Starting phenix.real_space_refine
on Mon May 12 06:53:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j18_35913/05_2025/8j18_35913.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j18_35913/05_2025/8j18_35913.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j18_35913/05_2025/8j18_35913.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j18_35913/05_2025/8j18_35913.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j18_35913/05_2025/8j18_35913.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j18_35913/05_2025/8j18_35913.cif"
  }
  resolution = 2.89
  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=   0.006 sd=   0.062
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      59      5.16       5
     C    5652      2.51       5
     N    1528      2.21       5
     O    1621      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8860
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1759
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 216}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 2591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2591
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
    Chain: "G"
      Number of atoms: 447
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 447
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "R"
      Number of atoms: 2300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2300
          Classifications: {'peptide': 291}
          Link IDs: {'PTRANS': 12, 'TRANS': 278}
          Chain breaks: 1
    Chain: "S"
      Number of atoms: 1748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1748
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'HXD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.50, per 1000 atoms: 0.62
  Number of scatterers: 8860
  At special positions: 0
  Unit cell: (109.5, 109.5, 121.91, 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      59     16.00
     O    1621      8.00
     N    1528      7.00
     C    5652      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  11 " - pdb=" SG  CYS R 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  93 " - pdb=" SG  CYS R 168 " 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: 2.48
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2120

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 13 sheets defined
      37.6% alpha, 22.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 4.055A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.536A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.415A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 271 through 279
      removed outlier: 3.827A  pdb=" N   LYS A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 328 through 351
      removed outlier: 4.101A  pdb=" N   VAL A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LYS A 349 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.771A  pdb=" N   ALA G  12 " --> pdb=" O   SER G   8 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.511A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'R' and resid 19 through 48
    Processing helix  chain 'R' and resid 49 through 52
    Processing helix  chain 'R' and resid 55 through 72
      removed outlier: 3.839A  pdb=" N   ILE R  59 " --> pdb=" O   PHE R  55 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 74 through 79
    Processing helix  chain 'R' and resid 90 through 124
      removed outlier: 4.160A  pdb=" N   ARG R  94 " --> pdb=" O   ALA R  90 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL R  95 " --> pdb=" O   THR R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 127 through 132
    Processing helix  chain 'R' and resid 133 through 153
      removed outlier: 3.756A  pdb=" N   VAL R 138 " --> pdb=" O   ALA R 134 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   TRP R 145 " --> pdb=" O   LEU R 141 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 155 through 157
      No H-bonds generated for 'chain 'R' and resid 155 through 157'
    Processing helix  chain 'R' and resid 175 through 213
    Processing helix  chain 'R' and resid 214 through 216
      No H-bonds generated for 'chain 'R' and resid 214 through 216'
    Processing helix  chain 'R' and resid 316 through 342
      Proline residue:  R 334  - end of helix
    Processing helix  chain 'R' and resid 350 through 370
      removed outlier: 3.616A  pdb=" N   TRP R 360 " --> pdb=" O   ALA R 356 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LEU R 361 " --> pdb=" O   ASN R 357 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ASN R 362 " --> pdb=" O   LEU R 358 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   GLY R 363 " --> pdb=" O   THR R 359 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   CYS R 364 " --> pdb=" O   TRP R 360 " (cutoff:3.500A)
      Proline residue:  R 367  - end of helix
    Processing helix  chain 'R' and resid 374 through 388
    Processing helix  chain 'R' and resid 389 through 394
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.827A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.577A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.474A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.854A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 4.113A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.508A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.445A  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: 6.983A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.610A  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 151
      removed outlier: 6.189A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.880A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.542A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.618A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.716A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 159 through 161
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.562A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142
    Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.297A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)

    448 hydrogen bonds defined for protein.
    1266 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: 2.77

  Time building geometry restraints manager: 2.83 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1412
        1.29 -     1.42: 2409
        1.42 -     1.55: 5131
        1.55 -     1.68: 9
        1.68 -     1.81: 82
  Bond restraints: 9043
  Sorted by residual:
  bond pdb=" C   THR R  35 "
       pdb=" O   THR R  35 "
    ideal  model  delta    sigma   weight residual
    1.236  1.162  0.074 1.16e-02 7.43e+03 4.11e+01
  bond pdb=" C   ASN B 313 "
       pdb=" O   ASN B 313 "
    ideal  model  delta    sigma   weight residual
    1.234  1.159  0.075 1.28e-02 6.10e+03 3.44e+01
  bond pdb=" C   ASP B 228 "
       pdb=" O   ASP B 228 "
    ideal  model  delta    sigma   weight residual
    1.234  1.177  0.057 1.21e-02 6.83e+03 2.25e+01
  bond pdb=" C   ARG R 176 "
       pdb=" O   ARG R 176 "
    ideal  model  delta    sigma   weight residual
    1.238  1.196  0.042 9.50e-03 1.11e+04 1.98e+01
  bond pdb=" C   ILE S 157 "
       pdb=" O   ILE S 157 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.044 9.90e-03 1.02e+04 1.93e+01
  ... (remaining 9038 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 11595
        1.35 -     2.71: 490
        2.71 -     4.06: 124
        4.06 -     5.41: 27
        5.41 -     6.76: 14
  Bond angle restraints: 12250
  Sorted by residual:
  angle pdb=" CA  THR R  35 "
        pdb=" C   THR R  35 "
        pdb=" O   THR R  35 "
      ideal   model   delta    sigma   weight residual
     120.90  114.94    5.96 1.03e+00 9.43e-01 3.35e+01
  angle pdb=" N   VAL R  78 "
        pdb=" CA  VAL R  78 "
        pdb=" C   VAL R  78 "
      ideal   model   delta    sigma   weight residual
     110.72  105.40    5.32 1.01e+00 9.80e-01 2.78e+01
  angle pdb=" CA  THR R  35 "
        pdb=" C   THR R  35 "
        pdb=" N   VAL R  36 "
      ideal   model   delta    sigma   weight residual
     117.02  123.00   -5.98 1.17e+00 7.31e-01 2.62e+01
  angle pdb=" N   ASP B 163 "
        pdb=" CA  ASP B 163 "
        pdb=" C   ASP B 163 "
      ideal   model   delta    sigma   weight residual
     111.56  105.01    6.55 1.38e+00 5.25e-01 2.25e+01
  angle pdb=" N   ASP B 228 "
        pdb=" CA  ASP B 228 "
        pdb=" C   ASP B 228 "
      ideal   model   delta    sigma   weight residual
     110.24  116.34   -6.10 1.30e+00 5.92e-01 2.20e+01
  ... (remaining 12245 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.35: 4718
       17.35 -    34.70: 468
       34.70 -    52.05: 128
       52.05 -    69.39: 33
       69.39 -    86.74: 13
  Dihedral angle restraints: 5360
    sinusoidal: 2070
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CA  VAL R  78 "
           pdb=" C   VAL R  78 "
           pdb=" N   ASP R  79 "
           pdb=" CA  ASP R  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.23   19.77     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  ARG S 191 "
           pdb=" C   ARG S 191 "
           pdb=" N   MET S 192 "
           pdb=" CA  MET S 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.07   17.93     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  PHE S  32 "
           pdb=" C   PHE S  32 "
           pdb=" N   GLY S  33 "
           pdb=" CA  GLY S  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.11   17.89     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 5357 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1235
       0.065 -    0.130: 145
       0.130 -    0.195: 15
       0.195 -    0.260: 4
       0.260 -    0.325: 1
  Chirality restraints: 1400
  Sorted by residual:
  chirality pdb=" CA  THR R  35 "
            pdb=" N   THR R  35 "
            pdb=" C   THR R  35 "
            pdb=" CB  THR R  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.20    0.33 2.00e-01 2.50e+01 2.65e+00
  chirality pdb=" CA  ARG R 176 "
            pdb=" N   ARG R 176 "
            pdb=" C   ARG R 176 "
            pdb=" CB  ARG R 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  TYR R 332 "
            pdb=" N   TYR R 332 "
            pdb=" C   TYR R 332 "
            pdb=" CB  TYR R 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 1397 not shown)

  Planarity restraints: 1544
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 312 "   -0.017 2.00e-02 2.50e+03   3.27e-02 1.07e+01
        pdb=" C   ASP B 312 "    0.057 2.00e-02 2.50e+03
        pdb=" O   ASP B 312 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ASN B 313 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R 175 "    0.015 2.00e-02 2.50e+03   3.01e-02 9.08e+00
        pdb=" C   GLY R 175 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   GLY R 175 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ARG R 176 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 247 "   -0.013 2.00e-02 2.50e+03   2.59e-02 6.72e+00
        pdb=" C   ASP B 247 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ASP B 247 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ALA B 248 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1541 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 478
        2.72 -     3.27: 9376
        3.27 -     3.81: 14676
        3.81 -     4.36: 18450
        4.36 -     4.90: 32221
  Nonbonded interactions: 75201
  Sorted by model distance:
  nonbonded pdb=" O   ASP R  79 "
            pdb=" OG1 THR R  80 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   ASP B 163 "
            pdb=" CG2 THR B 164 "
     model   vdw
     2.269 3.460
  nonbonded pdb=" OG1 THR B 164 "
            pdb=" O   HIS B 183 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   LYS G  32 "
            pdb=" OD1 ASP G  36 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   THR B  86 "
            pdb=" OG1 THR B  87 "
     model   vdw
     2.303 3.040
  ... (remaining 75196 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:             5.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          1.190
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     22.950
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  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:12.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
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      :  0.004   0.075   9045  Z= 0.265
  Angle     :  0.707   6.765  12254  Z= 0.430
  Chirality :  0.045   0.325   1400
  Planarity :  0.004   0.052   1544
  Dihedral  : 15.965  86.742   3234
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 20.15 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.25), residues: 1119
  helix:  0.95 (0.29), residues: 370
  sheet: -0.45 (0.29), residues: 290
  loop : -0.67 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R  83 
 PHE   0.009   0.001   PHE R 152 
 TYR   0.041   0.002   TYR S  59 
 ARG   0.007   0.001   ARG B  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16498 (  448)
  hydrogen bonds       : angle       7.30456 ( 1266)
  SS BOND              : bond        0.00425 (    2)
  SS BOND              : angle       0.29384 (    4)
  covalent geometry    : bond        0.00420 ( 9043)
  covalent geometry    : angle       0.70717 (12250)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 175
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 LEU cc_start: 0.8275 (mt) cc_final: 0.7683 (tp)
REVERT: B  124 TYR cc_start: 0.9060 (m-80) cc_final: 0.8703 (m-80)
REVERT: B  188 MET cc_start: 0.8746 (mmm) cc_final: 0.8331 (mmm)
REVERT: B  189 SER cc_start: 0.8703 (t) cc_final: 0.8260 (t)
REVERT: B  217 MET cc_start: 0.8116 (tpp) cc_final: 0.7897 (tpt)
REVERT: B  237 ASN cc_start: 0.8259 (t0) cc_final: 0.7993 (t0)
REVERT: B  259 GLN cc_start: 0.7583 (pt0) cc_final: 0.7085 (pt0)
REVERT: G   62 ARG cc_start: 0.7203 (ttm110) cc_final: 0.6820 (ttm110)
REVERT: R   81 TYR cc_start: 0.8313 (m-80) cc_final: 0.7856 (m-80)
REVERT: R  170 PHE cc_start: 0.8046 (p90) cc_final: 0.7081 (p90)
REVERT: R  171 ASP cc_start: 0.8440 (t0) cc_final: 0.7953 (t0)
REVERT: S    3 GLN cc_start: 0.7756 (tt0) cc_final: 0.7260 (pt0)
REVERT: S  218 ARG cc_start: 0.6257 (ptp-170) cc_final: 0.6011 (ptp90)
  outliers start: 12
  outliers final: 2
  residues processed: 182
  average time/residue: 1.3194
  time to fit residues: 255.0525
Evaluate side-chains
  149 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 147
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain R residue  390 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    5.9990
   chunk 84 optimal weight:    0.6980
   chunk 46 optimal weight:    9.9990
   chunk 28 optimal weight:    0.7980
   chunk 56 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 52 optimal weight:    9.9990
   chunk 64 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
A 333 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  83 HIS
R 202 HIS
** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 171 ASN
S 179 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.163197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.115888 restraints weight = 12095.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 2.85
r_work: 0.3301 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9045  Z= 0.168
  Angle     :  0.615   8.236  12254  Z= 0.324
  Chirality :  0.045   0.210   1400
  Planarity :  0.004   0.035   1544
  Dihedral  :  5.925  55.375   1252
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.04 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 19.73 %
    Favored  : 76.71 %
  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:  0.20 (0.25), residues: 1119
  helix:  1.37 (0.27), residues: 379
  sheet: -0.26 (0.29), residues: 286
  loop : -0.57 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 339 
 HIS   0.005   0.001   HIS R 393 
 PHE   0.020   0.002   PHE B 253 
 TYR   0.016   0.002   TYR B  59 
 ARG   0.007   0.001   ARG R  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04580 (  448)
  hydrogen bonds       : angle       5.08856 ( 1266)
  SS BOND              : bond        0.00409 (    2)
  SS BOND              : angle       0.61093 (    4)
  covalent geometry    : bond        0.00389 ( 9043)
  covalent geometry    : angle       0.61463 (12250)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 164
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 LEU cc_start: 0.8329 (mt) cc_final: 0.7793 (tp)
REVERT: B  188 MET cc_start: 0.8672 (mmm) cc_final: 0.8303 (mmm)
REVERT: B  189 SER cc_start: 0.8670 (t) cc_final: 0.8159 (t)
REVERT: B  217 MET cc_start: 0.8285 (tpp) cc_final: 0.8005 (tpt)
REVERT: B  259 GLN cc_start: 0.7538 (pt0) cc_final: 0.6974 (pt0)
REVERT: B  270 ILE cc_start: 0.9148 (tt) cc_final: 0.8908 (pp)
REVERT: G   36 ASP cc_start: 0.8270 (m-30) cc_final: 0.8037 (m-30)
REVERT: G   52 THR cc_start: 0.7474 (t) cc_final: 0.7131 (p)
REVERT: G   58 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8020 (mp0)
REVERT: G   62 ARG cc_start: 0.7160 (ttm110) cc_final: 0.6944 (ttm110)
REVERT: R    9 PHE cc_start: 0.7363 (m-80) cc_final: 0.7144 (m-10)
REVERT: R   74 GLN cc_start: 0.8798 (tp-100) cc_final: 0.8472 (tp-100)
REVERT: R  170 PHE cc_start: 0.7919 (p90) cc_final: 0.7024 (p90)
REVERT: R  171 ASP cc_start: 0.8355 (t0) cc_final: 0.7831 (t0)
REVERT: R  327 CYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7814 (t)
REVERT: S    3 GLN cc_start: 0.7522 (tt0) cc_final: 0.7134 (pt0)
REVERT: S   20 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8272 (mt)
REVERT: S   39 GLN cc_start: 0.8088 (tt0) cc_final: 0.7499 (tp40)
REVERT: S  233 LEU cc_start: 0.8091 (tp) cc_final: 0.7720 (mt)
REVERT: S  234 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7865 (mt-10)
  outliers start: 34
  outliers final: 12
  residues processed: 190
  average time/residue: 1.1176
  time to fit residues: 226.9369
Evaluate side-chains
  159 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  138 VAL
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  365 ILE
Chi-restraints excluded: chain R residue  390 ARG
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue  154 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 104 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 94 optimal weight:    0.2980
   chunk 101 optimal weight:    4.9990
   chunk 15 optimal weight:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   chunk 48 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 88 optimal weight:    9.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
R 204 GLN
** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.166003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.119045 restraints weight = 12054.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 2.93
r_work: 0.3358 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9045  Z= 0.117
  Angle     :  0.572   8.327  12254  Z= 0.295
  Chirality :  0.043   0.207   1400
  Planarity :  0.003   0.029   1544
  Dihedral  :  5.414  47.163   1252
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.04 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 19.62 %
    Favored  : 76.71 %
  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:  0.33 (0.25), residues: 1119
  helix:  1.48 (0.27), residues: 381
  sheet: -0.18 (0.29), residues: 284
  loop : -0.50 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 339 
 HIS   0.004   0.001   HIS R 393 
 PHE   0.016   0.001   PHE B 253 
 TYR   0.018   0.001   TYR B  59 
 ARG   0.007   0.000   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03911 (  448)
  hydrogen bonds       : angle       4.78315 ( 1266)
  SS BOND              : bond        0.00285 (    2)
  SS BOND              : angle       0.56066 (    4)
  covalent geometry    : bond        0.00256 ( 9043)
  covalent geometry    : angle       0.57169 (12250)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 172
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 LEU cc_start: 0.8338 (mt) cc_final: 0.7816 (tp)
REVERT: A  312 LYS cc_start: 0.8283 (mmtm) cc_final: 0.7955 (mmmt)
REVERT: A  318 GLU cc_start: 0.7920 (tt0) cc_final: 0.7287 (pm20)
REVERT: B   42 ARG cc_start: 0.7438 (tpp-160) cc_final: 0.7211 (tpp-160)
REVERT: B  188 MET cc_start: 0.8628 (mmm) cc_final: 0.8246 (mmm)
REVERT: B  189 SER cc_start: 0.8509 (t) cc_final: 0.8002 (t)
REVERT: B  217 MET cc_start: 0.8247 (tpp) cc_final: 0.7962 (tpt)
REVERT: B  259 GLN cc_start: 0.7505 (pt0) cc_final: 0.6857 (pt0)
REVERT: G   36 ASP cc_start: 0.8305 (m-30) cc_final: 0.8047 (m-30)
REVERT: G   44 HIS cc_start: 0.7226 (m90) cc_final: 0.7001 (m90)
REVERT: G   52 THR cc_start: 0.7424 (t) cc_final: 0.7194 (p)
REVERT: R   74 GLN cc_start: 0.8753 (tp-100) cc_final: 0.8469 (tp-100)
REVERT: R  170 PHE cc_start: 0.7790 (p90) cc_final: 0.6902 (p90)
REVERT: R  171 ASP cc_start: 0.8249 (t0) cc_final: 0.7737 (t0)
REVERT: R  327 CYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7645 (t)
REVERT: R  357 ASN cc_start: 0.9071 (m-40) cc_final: 0.8848 (m110)
REVERT: S    3 GLN cc_start: 0.7427 (tt0) cc_final: 0.7029 (pt0)
REVERT: S   39 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7294 (tp40)
REVERT: S  179 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7130 (mm-40)
REVERT: S  233 LEU cc_start: 0.7993 (tp) cc_final: 0.7620 (mt)
  outliers start: 35
  outliers final: 8
  residues processed: 192
  average time/residue: 1.0367
  time to fit residues: 214.2822
Evaluate side-chains
  158 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  390 ARG
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue  179 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 69 optimal weight:    0.6980
   chunk 103 optimal weight:    5.9990
   chunk 93 optimal weight:    6.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    0.3980
   chunk 59 optimal weight:    0.8980
   chunk 66 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   chunk 43 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
R 210 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.165719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.118555 restraints weight = 12084.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 2.93
r_work: 0.3360 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9045  Z= 0.123
  Angle     :  0.546   7.144  12254  Z= 0.285
  Chirality :  0.043   0.220   1400
  Planarity :  0.003   0.030   1544
  Dihedral  :  5.167  51.921   1252
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.31 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 22.88 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.25), residues: 1119
  helix:  1.50 (0.27), residues: 382
  sheet: -0.19 (0.28), residues: 298
  loop : -0.40 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 393 
 PHE   0.016   0.001   PHE B 253 
 TYR   0.020   0.001   TYR B  59 
 ARG   0.006   0.000   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  448)
  hydrogen bonds       : angle       4.71120 ( 1266)
  SS BOND              : bond        0.00294 (    2)
  SS BOND              : angle       0.58425 (    4)
  covalent geometry    : bond        0.00276 ( 9043)
  covalent geometry    : angle       0.54596 (12250)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 161
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
REVERT: A  232 LEU cc_start: 0.8426 (mt) cc_final: 0.7903 (tp)
REVERT: A  312 LYS cc_start: 0.8343 (mmtm) cc_final: 0.8006 (mmmt)
REVERT: B   42 ARG cc_start: 0.7514 (tpp-160) cc_final: 0.7241 (tpp-160)
REVERT: B  188 MET cc_start: 0.8635 (mmm) cc_final: 0.8247 (mmm)
REVERT: B  189 SER cc_start: 0.8512 (t) cc_final: 0.7998 (t)
REVERT: B  217 MET cc_start: 0.8229 (tpp) cc_final: 0.7955 (tpt)
REVERT: B  259 GLN cc_start: 0.7613 (pt0) cc_final: 0.7183 (pt0)
REVERT: B  262 MET cc_start: 0.7937 (ttp) cc_final: 0.7675 (ttp)
REVERT: G   36 ASP cc_start: 0.8308 (m-30) cc_final: 0.8010 (m-30)
REVERT: G   44 HIS cc_start: 0.7256 (m90) cc_final: 0.7034 (m90)
REVERT: R   52 ARG cc_start: 0.8413 (mtp180) cc_final: 0.8021 (mtp180)
REVERT: R   74 GLN cc_start: 0.8803 (tp-100) cc_final: 0.8529 (tp40)
REVERT: R  170 PHE cc_start: 0.7821 (p90) cc_final: 0.6934 (p90)
REVERT: R  171 ASP cc_start: 0.8265 (t0) cc_final: 0.7727 (t0)
REVERT: R  327 CYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7652 (t)
REVERT: S    3 GLN cc_start: 0.7481 (tt0) cc_final: 0.7006 (pt0)
REVERT: S   39 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7435 (tp40)
REVERT: S   59 TYR cc_start: 0.6857 (m-10) cc_final: 0.6632 (m-80)
REVERT: S  179 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7245 (mm-40)
REVERT: S  233 LEU cc_start: 0.8033 (tp) cc_final: 0.7706 (mt)
  outliers start: 28
  outliers final: 10
  residues processed: 177
  average time/residue: 1.1521
  time to fit residues: 217.9534
Evaluate side-chains
  156 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   22 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue  179 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 107 optimal weight:    7.9990
   chunk 85 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0870
   overall best weight:    1.5364

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 230 ASN
** R 210 GLN ** 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 = 0.3988 r_free = 0.3988 target = 0.163688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.116073 restraints weight = 12040.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.92
r_work: 0.3324 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9045  Z= 0.147
  Angle     :  0.566   9.007  12254  Z= 0.293
  Chirality :  0.043   0.235   1400
  Planarity :  0.003   0.030   1544
  Dihedral  :  4.998  58.599   1248
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.49 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 21.93 %
    Favored  : 73.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.25), residues: 1119
  helix:  1.61 (0.27), residues: 383
  sheet: -0.24 (0.28), residues: 298
  loop : -0.45 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 393 
 PHE   0.014   0.001   PHE B 253 
 TYR   0.024   0.002   TYR B  59 
 ARG   0.006   0.000   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03826 (  448)
  hydrogen bonds       : angle       4.70848 ( 1266)
  SS BOND              : bond        0.00334 (    2)
  SS BOND              : angle       0.62913 (    4)
  covalent geometry    : bond        0.00341 ( 9043)
  covalent geometry    : angle       0.56554 (12250)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 158
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
REVERT: A  232 LEU cc_start: 0.8521 (mt) cc_final: 0.8004 (tp)
REVERT: A  312 LYS cc_start: 0.8358 (mmtm) cc_final: 0.8034 (mmmt)
REVERT: A  330 LYS cc_start: 0.8208 (mmtp) cc_final: 0.7673 (mppt)
REVERT: B   44 GLN cc_start: 0.9026 (tt0) cc_final: 0.8762 (tp40)
REVERT: B  188 MET cc_start: 0.8599 (mmm) cc_final: 0.8269 (mmm)
REVERT: B  189 SER cc_start: 0.8594 (t) cc_final: 0.8051 (t)
REVERT: B  217 MET cc_start: 0.8224 (tpp) cc_final: 0.7947 (ppp)
REVERT: B  228 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6436 (p0)
REVERT: B  259 GLN cc_start: 0.7579 (pt0) cc_final: 0.6971 (pt0)
REVERT: B  262 MET cc_start: 0.7913 (ttp) cc_final: 0.7643 (ttp)
REVERT: G   36 ASP cc_start: 0.8304 (m-30) cc_final: 0.7973 (m-30)
REVERT: G   44 HIS cc_start: 0.7413 (m90) cc_final: 0.7072 (m-70)
REVERT: G   62 ARG cc_start: 0.7218 (ttm110) cc_final: 0.6980 (mtm-85)
REVERT: R   74 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8561 (tp-100)
REVERT: R   87 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.5193 (ttt-90)
REVERT: R  151 SER cc_start: 0.9228 (m) cc_final: 0.8833 (p)
REVERT: R  170 PHE cc_start: 0.7870 (p90) cc_final: 0.6954 (p90)
REVERT: R  341 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8492 (mm)
REVERT: S   39 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7131 (tp-100)
REVERT: S  179 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7264 (mm-40)
REVERT: S  233 LEU cc_start: 0.8037 (tp) cc_final: 0.7730 (mt)
  outliers start: 39
  outliers final: 18
  residues processed: 186
  average time/residue: 1.1609
  time to fit residues: 230.8725
Evaluate side-chains
  169 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   22 VAL
Chi-restraints excluded: chain R residue   67 LEU
Chi-restraints excluded: chain R residue   87 ARG
Chi-restraints excluded: chain R residue  138 VAL
Chi-restraints excluded: chain R residue  337 LEU
Chi-restraints excluded: chain R residue  341 LEU
Chi-restraints excluded: chain R residue  365 ILE
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue  179 GLN
Chi-restraints excluded: chain S residue  214 LEU
Chi-restraints excluded: chain S residue  232 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 107 optimal weight:    0.3980
   chunk 20 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 58 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
B  75 GLN
B 230 ASN
** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 357 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.164225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.116816 restraints weight = 12000.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.89
r_work: 0.3331 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9045  Z= 0.132
  Angle     :  0.558   8.181  12254  Z= 0.290
  Chirality :  0.043   0.230   1400
  Planarity :  0.003   0.035   1544
  Dihedral  :  4.879  57.888   1248
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.31 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 23.92 %
    Favored  : 72.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.25), residues: 1119
  helix:  1.65 (0.27), residues: 383
  sheet: -0.19 (0.28), residues: 298
  loop : -0.49 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 393 
 PHE   0.014   0.001   PHE B 253 
 TYR   0.019   0.001   TYR B  59 
 ARG   0.009   0.000   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03715 (  448)
  hydrogen bonds       : angle       4.68652 ( 1266)
  SS BOND              : bond        0.00311 (    2)
  SS BOND              : angle       0.60355 (    4)
  covalent geometry    : bond        0.00303 ( 9043)
  covalent geometry    : angle       0.55809 (12250)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 155
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
REVERT: A  232 LEU cc_start: 0.8525 (mt) cc_final: 0.8035 (tp)
REVERT: A  312 LYS cc_start: 0.8363 (mmtm) cc_final: 0.8019 (mmmt)
REVERT: A  330 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7651 (mppt)
REVERT: B   44 GLN cc_start: 0.9024 (tt0) cc_final: 0.8752 (tp40)
REVERT: B  188 MET cc_start: 0.8589 (mmm) cc_final: 0.8252 (mmm)
REVERT: B  189 SER cc_start: 0.8547 (t) cc_final: 0.8005 (t)
REVERT: B  228 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6454 (p0)
REVERT: B  259 GLN cc_start: 0.7585 (pt0) cc_final: 0.6991 (pt0)
REVERT: B  262 MET cc_start: 0.7927 (ttp) cc_final: 0.7683 (ttp)
REVERT: B  292 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.7871 (m-80)
REVERT: G   36 ASP cc_start: 0.8290 (m-30) cc_final: 0.7953 (m-30)
REVERT: G   44 HIS cc_start: 0.7386 (m90) cc_final: 0.7005 (m-70)
REVERT: G   62 ARG cc_start: 0.7255 (ttm110) cc_final: 0.7018 (mtm-85)
REVERT: R  151 SER cc_start: 0.9209 (m) cc_final: 0.8813 (p)
REVERT: R  170 PHE cc_start: 0.7869 (p90) cc_final: 0.6949 (p90)
REVERT: R  341 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8482 (mm)
REVERT: S   39 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7100 (tp-100)
REVERT: S   87 ARG cc_start: 0.5396 (OUTLIER) cc_final: 0.4959 (ptt90)
REVERT: S  179 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7264 (mm-40)
REVERT: S  233 LEU cc_start: 0.8025 (tp) cc_final: 0.7738 (mt)
  outliers start: 36
  outliers final: 17
  residues processed: 178
  average time/residue: 1.1055
  time to fit residues: 210.6888
Evaluate side-chains
  168 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 145
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   22 VAL
Chi-restraints excluded: chain R residue   67 LEU
Chi-restraints excluded: chain R residue  138 VAL
Chi-restraints excluded: chain R residue  337 LEU
Chi-restraints excluded: chain R residue  341 LEU
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue  179 GLN
Chi-restraints excluded: chain S residue  214 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 94 optimal weight:   20.0000
   chunk 63 optimal weight:    4.9990
   chunk 79 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 71 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.165138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.117957 restraints weight = 12126.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.87
r_work: 0.3349 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9045  Z= 0.120
  Angle     :  0.557   8.322  12254  Z= 0.288
  Chirality :  0.042   0.220   1400
  Planarity :  0.003   0.037   1544
  Dihedral  :  4.722  54.407   1248
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.49 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 25.50 %
    Favored  : 71.35 %
  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:  0.46 (0.25), residues: 1119
  helix:  1.65 (0.27), residues: 383
  sheet: -0.18 (0.28), residues: 296
  loop : -0.46 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 393 
 PHE   0.013   0.001   PHE B 253 
 TYR   0.017   0.001   TYR B  59 
 ARG   0.010   0.000   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03608 (  448)
  hydrogen bonds       : angle       4.63114 ( 1266)
  SS BOND              : bond        0.00290 (    2)
  SS BOND              : angle       0.58389 (    4)
  covalent geometry    : bond        0.00272 ( 9043)
  covalent geometry    : angle       0.55669 (12250)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 165
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
REVERT: A  232 LEU cc_start: 0.8517 (mt) cc_final: 0.8062 (tp)
REVERT: A  312 LYS cc_start: 0.8436 (mmtm) cc_final: 0.8116 (mmmt)
REVERT: A  330 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7662 (mppt)
REVERT: B   44 GLN cc_start: 0.9001 (tt0) cc_final: 0.8740 (tp40)
REVERT: B  175 GLN cc_start: 0.8201 (pt0) cc_final: 0.7500 (pp30)
REVERT: B  188 MET cc_start: 0.8594 (mmm) cc_final: 0.8270 (mmm)
REVERT: B  189 SER cc_start: 0.8520 (t) cc_final: 0.7993 (t)
REVERT: B  259 GLN cc_start: 0.7680 (pt0) cc_final: 0.7108 (pt0)
REVERT: B  262 MET cc_start: 0.8065 (ttp) cc_final: 0.7744 (ttp)
REVERT: B  292 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8047 (m-80)
REVERT: G   36 ASP cc_start: 0.8295 (m-30) cc_final: 0.7971 (m-30)
REVERT: G   44 HIS cc_start: 0.7444 (m90) cc_final: 0.7059 (m-70)
REVERT: G   62 ARG cc_start: 0.7303 (ttm110) cc_final: 0.6937 (tpp-160)
REVERT: R   74 GLN cc_start: 0.8875 (tp-100) cc_final: 0.8082 (tp-100)
REVERT: R  151 SER cc_start: 0.9182 (m) cc_final: 0.8656 (p)
REVERT: R  170 PHE cc_start: 0.7857 (p90) cc_final: 0.7018 (p90)
REVERT: R  178 TYR cc_start: 0.7546 (t80) cc_final: 0.7163 (t80)
REVERT: R  210 GLN cc_start: 0.7643 (mt0) cc_final: 0.7013 (mp10)
REVERT: R  341 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8505 (mm)
REVERT: S   39 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7135 (tp-100)
REVERT: S   87 ARG cc_start: 0.5414 (OUTLIER) cc_final: 0.4971 (ptt90)
REVERT: S  179 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7308 (mm-40)
REVERT: S  223 ASP cc_start: 0.5925 (m-30) cc_final: 0.5696 (m-30)
REVERT: S  227 TYR cc_start: 0.7485 (m-10) cc_final: 0.6778 (m-10)
REVERT: S  233 LEU cc_start: 0.8107 (tp) cc_final: 0.7894 (mt)
REVERT: S  234 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7562 (mt-10)
  outliers start: 30
  outliers final: 15
  residues processed: 186
  average time/residue: 1.0914
  time to fit residues: 218.0426
Evaluate side-chains
  168 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   67 LEU
Chi-restraints excluded: chain R residue  138 VAL
Chi-restraints excluded: chain R residue  337 LEU
Chi-restraints excluded: chain R residue  341 LEU
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue  154 SER
Chi-restraints excluded: chain S residue  179 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 95 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 67 optimal weight:    7.9990
   chunk 7 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 94 optimal weight:    7.9990
   chunk 108 optimal weight:    9.9990
   chunk 110 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
B 230 ASN
** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 357 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.164673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.117497 restraints weight = 12185.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.85
r_work: 0.3352 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9045  Z= 0.137
  Angle     :  0.590   8.447  12254  Z= 0.300
  Chirality :  0.043   0.231   1400
  Planarity :  0.003   0.040   1544
  Dihedral  :  4.719  51.421   1248
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.49 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 25.81 %
    Favored  : 70.93 %
  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:  0.40 (0.25), residues: 1119
  helix:  1.61 (0.27), residues: 383
  sheet: -0.20 (0.29), residues: 292
  loop : -0.51 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 393 
 PHE   0.014   0.001   PHE B 253 
 TYR   0.019   0.001   TYR R 119 
 ARG   0.010   0.001   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03677 (  448)
  hydrogen bonds       : angle       4.62934 ( 1266)
  SS BOND              : bond        0.00319 (    2)
  SS BOND              : angle       0.61026 (    4)
  covalent geometry    : bond        0.00316 ( 9043)
  covalent geometry    : angle       0.58950 (12250)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 155
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
REVERT: A  232 LEU cc_start: 0.8531 (mt) cc_final: 0.8084 (tp)
REVERT: A  312 LYS cc_start: 0.8434 (mmtm) cc_final: 0.8119 (mmmt)
REVERT: A  330 LYS cc_start: 0.8171 (mmtp) cc_final: 0.7622 (mppt)
REVERT: B   42 ARG cc_start: 0.7380 (tpp-160) cc_final: 0.7082 (tpp-160)
REVERT: B   44 GLN cc_start: 0.8994 (tt0) cc_final: 0.8742 (tp40)
REVERT: B  175 GLN cc_start: 0.8232 (pt0) cc_final: 0.7538 (pp30)
REVERT: B  188 MET cc_start: 0.8578 (mmm) cc_final: 0.8248 (mmm)
REVERT: B  189 SER cc_start: 0.8546 (t) cc_final: 0.8013 (t)
REVERT: B  228 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6509 (p0)
REVERT: B  259 GLN cc_start: 0.7663 (pt0) cc_final: 0.7144 (pt0)
REVERT: B  292 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8185 (m-80)
REVERT: G   36 ASP cc_start: 0.8260 (m-30) cc_final: 0.7917 (m-30)
REVERT: G   38 MET cc_start: 0.7822 (ttp) cc_final: 0.7077 (ttm)
REVERT: G   42 GLU cc_start: 0.7917 (pp20) cc_final: 0.7552 (pm20)
REVERT: G   44 HIS cc_start: 0.7427 (m90) cc_final: 0.7089 (m-70)
REVERT: R   52 ARG cc_start: 0.8431 (mtp180) cc_final: 0.7976 (mpp80)
REVERT: R   74 GLN cc_start: 0.8879 (tp-100) cc_final: 0.8198 (tp-100)
REVERT: R  151 SER cc_start: 0.9167 (m) cc_final: 0.8801 (p)
REVERT: R  170 PHE cc_start: 0.7850 (p90) cc_final: 0.6974 (p90)
REVERT: R  206 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7049 (ttmt)
REVERT: R  341 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8484 (mm)
REVERT: S   39 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7126 (tp-100)
REVERT: S   87 ARG cc_start: 0.5403 (OUTLIER) cc_final: 0.4993 (ptt90)
REVERT: S  179 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7308 (mm-40)
REVERT: S  233 LEU cc_start: 0.8101 (tp) cc_final: 0.7863 (mt)
REVERT: S  234 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7525 (mt-10)
  outliers start: 31
  outliers final: 17
  residues processed: 179
  average time/residue: 1.1200
  time to fit residues: 214.9528
Evaluate side-chains
  172 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   67 LEU
Chi-restraints excluded: chain R residue   81 TYR
Chi-restraints excluded: chain R residue  138 VAL
Chi-restraints excluded: chain R residue  206 LYS
Chi-restraints excluded: chain R residue  337 LEU
Chi-restraints excluded: chain R residue  341 LEU
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue  154 SER
Chi-restraints excluded: chain S residue  179 GLN
Chi-restraints excluded: chain S residue  214 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 43 optimal weight:    0.4980
   chunk 90 optimal weight:    0.9990
   chunk 56 optimal weight:    9.9990
   chunk 107 optimal weight:    9.9990
   chunk 109 optimal weight:    9.9990
   chunk 85 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
B 230 ASN
** R 210 GLN ** 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 = 0.4016 r_free = 0.4016 target = 0.166160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.118968 restraints weight = 12052.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.86
r_work: 0.3370 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9045  Z= 0.117
  Angle     :  0.582   8.356  12254  Z= 0.295
  Chirality :  0.042   0.226   1400
  Planarity :  0.004   0.076   1544
  Dihedral  :  4.639  49.740   1248
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.49 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 26.55 %
    Favored  : 70.51 %
  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:  0.44 (0.25), residues: 1119
  helix:  1.62 (0.27), residues: 384
  sheet: -0.14 (0.29), residues: 291
  loop : -0.51 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 393 
 PHE   0.014   0.001   PHE B 253 
 TYR   0.021   0.001   TYR B  59 
 ARG   0.019   0.001   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03548 (  448)
  hydrogen bonds       : angle       4.58091 ( 1266)
  SS BOND              : bond        0.00247 (    2)
  SS BOND              : angle       0.60485 (    4)
  covalent geometry    : bond        0.00264 ( 9043)
  covalent geometry    : angle       0.58181 (12250)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 165
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
REVERT: A  205 ARG cc_start: 0.8216 (mmm160) cc_final: 0.7674 (mmt-90)
REVERT: A  232 LEU cc_start: 0.8539 (mt) cc_final: 0.8105 (tp)
REVERT: A  312 LYS cc_start: 0.8422 (mmtm) cc_final: 0.8110 (mmmt)
REVERT: A  330 LYS cc_start: 0.8164 (mmtp) cc_final: 0.7567 (mppt)
REVERT: B   42 ARG cc_start: 0.7418 (tpp-160) cc_final: 0.7108 (tpp-160)
REVERT: B   44 GLN cc_start: 0.8995 (tt0) cc_final: 0.8743 (tp40)
REVERT: B  129 ARG cc_start: 0.8676 (ptp-110) cc_final: 0.8461 (ptm-80)
REVERT: B  175 GLN cc_start: 0.8210 (pt0) cc_final: 0.7507 (pp30)
REVERT: B  188 MET cc_start: 0.8564 (mmm) cc_final: 0.8238 (mmm)
REVERT: B  189 SER cc_start: 0.8517 (t) cc_final: 0.7996 (t)
REVERT: B  228 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6467 (p0)
REVERT: B  259 GLN cc_start: 0.7690 (pt0) cc_final: 0.7123 (pt0)
REVERT: B  292 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8131 (m-80)
REVERT: G   36 ASP cc_start: 0.8258 (m-30) cc_final: 0.7918 (m-30)
REVERT: G   44 HIS cc_start: 0.7404 (m90) cc_final: 0.7049 (m-70)
REVERT: G   62 ARG cc_start: 0.7158 (ttm110) cc_final: 0.6849 (mtm-85)
REVERT: R   52 ARG cc_start: 0.8398 (mtp180) cc_final: 0.7952 (mpp80)
REVERT: R   74 GLN cc_start: 0.8839 (tp-100) cc_final: 0.8189 (tp-100)
REVERT: R  151 SER cc_start: 0.9154 (m) cc_final: 0.8645 (p)
REVERT: R  170 PHE cc_start: 0.7821 (p90) cc_final: 0.6978 (p90)
REVERT: R  178 TYR cc_start: 0.7555 (t80) cc_final: 0.7155 (t80)
REVERT: R  206 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.6313 (ttmt)
REVERT: R  210 GLN cc_start: 0.7674 (mt0) cc_final: 0.7032 (mp10)
REVERT: R  341 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8471 (mm)
REVERT: R  353 MET cc_start: 0.7987 (mmm) cc_final: 0.7766 (mmm)
REVERT: S   39 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7165 (tp-100)
REVERT: S   87 ARG cc_start: 0.5355 (OUTLIER) cc_final: 0.4944 (ptt90)
REVERT: S  179 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7352 (mm-40)
REVERT: S  233 LEU cc_start: 0.8143 (tp) cc_final: 0.7938 (mt)
REVERT: S  234 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7635 (mt-10)
  outliers start: 28
  outliers final: 13
  residues processed: 189
  average time/residue: 1.1069
  time to fit residues: 224.2002
Evaluate side-chains
  171 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   81 TYR
Chi-restraints excluded: chain R residue  138 VAL
Chi-restraints excluded: chain R residue  206 LYS
Chi-restraints excluded: chain R residue  337 LEU
Chi-restraints excluded: chain R residue  341 LEU
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue  154 SER
Chi-restraints excluded: chain S residue  179 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    6.9990
   chunk 101 optimal weight:   20.0000
   chunk 89 optimal weight:    1.9990
   chunk 86 optimal weight:    7.9990
   chunk 8 optimal weight:    0.5980
   chunk 73 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 99 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 340 ASN
** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 357 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.164370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.116981 restraints weight = 12095.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.86
r_work: 0.3343 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9045  Z= 0.148
  Angle     :  0.610  11.288  12254  Z= 0.309
  Chirality :  0.043   0.233   1400
  Planarity :  0.004   0.077   1544
  Dihedral  :  4.757  46.998   1248
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.49 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 26.55 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.38 (0.25), residues: 1119
  helix:  1.56 (0.27), residues: 383
  sheet: -0.19 (0.29), residues: 294
  loop : -0.49 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 393 
 PHE   0.016   0.001   PHE B 253 
 TYR   0.025   0.002   TYR B  59 
 ARG   0.019   0.001   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03768 (  448)
  hydrogen bonds       : angle       4.65586 ( 1266)
  SS BOND              : bond        0.00321 (    2)
  SS BOND              : angle       0.61045 (    4)
  covalent geometry    : bond        0.00344 ( 9043)
  covalent geometry    : angle       0.60963 (12250)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 150
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 MET cc_start: 0.7920 (ttm) cc_final: 0.7485 (mtp)
REVERT: A  205 ARG cc_start: 0.8219 (mmm160) cc_final: 0.7706 (mmt-90)
REVERT: A  232 LEU cc_start: 0.8537 (mt) cc_final: 0.8106 (tp)
REVERT: A  271 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6396 (mttm)
REVERT: A  312 LYS cc_start: 0.8398 (mmtm) cc_final: 0.8097 (mmmt)
REVERT: A  330 LYS cc_start: 0.8144 (mmtp) cc_final: 0.7570 (mppt)
REVERT: B   42 ARG cc_start: 0.7424 (tpp-160) cc_final: 0.7119 (tpp-160)
REVERT: B   44 GLN cc_start: 0.8984 (tt0) cc_final: 0.8738 (tp40)
REVERT: B  175 GLN cc_start: 0.8249 (pt0) cc_final: 0.7556 (pp30)
REVERT: B  188 MET cc_start: 0.8593 (mmm) cc_final: 0.8271 (mmm)
REVERT: B  189 SER cc_start: 0.8614 (t) cc_final: 0.8094 (t)
REVERT: B  228 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6452 (p0)
REVERT: B  259 GLN cc_start: 0.7709 (pt0) cc_final: 0.7190 (pt0)
REVERT: B  292 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8215 (m-80)
REVERT: G   36 ASP cc_start: 0.8275 (m-30) cc_final: 0.7947 (m-30)
REVERT: G   44 HIS cc_start: 0.7496 (m90) cc_final: 0.7169 (m-70)
REVERT: G   58 GLU cc_start: 0.8879 (mm-30) cc_final: 0.7959 (mp0)
REVERT: G   62 ARG cc_start: 0.7145 (ttm110) cc_final: 0.6707 (tpp-160)
REVERT: R   52 ARG cc_start: 0.8447 (mtp180) cc_final: 0.7810 (tpp80)
REVERT: R   74 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8216 (tp-100)
REVERT: R  151 SER cc_start: 0.9160 (m) cc_final: 0.8801 (p)
REVERT: R  170 PHE cc_start: 0.7879 (p90) cc_final: 0.7000 (p90)
REVERT: R  210 GLN cc_start: 0.7681 (mt0) cc_final: 0.7053 (mp10)
REVERT: R  353 MET cc_start: 0.7997 (mmm) cc_final: 0.7769 (mmm)
REVERT: S   39 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7206 (tp-100)
REVERT: S   87 ARG cc_start: 0.5370 (OUTLIER) cc_final: 0.4989 (ptt90)
REVERT: S  179 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7261 (mm-40)
REVERT: S  233 LEU cc_start: 0.8180 (tp) cc_final: 0.7974 (mt)
  outliers start: 26
  outliers final: 17
  residues processed: 170
  average time/residue: 1.1494
  time to fit residues: 209.0843
Evaluate side-chains
  170 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   81 TYR
Chi-restraints excluded: chain R residue  138 VAL
Chi-restraints excluded: chain R residue  337 LEU
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue  154 SER
Chi-restraints excluded: chain S residue  179 GLN
Chi-restraints excluded: chain S residue  214 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 109 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 91 optimal weight:    7.9990
   chunk 93 optimal weight:    0.3980
   chunk 17 optimal weight:    0.0980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
R  74 GLN
** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.167700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.120448 restraints weight = 11967.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 2.88
r_work: 0.3383 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9045  Z= 0.110
  Angle     :  0.591  11.252  12254  Z= 0.297
  Chirality :  0.042   0.194   1400
  Planarity :  0.004   0.081   1544
  Dihedral  :  4.498  44.193   1248
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.49 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 26.97 %
    Favored  : 70.62 %
  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:  0.47 (0.25), residues: 1119
  helix:  1.61 (0.27), residues: 383
  sheet: -0.05 (0.29), residues: 291
  loop : -0.50 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 393 
 PHE   0.014   0.001   PHE B 253 
 TYR   0.020   0.001   TYR B  59 
 ARG   0.019   0.001   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03492 (  448)
  hydrogen bonds       : angle       4.53052 ( 1266)
  SS BOND              : bond        0.00227 (    2)
  SS BOND              : angle       0.47389 (    4)
  covalent geometry    : bond        0.00242 ( 9043)
  covalent geometry    : angle       0.59110 (12250)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6998.58 seconds
wall clock time: 121 minutes 33.23 seconds (7293.23 seconds total)