Starting phenix.real_space_refine
on Wed Mar 12 17:49:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w87_37347/03_2025/8w87_37347_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w87_37347/03_2025/8w87_37347.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w87_37347/03_2025/8w87_37347.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w87_37347/03_2025/8w87_37347.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w87_37347/03_2025/8w87_37347_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w87_37347/03_2025/8w87_37347_neut.cif"
  }
  resolution = 2.8
  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=   0.001 sd=   0.047
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      63      5.16       5
     C    5235      2.51       5
     N    1415      2.21       5
     O    1515      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8228
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1906
          Classifications: {'peptide': 234}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "B"
      Number of atoms: 2593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2593
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "R"
      Number of atoms: 2315
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2315
          Classifications: {'peptide': 289}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 11, 'TRANS': 277}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 31
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 23
    Chain: "R"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Unusual residues: {'B40': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.13, per 1000 atoms: 0.62
  Number of scatterers: 8228
  At special positions: 0
  Unit cell: (82.4, 98.88, 132.664, 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      63     16.00
     O    1515      8.00
     N    1415      7.00
     C    5235      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 182 " distance=2.26

  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: 2.21
  Conformation dependent library (CDL) restraints added in 946.1 milliseconds
  

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  B40 R 501 "
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 10 sheets defined
      44.2% alpha, 20.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 33
    Processing helix  chain 'A' and resid 52 through 62
      removed outlier: 3.934A  pdb=" N   ILE A  62 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 223
      removed outlier: 3.511A  pdb=" N   PHE A 222 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 238
      No H-bonds generated for 'chain 'A' and resid 236 through 238'
    Processing helix  chain 'A' and resid 239 through 253
    Processing helix  chain 'A' and resid 267 through 278
    Processing helix  chain 'A' and resid 281 through 285
    Processing helix  chain 'A' and resid 286 through 291
    Processing helix  chain 'A' and resid 305 through 326
      removed outlier: 3.749A  pdb=" N   ILE A 322 " --> pdb=" O   GLU A 318 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   SER A 326 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 365
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.524A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.812A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 20 through 51
    Processing helix  chain 'R' and resid 56 through 76
    Processing helix  chain 'R' and resid 76 through 87
    Processing helix  chain 'R' and resid 91 through 127
      removed outlier: 4.282A  pdb=" N   PHE R  95 " --> pdb=" O   PHE R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 130 through 135
    Processing helix  chain 'R' and resid 136 through 161
      Proline residue:  R 151  - end of helix
    Processing helix  chain 'R' and resid 168 through 180
    Processing helix  chain 'R' and resid 187 through 199
    Processing helix  chain 'R' and resid 199 through 231
      removed outlier: 3.990A  pdb=" N   LEU R 231 " --> pdb=" O   ALA R 227 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 247 through 278
      removed outlier: 3.610A  pdb=" N   PHE R 260 " --> pdb=" O   VAL R 256 " (cutoff:3.500A)
      Proline residue:  R 266  - end of helix
      Proline residue:  R 275  - end of helix
    Processing helix  chain 'R' and resid 284 through 305
      removed outlier: 3.631A  pdb=" N   SER R 297 " --> pdb=" O   GLY R 293 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 320
    Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 198
      removed outlier: 4.685A  pdb=" N   VAL A 208 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 8.103A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ALA A 227 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   ILE A 228 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   PHE A 264 " --> pdb=" O   ILE A 228 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   PHE A 230 " --> pdb=" O   PHE A 264 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ASN A 266 " --> pdb=" O   PHE A 230 " (cutoff:3.500A)
      removed outlier: 5.963A  pdb=" N   VAL A 232 " --> pdb=" O   ASN A 266 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.944A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.532A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.358A  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: 6.743A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.234A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.556A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.232A  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: 3.839A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.695A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.840A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.851A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    463 hydrogen bonds defined for protein.
    1320 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: 2.70

  Time building geometry restraints manager: 2.47 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1386
        1.32 -     1.44: 2303
        1.44 -     1.57: 4625
        1.57 -     1.69: 0
        1.69 -     1.81: 92
  Bond restraints: 8406
  Sorted by residual:
  bond pdb=" C   THR R 102 "
       pdb=" N   ASP R 103 "
    ideal  model  delta    sigma   weight residual
    1.334  1.415 -0.082 1.23e-02 6.61e+03 4.39e+01
  bond pdb=" C   ASP R 103 "
       pdb=" N   ILE R 104 "
    ideal  model  delta    sigma   weight residual
    1.334  1.258  0.076 1.25e-02 6.40e+03 3.74e+01
  bond pdb=" C   ASP R 103 "
       pdb=" O   ASP R 103 "
    ideal  model  delta    sigma   weight residual
    1.236  1.200  0.036 1.15e-02 7.56e+03 9.89e+00
  bond pdb=" CB  ASP R 103 "
       pdb=" CG  ASP R 103 "
    ideal  model  delta    sigma   weight residual
    1.516  1.459  0.057 2.50e-02 1.60e+03 5.29e+00
  bond pdb=" CA  ASP R 103 "
       pdb=" CB  ASP R 103 "
    ideal  model  delta    sigma   weight residual
    1.530  1.557 -0.027 1.57e-02 4.06e+03 3.05e+00
  ... (remaining 8401 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 11276
        2.16 -     4.33: 97
        4.33 -     6.49: 9
        6.49 -     8.65: 0
        8.65 -    10.82: 2
  Bond angle restraints: 11384
  Sorted by residual:
  angle pdb=" C   ASP R 103 "
        pdb=" CA  ASP R 103 "
        pdb=" CB  ASP R 103 "
      ideal   model   delta    sigma   weight residual
     110.96  105.05    5.91 1.54e+00 4.22e-01 1.47e+01
  angle pdb=" CA  B40 R 501 "
        pdb=" N   B40 R 501 "
        pdb=" CM  B40 R 501 "
      ideal   model   delta    sigma   weight residual
     115.05  104.23   10.82 3.00e+00 1.11e-01 1.30e+01
  angle pdb=" N   B40 R 501 "
        pdb=" CA  B40 R 501 "
        pdb=" C   B40 R 501 "
      ideal   model   delta    sigma   weight residual
     114.49  104.29   10.20 3.00e+00 1.11e-01 1.16e+01
  angle pdb=" N   VAL R 150 "
        pdb=" CA  VAL R 150 "
        pdb=" C   VAL R 150 "
      ideal   model   delta    sigma   weight residual
     112.35  108.63    3.72 1.20e+00 6.94e-01 9.62e+00
  angle pdb=" N   SER B 331 "
        pdb=" CA  SER B 331 "
        pdb=" C   SER B 331 "
      ideal   model   delta    sigma   weight residual
     108.60  112.56   -3.96 1.46e+00 4.69e-01 7.37e+00
  ... (remaining 11379 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.64: 4508
       19.64 -    39.29: 381
       39.29 -    58.93: 79
       58.93 -    78.58: 16
       78.58 -    98.22: 6
  Dihedral angle restraints: 4990
    sinusoidal: 1945
      harmonic: 3045
  Sorted by residual:
  dihedral pdb=" CA  PHE B 292 "
           pdb=" C   PHE B 292 "
           pdb=" N   ASN B 293 "
           pdb=" CA  ASN B 293 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.73   18.27     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.49  -17.51     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CB  B40 R 501 "
           pdb=" N   B40 R 501 "
           pdb=" CA  B40 R 501 "
           pdb=" CM  B40 R 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     168.08  -93.70  -98.22     1      3.00e+01 1.11e-03 1.22e+01
  ... (remaining 4987 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1106
       0.056 -    0.113: 144
       0.113 -    0.169: 23
       0.169 -    0.226: 1
       0.226 -    0.282: 1
  Chirality restraints: 1275
  Sorted by residual:
  chirality pdb=" CA  B40 R 501 "
            pdb=" N   B40 R 501 "
            pdb=" C   B40 R 501 "
            pdb=" CB  B40 R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42   -2.71    0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" CA  ASP R 103 "
            pdb=" N   ASP R 103 "
            pdb=" C   ASP R 103 "
            pdb=" CB  ASP R 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.70e-01
  chirality pdb=" CA  PHE B 292 "
            pdb=" N   PHE B 292 "
            pdb=" C   PHE B 292 "
            pdb=" CB  PHE B 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.95e-01
  ... (remaining 1272 not shown)

  Planarity restraints: 1448
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 284 "    0.017 2.00e-02 2.50e+03   3.43e-02 1.18e+01
        pdb=" C   THR R 284 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   THR R 284 "    0.022 2.00e-02 2.50e+03
        pdb=" N   LEU R 285 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R 282 "    0.056 5.00e-02 4.00e+02   8.32e-02 1.11e+01
        pdb=" N   PRO R 283 "   -0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO R 283 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO R 283 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  19 "   -0.182 9.50e-02 1.11e+02   8.20e-02 4.90e+00
        pdb=" NE  ARG B  19 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  19 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  19 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  19 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1445 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 594
        2.73 -     3.28: 8380
        3.28 -     3.82: 13939
        3.82 -     4.36: 17219
        4.36 -     4.90: 30105
  Nonbonded interactions: 70237
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 195 "
            pdb=" OG1 THR B 196 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" O   ASN A 188 "
            pdb=" OG  SER A 189 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" C   B40 R 501 "
            pdb=" CM  B40 R 501 "
     model   vdw
     2.251 3.104
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OE2 GLU B 260 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.319 3.040
  ... (remaining 70232 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:             1.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.230
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  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:15.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
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      :  0.003   0.082   8406  Z= 0.217
  Angle     :  0.561  10.817  11384  Z= 0.318
  Chirality :  0.041   0.282   1275
  Planarity :  0.005   0.083   1448
  Dihedral  : 15.674  98.222   3019
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 16.10 %
    Favored  : 83.45 %
  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:  1.49 (0.27), residues: 1031
  helix:  2.26 (0.25), residues: 416
  sheet:  0.46 (0.34), residues: 228
  loop : -0.01 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 291 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.011   0.001   PHE R  70 
 TYR   0.008   0.001   TYR A 313 
 ARG   0.015   0.001   ARG B  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 128
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
REVERT: A  330 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7653 (mtm110)
REVERT: B   17 GLN cc_start: 0.6251 (tt0) cc_final: 0.6005 (tm130)
  outliers start: 4
  outliers final: 3
  residues processed: 130
  average time/residue: 1.3560
  time to fit residues: 186.4171
Evaluate side-chains
  124 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 121
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain R residue   80 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 76 optimal weight:    6.9990
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    8.9990
   chunk 51 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 237 ASN
B 239 ASN
N 123 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.150612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.105899 restraints weight = 9277.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 2.31
r_work: 0.3118 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.1052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8406  Z= 0.188
  Angle     :  0.527   6.456  11384  Z= 0.287
  Chirality :  0.042   0.157   1275
  Planarity :  0.004   0.065   1448
  Dihedral  :  5.454  57.502   1149
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.08 %
    Favored  : 83.78 %
  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:  1.64 (0.27), residues: 1031
  helix:  2.36 (0.25), residues: 415
  sheet:  0.55 (0.36), residues: 213
  loop :  0.10 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 169 
 HIS   0.004   0.001   HIS G  44 
 PHE   0.021   0.001   PHE R 165 
 TYR   0.031   0.001   TYR R  27 
 ARG   0.008   0.000   ARG B  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
REVERT: A  200 LYS cc_start: 0.8671 (mttp) cc_final: 0.8125 (mmtm)
REVERT: A  213 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7638 (p0)
REVERT: A  318 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7845 (mm-30)
REVERT: A  321 ARG cc_start: 0.7216 (mtp85) cc_final: 0.6987 (mtm-85)
REVERT: A  355 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7772 (t0)
REVERT: B  214 ARG cc_start: 0.8305 (mmm-85) cc_final: 0.7367 (mpp80)
REVERT: B  243 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7980 (p)
REVERT: R   80 SER cc_start: 0.7660 (t) cc_final: 0.6818 (p)
  outliers start: 19
  outliers final: 7
  residues processed: 151
  average time/residue: 1.5871
  time to fit residues: 253.6343
Evaluate side-chains
  138 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 1.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain R residue   96 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 56 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 74 optimal weight:    0.3980
   chunk 45 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0470
   chunk 94 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 237 ASN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.152471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.107653 restraints weight = 9344.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.31
r_work: 0.3145 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8406  Z= 0.151
  Angle     :  0.481   6.066  11384  Z= 0.262
  Chirality :  0.041   0.151   1275
  Planarity :  0.004   0.058   1448
  Dihedral  :  4.909  55.740   1148
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.75 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.27), residues: 1031
  helix:  2.37 (0.25), residues: 422
  sheet:  0.57 (0.36), residues: 215
  loop :  0.15 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 169 
 HIS   0.003   0.001   HIS G  44 
 PHE   0.012   0.001   PHE A 196 
 TYR   0.008   0.001   TYR N  95 
 ARG   0.006   0.000   ARG B  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 LYS cc_start: 0.8659 (mttp) cc_final: 0.8131 (mmtm)
REVERT: A  317 ASP cc_start: 0.8260 (m-30) cc_final: 0.7988 (m-30)
REVERT: A  318 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7845 (mm-30)
REVERT: A  355 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7814 (t0)
REVERT: B   17 GLN cc_start: 0.5893 (tt0) cc_final: 0.5693 (tm130)
REVERT: B  175 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7290 (mp10)
REVERT: R  135 MET cc_start: 0.8398 (mmp) cc_final: 0.8046 (mmt)
  outliers start: 23
  outliers final: 11
  residues processed: 162
  average time/residue: 1.3904
  time to fit residues: 238.4827
Evaluate side-chains
  145 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 1.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  176 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 32 optimal weight:    0.3980
   chunk 10 optimal weight:    0.0870
   chunk 71 optimal weight:    0.1980
   chunk 63 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 58 optimal weight:    7.9990
   chunk 57 optimal weight:    7.9990
   overall best weight:    1.7362

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 237 ASN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.148663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.103538 restraints weight = 9321.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 2.29
r_work: 0.3084 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8406  Z= 0.279
  Angle     :  0.528   6.360  11384  Z= 0.285
  Chirality :  0.043   0.155   1275
  Planarity :  0.004   0.055   1448
  Dihedral  :  5.235  58.789   1148
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 16.78 %
    Favored  : 80.29 %
  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:  1.49 (0.26), residues: 1031
  helix:  2.23 (0.25), residues: 421
  sheet:  0.53 (0.36), residues: 213
  loop : -0.04 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 218 
 HIS   0.004   0.001   HIS G  44 
 PHE   0.017   0.002   PHE R 165 
 TYR   0.015   0.001   TYR R  27 
 ARG   0.008   0.000   ARG B  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7558 (mptt)
REVERT: A  200 LYS cc_start: 0.8705 (mttp) cc_final: 0.8159 (mmtm)
REVERT: A  213 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7286 (p0)
REVERT: A  355 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7797 (t0)
REVERT: B  175 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7344 (mp10)
REVERT: R   23 ARG cc_start: 0.5770 (OUTLIER) cc_final: 0.5122 (ptt90)
REVERT: R   80 SER cc_start: 0.7600 (t) cc_final: 0.6751 (p)
  outliers start: 26
  outliers final: 14
  residues processed: 149
  average time/residue: 1.2034
  time to fit residues: 190.6247
Evaluate side-chains
  148 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain R residue   23 ARG
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  176 VAL
Chi-restraints excluded: chain R residue  182 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 79 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 97 optimal weight:    0.2980
   chunk 14 optimal weight:    0.8980
   chunk 88 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.151296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.106105 restraints weight = 9299.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.31
r_work: 0.3121 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8406  Z= 0.161
  Angle     :  0.474   5.861  11384  Z= 0.257
  Chirality :  0.041   0.150   1275
  Planarity :  0.004   0.055   1448
  Dihedral  :  4.947  55.820   1148
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 16.89 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.58 (0.27), residues: 1031
  helix:  2.31 (0.25), residues: 422
  sheet:  0.46 (0.36), residues: 217
  loop :  0.07 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 169 
 HIS   0.002   0.001   HIS A 331 
 PHE   0.012   0.001   PHE A 196 
 TYR   0.011   0.001   TYR R 279 
 ARG   0.009   0.000   ARG B  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 137
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7580 (mptt)
REVERT: A  200 LYS cc_start: 0.8672 (mttp) cc_final: 0.8147 (mmtm)
REVERT: A  213 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7235 (p0)
REVERT: A  317 ASP cc_start: 0.8247 (m-30) cc_final: 0.7976 (m-30)
REVERT: A  355 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7804 (t0)
REVERT: B  175 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7307 (mp10)
REVERT: R   23 ARG cc_start: 0.5778 (OUTLIER) cc_final: 0.5128 (ptt90)
REVERT: R  135 MET cc_start: 0.8390 (mmp) cc_final: 0.8011 (mmt)
  outliers start: 27
  outliers final: 17
  residues processed: 156
  average time/residue: 1.2035
  time to fit residues: 199.5081
Evaluate side-chains
  154 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain R residue   23 ARG
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  176 VAL
Chi-restraints excluded: chain R residue  207 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.151144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.106192 restraints weight = 9315.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.31
r_work: 0.3094 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8406  Z= 0.172
  Angle     :  0.476   5.682  11384  Z= 0.259
  Chirality :  0.041   0.149   1275
  Planarity :  0.004   0.053   1448
  Dihedral  :  4.847  55.217   1148
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 16.78 %
    Favored  : 79.73 %
  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:  1.58 (0.27), residues: 1031
  helix:  2.32 (0.25), residues: 422
  sheet:  0.47 (0.36), residues: 217
  loop :  0.04 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 169 
 HIS   0.003   0.001   HIS G  44 
 PHE   0.015   0.001   PHE R 165 
 TYR   0.010   0.001   TYR N  60 
 ARG   0.008   0.000   ARG B  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 136
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7085 (tmtt)
REVERT: A  200 LYS cc_start: 0.8629 (mttp) cc_final: 0.8090 (mmtm)
REVERT: A  213 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7144 (p0)
REVERT: A  317 ASP cc_start: 0.8142 (m-30) cc_final: 0.7868 (m-30)
REVERT: A  355 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7703 (t0)
REVERT: B  175 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7255 (mp10)
REVERT: R   23 ARG cc_start: 0.5713 (OUTLIER) cc_final: 0.5056 (ptt90)
REVERT: R  135 MET cc_start: 0.8305 (mmp) cc_final: 0.7968 (mmt)
  outliers start: 31
  outliers final: 16
  residues processed: 157
  average time/residue: 1.1765
  time to fit residues: 196.5292
Evaluate side-chains
  154 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain R residue   23 ARG
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  176 VAL
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  207 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   chunk 84 optimal weight:    0.6980
   chunk 96 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.151336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.106248 restraints weight = 9322.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.32
r_work: 0.3119 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8406  Z= 0.176
  Angle     :  0.477   5.565  11384  Z= 0.259
  Chirality :  0.041   0.148   1275
  Planarity :  0.004   0.054   1448
  Dihedral  :  4.791  54.905   1148
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 17.68 %
    Favored  : 79.28 %
  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:  1.60 (0.27), residues: 1031
  helix:  2.34 (0.25), residues: 422
  sheet:  0.52 (0.36), residues: 215
  loop :  0.04 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 169 
 HIS   0.003   0.001   HIS A 331 
 PHE   0.013   0.001   PHE A 196 
 TYR   0.014   0.001   TYR R  27 
 ARG   0.010   0.000   ARG B  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7065 (tmtt)
REVERT: A  200 LYS cc_start: 0.8638 (mttp) cc_final: 0.8097 (mmtt)
REVERT: A  213 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7112 (p0)
REVERT: A  317 ASP cc_start: 0.8151 (m-30) cc_final: 0.7847 (m-30)
REVERT: A  355 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7727 (t0)
REVERT: B  175 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7261 (mp10)
REVERT: R   23 ARG cc_start: 0.5771 (OUTLIER) cc_final: 0.5047 (ptt90)
REVERT: R  135 MET cc_start: 0.8310 (mmp) cc_final: 0.7959 (mmt)
  outliers start: 27
  outliers final: 17
  residues processed: 154
  average time/residue: 1.3168
  time to fit residues: 215.3117
Evaluate side-chains
  153 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain R residue   23 ARG
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  176 VAL
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  207 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 80 optimal weight:    6.9990
   chunk 57 optimal weight:    9.9990
   chunk 1 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 259 GLN
R 296 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.149457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.104166 restraints weight = 9409.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.32
r_work: 0.3094 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8406  Z= 0.244
  Angle     :  0.514   6.905  11384  Z= 0.277
  Chirality :  0.042   0.150   1275
  Planarity :  0.004   0.058   1448
  Dihedral  :  4.879  55.186   1148
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.13 %
    Favored  : 78.83 %
  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:  1.49 (0.26), residues: 1031
  helix:  2.27 (0.25), residues: 420
  sheet:  0.46 (0.36), residues: 215
  loop : -0.04 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 218 
 HIS   0.004   0.001   HIS R  63 
 PHE   0.014   0.001   PHE A 196 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.018   0.000   ARG B  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 133
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7075 (tmtt)
REVERT: A  200 LYS cc_start: 0.8651 (mttp) cc_final: 0.8097 (mmtm)
REVERT: A  213 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7111 (p0)
REVERT: A  355 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7709 (t0)
REVERT: B  175 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7267 (mp10)
REVERT: B  292 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8108 (m-10)
REVERT: R   23 ARG cc_start: 0.5733 (OUTLIER) cc_final: 0.5031 (ptt90)
REVERT: R  135 MET cc_start: 0.8276 (mmp) cc_final: 0.7986 (mmt)
  outliers start: 27
  outliers final: 17
  residues processed: 152
  average time/residue: 1.5171
  time to fit residues: 245.0448
Evaluate side-chains
  154 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue  197 GLN
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain R residue   23 ARG
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  176 VAL
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  207 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 80 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.151009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.105812 restraints weight = 9488.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.34
r_work: 0.3119 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8406  Z= 0.183
  Angle     :  0.490   7.032  11384  Z= 0.265
  Chirality :  0.041   0.146   1275
  Planarity :  0.004   0.078   1448
  Dihedral  :  4.680  54.418   1148
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 18.02 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.26), residues: 1031
  helix:  2.31 (0.25), residues: 421
  sheet:  0.52 (0.36), residues: 215
  loop : -0.01 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R 291 
 HIS   0.003   0.001   HIS A 331 
 PHE   0.013   0.001   PHE R 154 
 TYR   0.012   0.001   TYR R  27 
 ARG   0.019   0.000   ARG B  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 135
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7101 (tmtt)
REVERT: A  200 LYS cc_start: 0.8691 (mttp) cc_final: 0.8140 (mmtt)
REVERT: A  213 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7167 (p0)
REVERT: A  317 ASP cc_start: 0.8225 (m-30) cc_final: 0.7936 (m-30)
REVERT: A  355 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7808 (t0)
REVERT: B  175 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7416 (mp10)
REVERT: B  217 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.8039 (ppp)
REVERT: R   23 ARG cc_start: 0.5722 (OUTLIER) cc_final: 0.5017 (ptt90)
REVERT: R  135 MET cc_start: 0.8393 (mmp) cc_final: 0.8009 (mmt)
  outliers start: 31
  outliers final: 16
  residues processed: 157
  average time/residue: 1.2432
  time to fit residues: 207.0605
Evaluate side-chains
  153 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue  197 GLN
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain R residue   23 ARG
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  176 VAL
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  207 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 81 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 98 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 92 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.151459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.106420 restraints weight = 9359.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.31
r_work: 0.3126 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8406  Z= 0.170
  Angle     :  0.483   6.047  11384  Z= 0.262
  Chirality :  0.041   0.146   1275
  Planarity :  0.004   0.057   1448
  Dihedral  :  4.515  54.914   1146
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 18.47 %
    Favored  : 78.72 %
  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:  1.60 (0.27), residues: 1031
  helix:  2.33 (0.25), residues: 422
  sheet:  0.55 (0.36), residues: 215
  loop :  0.02 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R 291 
 HIS   0.003   0.001   HIS A 331 
 PHE   0.014   0.001   PHE R 154 
 TYR   0.012   0.001   TYR R 279 
 ARG   0.013   0.000   ARG B  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 135
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7131 (tmtt)
REVERT: A  200 LYS cc_start: 0.8679 (mttp) cc_final: 0.8133 (mmtt)
REVERT: A  213 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7200 (p0)
REVERT: A  355 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7812 (t0)
REVERT: B  186 ASP cc_start: 0.7910 (m-30) cc_final: 0.7578 (m-30)
REVERT: B  217 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8058 (ppp)
REVERT: N   46 GLU cc_start: 0.8143 (tt0) cc_final: 0.7793 (pt0)
REVERT: R   23 ARG cc_start: 0.5711 (OUTLIER) cc_final: 0.5014 (ptt90)
REVERT: R  135 MET cc_start: 0.8400 (mmp) cc_final: 0.7973 (mmt)
  outliers start: 25
  outliers final: 16
  residues processed: 152
  average time/residue: 1.2896
  time to fit residues: 207.6265
Evaluate side-chains
  149 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  355 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain R residue   23 ARG
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  176 VAL
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  207 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 91 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 94 optimal weight:    8.9990
   chunk 83 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 88 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.149025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.103767 restraints weight = 9526.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 2.33
r_work: 0.3089 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8406  Z= 0.260
  Angle     :  0.531   7.258  11384  Z= 0.287
  Chirality :  0.043   0.148   1275
  Planarity :  0.004   0.076   1448
  Dihedral  :  4.728  54.810   1146
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.03 %
    Favored  : 78.27 %
  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:  1.46 (0.26), residues: 1031
  helix:  2.26 (0.25), residues: 420
  sheet:  0.44 (0.35), residues: 223
  loop : -0.08 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 218 
 HIS   0.004   0.001   HIS R  63 
 PHE   0.014   0.001   PHE A 196 
 TYR   0.013   0.001   TYR R 279 
 ARG   0.019   0.001   ARG B  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7625.52 seconds
wall clock time: 134 minutes 46.99 seconds (8086.99 seconds total)