outliers start: 26
  outliers final: 21
  residues processed: 261
  average time/residue: 0.2940
  time to fit residues: 97.4983
Evaluate side-chains
  271 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 247
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue   69 VAL
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  112 SER
Chi-restraints excluded: chain R residue  129 HIS
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  199 THR
Chi-restraints excluded: chain R residue  273 GLN
Chi-restraints excluded: chain R residue  302 VAL
Chi-restraints excluded: chain R residue  304 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0060
   chunk 83 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
A 331 ASN
R  57 HIS
** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.105541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.092474 restraints weight = 12826.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.56
r_work: 0.3185 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.4137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7308  Z= 0.130
  Angle     :  0.599  12.822   9885  Z= 0.312
  Chirality :  0.044   0.177   1137
  Planarity :  0.004   0.038   1241
  Dihedral  :  5.217  46.365   1003
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 27.65 %
    Favored  : 69.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.28), residues: 893
  helix:  1.10 (0.27), residues: 405
  sheet: -0.03 (0.40), residues: 162
  loop : -1.23 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.002   0.000   HIS B  54 
 PHE   0.033   0.001   PHE R  74 
 TYR   0.011   0.001   TYR B 124 
 ARG   0.007   0.001   ARG R 267 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03718 (  388)
  hydrogen bonds       : angle       4.57010 ( 1116)
  SS BOND              : bond        0.00121 (    1)
  SS BOND              : angle       2.31840 (    2)
  covalent geometry    : bond        0.00294 ( 7307)
  covalent geometry    : angle       0.59797 ( 9883)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4769.73 seconds
wall clock time: 85 minutes 21.45 seconds (5121.45 seconds total)