Starting phenix.real_space_refine
on Wed Jan 15 18:56:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xjl_38400/01_2025/8xjl_38400.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xjl_38400/01_2025/8xjl_38400.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xjl_38400/01_2025/8xjl_38400.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xjl_38400/01_2025/8xjl_38400.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xjl_38400/01_2025/8xjl_38400.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xjl_38400/01_2025/8xjl_38400.cif"
  }
  resolution = 2.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
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      62      5.16       5
     C    5624      2.51       5
     N    1513      2.21       5
     O    1647      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8846
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1821
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 217}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 2622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 342, 2622
          Classifications: {'peptide': 342}
          Link IDs: {'PTRANS': 5, 'TRANS': 336}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "E"
      Number of atoms: 1771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1771
          Classifications: {'peptide': 230}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2171
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 5, 'TRANS': 281}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 102
          Unresolved non-hydrogen angles: 121
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 60
    Chain: "R"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'UGU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.94, per 1000 atoms: 0.56
  Number of scatterers: 8846
  At special positions: 0
  Unit cell: (105.93, 116.63, 111.28, 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      62     16.00
     O    1647      8.00
     N    1513      7.00
     C    5624      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  21 " - pdb=" SG  CYS E  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 108 " - pdb=" SG  CYS R 186 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.26
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 14 sheets defined
      40.7% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.530A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 101
    Processing helix  chain 'A' and resid 117 through 130
    Processing helix  chain 'A' and resid 131 through 135
      removed outlier: 4.090A  pdb=" N   ARG A 135 " --> pdb=" O   ARG A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.189A  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 183 through 204
      removed outlier: 3.683A  pdb=" N   PHE A 197 " --> pdb=" O   ILE A 193 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   SER A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 245
      removed outlier: 3.508A  pdb=" N   ASP A 233 " --> pdb=" O   ASN A 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 24
      removed outlier: 3.658A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'E' and resid 27 through 31
    Processing helix  chain 'E' and resid 52 through 55
      removed outlier: 4.114A  pdb=" N   GLY E  55 " --> pdb=" O   SER E  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 52 through 55'
    Processing helix  chain 'E' and resid 86 through 90
      removed outlier: 3.630A  pdb=" N   THR E  90 " --> pdb=" O   SER E  87 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 29 through 59
      removed outlier: 4.044A  pdb=" N   SER R  33 " --> pdb=" O   SER R  29 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLN R  56 " --> pdb=" O   MET R  52 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 64 through 94
    Processing helix  chain 'R' and resid 97 through 102
    Processing helix  chain 'R' and resid 105 through 139
      removed outlier: 3.538A  pdb=" N   SER R 109 " --> pdb=" O   ASN R 105 " (cutoff:3.500A)
      Proline residue:  R 122  - end of helix
    Processing helix  chain 'R' and resid 139 through 146
    Processing helix  chain 'R' and resid 148 through 168
    Processing helix  chain 'R' and resid 168 through 173
    Processing helix  chain 'R' and resid 195 through 232
      removed outlier: 4.138A  pdb=" N   LEU R 202 " --> pdb=" O   ASP R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 243 through 276
      removed outlier: 3.679A  pdb=" N   TRP R 262 " --> pdb=" O   SER R 258 " (cutoff:3.500A)
      Proline residue:  R 264  - end of helix
      removed outlier: 3.613A  pdb=" N   THR R 268 " --> pdb=" O   PRO R 264 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 277 through 279
      No H-bonds generated for 'chain 'R' and resid 277 through 279'
    Processing helix  chain 'R' and resid 282 through 305
      removed outlier: 3.637A  pdb=" N   ASN R 296 " --> pdb=" O   MET R 292 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   GLN R 297 " --> pdb=" O   ALA R 293 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 321
      removed outlier: 3.626A  pdb=" N   ASN R 314 " --> pdb=" O   ALA R 310 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 76
      removed outlier: 4.598A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   GLY A  40 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 9.573A  pdb=" N   ALA A 105 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   ILE A 107 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 8.657A  pdb=" N   ASP A 111 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51
      removed outlier: 5.689A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.800A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.016A  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: 4.165A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.506A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.761A  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: 4.253A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.506A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.769A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.606A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11
      removed outlier: 6.682A  pdb=" N   MET E  33 " --> pdb=" O   TYR E  49 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   TYR E  49 " --> pdb=" O   MET E  33 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   TRP E  35 " --> pdb=" O   VAL E  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11
      removed outlier: 4.344A  pdb=" N   PHE E 109 " --> pdb=" O   ARG E  97 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.331A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 178 through 179

    486 hydrogen bonds defined for protein.
    1365 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.76

  Time building geometry restraints manager: 2.60 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: 2875
        1.34 -     1.46: 2140
        1.46 -     1.58: 3915
        1.58 -     1.69: 3
        1.69 -     1.81: 90
  Bond restraints: 9023
  Sorted by residual:
  bond pdb=" C11 UGU R 601 "
       pdb=" C12 UGU R 601 "
    ideal  model  delta    sigma   weight residual
    1.530  1.316  0.214 2.00e-02 2.50e+03 1.14e+02
  bond pdb=" C8  UGU R 601 "
       pdb=" C9  UGU R 601 "
    ideal  model  delta    sigma   weight residual
    1.531  1.338  0.193 2.00e-02 2.50e+03 9.35e+01
  bond pdb=" C12 UGU R 601 "
       pdb=" C8  UGU R 601 "
    ideal  model  delta    sigma   weight residual
    1.548  1.694 -0.146 2.00e-02 2.50e+03 5.30e+01
  bond pdb=" C10 UGU R 601 "
       pdb=" C11 UGU R 601 "
    ideal  model  delta    sigma   weight residual
    1.550  1.616 -0.066 2.00e-02 2.50e+03 1.11e+01
  bond pdb=" C6  UGU R 601 "
       pdb=" C7  UGU R 601 "
    ideal  model  delta    sigma   weight residual
    1.502  1.561 -0.059 2.00e-02 2.50e+03 8.70e+00
  ... (remaining 9018 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.95: 12194
        2.95 -     5.90: 23
        5.90 -     8.85: 1
        8.85 -    11.80: 1
       11.80 -    14.75: 3
  Bond angle restraints: 12222
  Sorted by residual:
  angle pdb=" C12 UGU R 601 "
        pdb=" C13 UGU R 601 "
        pdb=" C14 UGU R 601 "
      ideal   model   delta    sigma   weight residual
     127.73  112.98   14.75 3.00e+00 1.11e-01 2.42e+01
  angle pdb=" C5  UGU R 601 "
        pdb=" C6  UGU R 601 "
        pdb=" C7  UGU R 601 "
      ideal   model   delta    sigma   weight residual
     128.14  113.61   14.53 3.00e+00 1.11e-01 2.34e+01
  angle pdb=" C13 UGU R 601 "
        pdb=" C14 UGU R 601 "
        pdb=" C15 UGU R 601 "
      ideal   model   delta    sigma   weight residual
     126.10  112.83   13.27 3.00e+00 1.11e-01 1.96e+01
  angle pdb=" C4  UGU R 601 "
        pdb=" C5  UGU R 601 "
        pdb=" C6  UGU R 601 "
      ideal   model   delta    sigma   weight residual
     128.19  116.86   11.33 3.00e+00 1.11e-01 1.43e+01
  angle pdb=" C11 UGU R 601 "
        pdb=" C12 UGU R 601 "
        pdb=" C13 UGU R 601 "
      ideal   model   delta    sigma   weight residual
     117.79  110.36    7.43 3.00e+00 1.11e-01 6.13e+00
  ... (remaining 12217 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.54: 5316
       33.54 -    67.07: 47
       67.07 -   100.61: 4
      100.61 -   134.15: 0
      134.15 -   167.68: 1
  Dihedral angle restraints: 5368
    sinusoidal: 2073
      harmonic: 3295
  Sorted by residual:
  dihedral pdb=" C16 UGU R 601 "
           pdb=" C17 UGU R 601 "
           pdb=" C18 UGU R 601 "
           pdb=" C19 UGU R 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     297.02  129.34  167.68     1      3.00e+01 1.11e-03 2.11e+01
  dihedral pdb=" CA  ARG E 191 "
           pdb=" C   ARG E 191 "
           pdb=" N   MET E 192 "
           pdb=" CA  MET E 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.82   17.18     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CA  PHE E  31 "
           pdb=" C   PHE E  31 "
           pdb=" N   GLY E  32 "
           pdb=" CA  GLY E  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.04   16.96     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 5365 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1276
       0.068 -    0.136: 118
       0.136 -    0.204: 2
       0.204 -    0.272: 1
       0.272 -    0.340: 1
  Chirality restraints: 1398
  Sorted by residual:
  chirality pdb=" C12 UGU R 601 "
            pdb=" C11 UGU R 601 "
            pdb=" C13 UGU R 601 "
            pdb=" C8  UGU R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.76   -0.34 2.00e-01 2.50e+01 2.88e+00
  chirality pdb=" C9  UGU R 601 "
            pdb=" C10 UGU R 601 "
            pdb=" C8  UGU R 601 "
            pdb=" O3  UGU R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.72   -2.46   -0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" C8  UGU R 601 "
            pdb=" C12 UGU R 601 "
            pdb=" C7  UGU R 601 "
            pdb=" C9  UGU R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.54   -2.73    0.19 2.00e-01 2.50e+01 9.24e-01
  ... (remaining 1395 not shown)

  Planarity restraints: 1548
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.029 5.00e-02 4.00e+02   4.32e-02 2.99e+00
        pdb=" N   PRO B 236 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "    0.020 5.00e-02 4.00e+02   2.96e-02 1.40e+00
        pdb=" N   PRO B 194 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C  59 "    0.017 5.00e-02 4.00e+02   2.53e-02 1.03e+00
        pdb=" N   PRO C  60 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO C  60 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO C  60 "    0.014 5.00e-02 4.00e+02
  ... (remaining 1545 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1379
        2.76 -     3.30: 8377
        3.30 -     3.83: 14805
        3.83 -     4.37: 18525
        4.37 -     4.90: 31741
  Nonbonded interactions: 74827
  Sorted by model distance:
  nonbonded pdb=" O   ARG R 291 "
            pdb=" CG2 THR R 294 "
     model   vdw
     2.225 3.460
  nonbonded pdb=" O   VAL R 303 "
            pdb=" NH2 ARG R 308 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" O   LYS C  20 "
            pdb=" ND2 ASN C  24 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" NE2 GLN A  52 "
            pdb=" O   ALA A 218 "
     model   vdw
     2.286 3.120
  ... (remaining 74822 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.300
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.860
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.214   9023  Z= 0.287
  Angle     :  0.477  14.755  12222  Z= 0.223
  Chirality :  0.041   0.340   1398
  Planarity :  0.003   0.043   1548
  Dihedral  : 10.361 167.683   3231
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  3.38 %
    Favored  : 95.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.28 (0.25), residues: 1122
  helix:  1.35 (0.25), residues: 414
  sheet:  1.07 (0.33), residues: 267
  loop :  0.37 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 209 
 PHE   0.012   0.001   PHE B 151 
 TYR   0.011   0.001   TYR E 190 
 ARG   0.003   0.000   ARG E  37 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 209
  time to evaluate  : 0.947 
Fit side-chains
REVERT: E   42 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7808 (mmtp)
REVERT: E  140 MET cc_start: 0.8395 (mmm) cc_final: 0.8174 (mmp)
REVERT: E  210 THR cc_start: 0.8082 (p) cc_final: 0.7849 (p)
REVERT: R   57 ARG cc_start: 0.7428 (ttm170) cc_final: 0.7096 (mtm-85)
REVERT: R  198 ASP cc_start: 0.8000 (t0) cc_final: 0.7693 (t0)
  outliers start: 10
  outliers final: 3
  residues processed: 218
  average time/residue: 1.3034
  time to fit residues: 301.7725
Evaluate side-chains
  144 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 141
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  209 HIS
Chi-restraints excluded: chain R residue   28 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   chunk 57 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 101 optimal weight:    4.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 244 ASN
B  88 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 ASN
R 143 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.152912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.121127 restraints weight = 10261.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 1.73
r_work: 0.3187 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9023  Z= 0.202
  Angle     :  0.522   6.521  12222  Z= 0.283
  Chirality :  0.042   0.145   1398
  Planarity :  0.004   0.044   1548
  Dihedral  :  6.771 130.712   1270
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 11.18 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  2.09 (0.26), residues: 1122
  helix:  2.68 (0.24), residues: 411
  sheet:  1.03 (0.32), residues: 263
  loop :  0.46 (0.32), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 295 
 HIS   0.005   0.001   HIS R  81 
 PHE   0.014   0.001   PHE R 101 
 TYR   0.016   0.001   TYR E 190 
 ARG   0.005   0.000   ARG A 194 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 0.931 
Fit side-chains
REVERT: A  132 ARG cc_start: 0.7750 (tpt90) cc_final: 0.7364 (tpm170)
REVERT: A  183 ASP cc_start: 0.7976 (t70) cc_final: 0.7726 (t70)
REVERT: A  230 ASP cc_start: 0.7697 (m-30) cc_final: 0.7407 (m-30)
REVERT: E   42 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7794 (mmtp)
REVERT: E   45 GLU cc_start: 0.7751 (pt0) cc_final: 0.7530 (pt0)
REVERT: E   64 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7751 (tttm)
REVERT: E  140 MET cc_start: 0.8419 (mmm) cc_final: 0.8143 (mmp)
REVERT: R  285 THR cc_start: 0.6999 (m) cc_final: 0.6715 (p)
  outliers start: 28
  outliers final: 12
  residues processed: 165
  average time/residue: 1.2345
  time to fit residues: 217.1420
Evaluate side-chains
  143 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  209 HIS
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain R residue   28 LEU
Chi-restraints excluded: chain R residue   67 LEU
Chi-restraints excluded: chain R residue  139 LYS
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  294 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 24 optimal weight:   10.0000
   chunk 21 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 81 optimal weight:   10.0000
   chunk 93 optimal weight:    6.9990
   chunk 71 optimal weight:    0.8980
   chunk 69 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
A 119 GLN
A 209 HIS
B 156 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 186 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.150897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.118325 restraints weight = 10416.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.82
r_work: 0.3161 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9023  Z= 0.170
  Angle     :  0.492   6.568  12222  Z= 0.261
  Chirality :  0.040   0.133   1398
  Planarity :  0.003   0.044   1548
  Dihedral  :  5.843  90.670   1268
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 12.24 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  2.21 (0.26), residues: 1122
  helix:  2.96 (0.24), residues: 414
  sheet:  0.83 (0.31), residues: 273
  loop :  0.49 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R  81 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.015   0.001   TYR E 190 
 ARG   0.006   0.000   ARG A 225 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A  222 GLU cc_start: 0.7301 (tt0) cc_final: 0.7090 (tp30)
REVERT: A  230 ASP cc_start: 0.7594 (m-30) cc_final: 0.7378 (m-30)
REVERT: C   28 ILE cc_start: 0.8363 (pt) cc_final: 0.7967 (tt)
REVERT: E   42 LYS cc_start: 0.8361 (mmtm) cc_final: 0.8051 (mmtp)
REVERT: E   64 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7705 (tttm)
REVERT: E  140 MET cc_start: 0.8334 (mmm) cc_final: 0.8111 (mmp)
REVERT: R   84 ASN cc_start: 0.7679 (m-40) cc_final: 0.7385 (m110)
REVERT: R  285 THR cc_start: 0.7083 (m) cc_final: 0.6865 (p)
  outliers start: 24
  outliers final: 12
  residues processed: 148
  average time/residue: 1.2249
  time to fit residues: 193.9168
Evaluate side-chains
  137 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain E residue   18 LYS
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain R residue   28 LEU
Chi-restraints excluded: chain R residue   48 ILE
Chi-restraints excluded: chain R residue   67 LEU
Chi-restraints excluded: chain R residue  139 LYS
Chi-restraints excluded: chain R residue  303 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 108 optimal weight:   20.0000
   chunk 4 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0370
   chunk 30 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.8062

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 116 ASN
A 119 GLN
B 156 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.151971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.118904 restraints weight = 10243.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 1.73
r_work: 0.3123 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9023  Z= 0.163
  Angle     :  0.472   6.442  12222  Z= 0.252
  Chirality :  0.040   0.135   1398
  Planarity :  0.003   0.045   1548
  Dihedral  :  5.457  87.626   1266
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 13.40 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  2.22 (0.26), residues: 1122
  helix:  3.10 (0.24), residues: 414
  sheet:  0.68 (0.30), residues: 276
  loop :  0.46 (0.32), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A  82 
 PHE   0.021   0.001   PHE R 200 
 TYR   0.016   0.001   TYR R 188 
 ARG   0.005   0.000   ARG A 225 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 LYS cc_start: 0.7670 (mtpt) cc_final: 0.7223 (mptt)
REVERT: A  101 ASN cc_start: 0.7614 (t0) cc_final: 0.7359 (t0)
REVERT: A  115 TYR cc_start: 0.8431 (m-80) cc_final: 0.8132 (m-80)
REVERT: A  132 ARG cc_start: 0.7749 (tpt90) cc_final: 0.7246 (tpm170)
REVERT: C   21 MET cc_start: 0.7126 (mtm) cc_final: 0.6845 (mpm)
REVERT: C   28 ILE cc_start: 0.8315 (pt) cc_final: 0.7923 (tt)
REVERT: E   42 LYS cc_start: 0.8387 (mmtm) cc_final: 0.8039 (mmtp)
REVERT: E   64 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7763 (tttm)
REVERT: E  219 LEU cc_start: 0.8646 (tp) cc_final: 0.8214 (mm)
REVERT: E  220 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7069 (mp0)
REVERT: R   84 ASN cc_start: 0.7646 (m-40) cc_final: 0.7370 (m110)
REVERT: R   90 PHE cc_start: 0.6978 (t80) cc_final: 0.6772 (t80)
REVERT: R  141 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8383 (mt)
REVERT: R  207 PHE cc_start: 0.7634 (t80) cc_final: 0.7399 (t80)
  outliers start: 27
  outliers final: 14
  residues processed: 147
  average time/residue: 1.2305
  time to fit residues: 193.4644
Evaluate side-chains
  141 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain E residue   18 LYS
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain E residue  220 GLU
Chi-restraints excluded: chain R residue   28 LEU
Chi-restraints excluded: chain R residue   48 ILE
Chi-restraints excluded: chain R residue   67 LEU
Chi-restraints excluded: chain R residue  139 LYS
Chi-restraints excluded: chain R residue  141 ILE
Chi-restraints excluded: chain R residue  303 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 25 optimal weight:    8.9990
   chunk 95 optimal weight:    0.7980
   chunk 96 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
A 119 GLN
B 156 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.150782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.118016 restraints weight = 10362.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 1.74
r_work: 0.3137 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9023  Z= 0.191
  Angle     :  0.491   6.480  12222  Z= 0.262
  Chirality :  0.041   0.134   1398
  Planarity :  0.003   0.045   1548
  Dihedral  :  5.440  82.155   1266
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 13.61 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  2.12 (0.26), residues: 1122
  helix:  3.01 (0.24), residues: 420
  sheet:  0.59 (0.30), residues: 279
  loop :  0.41 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A  82 
 PHE   0.015   0.001   PHE R 200 
 TYR   0.016   0.001   TYR R 188 
 ARG   0.004   0.000   ARG A 225 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 1.128 
Fit side-chains
REVERT: A   73 LYS cc_start: 0.7728 (mtpt) cc_final: 0.7229 (mptt)
REVERT: A  101 ASN cc_start: 0.7715 (t0) cc_final: 0.7433 (t0)
REVERT: A  132 ARG cc_start: 0.7701 (tpt90) cc_final: 0.7452 (tpt90)
REVERT: A  183 ASP cc_start: 0.7886 (t70) cc_final: 0.7555 (t70)
REVERT: C   21 MET cc_start: 0.7156 (mtm) cc_final: 0.6886 (mpm)
REVERT: C   28 ILE cc_start: 0.8227 (pt) cc_final: 0.7840 (tt)
REVERT: E   42 LYS cc_start: 0.8403 (mmtm) cc_final: 0.8062 (mmtp)
REVERT: E  220 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7064 (mp0)
REVERT: R  141 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8356 (mt)
REVERT: R  207 PHE cc_start: 0.7627 (t80) cc_final: 0.7385 (t80)
  outliers start: 28
  outliers final: 15
  residues processed: 150
  average time/residue: 1.2646
  time to fit residues: 202.6819
Evaluate side-chains
  143 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain E residue   18 LYS
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain E residue  220 GLU
Chi-restraints excluded: chain R residue   28 LEU
Chi-restraints excluded: chain R residue   48 ILE
Chi-restraints excluded: chain R residue   67 LEU
Chi-restraints excluded: chain R residue  139 LYS
Chi-restraints excluded: chain R residue  141 ILE
Chi-restraints excluded: chain R residue  303 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 22 optimal weight:   20.0000
   chunk 104 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0870
   chunk 37 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 63 optimal weight:    6.9990
   overall best weight:    1.5764

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

Flipped N/Q/H residues before XYZ refinement:
A 119 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.149182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.116296 restraints weight = 10304.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 1.78
r_work: 0.3089 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9023  Z= 0.246
  Angle     :  0.528   8.173  12222  Z= 0.281
  Chirality :  0.042   0.143   1398
  Planarity :  0.004   0.045   1548
  Dihedral  :  5.645  81.670   1266
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.35 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.94 (0.25), residues: 1122
  helix:  2.79 (0.24), residues: 421
  sheet:  0.55 (0.30), residues: 279
  loop :  0.33 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  96 
 HIS   0.005   0.001   HIS A  82 
 PHE   0.014   0.002   PHE B 199 
 TYR   0.018   0.002   TYR R 188 
 ARG   0.004   0.000   ARG A 225 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7306 (mptt)
REVERT: A  101 ASN cc_start: 0.7891 (t0) cc_final: 0.7619 (t0)
REVERT: A  115 TYR cc_start: 0.8453 (m-80) cc_final: 0.8223 (m-80)
REVERT: A  132 ARG cc_start: 0.7716 (tpt90) cc_final: 0.7462 (tpt90)
REVERT: A  183 ASP cc_start: 0.7914 (t70) cc_final: 0.7562 (t70)
REVERT: A  230 ASP cc_start: 0.7728 (m-30) cc_final: 0.7484 (m-30)
REVERT: C   21 MET cc_start: 0.7209 (mtm) cc_final: 0.6894 (mpm)
REVERT: C   28 ILE cc_start: 0.8246 (pt) cc_final: 0.7847 (tt)
REVERT: E   42 LYS cc_start: 0.8431 (mmtm) cc_final: 0.8074 (mmtp)
REVERT: E  219 LEU cc_start: 0.8569 (tp) cc_final: 0.8129 (mm)
REVERT: R   90 PHE cc_start: 0.6824 (t80) cc_final: 0.6607 (t80)
REVERT: R  141 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8349 (mt)
REVERT: R  207 PHE cc_start: 0.7647 (t80) cc_final: 0.7417 (t80)
  outliers start: 25
  outliers final: 13
  residues processed: 140
  average time/residue: 1.2987
  time to fit residues: 193.5404
Evaluate side-chains
  139 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain E residue   18 LYS
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain R residue   28 LEU
Chi-restraints excluded: chain R residue   48 ILE
Chi-restraints excluded: chain R residue   67 LEU
Chi-restraints excluded: chain R residue  139 LYS
Chi-restraints excluded: chain R residue  141 ILE
Chi-restraints excluded: chain R residue  303 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 90 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 104 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.148792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.116037 restraints weight = 10340.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 1.77
r_work: 0.3077 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9023  Z= 0.265
  Angle     :  0.545   8.182  12222  Z= 0.290
  Chirality :  0.042   0.141   1398
  Planarity :  0.004   0.043   1548
  Dihedral  :  5.769  80.728   1266
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.87 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.79 (0.25), residues: 1122
  helix:  2.67 (0.24), residues: 421
  sheet:  0.51 (0.30), residues: 269
  loop :  0.22 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  96 
 HIS   0.005   0.001   HIS A  82 
 PHE   0.015   0.002   PHE B 199 
 TYR   0.018   0.002   TYR R 188 
 ARG   0.004   0.000   ARG A 225 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 LYS cc_start: 0.7822 (mtpt) cc_final: 0.7418 (mptt)
REVERT: A  101 ASN cc_start: 0.7958 (t0) cc_final: 0.7696 (t0)
REVERT: A  132 ARG cc_start: 0.7743 (tpt90) cc_final: 0.7492 (tpt90)
REVERT: A  183 ASP cc_start: 0.7924 (t70) cc_final: 0.7584 (t70)
REVERT: A  230 ASP cc_start: 0.7731 (m-30) cc_final: 0.7489 (m-30)
REVERT: C   21 MET cc_start: 0.7210 (mtm) cc_final: 0.6875 (mpm)
REVERT: C   28 ILE cc_start: 0.8322 (pt) cc_final: 0.7905 (tt)
REVERT: E   42 LYS cc_start: 0.8447 (mmtm) cc_final: 0.8044 (mmtp)
REVERT: R  141 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8370 (mt)
REVERT: R  207 PHE cc_start: 0.7580 (t80) cc_final: 0.7359 (t80)
  outliers start: 25
  outliers final: 15
  residues processed: 140
  average time/residue: 1.3208
  time to fit residues: 196.8881
Evaluate side-chains
  137 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue   18 LYS
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain R residue   28 LEU
Chi-restraints excluded: chain R residue   67 LEU
Chi-restraints excluded: chain R residue  139 LYS
Chi-restraints excluded: chain R residue  141 ILE
Chi-restraints excluded: chain R residue  303 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 58 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 101 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 104 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 112 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.149630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.116850 restraints weight = 10500.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.78
r_work: 0.3098 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9023  Z= 0.199
  Angle     :  0.513   7.734  12222  Z= 0.273
  Chirality :  0.041   0.135   1398
  Planarity :  0.003   0.045   1548
  Dihedral  :  5.698  77.845   1266
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.72 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.86 (0.25), residues: 1122
  helix:  2.81 (0.24), residues: 421
  sheet:  0.51 (0.30), residues: 275
  loop :  0.17 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A  82 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.015   0.001   TYR R 188 
 ARG   0.004   0.000   ARG R 133 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7436 (mptt)
REVERT: A  101 ASN cc_start: 0.7919 (t0) cc_final: 0.7643 (t0)
REVERT: A  132 ARG cc_start: 0.7738 (tpt90) cc_final: 0.7485 (tpt90)
REVERT: A  183 ASP cc_start: 0.7917 (t70) cc_final: 0.7579 (t70)
REVERT: B   78 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8775 (mmtt)
REVERT: C   21 MET cc_start: 0.7208 (mtm) cc_final: 0.6884 (mpm)
REVERT: C   28 ILE cc_start: 0.8283 (pt) cc_final: 0.7854 (tt)
REVERT: E   42 LYS cc_start: 0.8446 (mmtm) cc_final: 0.8043 (mmtp)
REVERT: R  141 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8373 (mt)
REVERT: R  207 PHE cc_start: 0.7648 (t80) cc_final: 0.7428 (t80)
  outliers start: 21
  outliers final: 15
  residues processed: 137
  average time/residue: 1.3194
  time to fit residues: 192.3972
Evaluate side-chains
  138 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain E residue   18 LYS
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain R residue   28 LEU
Chi-restraints excluded: chain R residue   48 ILE
Chi-restraints excluded: chain R residue   67 LEU
Chi-restraints excluded: chain R residue  139 LYS
Chi-restraints excluded: chain R residue  141 ILE
Chi-restraints excluded: chain R residue  303 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 6 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 92 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 112 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.150035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.117457 restraints weight = 10415.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.77
r_work: 0.3096 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9023  Z= 0.227
  Angle     :  0.528   7.858  12222  Z= 0.281
  Chirality :  0.042   0.138   1398
  Planarity :  0.003   0.045   1548
  Dihedral  :  5.730  72.204   1266
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.93 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.84 (0.25), residues: 1122
  helix:  2.84 (0.24), residues: 415
  sheet:  0.47 (0.30), residues: 275
  loop :  0.19 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  63 
 HIS   0.005   0.001   HIS A  82 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.016   0.001   TYR R 188 
 ARG   0.004   0.000   ARG R 133 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 LYS cc_start: 0.7789 (mtpt) cc_final: 0.7454 (mptt)
REVERT: A  101 ASN cc_start: 0.7948 (t0) cc_final: 0.7705 (t0)
REVERT: A  132 ARG cc_start: 0.7741 (tpt90) cc_final: 0.7489 (tpt90)
REVERT: A  183 ASP cc_start: 0.7929 (t70) cc_final: 0.7598 (t70)
REVERT: C   21 MET cc_start: 0.7226 (mtm) cc_final: 0.6885 (mpm)
REVERT: C   28 ILE cc_start: 0.8286 (pt) cc_final: 0.7853 (tt)
REVERT: E   42 LYS cc_start: 0.8450 (mmtm) cc_final: 0.8019 (tppp)
REVERT: R  141 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8390 (mt)
REVERT: R  207 PHE cc_start: 0.7594 (t80) cc_final: 0.7358 (t80)
  outliers start: 19
  outliers final: 16
  residues processed: 134
  average time/residue: 1.2959
  time to fit residues: 184.9107
Evaluate side-chains
  138 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue   18 LYS
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain R residue   28 LEU
Chi-restraints excluded: chain R residue   48 ILE
Chi-restraints excluded: chain R residue   67 LEU
Chi-restraints excluded: chain R residue  139 LYS
Chi-restraints excluded: chain R residue  141 ILE
Chi-restraints excluded: chain R residue  303 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 101 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 82 optimal weight:    6.9990
   chunk 93 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 94 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 73 optimal weight:    0.1980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 112 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.150520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.117899 restraints weight = 10490.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 1.78
r_work: 0.3139 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9023  Z= 0.180
  Angle     :  0.507   7.519  12222  Z= 0.269
  Chirality :  0.041   0.141   1398
  Planarity :  0.003   0.046   1548
  Dihedral  :  5.627  66.176   1266
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 16.24 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.99 (0.26), residues: 1122
  helix:  3.01 (0.24), residues: 414
  sheet:  0.51 (0.30), residues: 274
  loop :  0.26 (0.32), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A  82 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.015   0.001   TYR E 190 
 ARG   0.005   0.000   ARG R 133 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 LYS cc_start: 0.7751 (mtpt) cc_final: 0.7453 (mptt)
REVERT: A  101 ASN cc_start: 0.7856 (t0) cc_final: 0.7587 (t0)
REVERT: A  132 ARG cc_start: 0.7732 (tpt90) cc_final: 0.7489 (tpt90)
REVERT: A  183 ASP cc_start: 0.7911 (t70) cc_final: 0.7589 (t70)
REVERT: B   46 ARG cc_start: 0.8090 (mmm160) cc_final: 0.7637 (mmm-85)
REVERT: C   21 MET cc_start: 0.7222 (mtm) cc_final: 0.6899 (mpm)
REVERT: C   28 ILE cc_start: 0.8252 (pt) cc_final: 0.7841 (tt)
REVERT: E   42 LYS cc_start: 0.8404 (mmtm) cc_final: 0.7990 (tppp)
REVERT: R  141 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8361 (mt)
REVERT: R  207 PHE cc_start: 0.7628 (t80) cc_final: 0.7426 (t80)
  outliers start: 18
  outliers final: 15
  residues processed: 138
  average time/residue: 1.3088
  time to fit residues: 192.5980
Evaluate side-chains
  137 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  217 CYS
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue   18 LYS
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain R residue   28 LEU
Chi-restraints excluded: chain R residue   48 ILE
Chi-restraints excluded: chain R residue   67 LEU
Chi-restraints excluded: chain R residue  139 LYS
Chi-restraints excluded: chain R residue  141 ILE
Chi-restraints excluded: chain R residue  303 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 109 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0970
   chunk 53 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   chunk 57 optimal weight:    6.9990
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 112 GLN
R 250 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.151308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.118865 restraints weight = 10446.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.75
r_work: 0.3133 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9023  Z= 0.161
  Angle     :  0.492   7.554  12222  Z= 0.262
  Chirality :  0.040   0.133   1398
  Planarity :  0.003   0.047   1548
  Dihedral  :  5.452  56.815   1266
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 16.46 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  2.07 (0.26), residues: 1122
  helix:  3.18 (0.24), residues: 410
  sheet:  0.47 (0.30), residues: 276
  loop :  0.28 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A  82 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.014   0.001   TYR E 190 
 ARG   0.003   0.000   ARG A 225 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7576.23 seconds
wall clock time: 134 minutes 20.09 seconds (8060.09 seconds total)