Starting phenix.real_space_refine
on Fri Jul 25 04:23:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lwp_63455/07_2025/9lwp_63455.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lwp_63455/07_2025/9lwp_63455.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lwp_63455/07_2025/9lwp_63455.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lwp_63455/07_2025/9lwp_63455.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lwp_63455/07_2025/9lwp_63455.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lwp_63455/07_2025/9lwp_63455.cif"
  }
  resolution = 2.93
  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=   0.067
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      42      5.16       5
     C    4371      2.51       5
     N    1183      2.21       5
     O    1248      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6844
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "R"
      Number of atoms: 2165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2165
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 10, 'TRANS': 260}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 1650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1650
          Classifications: {'peptide': 211}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 4, 'TRANS': 206}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 85
          Unresolved non-hydrogen angles: 100
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 54
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
  Time building chain proxies: 4.05, per 1000 atoms: 0.59
  Number of scatterers: 6844
  At special positions: 0
  Unit cell: (77.112, 100.674, 127.449, 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      42     16.00
     O    1248      8.00
     N    1183      7.00
     C    4371      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.36
  Conformation dependent library (CDL) restraints added in 880.9 milliseconds
  

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1666

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 8 sheets defined
      46.8% alpha, 18.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'R' and resid 48 through 75
      removed outlier: 3.605A  pdb=" N   ILE R  52 " --> pdb=" O   CYS R  48 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   THR R  53 " --> pdb=" O   ALA R  49 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 80 through 108
      removed outlier: 3.552A  pdb=" N   ILE R  84 " --> pdb=" O   THR R  80 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   PHE R  85 " --> pdb=" O   VAL R  81 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ILE R  86 " --> pdb=" O   PRO R  82 " (cutoff:3.500A)
      Proline residue:  R 102  - end of helix
    Processing helix  chain 'R' and resid 118 through 119
      No H-bonds generated for 'chain 'R' and resid 118 through 119'
    Processing helix  chain 'R' and resid 121 through 121
      No H-bonds generated for 'chain 'R' and resid 121 through 121'
    Processing helix  chain 'R' and resid 122 through 151
    Processing helix  chain 'R' and resid 160 through 180
    Processing helix  chain 'R' and resid 181 through 183
      No H-bonds generated for 'chain 'R' and resid 181 through 183'
    Processing helix  chain 'R' and resid 211 through 227
    Processing helix  chain 'R' and resid 227 through 248
    Processing helix  chain 'R' and resid 259 through 297
      Proline residue:  R 286  - end of helix
    Processing helix  chain 'R' and resid 308 through 334
      removed outlier: 4.012A  pdb=" N   ASN R 322 " --> pdb=" O   LEU R 318 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   SER R 323 " --> pdb=" O   ALA R 319 " (cutoff:3.500A)
      Proline residue:  R 327  - end of helix
      removed outlier: 3.915A  pdb=" N   LEU R 330 " --> pdb=" O   ASN R 326 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 334 through 344
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 46 through 50
      removed outlier: 3.560A  pdb=" N   ILE A  49 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   VAL A  50 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 46 through 50'
    Processing helix  chain 'A' and resid 95 through 100
      removed outlier: 3.519A  pdb=" N   GLN A  98 " --> pdb=" O   LYS A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 130
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.164A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 184 through 203
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.580A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.669A  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 sheet with id=AA1, first strand: chain 'A' and resid 69 through 76
      removed outlier: 4.725A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   ILE A 107 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.650A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.817A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.720A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.674A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.405A  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: 6.872A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.803A  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: 3.619A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.211A  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: 4.042A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 5.885A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    373 hydrogen bonds defined for protein.
    1095 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.90

  Time building geometry restraints manager: 1.65 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2210
        1.34 -     1.46: 1621
        1.46 -     1.58: 3088
        1.58 -     1.69: 0
        1.69 -     1.81: 57
  Bond restraints: 6976
  Sorted by residual:
  bond pdb=" CB  ASN A  43 "
       pdb=" CG  ASN A  43 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 2.50e-02 1.60e+03 1.57e+00
  bond pdb=" C   LEU R 180 "
       pdb=" N   PRO R 181 "
    ideal  model  delta    sigma   weight residual
    1.334  1.360 -0.027 2.34e-02 1.83e+03 1.29e+00
  bond pdb=" CA  ASN A  43 "
       pdb=" CB  ASN A  43 "
    ideal  model  delta    sigma   weight residual
    1.533  1.550 -0.016 1.66e-02 3.63e+03 9.47e-01
  bond pdb=" C   ILE R 251 "
       pdb=" N   PRO R 252 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 2.34e-02 1.83e+03 8.06e-01
  bond pdb=" CB  VAL R 273 "
       pdb=" CG1 VAL R 273 "
    ideal  model  delta    sigma   weight residual
    1.521  1.492  0.029 3.30e-02 9.18e+02 7.49e-01
  ... (remaining 6971 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 9356
        1.88 -     3.75: 80
        3.75 -     5.63: 12
        5.63 -     7.50: 2
        7.50 -     9.38: 1
  Bond angle restraints: 9451
  Sorted by residual:
  angle pdb=" CA  LEU R 223 "
        pdb=" CB  LEU R 223 "
        pdb=" CG  LEU R 223 "
      ideal   model   delta    sigma   weight residual
     116.30  125.68   -9.38 3.50e+00 8.16e-02 7.18e+00
  angle pdb=" CA  ASN A  43 "
        pdb=" CB  ASN A  43 "
        pdb=" CG  ASN A  43 "
      ideal   model   delta    sigma   weight residual
     112.60  115.05   -2.45 1.00e+00 1.00e+00 6.01e+00
  angle pdb=" C   GLN R 256 "
        pdb=" N   SER R 257 "
        pdb=" CA  SER R 257 "
      ideal   model   delta    sigma   weight residual
     125.66  129.64   -3.98 1.85e+00 2.92e-01 4.64e+00
  angle pdb=" C   ALA R 319 "
        pdb=" N   PHE R 320 "
        pdb=" CA  PHE R 320 "
      ideal   model   delta    sigma   weight residual
     122.38  118.64    3.74 1.81e+00 3.05e-01 4.28e+00
  angle pdb=" CA  ASN B 155 "
        pdb=" C   ASN B 155 "
        pdb=" O   ASN B 155 "
      ideal   model   delta    sigma   weight residual
     119.08  121.20   -2.12 1.03e+00 9.43e-01 4.23e+00
  ... (remaining 9446 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 3657
       17.44 -    34.87: 388
       34.87 -    52.30: 97
       52.30 -    69.74: 6
       69.74 -    87.17: 3
  Dihedral angle restraints: 4151
    sinusoidal: 1594
      harmonic: 2557
  Sorted by residual:
  dihedral pdb=" CG  ARG A 188 "
           pdb=" CD  ARG A 188 "
           pdb=" NE  ARG A 188 "
           pdb=" CZ  ARG A 188 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.77  -43.77     2      1.50e+01 4.44e-03 1.02e+01
  dihedral pdb=" CG  ARG B 304 "
           pdb=" CD  ARG B 304 "
           pdb=" NE  ARG B 304 "
           pdb=" CZ  ARG B 304 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -131.72   41.72     2      1.50e+01 4.44e-03 9.45e+00
  dihedral pdb=" CA  ARG R 271 "
           pdb=" CB  ARG R 271 "
           pdb=" CG  ARG R 271 "
           pdb=" CD  ARG R 271 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  127.45   52.55     3      1.50e+01 4.44e-03 9.13e+00
  ... (remaining 4148 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 664
       0.028 -    0.055: 273
       0.055 -    0.082: 95
       0.082 -    0.110: 46
       0.110 -    0.137: 22
  Chirality restraints: 1100
  Sorted by residual:
  chirality pdb=" CA  PRO R 252 "
            pdb=" N   PRO R 252 "
            pdb=" C   PRO R 252 "
            pdb=" CB  PRO R 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.72e-01
  chirality pdb=" CA  ILE A 140 "
            pdb=" N   ILE A 140 "
            pdb=" C   ILE A 140 "
            pdb=" CB  ILE A 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.20e-01
  chirality pdb=" CA  PRO R 102 "
            pdb=" N   PRO R 102 "
            pdb=" C   PRO R 102 "
            pdb=" CB  PRO R 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.04e-01
  ... (remaining 1097 not shown)

  Planarity restraints: 1186
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 251 "   -0.028 5.00e-02 4.00e+02   4.22e-02 2.85e+00
        pdb=" N   PRO R 252 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO R 252 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO R 252 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 223 "    0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   LEU R 223 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   LEU R 223 "    0.010 2.00e-02 2.50e+03
        pdb=" N   VAL R 224 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 180 "   -0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO R 181 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO R 181 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO R 181 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1183 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 103
        2.66 -     3.22: 6494
        3.22 -     3.78: 10904
        3.78 -     4.34: 14745
        4.34 -     4.90: 24570
  Nonbonded interactions: 56816
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.104 3.040
  nonbonded pdb=" O   CYS B 218 "
            pdb=" NE2 GLN G  18 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" NH2 ARG R 268 "
            pdb=" O   TRP R 332 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.245 3.040
  ... (remaining 56811 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=0.00 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:             1.130
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.850
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7006
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6976  Z= 0.118
  Angle     :  0.504   9.379   9451  Z= 0.279
  Chirality :  0.040   0.137   1100
  Planarity :  0.004   0.042   1186
  Dihedral  : 14.803  87.172   2485
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.17 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 14.91 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.28), residues: 852
  helix:  1.82 (0.26), residues: 381
  sheet:  0.34 (0.38), residues: 188
  loop : -0.81 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 332 
 HIS   0.004   0.001   HIS R 308 
 PHE   0.022   0.001   PHE R 320 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.011   0.000   ARG A 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13840 (  373)
  hydrogen bonds       : angle       5.66140 ( 1095)
  covalent geometry    : bond        0.00238 ( 6976)
  covalent geometry    : angle       0.50445 ( 9451)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   78 MET cc_start: 0.6771 (ptm) cc_final: 0.6492 (ptp)
REVERT: R  147 LYS cc_start: 0.8034 (ttmm) cc_final: 0.7572 (ttpt)
REVERT: R  210 LYS cc_start: 0.5315 (mmtt) cc_final: 0.3968 (mptp)
REVERT: R  220 LEU cc_start: 0.7416 (tt) cc_final: 0.6752 (tp)
REVERT: A   32 ARG cc_start: 0.6674 (mmt-90) cc_final: 0.5749 (mtm180)
REVERT: B  110 ASN cc_start: 0.8393 (m-40) cc_final: 0.8139 (m-40)
REVERT: B  217 MET cc_start: 0.6570 (pmm) cc_final: 0.6183 (pmt)
REVERT: B  262 MET cc_start: 0.7331 (tpt) cc_final: 0.7071 (tpp)
REVERT: B  325 MET cc_start: 0.8297 (ttm) cc_final: 0.7991 (tpt)
  outliers start: 7
  outliers final: 3
  residues processed: 74
  average time/residue: 1.0765
  time to fit residues: 84.8337
Evaluate side-chains
  69 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain B residue  146 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0570
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   overall best weight:    0.7502

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
B 119 ASN
B 220 GLN
B 268 ASN
B 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.198248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.159205 restraints weight = 7126.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 1.95
r_work: 0.3585 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3451 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.0848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6976  Z= 0.151
  Angle     :  0.523   7.681   9451  Z= 0.284
  Chirality :  0.042   0.160   1100
  Planarity :  0.004   0.049   1186
  Dihedral  :  4.166  40.616    945
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.29 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 14.36 %
    Favored  : 82.52 %
  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:  0.79 (0.28), residues: 852
  helix:  1.72 (0.25), residues: 376
  sheet:  0.40 (0.39), residues: 185
  loop : -0.95 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R 294 
 PHE   0.018   0.001   PHE R 320 
 TYR   0.020   0.001   TYR B  59 
 ARG   0.007   0.001   ARG A 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04436 (  373)
  hydrogen bonds       : angle       4.68743 ( 1095)
  covalent geometry    : bond        0.00345 ( 6976)
  covalent geometry    : angle       0.52322 ( 9451)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 77
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
REVERT: R   78 MET cc_start: 0.6648 (ptm) cc_final: 0.6133 (ptp)
REVERT: R  127 ARG cc_start: 0.5485 (ttp80) cc_final: 0.4863 (ttp-170)
REVERT: R  147 LYS cc_start: 0.8082 (ttmm) cc_final: 0.7588 (ttmm)
REVERT: R  210 LYS cc_start: 0.5415 (mmtt) cc_final: 0.3978 (mptp)
REVERT: R  220 LEU cc_start: 0.7492 (tt) cc_final: 0.6869 (tp)
REVERT: A   32 ARG cc_start: 0.6793 (mmt-90) cc_final: 0.5782 (mtm180)
REVERT: A   72 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8416 (p)
REVERT: A   77 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7727 (m-30)
REVERT: B  110 ASN cc_start: 0.8312 (m-40) cc_final: 0.8100 (m-40)
REVERT: B  200 VAL cc_start: 0.8945 (p) cc_final: 0.8603 (m)
REVERT: B  217 MET cc_start: 0.6395 (pmm) cc_final: 0.5986 (pmt)
REVERT: B  219 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6796 (mpt90)
REVERT: B  325 MET cc_start: 0.8223 (ttm) cc_final: 0.7884 (tpt)
  outliers start: 23
  outliers final: 10
  residues processed: 90
  average time/residue: 0.9711
  time to fit residues: 93.2841
Evaluate side-chains
  84 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   53 THR
Chi-restraints excluded: chain R residue  218 SER
Chi-restraints excluded: chain R residue  307 MET
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  267 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 75 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 47 optimal weight:    0.2980
   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 101 ASN
B 220 GLN
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.198494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.159058 restraints weight = 7177.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3751 rms_B_bonded: 2.00
r_work: 0.3559 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3422 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.1129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6976  Z= 0.129
  Angle     :  0.489   7.415   9451  Z= 0.265
  Chirality :  0.042   0.154   1100
  Planarity :  0.004   0.051   1186
  Dihedral  :  4.134  40.821    944
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.29 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 16.94 %
    Favored  : 79.40 %
  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:  0.96 (0.28), residues: 852
  helix:  1.87 (0.25), residues: 375
  sheet:  0.50 (0.38), residues: 192
  loop : -0.93 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 294 
 PHE   0.019   0.001   PHE R 320 
 TYR   0.016   0.001   TYR B  59 
 ARG   0.004   0.000   ARG A 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04151 (  373)
  hydrogen bonds       : angle       4.46638 ( 1095)
  covalent geometry    : bond        0.00287 ( 6976)
  covalent geometry    : angle       0.48950 ( 9451)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 78
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
REVERT: R   78 MET cc_start: 0.6694 (ptm) cc_final: 0.6051 (ptp)
REVERT: R  147 LYS cc_start: 0.8106 (ttmm) cc_final: 0.7710 (ttpm)
REVERT: R  210 LYS cc_start: 0.5574 (mmtt) cc_final: 0.4119 (mptp)
REVERT: R  220 LEU cc_start: 0.7634 (tt) cc_final: 0.6937 (tp)
REVERT: R  317 VAL cc_start: 0.8298 (t) cc_final: 0.8031 (m)
REVERT: A   25 GLU cc_start: 0.7427 (tt0) cc_final: 0.7032 (tt0)
REVERT: A   72 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8480 (p)
REVERT: A   73 LYS cc_start: 0.8268 (mttt) cc_final: 0.8060 (mmtt)
REVERT: A   77 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7649 (m-30)
REVERT: A  136 THR cc_start: 0.8842 (t) cc_final: 0.8568 (m)
REVERT: B  200 VAL cc_start: 0.8982 (p) cc_final: 0.8678 (m)
REVERT: B  217 MET cc_start: 0.6487 (pmm) cc_final: 0.6111 (pmt)
REVERT: B  219 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6646 (mpt90)
REVERT: B  325 MET cc_start: 0.8290 (ttm) cc_final: 0.7933 (tpt)
  outliers start: 27
  outliers final: 12
  residues processed: 93
  average time/residue: 0.9976
  time to fit residues: 99.0341
Evaluate side-chains
  85 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 SER
Chi-restraints excluded: chain R residue  248 THR
Chi-restraints excluded: chain R residue  307 MET
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 14 optimal weight:    0.4980
   chunk 59 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 49 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.196309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.156253 restraints weight = 7210.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 2.08
r_work: 0.3527 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3390 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.1380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6976  Z= 0.150
  Angle     :  0.509   8.103   9451  Z= 0.274
  Chirality :  0.042   0.153   1100
  Planarity :  0.004   0.051   1186
  Dihedral  :  4.234  40.630    944
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.64 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 16.53 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.28), residues: 852
  helix:  1.78 (0.25), residues: 376
  sheet:  0.47 (0.38), residues: 192
  loop : -0.95 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 294 
 PHE   0.018   0.001   PHE R 320 
 TYR   0.020   0.001   TYR B  59 
 ARG   0.004   0.000   ARG B 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04308 (  373)
  hydrogen bonds       : angle       4.45513 ( 1095)
  covalent geometry    : bond        0.00349 ( 6976)
  covalent geometry    : angle       0.50917 ( 9451)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 85
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
REVERT: R   78 MET cc_start: 0.6753 (ptm) cc_final: 0.6039 (ptp)
REVERT: R   99 THR cc_start: 0.7063 (m) cc_final: 0.6375 (p)
REVERT: R  147 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7754 (ttpt)
REVERT: R  210 LYS cc_start: 0.5256 (mmtt) cc_final: 0.3759 (mptp)
REVERT: R  220 LEU cc_start: 0.7744 (tt) cc_final: 0.7084 (tp)
REVERT: A   25 GLU cc_start: 0.7438 (tt0) cc_final: 0.7021 (tt0)
REVERT: A   32 ARG cc_start: 0.6870 (mmt-90) cc_final: 0.5996 (ptp90)
REVERT: A   77 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7771 (m-30)
REVERT: A  136 THR cc_start: 0.8823 (t) cc_final: 0.8574 (m)
REVERT: A  153 VAL cc_start: 0.7525 (p) cc_final: 0.7217 (m)
REVERT: B  137 ARG cc_start: 0.7227 (tpp-160) cc_final: 0.6963 (tpp-160)
REVERT: B  171 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.7236 (mp)
REVERT: B  200 VAL cc_start: 0.8976 (p) cc_final: 0.8616 (m)
REVERT: B  217 MET cc_start: 0.6507 (pmm) cc_final: 0.6134 (pmt)
REVERT: B  219 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6415 (mpt90)
REVERT: B  234 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.7989 (m-80)
REVERT: B  325 MET cc_start: 0.8338 (ttm) cc_final: 0.7980 (tpt)
  outliers start: 33
  outliers final: 18
  residues processed: 107
  average time/residue: 0.9902
  time to fit residues: 112.9959
Evaluate side-chains
  102 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   53 THR
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   87 THR
Chi-restraints excluded: chain R residue  128 LEU
Chi-restraints excluded: chain R residue  218 SER
Chi-restraints excluded: chain R residue  248 THR
Chi-restraints excluded: chain R residue  307 MET
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  275 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 52 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0270
   chunk 40 optimal weight:    6.9990
   chunk 19 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
B 220 GLN
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.197722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.158382 restraints weight = 7127.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3763 rms_B_bonded: 1.99
r_work: 0.3576 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.1536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6976  Z= 0.123
  Angle     :  0.484   7.693   9451  Z= 0.262
  Chirality :  0.041   0.150   1100
  Planarity :  0.004   0.051   1186
  Dihedral  :  4.154  40.538    944
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.64 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 17.62 %
    Favored  : 78.32 %
  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:  1.01 (0.28), residues: 852
  helix:  1.89 (0.25), residues: 377
  sheet:  0.50 (0.38), residues: 192
  loop : -0.87 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 294 
 PHE   0.020   0.001   PHE R 320 
 TYR   0.012   0.001   TYR B  59 
 ARG   0.005   0.000   ARG B 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03979 (  373)
  hydrogen bonds       : angle       4.35434 ( 1095)
  covalent geometry    : bond        0.00276 ( 6976)
  covalent geometry    : angle       0.48423 ( 9451)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 80
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
REVERT: R   78 MET cc_start: 0.6757 (ptm) cc_final: 0.6035 (ptp)
REVERT: R   99 THR cc_start: 0.7012 (m) cc_final: 0.6401 (p)
REVERT: R  147 LYS cc_start: 0.8072 (ttmm) cc_final: 0.7644 (ttpm)
REVERT: R  210 LYS cc_start: 0.5444 (mmtt) cc_final: 0.4069 (mptp)
REVERT: R  220 LEU cc_start: 0.7655 (tt) cc_final: 0.7005 (tp)
REVERT: A   25 GLU cc_start: 0.7400 (tt0) cc_final: 0.6993 (tt0)
REVERT: A   32 ARG cc_start: 0.6885 (mmt-90) cc_final: 0.6011 (ptp90)
REVERT: A   73 LYS cc_start: 0.8310 (mmtt) cc_final: 0.8024 (mmtt)
REVERT: A   77 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7726 (m-30)
REVERT: A  136 THR cc_start: 0.8715 (t) cc_final: 0.8462 (m)
REVERT: B   78 LYS cc_start: 0.8538 (tppp) cc_final: 0.8228 (tppt)
REVERT: B  200 VAL cc_start: 0.8956 (p) cc_final: 0.8656 (m)
REVERT: B  217 MET cc_start: 0.6567 (pmm) cc_final: 0.6207 (pmt)
REVERT: B  219 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6403 (mpt90)
REVERT: B  262 MET cc_start: 0.7437 (tpt) cc_final: 0.7171 (tpp)
REVERT: B  284 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8143 (mp)
REVERT: B  325 MET cc_start: 0.8303 (ttm) cc_final: 0.7961 (tpt)
  outliers start: 30
  outliers final: 20
  residues processed: 100
  average time/residue: 0.9146
  time to fit residues: 97.9204
Evaluate side-chains
  101 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   87 THR
Chi-restraints excluded: chain R residue  180 LEU
Chi-restraints excluded: chain R residue  218 SER
Chi-restraints excluded: chain R residue  248 THR
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain R residue  307 MET
Chi-restraints excluded: chain R residue  324 CYS
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  284 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 79 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 72 optimal weight:    0.5980
   chunk 50 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  80 ASN
A 101 ASN
B 220 GLN
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.194321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.155931 restraints weight = 7179.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 1.93
r_work: 0.3530 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3396 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6976  Z= 0.148
  Angle     :  0.507   8.481   9451  Z= 0.272
  Chirality :  0.042   0.149   1100
  Planarity :  0.004   0.050   1186
  Dihedral  :  4.221  40.188    944
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.17 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 18.16 %
    Favored  : 77.10 %
  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:  0.94 (0.28), residues: 852
  helix:  1.84 (0.25), residues: 377
  sheet:  0.46 (0.38), residues: 194
  loop : -0.90 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 294 
 PHE   0.018   0.001   PHE R 320 
 TYR   0.017   0.001   TYR B  59 
 ARG   0.008   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04227 (  373)
  hydrogen bonds       : angle       4.39000 ( 1095)
  covalent geometry    : bond        0.00343 ( 6976)
  covalent geometry    : angle       0.50698 ( 9451)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 79
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
REVERT: R   78 MET cc_start: 0.6740 (ptm) cc_final: 0.6514 (ptm)
REVERT: R   99 THR cc_start: 0.7013 (m) cc_final: 0.6367 (p)
REVERT: R  147 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7781 (ttpt)
REVERT: R  220 LEU cc_start: 0.7742 (tt) cc_final: 0.7112 (tp)
REVERT: A   25 GLU cc_start: 0.7460 (tt0) cc_final: 0.7046 (tt0)
REVERT: A   32 ARG cc_start: 0.6868 (mmt-90) cc_final: 0.6077 (ptp90)
REVERT: A   73 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8134 (mmtt)
REVERT: A   77 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7781 (m-30)
REVERT: A  136 THR cc_start: 0.8722 (t) cc_final: 0.8486 (m)
REVERT: A  153 VAL cc_start: 0.7570 (p) cc_final: 0.7253 (m)
REVERT: B   46 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7294 (mtp-110)
REVERT: B   78 LYS cc_start: 0.8583 (tppp) cc_final: 0.8282 (tppt)
REVERT: B  137 ARG cc_start: 0.7209 (tpp-160) cc_final: 0.6956 (tpp-160)
REVERT: B  171 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7277 (mp)
REVERT: B  200 VAL cc_start: 0.8976 (p) cc_final: 0.8765 (m)
REVERT: B  217 MET cc_start: 0.6626 (pmm) cc_final: 0.6258 (pmt)
REVERT: B  219 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6440 (mpt90)
REVERT: B  262 MET cc_start: 0.7458 (tpt) cc_final: 0.7218 (tpp)
REVERT: B  284 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8188 (mp)
REVERT: B  325 MET cc_start: 0.8364 (ttm) cc_final: 0.8010 (tpt)
  outliers start: 35
  outliers final: 23
  residues processed: 104
  average time/residue: 0.9035
  time to fit residues: 100.6897
Evaluate side-chains
  107 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   87 THR
Chi-restraints excluded: chain R residue  128 LEU
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  180 LEU
Chi-restraints excluded: chain R residue  218 SER
Chi-restraints excluded: chain R residue  248 THR
Chi-restraints excluded: chain R residue  307 MET
Chi-restraints excluded: chain R residue  318 LEU
Chi-restraints excluded: chain R residue  324 CYS
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  284 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 16 optimal weight:    0.0770
   chunk 48 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 71 optimal weight:    0.1980
   chunk 53 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 62 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
R 258 HIS
A 101 ASN
B 220 GLN
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.197467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.158024 restraints weight = 7163.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 1.99
r_work: 0.3550 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3413 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7072
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6976  Z= 0.118
  Angle     :  0.481   7.919   9451  Z= 0.259
  Chirality :  0.041   0.148   1100
  Planarity :  0.004   0.051   1186
  Dihedral  :  4.144  43.594    944
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.64 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 18.97 %
    Favored  : 76.42 %
  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:  1.08 (0.28), residues: 852
  helix:  1.97 (0.25), residues: 377
  sheet:  0.56 (0.38), residues: 190
  loop : -0.88 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.002   0.001   HIS R 294 
 PHE   0.019   0.001   PHE R 320 
 TYR   0.011   0.001   TYR B  59 
 ARG   0.004   0.000   ARG B 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03892 (  373)
  hydrogen bonds       : angle       4.28832 ( 1095)
  covalent geometry    : bond        0.00259 ( 6976)
  covalent geometry    : angle       0.48135 ( 9451)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 80
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
REVERT: R   78 MET cc_start: 0.6716 (ptm) cc_final: 0.6490 (ptm)
REVERT: R   99 THR cc_start: 0.7124 (m) cc_final: 0.6480 (p)
REVERT: R  121 LYS cc_start: 0.6978 (mtpt) cc_final: 0.6205 (mmmt)
REVERT: R  147 LYS cc_start: 0.8103 (ttmm) cc_final: 0.7657 (ttpm)
REVERT: R  220 LEU cc_start: 0.7637 (tt) cc_final: 0.7012 (tp)
REVERT: A   25 GLU cc_start: 0.7391 (tt0) cc_final: 0.6984 (tt0)
REVERT: A   32 ARG cc_start: 0.6830 (mmt-90) cc_final: 0.6011 (ptp90)
REVERT: A   72 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8277 (p)
REVERT: A   73 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7997 (mmmt)
REVERT: A  136 THR cc_start: 0.8698 (t) cc_final: 0.8463 (m)
REVERT: A  153 VAL cc_start: 0.7608 (p) cc_final: 0.7282 (m)
REVERT: B   78 LYS cc_start: 0.8530 (tppp) cc_final: 0.8236 (tppt)
REVERT: B  200 VAL cc_start: 0.8992 (p) cc_final: 0.8705 (m)
REVERT: B  217 MET cc_start: 0.6609 (pmm) cc_final: 0.6246 (pmt)
REVERT: B  219 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6350 (mpt90)
REVERT: B  262 MET cc_start: 0.7449 (tpt) cc_final: 0.7195 (tpp)
REVERT: B  284 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8144 (mp)
REVERT: B  325 MET cc_start: 0.8309 (ttm) cc_final: 0.7968 (mmt)
  outliers start: 34
  outliers final: 19
  residues processed: 105
  average time/residue: 0.8895
  time to fit residues: 100.4135
Evaluate side-chains
  97 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   87 THR
Chi-restraints excluded: chain R residue  128 LEU
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  180 LEU
Chi-restraints excluded: chain R residue  218 SER
Chi-restraints excluded: chain R residue  248 THR
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain R residue  307 MET
Chi-restraints excluded: chain R residue  324 CYS
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  284 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 82 optimal weight:    6.9990
   chunk 8 optimal weight:    0.5980
   chunk 79 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.196258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.156577 restraints weight = 7157.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 1.99
r_work: 0.3535 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3398 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6976  Z= 0.134
  Angle     :  0.495   7.883   9451  Z= 0.265
  Chirality :  0.042   0.147   1100
  Planarity :  0.004   0.050   1186
  Dihedral  :  4.212  50.169    944
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.40 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 19.78 %
    Favored  : 76.29 %
  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:  1.06 (0.28), residues: 852
  helix:  1.94 (0.25), residues: 377
  sheet:  0.58 (0.38), residues: 190
  loop : -0.89 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 294 
 PHE   0.019   0.001   PHE R 320 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.005   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04095 (  373)
  hydrogen bonds       : angle       4.32365 ( 1095)
  covalent geometry    : bond        0.00306 ( 6976)
  covalent geometry    : angle       0.49504 ( 9451)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 78
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
REVERT: R   99 THR cc_start: 0.7100 (m) cc_final: 0.6450 (p)
REVERT: R  121 LYS cc_start: 0.7046 (mtpt) cc_final: 0.6179 (mmmt)
REVERT: R  147 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7657 (ttpm)
REVERT: R  220 LEU cc_start: 0.7637 (tt) cc_final: 0.7017 (tp)
REVERT: R  291 TYR cc_start: 0.7270 (t80) cc_final: 0.6906 (t80)
REVERT: A   25 GLU cc_start: 0.7413 (tt0) cc_final: 0.7006 (tt0)
REVERT: A   32 ARG cc_start: 0.6774 (mmt-90) cc_final: 0.5922 (ptp90)
REVERT: A  136 THR cc_start: 0.8683 (t) cc_final: 0.8460 (m)
REVERT: A  153 VAL cc_start: 0.7646 (p) cc_final: 0.7329 (m)
REVERT: B   46 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7275 (mtp-110)
REVERT: B   78 LYS cc_start: 0.8551 (tppp) cc_final: 0.8262 (tppt)
REVERT: B  137 ARG cc_start: 0.7189 (tpp-160) cc_final: 0.6865 (tpp80)
REVERT: B  200 VAL cc_start: 0.8953 (p) cc_final: 0.8687 (m)
REVERT: B  217 MET cc_start: 0.6603 (pmm) cc_final: 0.6239 (pmt)
REVERT: B  219 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6291 (mpt90)
REVERT: B  262 MET cc_start: 0.7447 (tpt) cc_final: 0.7176 (tpp)
REVERT: B  284 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8150 (mp)
REVERT: B  325 MET cc_start: 0.8329 (ttm) cc_final: 0.7985 (mmt)
  outliers start: 29
  outliers final: 22
  residues processed: 98
  average time/residue: 0.9761
  time to fit residues: 102.0703
Evaluate side-chains
  102 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   87 THR
Chi-restraints excluded: chain R residue  128 LEU
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  180 LEU
Chi-restraints excluded: chain R residue  218 SER
Chi-restraints excluded: chain R residue  248 THR
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain R residue  307 MET
Chi-restraints excluded: chain R residue  324 CYS
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  284 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0970
   chunk 81 optimal weight:   20.0000
   chunk 26 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.196417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.156635 restraints weight = 7165.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 2.00
r_work: 0.3539 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3403 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6976  Z= 0.133
  Angle     :  0.496   8.291   9451  Z= 0.266
  Chirality :  0.042   0.147   1100
  Planarity :  0.004   0.051   1186
  Dihedral  :  4.294  57.005    944
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.52 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 19.92 %
    Favored  : 76.29 %
  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:  1.06 (0.28), residues: 852
  helix:  1.96 (0.25), residues: 377
  sheet:  0.55 (0.38), residues: 190
  loop : -0.90 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.011   0.001   HIS A  82 
 PHE   0.019   0.001   PHE R 320 
 TYR   0.009   0.001   TYR R  54 
 ARG   0.005   0.000   ARG B 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04053 (  373)
  hydrogen bonds       : angle       4.31502 ( 1095)
  covalent geometry    : bond        0.00303 ( 6976)
  covalent geometry    : angle       0.49602 ( 9451)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   78 MET cc_start: 0.6759 (ptm) cc_final: 0.6167 (ptp)
REVERT: R   99 THR cc_start: 0.7094 (m) cc_final: 0.6466 (p)
REVERT: R  147 LYS cc_start: 0.8103 (ttmm) cc_final: 0.7651 (ttpm)
REVERT: R  210 LYS cc_start: 0.5018 (mptt) cc_final: 0.4671 (mmtp)
REVERT: R  220 LEU cc_start: 0.7627 (tt) cc_final: 0.7018 (tp)
REVERT: R  291 TYR cc_start: 0.7347 (t80) cc_final: 0.6963 (t80)
REVERT: A   25 GLU cc_start: 0.7412 (tt0) cc_final: 0.6996 (tt0)
REVERT: A   32 ARG cc_start: 0.6801 (mmt-90) cc_final: 0.5932 (ptp90)
REVERT: A   72 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8499 (p)
REVERT: A  136 THR cc_start: 0.8685 (t) cc_final: 0.8463 (m)
REVERT: A  153 VAL cc_start: 0.7606 (p) cc_final: 0.7292 (m)
REVERT: B   46 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7274 (mtp-110)
REVERT: B   78 LYS cc_start: 0.8582 (tppp) cc_final: 0.8286 (tppt)
REVERT: B  137 ARG cc_start: 0.7168 (tpp-160) cc_final: 0.6918 (tpp-160)
REVERT: B  200 VAL cc_start: 0.8986 (p) cc_final: 0.8717 (m)
REVERT: B  217 MET cc_start: 0.6678 (pmm) cc_final: 0.6300 (pmt)
REVERT: B  219 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6275 (mpt90)
REVERT: B  262 MET cc_start: 0.7447 (tpt) cc_final: 0.7172 (tpp)
REVERT: B  284 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8144 (mp)
REVERT: B  325 MET cc_start: 0.8332 (ttm) cc_final: 0.7986 (mmt)
  outliers start: 28
  outliers final: 21
  residues processed: 99
  average time/residue: 1.0129
  time to fit residues: 106.7160
Evaluate side-chains
  105 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   87 THR
Chi-restraints excluded: chain R residue  128 LEU
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  180 LEU
Chi-restraints excluded: chain R residue  218 SER
Chi-restraints excluded: chain R residue  248 THR
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain R residue  307 MET
Chi-restraints excluded: chain R residue  324 CYS
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  284 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 72 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 60 optimal weight:    0.4980
   chunk 33 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 83 optimal weight:   20.0000
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.195213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.154912 restraints weight = 7234.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 2.03
r_work: 0.3523 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7162
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6976  Z= 0.148
  Angle     :  0.513   8.385   9451  Z= 0.274
  Chirality :  0.043   0.148   1100
  Planarity :  0.004   0.050   1186
  Dihedral  :  4.355  57.617    944
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.52 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 20.33 %
    Favored  : 75.88 %
  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:  1.00 (0.28), residues: 852
  helix:  1.92 (0.25), residues: 377
  sheet:  0.49 (0.38), residues: 190
  loop : -0.93 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.010   0.001   HIS A  82 
 PHE   0.018   0.001   PHE R 320 
 TYR   0.008   0.001   TYR R  54 
 ARG   0.004   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04260 (  373)
  hydrogen bonds       : angle       4.37282 ( 1095)
  covalent geometry    : bond        0.00344 ( 6976)
  covalent geometry    : angle       0.51257 ( 9451)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   78 MET cc_start: 0.6739 (ptm) cc_final: 0.6215 (ptp)
REVERT: R   99 THR cc_start: 0.7164 (m) cc_final: 0.6584 (p)
REVERT: R  147 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7701 (ttpm)
REVERT: R  210 LYS cc_start: 0.5249 (mptt) cc_final: 0.4673 (mmtp)
REVERT: R  220 LEU cc_start: 0.7606 (tt) cc_final: 0.7021 (tp)
REVERT: R  291 TYR cc_start: 0.7409 (t80) cc_final: 0.7048 (t80)
REVERT: A   25 GLU cc_start: 0.7442 (tt0) cc_final: 0.7045 (tt0)
REVERT: A   32 ARG cc_start: 0.6918 (mmt-90) cc_final: 0.6047 (ptp90)
REVERT: A   72 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8514 (p)
REVERT: A  136 THR cc_start: 0.8696 (t) cc_final: 0.8473 (m)
REVERT: A  153 VAL cc_start: 0.7715 (p) cc_final: 0.7412 (m)
REVERT: B   46 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7286 (mtp-110)
REVERT: B   78 LYS cc_start: 0.8616 (tppp) cc_final: 0.8332 (tppt)
REVERT: B  137 ARG cc_start: 0.7234 (tpp-160) cc_final: 0.6989 (tpp-160)
REVERT: B  186 ASP cc_start: 0.7564 (m-30) cc_final: 0.7185 (m-30)
REVERT: B  217 MET cc_start: 0.6743 (pmm) cc_final: 0.6372 (pmt)
REVERT: B  219 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6380 (mpt90)
REVERT: B  262 MET cc_start: 0.7456 (tpt) cc_final: 0.7212 (tpp)
REVERT: B  284 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8142 (mp)
REVERT: B  325 MET cc_start: 0.8362 (ttm) cc_final: 0.8014 (mmt)
  outliers start: 28
  outliers final: 19
  residues processed: 104
  average time/residue: 1.0012
  time to fit residues: 112.1384
Evaluate side-chains
  103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   87 THR
Chi-restraints excluded: chain R residue  128 LEU
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  180 LEU
Chi-restraints excluded: chain R residue  218 SER
Chi-restraints excluded: chain R residue  248 THR
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain R residue  324 CYS
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  284 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 83 optimal weight:   20.0000
   chunk 69 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 79 optimal weight:    0.5980
   chunk 64 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 75 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:
A 101 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.195688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.156398 restraints weight = 7199.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 2.01
r_work: 0.3527 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6976  Z= 0.143
  Angle     :  0.509   8.212   9451  Z= 0.273
  Chirality :  0.042   0.148   1100
  Planarity :  0.004   0.049   1186
  Dihedral  :  4.336  55.233    944
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.76 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 20.87 %
    Favored  : 75.47 %
  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:  0.99 (0.29), residues: 852
  helix:  1.94 (0.25), residues: 377
  sheet:  0.36 (0.38), residues: 192
  loop : -0.88 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.008   0.001   HIS A  82 
 PHE   0.019   0.001   PHE R 320 
 TYR   0.010   0.001   TYR R  54 
 ARG   0.004   0.000   ARG B 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04190 (  373)
  hydrogen bonds       : angle       4.39267 ( 1095)
  covalent geometry    : bond        0.00332 ( 6976)
  covalent geometry    : angle       0.50879 ( 9451)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5048.64 seconds
wall clock time: 87 minutes 0.29 seconds (5220.29 seconds total)