Starting phenix.real_space_refine
on Fri Jul 25 18:51:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8s2t_19683/07_2025/8s2t_19683.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8s2t_19683/07_2025/8s2t_19683.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8s2t_19683/07_2025/8s2t_19683.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8s2t_19683/07_2025/8s2t_19683.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8s2t_19683/07_2025/8s2t_19683.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8s2t_19683/07_2025/8s2t_19683.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
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    5045      2.51       5
     N    1400      2.21       5
     O    1457      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7955
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1673
          Classifications: {'peptide': 196}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 189}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 2269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2269
          Classifications: {'peptide': 285}
          Link IDs: {'PTRANS': 10, 'TRANS': 274}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'5FW': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.45, per 1000 atoms: 0.69
  Number of scatterers: 7955
  At special positions: 0
  Unit cell: (82.7105, 100.839, 129.164, 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    1457      8.00
     N    1400      7.00
     C    5045      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R 131 " - pdb=" SG  CYS R 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 209 " - pdb=" SG  CYS R 215 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.01
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1888

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 10 sheets defined
      43.4% alpha, 21.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 38
      removed outlier: 3.655A  pdb=" N   GLU A  15 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 225
      removed outlier: 4.002A  pdb=" N   ASN A 225 " --> pdb=" O   GLN A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 264
    Processing helix  chain 'A' and resid 293 through 297
    Processing helix  chain 'A' and resid 298 through 304
    Processing helix  chain 'A' and resid 317 through 336
    Processing helix  chain 'A' and resid 354 through 377
    Processing helix  chain 'B' and resid 4 through 24
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'C' and resid 7 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 74 through 76
      No H-bonds generated for 'chain 'N' and resid 74 through 76'
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 56 through 86
    Processing helix  chain 'R' and resid 87 through 90
    Processing helix  chain 'R' and resid 92 through 111
      removed outlier: 3.753A  pdb=" N   PHE R  96 " --> pdb=" O   LEU R  92 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 111 through 121
      removed outlier: 4.130A  pdb=" N   THR R 117 " --> pdb=" O   PRO R 113 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ILE R 118 " --> pdb=" O   PHE R 114 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 127 through 162
      removed outlier: 3.914A  pdb=" N   CYS R 131 " --> pdb=" O   GLY R 127 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 165 through 170
    Processing helix  chain 'R' and resid 171 through 188
    Processing helix  chain 'R' and resid 190 through 196
    Processing helix  chain 'R' and resid 203 through 209
    Processing helix  chain 'R' and resid 221 through 233
    Processing helix  chain 'R' and resid 233 through 263
      removed outlier: 4.137A  pdb=" N   CYS R 261 " --> pdb=" O   LYS R 257 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 320 through 349
      Proline residue:  R 339  - end of helix
    Processing helix  chain 'R' and resid 355 through 368
    Processing helix  chain 'R' and resid 368 through 373
    Processing helix  chain 'R' and resid 374 through 376
      No H-bonds generated for 'chain 'R' and resid 374 through 376'
    Processing helix  chain 'R' and resid 380 through 392
    Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 200
      removed outlier: 6.207A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 206 " (cutoff:3.500A)
      removed outlier: 7.710A  pdb=" N   PHE A 208 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   ILE A 231 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   VAL A 233 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   VAL A 273 " --> pdb=" O   TYR A 346 " (cutoff:3.500A)
      removed outlier: 7.530A  pdb=" N   HIS A 348 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   LEU A 275 " --> pdb=" O   HIS A 348 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.724A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.684A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.298A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.792A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.396A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.908A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.356A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.515A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.705A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    428 hydrogen bonds defined for protein.
    1203 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: 2.43

  Time building geometry restraints manager: 2.18 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1383
        1.30 -     1.44: 2383
        1.44 -     1.57: 4235
        1.57 -     1.70: 47
        1.70 -     1.84: 71
  Bond restraints: 8119
  Sorted by residual:
  bond pdb=" CB  HIS B 225 "
       pdb=" CG  HIS B 225 "
    ideal  model  delta    sigma   weight residual
    1.497  1.371  0.126 1.40e-02 5.10e+03 8.15e+01
  bond pdb=" NE  ARG C  62 "
       pdb=" CZ  ARG C  62 "
    ideal  model  delta    sigma   weight residual
    1.326  1.400 -0.074 1.10e-02 8.26e+03 4.56e+01
  bond pdb=" CB  ARG A 218 "
       pdb=" CG  ARG A 218 "
    ideal  model  delta    sigma   weight residual
    1.520  1.337  0.183 3.00e-02 1.11e+03 3.73e+01
  bond pdb=" CB  ASP B 205 "
       pdb=" CG  ASP B 205 "
    ideal  model  delta    sigma   weight residual
    1.516  1.365  0.151 2.50e-02 1.60e+03 3.63e+01
  bond pdb=" CB  HIS B 142 "
       pdb=" CG  HIS B 142 "
    ideal  model  delta    sigma   weight residual
    1.497  1.413  0.084 1.40e-02 5.10e+03 3.57e+01
  ... (remaining 8114 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 9584
        2.60 -     5.21: 1228
        5.21 -     7.81: 166
        7.81 -    10.42: 18
       10.42 -    13.02: 3
  Bond angle restraints: 10999
  Sorted by residual:
  angle pdb=" N   ARG B 197 "
        pdb=" CA  ARG B 197 "
        pdb=" C   ARG B 197 "
      ideal   model   delta    sigma   weight residual
     114.04  101.02   13.02 1.24e+00 6.50e-01 1.10e+02
  angle pdb=" C   SER R 162 "
        pdb=" N   PRO R 163 "
        pdb=" CA  PRO R 163 "
      ideal   model   delta    sigma   weight residual
     119.56  128.23   -8.67 1.01e+00 9.80e-01 7.37e+01
  angle pdb=" N   VAL N 110 "
        pdb=" CA  VAL N 110 "
        pdb=" C   VAL N 110 "
      ideal   model   delta    sigma   weight residual
     109.58   99.00   10.58 1.29e+00 6.01e-01 6.72e+01
  angle pdb=" C   ASP C  48 "
        pdb=" N   PRO C  49 "
        pdb=" CA  PRO C  49 "
      ideal   model   delta    sigma   weight residual
     119.56  127.71   -8.15 1.02e+00 9.61e-01 6.39e+01
  angle pdb=" CA  HIS A 206 "
        pdb=" CB  HIS A 206 "
        pdb=" CG  HIS A 206 "
      ideal   model   delta    sigma   weight residual
     113.80  121.66   -7.86 1.00e+00 1.00e+00 6.17e+01
  ... (remaining 10994 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 4669
       17.89 -    35.78: 125
       35.78 -    53.67: 27
       53.67 -    71.56: 11
       71.56 -    89.45: 5
  Dihedral angle restraints: 4837
    sinusoidal: 1925
      harmonic: 2912
  Sorted by residual:
  dihedral pdb=" C   TRP B  82 "
           pdb=" N   TRP B  82 "
           pdb=" CA  TRP B  82 "
           pdb=" CB  TRP B  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.93   -9.67     0      2.50e+00 1.60e-01 1.50e+01
  dihedral pdb=" C   HIS A 206 "
           pdb=" N   HIS A 206 "
           pdb=" CA  HIS A 206 "
           pdb=" CB  HIS A 206 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.24    9.64     0      2.50e+00 1.60e-01 1.49e+01
  dihedral pdb=" CA  ASP N 106 "
           pdb=" CB  ASP N 106 "
           pdb=" CG  ASP N 106 "
           pdb=" OD1 ASP N 106 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.81   57.81     1      2.00e+01 2.50e-03 1.12e+01
  ... (remaining 4834 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 768
       0.087 -    0.173: 350
       0.173 -    0.259: 83
       0.259 -    0.346: 24
       0.346 -    0.432: 6
  Chirality restraints: 1231
  Sorted by residual:
  chirality pdb=" CA  TYR R 244 "
            pdb=" N   TYR R 244 "
            pdb=" C   TYR R 244 "
            pdb=" CB  TYR R 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.67e+00
  chirality pdb=" CB  VAL A 353 "
            pdb=" CA  VAL A 353 "
            pdb=" CG1 VAL A 353 "
            pdb=" CG2 VAL A 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -3.04    0.41 2.00e-01 2.50e+01 4.30e+00
  chirality pdb=" CA  TRP R 337 "
            pdb=" N   TRP R 337 "
            pdb=" C   TRP R 337 "
            pdb=" CB  TRP R 337 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.58e+00
  ... (remaining 1228 not shown)

  Planarity restraints: 1404
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  40 "    0.057 2.00e-02 2.50e+03   3.39e-02 2.29e+01
        pdb=" CG  TYR C  40 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  40 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  40 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  40 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  40 "   -0.027 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  40 "   -0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR C  40 "    0.059 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  99 "    0.061 2.00e-02 2.50e+03   2.98e-02 2.21e+01
        pdb=" CG  TRP B  99 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  99 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  99 "   -0.036 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  99 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  99 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  99 "   -0.036 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  99 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  99 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  99 "    0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  63 "   -0.058 2.00e-02 2.50e+03   2.82e-02 1.99e+01
        pdb=" CG  TRP B  63 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  63 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  63 "    0.035 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  63 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  63 "    0.010 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  63 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  63 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  63 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  63 "   -0.030 2.00e-02 2.50e+03
  ... (remaining 1401 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 2854
        2.85 -     3.36: 7983
        3.36 -     3.87: 14243
        3.87 -     4.39: 17710
        4.39 -     4.90: 27899
  Nonbonded interactions: 70689
  Sorted by model distance:
  nonbonded pdb=" N   ASP R 356 "
            pdb=" OD1 ASP R 356 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" OD2 ASP A  33 "
            pdb=" NZ  LYS B  78 "
     model   vdw
     2.373 3.120
  nonbonded pdb=" N   ASP R 204 "
            pdb=" OD1 ASP R 204 "
     model   vdw
     2.381 3.120
  nonbonded pdb=" O   TRP N  47 "
            pdb=" OG1 THR N  61 "
     model   vdw
     2.386 3.040
  ... (remaining 70684 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:             2.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.830
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
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      :  0.025   0.183   8123  Z= 1.318
  Angle     :  1.810  13.022  11007  Z= 1.238
  Chirality :  0.105   0.432   1231
  Planarity :  0.010   0.123   1404
  Dihedral  : 10.263  89.446   2937
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 1.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.11 %
  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:  0.52 (0.26), residues: 982
  helix:  0.01 (0.23), residues: 388
  sheet:  1.19 (0.34), residues: 198
  loop :  0.47 (0.34), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.011   TRP B  99 
 HIS   0.016   0.004   HIS B 225 
 PHE   0.037   0.007   PHE R 164 
 TYR   0.059   0.008   TYR C  40 
 ARG   0.010   0.001   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14470 (  428)
  hydrogen bonds       : angle       7.06771 ( 1203)
  SS BOND              : bond        0.00614 (    4)
  SS BOND              : angle       4.23785 (    8)
  covalent geometry    : bond        0.02482 ( 8119)
  covalent geometry    : angle       1.80725 (10999)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  324 LYS cc_start: 0.8015 (tttt) cc_final: 0.7691 (ttmm)
REVERT: R  355 PRO cc_start: 0.8131 (Cg_exo) cc_final: 0.7918 (Cg_endo)
  outliers start: 0
  outliers final: 0
  residues processed: 270
  average time/residue: 0.2682
  time to fit residues: 90.6222
Evaluate side-chains
  162 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    0.6980
   chunk 73 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 88 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A 206 HIS
A 373 HIS
N 120 GLN
** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 373 ASN ** 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 = 0.3800 r_free = 0.3800 target = 0.127829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.107689 restraints weight = 13149.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.51
r_work: 0.3391 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.3237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   8123  Z= 0.205
  Angle     :  0.705   8.166  11007  Z= 0.385
  Chirality :  0.047   0.337   1231
  Planarity :  0.005   0.044   1404
  Dihedral  :  5.979  42.589   1106
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  :  9.95 %
    Favored  : 87.70 %
  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:  0.73 (0.26), residues: 982
  helix:  1.03 (0.25), residues: 397
  sheet:  0.48 (0.33), residues: 187
  loop :  0.08 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 199 
 HIS   0.010   0.002   HIS A 206 
 PHE   0.026   0.002   PHE N  68 
 TYR   0.027   0.002   TYR N  60 
 ARG   0.007   0.001   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05291 (  428)
  hydrogen bonds       : angle       5.44040 ( 1203)
  SS BOND              : bond        0.00271 (    4)
  SS BOND              : angle       2.07594 (    8)
  covalent geometry    : bond        0.00454 ( 8119)
  covalent geometry    : angle       0.70315 (10999)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 199
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 ASN cc_start: 0.9144 (m-40) cc_final: 0.8913 (m110)
REVERT: A  358 ILE cc_start: 0.9176 (tt) cc_final: 0.8874 (tp)
REVERT: A  367 ASP cc_start: 0.7913 (m-30) cc_final: 0.7712 (m-30)
REVERT: B   13 GLN cc_start: 0.8786 (tt0) cc_final: 0.8415 (pt0)
REVERT: B  111 TYR cc_start: 0.8742 (m-80) cc_final: 0.8394 (m-80)
REVERT: B  130 GLU cc_start: 0.7178 (pt0) cc_final: 0.6953 (pt0)
REVERT: B  134 ARG cc_start: 0.7668 (ptp-170) cc_final: 0.7401 (ptm160)
REVERT: B  172 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8093 (mp0)
REVERT: B  291 ASP cc_start: 0.7495 (t70) cc_final: 0.6977 (t70)
REVERT: B  339 TRP cc_start: 0.8855 (m100) cc_final: 0.8354 (m-10)
REVERT: C   58 GLU cc_start: 0.7979 (mp0) cc_final: 0.7636 (mp0)
REVERT: N   95 TYR cc_start: 0.8654 (m-80) cc_final: 0.8216 (m-80)
REVERT: N  105 ARG cc_start: 0.8386 (mtp-110) cc_final: 0.8121 (mtp-110)
REVERT: R  110 LEU cc_start: 0.7908 (mp) cc_final: 0.6924 (tt)
REVERT: R  324 LYS cc_start: 0.7282 (tttt) cc_final: 0.6961 (ttmm)
REVERT: R  328 ILE cc_start: 0.8632 (mt) cc_final: 0.8357 (tt)
REVERT: R  335 LEU cc_start: 0.7942 (tp) cc_final: 0.7422 (mp)
  outliers start: 20
  outliers final: 13
  residues processed: 208
  average time/residue: 0.2234
  time to fit residues: 60.6475
Evaluate side-chains
  182 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 169
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   88 ARG
Chi-restraints excluded: chain R residue  125 GLU
Chi-restraints excluded: chain R residue  189 VAL
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain R residue  232 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 74 optimal weight:    0.8980
   chunk 75 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
N  31 ASN
** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.124413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.104117 restraints weight = 13474.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 2.54
r_work: 0.3337 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.4003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   8123  Z= 0.208
  Angle     :  0.643   6.956  11007  Z= 0.346
  Chirality :  0.045   0.294   1231
  Planarity :  0.005   0.048   1404
  Dihedral  :  5.848  45.994   1106
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 12.53 %
    Favored  : 84.54 %
  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:  0.66 (0.27), residues: 982
  helix:  1.07 (0.25), residues: 401
  sheet: -0.14 (0.33), residues: 198
  loop :  0.28 (0.34), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 199 
 HIS   0.008   0.002   HIS C  44 
 PHE   0.028   0.002   PHE N  68 
 TYR   0.027   0.002   TYR N  60 
 ARG   0.005   0.001   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04557 (  428)
  hydrogen bonds       : angle       5.17257 ( 1203)
  SS BOND              : bond        0.00318 (    4)
  SS BOND              : angle       1.85206 (    8)
  covalent geometry    : bond        0.00472 ( 8119)
  covalent geometry    : angle       0.64164 (10999)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 190
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 ILE cc_start: 0.9163 (tt) cc_final: 0.8922 (tp)
REVERT: B    6 GLN cc_start: 0.8940 (mt0) cc_final: 0.8713 (mp10)
REVERT: B   59 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.7003 (m-80)
REVERT: B  111 TYR cc_start: 0.8810 (m-80) cc_final: 0.8571 (m-80)
REVERT: B  118 ASP cc_start: 0.8121 (m-30) cc_final: 0.7685 (m-30)
REVERT: B  134 ARG cc_start: 0.7662 (ptp-170) cc_final: 0.7387 (ptm160)
REVERT: B  315 VAL cc_start: 0.8198 (t) cc_final: 0.7974 (t)
REVERT: B  334 SER cc_start: 0.9219 (m) cc_final: 0.8988 (m)
REVERT: B  339 TRP cc_start: 0.8872 (m100) cc_final: 0.8649 (m-10)
REVERT: C   42 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8071 (mm-30)
REVERT: C   58 GLU cc_start: 0.8025 (mp0) cc_final: 0.7729 (mp0)
REVERT: N   95 TYR cc_start: 0.8709 (m-80) cc_final: 0.8383 (m-80)
REVERT: N  105 ARG cc_start: 0.8416 (mtp180) cc_final: 0.8208 (mtp-110)
REVERT: R  110 LEU cc_start: 0.7924 (mp) cc_final: 0.6938 (tt)
REVERT: R  320 GLN cc_start: 0.4987 (mt0) cc_final: 0.4773 (pt0)
REVERT: R  324 LYS cc_start: 0.7182 (tttt) cc_final: 0.6765 (ttmm)
REVERT: R  335 LEU cc_start: 0.8033 (tp) cc_final: 0.7621 (mp)
  outliers start: 25
  outliers final: 18
  residues processed: 204
  average time/residue: 0.2542
  time to fit residues: 69.7342
Evaluate side-chains
  189 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 170
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue   88 ARG
Chi-restraints excluded: chain R residue  125 GLU
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain R residue  232 SER
Chi-restraints excluded: chain R residue  346 VAL
Chi-restraints excluded: chain R residue  360 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 93 optimal weight:    0.2980
   chunk 54 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0970
   chunk 43 optimal weight:    0.8980
   chunk 94 optimal weight:    0.5980
   chunk 87 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0870
   overall best weight:    0.3556

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

Flipped N/Q/H residues before XYZ refinement:
A 257 ASN
A 264 ASN
B  75 GLN
** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 373 ASN ** 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 = 0.3780 r_free = 0.3780 target = 0.126826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.106450 restraints weight = 13224.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.58
r_work: 0.3361 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.4414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8123  Z= 0.143
  Angle     :  0.614   9.926  11007  Z= 0.327
  Chirality :  0.043   0.258   1231
  Planarity :  0.004   0.045   1404
  Dihedral  :  5.720  54.959   1106
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 14.05 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.79 (0.27), residues: 982
  helix:  1.30 (0.26), residues: 392
  sheet:  0.00 (0.33), residues: 200
  loop :  0.18 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP R 199 
 HIS   0.005   0.001   HIS C  44 
 PHE   0.015   0.002   PHE A 301 
 TYR   0.023   0.002   TYR N  80 
 ARG   0.003   0.000   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04095 (  428)
  hydrogen bonds       : angle       5.06293 ( 1203)
  SS BOND              : bond        0.00887 (    4)
  SS BOND              : angle       4.04846 (    8)
  covalent geometry    : bond        0.00321 ( 8119)
  covalent geometry    : angle       0.60433 (10999)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 178
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 TYR cc_start: 0.8675 (t80) cc_final: 0.8439 (t80)
REVERT: A  358 ILE cc_start: 0.9168 (tt) cc_final: 0.8910 (tp)
REVERT: B    6 GLN cc_start: 0.8958 (mt0) cc_final: 0.8716 (mp10)
REVERT: B    9 GLN cc_start: 0.8528 (tp40) cc_final: 0.8014 (tp40)
REVERT: B   59 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.6883 (m-80)
REVERT: B  111 TYR cc_start: 0.8793 (m-80) cc_final: 0.8589 (m-80)
REVERT: B  118 ASP cc_start: 0.8232 (m-30) cc_final: 0.7918 (m-30)
REVERT: B  130 GLU cc_start: 0.7340 (pt0) cc_final: 0.7098 (pt0)
REVERT: B  134 ARG cc_start: 0.7806 (ptp-170) cc_final: 0.7368 (ptm-80)
REVERT: C   42 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8119 (mm-30)
REVERT: C   58 GLU cc_start: 0.8020 (mp0) cc_final: 0.7384 (mp0)
REVERT: N  117 TYR cc_start: 0.8470 (m-80) cc_final: 0.7804 (m-80)
REVERT: R  104 ASP cc_start: 0.8294 (m-30) cc_final: 0.8058 (t0)
REVERT: R  110 LEU cc_start: 0.7876 (mp) cc_final: 0.6957 (tt)
REVERT: R  320 GLN cc_start: 0.4964 (mt0) cc_final: 0.4763 (pt0)
REVERT: R  324 LYS cc_start: 0.7050 (tttt) cc_final: 0.6627 (ttmt)
REVERT: R  335 LEU cc_start: 0.7904 (tp) cc_final: 0.7451 (mp)
  outliers start: 24
  outliers final: 15
  residues processed: 193
  average time/residue: 0.2091
  time to fit residues: 53.9669
Evaluate side-chains
  183 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 167
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue   88 ARG
Chi-restraints excluded: chain R residue  125 GLU
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain R residue  232 SER
Chi-restraints excluded: chain R residue  243 VAL
Chi-restraints excluded: chain R residue  328 ILE
Chi-restraints excluded: chain R residue  346 VAL
Chi-restraints excluded: chain R residue  360 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 19 optimal weight:    0.2980
   chunk 12 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0980
   chunk 51 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 253 GLN
** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.123269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.102871 restraints weight = 13227.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.57
r_work: 0.3311 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.4628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079   8123  Z= 0.196
  Angle     :  0.647   9.320  11007  Z= 0.341
  Chirality :  0.046   0.375   1231
  Planarity :  0.004   0.047   1404
  Dihedral  :  5.653  48.419   1106
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 14.29 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.68 (0.27), residues: 982
  helix:  1.26 (0.26), residues: 397
  sheet: -0.18 (0.35), residues: 194
  loop :  0.12 (0.34), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 364 
 HIS   0.006   0.001   HIS C  44 
 PHE   0.019   0.002   PHE N  68 
 TYR   0.022   0.002   TYR N  60 
 ARG   0.005   0.000   ARG A 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04116 (  428)
  hydrogen bonds       : angle       4.97755 ( 1203)
  SS BOND              : bond        0.00754 (    4)
  SS BOND              : angle       3.76661 (    8)
  covalent geometry    : bond        0.00451 ( 8119)
  covalent geometry    : angle       0.63937 (10999)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 180
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 TYR cc_start: 0.8613 (t80) cc_final: 0.8397 (t80)
REVERT: A  358 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8939 (tp)
REVERT: B    6 GLN cc_start: 0.8955 (mt0) cc_final: 0.8688 (mp10)
REVERT: B    9 GLN cc_start: 0.8659 (tp40) cc_final: 0.8432 (tp40)
REVERT: B   59 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.7022 (m-80)
REVERT: B  130 GLU cc_start: 0.7315 (pt0) cc_final: 0.7025 (pt0)
REVERT: B  134 ARG cc_start: 0.7763 (ptp-170) cc_final: 0.7311 (ptm-80)
REVERT: B  214 ARG cc_start: 0.8363 (mmm-85) cc_final: 0.8160 (mmm-85)
REVERT: B  234 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8554 (m-80)
REVERT: C   11 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7847 (pt0)
REVERT: C   58 GLU cc_start: 0.8065 (mp0) cc_final: 0.7418 (mp0)
REVERT: N   13 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8383 (mm-40)
REVERT: N  117 TYR cc_start: 0.8564 (m-80) cc_final: 0.7919 (m-80)
REVERT: R  110 LEU cc_start: 0.7878 (mp) cc_final: 0.6851 (tt)
REVERT: R  324 LYS cc_start: 0.6875 (tttt) cc_final: 0.6350 (ttmm)
REVERT: R  335 LEU cc_start: 0.7987 (tp) cc_final: 0.7524 (mp)
  outliers start: 34
  outliers final: 22
  residues processed: 195
  average time/residue: 0.2129
  time to fit residues: 55.0563
Evaluate side-chains
  190 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 165
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   88 ARG
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain R residue  232 SER
Chi-restraints excluded: chain R residue  243 VAL
Chi-restraints excluded: chain R residue  346 VAL
Chi-restraints excluded: chain R residue  365 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 253 GLN
N  31 ASN
** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.121755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.101404 restraints weight = 13337.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 2.56
r_work: 0.3294 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.4835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   8123  Z= 0.205
  Angle     :  0.649   9.374  11007  Z= 0.340
  Chirality :  0.046   0.365   1231
  Planarity :  0.004   0.045   1404
  Dihedral  :  5.637  44.470   1106
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 15.11 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.66 (0.27), residues: 982
  helix:  1.36 (0.26), residues: 389
  sheet: -0.29 (0.35), residues: 196
  loop :  0.04 (0.34), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 364 
 HIS   0.006   0.001   HIS C  44 
 PHE   0.017   0.002   PHE N  68 
 TYR   0.018   0.002   TYR B 264 
 ARG   0.004   0.000   ARG A 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04015 (  428)
  hydrogen bonds       : angle       5.06283 ( 1203)
  SS BOND              : bond        0.00737 (    4)
  SS BOND              : angle       3.71987 (    8)
  covalent geometry    : bond        0.00470 ( 8119)
  covalent geometry    : angle       0.64118 (10999)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 175
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 TYR cc_start: 0.8649 (t80) cc_final: 0.8412 (t80)
REVERT: A  358 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8927 (tp)
REVERT: B    6 GLN cc_start: 0.8956 (mt0) cc_final: 0.8691 (mp10)
REVERT: B    9 GLN cc_start: 0.8621 (tp40) cc_final: 0.8318 (tp40)
REVERT: B   59 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.7025 (m-80)
REVERT: B  134 ARG cc_start: 0.7778 (ptp-170) cc_final: 0.7282 (ptm-80)
REVERT: B  234 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8576 (m-80)
REVERT: C   11 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7833 (pt0)
REVERT: C   58 GLU cc_start: 0.8121 (mp0) cc_final: 0.7512 (mp0)
REVERT: N   13 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8449 (mm-40)
REVERT: N  117 TYR cc_start: 0.8608 (m-80) cc_final: 0.7938 (m-80)
REVERT: R  104 ASP cc_start: 0.8408 (m-30) cc_final: 0.8203 (t0)
REVERT: R  110 LEU cc_start: 0.7994 (mp) cc_final: 0.7042 (tt)
REVERT: R  324 LYS cc_start: 0.7084 (tttt) cc_final: 0.6472 (ttmm)
REVERT: R  330 MET cc_start: 0.7805 (mmm) cc_final: 0.7323 (mmt)
REVERT: R  335 LEU cc_start: 0.8006 (tp) cc_final: 0.7533 (mp)
  outliers start: 37
  outliers final: 26
  residues processed: 194
  average time/residue: 0.2141
  time to fit residues: 55.3440
Evaluate side-chains
  197 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 168
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  324 LYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   88 ARG
Chi-restraints excluded: chain R residue  121 TRP
Chi-restraints excluded: chain R residue  125 GLU
Chi-restraints excluded: chain R residue  219 VAL
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain R residue  232 SER
Chi-restraints excluded: chain R residue  243 VAL
Chi-restraints excluded: chain R residue  328 ILE
Chi-restraints excluded: chain R residue  346 VAL
Chi-restraints excluded: chain R residue  365 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.121297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.100841 restraints weight = 13496.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.58
r_work: 0.3283 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.4967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   8123  Z= 0.205
  Angle     :  0.653   8.766  11007  Z= 0.343
  Chirality :  0.047   0.364   1231
  Planarity :  0.004   0.049   1404
  Dihedral  :  5.661  42.543   1106
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 15.46 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.60 (0.28), residues: 982
  helix:  1.37 (0.26), residues: 389
  sheet: -0.62 (0.35), residues: 209
  loop :  0.17 (0.35), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP R 364 
 HIS   0.007   0.001   HIS C  44 
 PHE   0.016   0.002   PHE R 341 
 TYR   0.025   0.002   TYR N  60 
 ARG   0.004   0.000   ARG A 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04027 (  428)
  hydrogen bonds       : angle       5.07028 ( 1203)
  SS BOND              : bond        0.00668 (    4)
  SS BOND              : angle       3.57622 (    8)
  covalent geometry    : bond        0.00470 ( 8119)
  covalent geometry    : angle       0.64582 (10999)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 173
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 TYR cc_start: 0.8663 (t80) cc_final: 0.8445 (t80)
REVERT: A  199 GLN cc_start: 0.8267 (tt0) cc_final: 0.7832 (tt0)
REVERT: A  358 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8947 (tp)
REVERT: B    6 GLN cc_start: 0.8967 (mt0) cc_final: 0.8463 (mt0)
REVERT: B   59 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.6864 (m-80)
REVERT: B  134 ARG cc_start: 0.7713 (ptp-170) cc_final: 0.7226 (ptm-80)
REVERT: B  234 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8605 (m-80)
REVERT: C   11 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7776 (pt0)
REVERT: C   58 GLU cc_start: 0.8193 (mp0) cc_final: 0.7580 (mp0)
REVERT: N   13 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8437 (mm-40)
REVERT: N   87 LYS cc_start: 0.8596 (mttm) cc_final: 0.8393 (mtmm)
REVERT: R  104 ASP cc_start: 0.8439 (m-30) cc_final: 0.8206 (t0)
REVERT: R  110 LEU cc_start: 0.8043 (mp) cc_final: 0.7105 (tt)
REVERT: R  324 LYS cc_start: 0.7056 (tttt) cc_final: 0.6453 (ttmm)
REVERT: R  330 MET cc_start: 0.7779 (mmm) cc_final: 0.7258 (mmm)
REVERT: R  335 LEU cc_start: 0.8030 (tp) cc_final: 0.7563 (mp)
  outliers start: 41
  outliers final: 28
  residues processed: 194
  average time/residue: 0.2160
  time to fit residues: 55.9031
Evaluate side-chains
  194 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 163
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  324 LYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain R residue   88 ARG
Chi-restraints excluded: chain R residue  121 TRP
Chi-restraints excluded: chain R residue  125 GLU
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  151 VAL
Chi-restraints excluded: chain R residue  219 VAL
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain R residue  232 SER
Chi-restraints excluded: chain R residue  243 VAL
Chi-restraints excluded: chain R residue  328 ILE
Chi-restraints excluded: chain R residue  346 VAL
Chi-restraints excluded: chain R residue  365 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 76 optimal weight:    0.4980
   chunk 66 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.122348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.102059 restraints weight = 13541.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 2.60
r_work: 0.3299 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.5122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8123  Z= 0.170
  Angle     :  0.634   9.181  11007  Z= 0.331
  Chirality :  0.046   0.359   1231
  Planarity :  0.004   0.046   1404
  Dihedral  :  5.565  42.178   1106
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 16.04 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.70 (0.28), residues: 982
  helix:  1.47 (0.26), residues: 390
  sheet: -0.43 (0.35), residues: 208
  loop :  0.11 (0.35), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP R 364 
 HIS   0.004   0.001   HIS C  44 
 PHE   0.015   0.002   PHE R 340 
 TYR   0.024   0.002   TYR N  80 
 ARG   0.004   0.000   ARG A 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03915 (  428)
  hydrogen bonds       : angle       5.07621 ( 1203)
  SS BOND              : bond        0.00562 (    4)
  SS BOND              : angle       3.22403 (    8)
  covalent geometry    : bond        0.00390 ( 8119)
  covalent geometry    : angle       0.62780 (10999)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 166
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 TYR cc_start: 0.8658 (t80) cc_final: 0.8418 (t80)
REVERT: A  199 GLN cc_start: 0.8270 (tt0) cc_final: 0.7843 (tt0)
REVERT: A  208 PHE cc_start: 0.7599 (m-80) cc_final: 0.7005 (m-80)
REVERT: A  277 LEU cc_start: 0.9003 (mm) cc_final: 0.8688 (mm)
REVERT: A  358 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8939 (tp)
REVERT: B   59 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.6879 (m-80)
REVERT: B  134 ARG cc_start: 0.7740 (ptp-170) cc_final: 0.7241 (ptm-80)
REVERT: B  234 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8529 (m-80)
REVERT: B  264 TYR cc_start: 0.8834 (m-80) cc_final: 0.8274 (m-80)
REVERT: C   11 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7798 (pm20)
REVERT: C   58 GLU cc_start: 0.8245 (mp0) cc_final: 0.7756 (mp0)
REVERT: N   13 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8547 (mm-40)
REVERT: R  104 ASP cc_start: 0.8425 (m-30) cc_final: 0.8221 (t0)
REVERT: R  110 LEU cc_start: 0.7934 (mp) cc_final: 0.7134 (tt)
REVERT: R  324 LYS cc_start: 0.7027 (tttt) cc_final: 0.6410 (ttmm)
REVERT: R  330 MET cc_start: 0.7762 (mmm) cc_final: 0.7228 (mmm)
REVERT: R  335 LEU cc_start: 0.8003 (tp) cc_final: 0.7547 (mp)
  outliers start: 34
  outliers final: 27
  residues processed: 187
  average time/residue: 0.2284
  time to fit residues: 56.6210
Evaluate side-chains
  189 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 159
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  324 LYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain R residue   88 ARG
Chi-restraints excluded: chain R residue  121 TRP
Chi-restraints excluded: chain R residue  125 GLU
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  151 VAL
Chi-restraints excluded: chain R residue  219 VAL
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain R residue  232 SER
Chi-restraints excluded: chain R residue  243 VAL
Chi-restraints excluded: chain R residue  346 VAL
Chi-restraints excluded: chain R residue  354 VAL
Chi-restraints excluded: chain R residue  365 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0980
   chunk 83 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.120977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.101607 restraints weight = 13680.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 2.56
r_work: 0.3320 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.5196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8123  Z= 0.174
  Angle     :  0.636   8.211  11007  Z= 0.331
  Chirality :  0.046   0.337   1231
  Planarity :  0.004   0.050   1404
  Dihedral  :  5.533  42.288   1106
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 15.69 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.73 (0.28), residues: 982
  helix:  1.55 (0.26), residues: 389
  sheet: -0.44 (0.35), residues: 208
  loop :  0.07 (0.35), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP R 364 
 HIS   0.006   0.001   HIS C  44 
 PHE   0.015   0.002   PHE R 340 
 TYR   0.025   0.002   TYR N  80 
 ARG   0.005   0.000   ARG A 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03877 (  428)
  hydrogen bonds       : angle       5.06477 ( 1203)
  SS BOND              : bond        0.00620 (    4)
  SS BOND              : angle       3.17557 (    8)
  covalent geometry    : bond        0.00401 ( 8119)
  covalent geometry    : angle       0.63063 (10999)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 162
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 TYR cc_start: 0.8663 (t80) cc_final: 0.8431 (t80)
REVERT: A  199 GLN cc_start: 0.8231 (tt0) cc_final: 0.7839 (tt0)
REVERT: A  208 PHE cc_start: 0.7678 (m-80) cc_final: 0.7093 (m-80)
REVERT: A  277 LEU cc_start: 0.8993 (mm) cc_final: 0.8683 (mm)
REVERT: A  303 ARG cc_start: 0.7267 (ttp80) cc_final: 0.6958 (tpp-160)
REVERT: A  358 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8961 (tp)
REVERT: B   59 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.6898 (m-80)
REVERT: B  134 ARG cc_start: 0.7775 (ptp-170) cc_final: 0.7296 (ptm-80)
REVERT: B  234 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8552 (m-80)
REVERT: B  264 TYR cc_start: 0.8860 (m-80) cc_final: 0.8210 (m-80)
REVERT: C   11 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7765 (pm20)
REVERT: C   58 GLU cc_start: 0.8313 (mp0) cc_final: 0.7678 (mp0)
REVERT: N   13 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8505 (mm-40)
REVERT: N   34 MET cc_start: 0.8409 (tpt) cc_final: 0.8145 (mmm)
REVERT: R  110 LEU cc_start: 0.8002 (mp) cc_final: 0.7118 (tt)
REVERT: R  324 LYS cc_start: 0.7051 (tttt) cc_final: 0.6427 (ttmm)
REVERT: R  330 MET cc_start: 0.7772 (mmm) cc_final: 0.7221 (mmm)
REVERT: R  335 LEU cc_start: 0.8012 (tp) cc_final: 0.7543 (mp)
  outliers start: 37
  outliers final: 28
  residues processed: 185
  average time/residue: 0.2342
  time to fit residues: 57.7288
Evaluate side-chains
  191 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 160
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  324 LYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain R residue   88 ARG
Chi-restraints excluded: chain R residue  121 TRP
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  151 VAL
Chi-restraints excluded: chain R residue  219 VAL
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain R residue  232 SER
Chi-restraints excluded: chain R residue  243 VAL
Chi-restraints excluded: chain R residue  346 VAL
Chi-restraints excluded: chain R residue  354 VAL
Chi-restraints excluded: chain R residue  365 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 62 optimal weight:    0.4980
   chunk 37 optimal weight:    0.7980
   chunk 80 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.122575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.102469 restraints weight = 13411.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.59
r_work: 0.3327 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.5322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8123  Z= 0.171
  Angle     :  0.638   8.385  11007  Z= 0.332
  Chirality :  0.046   0.321   1231
  Planarity :  0.004   0.047   1404
  Dihedral  :  5.501  42.528   1106
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 16.16 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.66 (0.28), residues: 982
  helix:  1.51 (0.26), residues: 389
  sheet: -0.47 (0.34), residues: 218
  loop :  0.02 (0.35), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 364 
 HIS   0.004   0.001   HIS C  44 
 PHE   0.014   0.002   PHE R 341 
 TYR   0.021   0.002   TYR N  80 
 ARG   0.004   0.000   ARG A 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03888 (  428)
  hydrogen bonds       : angle       5.07321 ( 1203)
  SS BOND              : bond        0.00602 (    4)
  SS BOND              : angle       3.07235 (    8)
  covalent geometry    : bond        0.00395 ( 8119)
  covalent geometry    : angle       0.63326 (10999)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 163
  time to evaluate  : 1.463 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 TYR cc_start: 0.8663 (t80) cc_final: 0.8430 (t80)
REVERT: A  199 GLN cc_start: 0.8209 (tt0) cc_final: 0.7829 (tt0)
REVERT: A  208 PHE cc_start: 0.7678 (m-80) cc_final: 0.7111 (m-80)
REVERT: A  277 LEU cc_start: 0.8985 (mm) cc_final: 0.8651 (mm)
REVERT: A  303 ARG cc_start: 0.7394 (ttp80) cc_final: 0.7080 (tpp-160)
REVERT: A  358 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8958 (tp)
REVERT: B   59 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.6934 (m-80)
REVERT: B  134 ARG cc_start: 0.7753 (ptp-170) cc_final: 0.7272 (ptm-80)
REVERT: B  234 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8570 (m-80)
REVERT: B  264 TYR cc_start: 0.8736 (m-80) cc_final: 0.8048 (m-80)
REVERT: C   11 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7852 (pm20)
REVERT: C   58 GLU cc_start: 0.8288 (mp0) cc_final: 0.7655 (mp0)
REVERT: N   13 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8491 (mm-40)
REVERT: N   34 MET cc_start: 0.8413 (tpt) cc_final: 0.8136 (mmm)
REVERT: R  110 LEU cc_start: 0.8022 (mp) cc_final: 0.7202 (tt)
REVERT: R  324 LYS cc_start: 0.7017 (tttt) cc_final: 0.6384 (ttmm)
REVERT: R  330 MET cc_start: 0.7754 (mmm) cc_final: 0.7196 (mmm)
REVERT: R  335 LEU cc_start: 0.8050 (tp) cc_final: 0.7562 (mp)
  outliers start: 33
  outliers final: 27
  residues processed: 183
  average time/residue: 0.2403
  time to fit residues: 59.0239
Evaluate side-chains
  185 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 155
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  324 LYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain R residue   88 ARG
Chi-restraints excluded: chain R residue  121 TRP
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  151 VAL
Chi-restraints excluded: chain R residue  219 VAL
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain R residue  232 SER
Chi-restraints excluded: chain R residue  243 VAL
Chi-restraints excluded: chain R residue  346 VAL
Chi-restraints excluded: chain R residue  354 VAL
Chi-restraints excluded: chain R residue  365 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 83 optimal weight:    0.0060
   chunk 64 optimal weight:    0.6980
   chunk 85 optimal weight:    4.9990
   chunk 32 optimal weight:    0.4980
   chunk 95 optimal weight:    0.0370
   chunk 60 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.3874

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

Flipped N/Q/H residues before XYZ refinement:
** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.125404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.105473 restraints weight = 13465.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 2.61
r_work: 0.3356 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.5499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8123  Z= 0.137
  Angle     :  0.623  11.282  11007  Z= 0.322
  Chirality :  0.045   0.405   1231
  Planarity :  0.004   0.050   1404
  Dihedral  :  5.382  43.053   1106
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 16.16 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.69 (0.28), residues: 982
  helix:  1.60 (0.26), residues: 389
  sheet: -0.49 (0.34), residues: 219
  loop : -0.02 (0.35), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP R 364 
 HIS   0.004   0.001   HIS C  44 
 PHE   0.012   0.001   PHE R 341 
 TYR   0.014   0.001   TYR N  60 
 ARG   0.006   0.000   ARG N 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03773 (  428)
  hydrogen bonds       : angle       5.00562 ( 1203)
  SS BOND              : bond        0.00534 (    4)
  SS BOND              : angle       2.60460 (    8)
  covalent geometry    : bond        0.00312 ( 8119)
  covalent geometry    : angle       0.61887 (10999)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3797.56 seconds
wall clock time: 66 minutes 32.32 seconds (3992.32 seconds total)