Starting phenix.real_space_refine
on Tue May 13 13:32:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y65_33634/05_2025/7y65_33634_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y65_33634/05_2025/7y65_33634.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y65_33634/05_2025/7y65_33634.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y65_33634/05_2025/7y65_33634.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y65_33634/05_2025/7y65_33634_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y65_33634/05_2025/7y65_33634_neut.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.047
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2112 atoms to isotropic.
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      60      5.16       5
     C    5584      2.51       5
     N    1476      2.21       5
     O    1601      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8721
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1813
          Classifications: {'peptide': 226}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 223}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2611
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "C"
      Number of atoms: 474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 474
          Classifications: {'peptide': 61}
          Link IDs: {'PTRANS': 4, 'TRANS': 56}
    Chain: "L"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 50
          Classifications: {'peptide': 5}
          Link IDs: {'PTRANS': 1, 'TRANS': 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Planarities with less than four sites: {'ZAL:plan-1': 1, 'ALC:plan-1': 1, 'MEA:plan-2': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "L"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1, 'PEPT-D': 1}
    Chain: "S"
      Number of atoms: 1515
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1515
          Classifications: {'peptide': 194}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 2246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2246
          Classifications: {'peptide': 283}
          Link IDs: {'PTRANS': 13, 'TRANS': 269}
  Time building chain proxies: 5.26, per 1000 atoms: 0.60
  Number of scatterers: 8721
  At special positions: 0
  Unit cell: (85.85, 115.6, 130.9, 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      60     16.00
     O    1601      8.00
     N    1476      7.00
     C    5584      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 109 " - pdb=" SG  CYS D 188 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.41
  Conformation dependent library (CDL) restraints added in 958.2 milliseconds
  

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DAR L   6 "
      Input volumes are d-peptide like
        pdb=" CB  ZAL L   4 "
  Number of C-beta restraints generated:  2076

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 14 sheets defined
      38.1% alpha, 20.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 28
      removed outlier: 3.680A  pdb=" N   GLU A  28 " --> pdb=" O   ARG A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.542A  pdb=" N   GLU A 245 " --> pdb=" O   ASN A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.672A  pdb=" N   PHE A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.962A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.525A  pdb=" N   CYS A 351 " --> pdb=" O   ASN A 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 25
      removed outlier: 3.796A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 23
    Processing helix  chain 'C' and resid 29 through 45
      removed outlier: 3.600A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 48
      No H-bonds generated for 'chain 'C' and resid 46 through 48'
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.643A  pdb=" N   SER S  31 " --> pdb=" O   ALA S  28 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   PHE S  32 " --> pdb=" O   PHE S  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 28 through 32'
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.919A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'D' and resid 34 through 65
      removed outlier: 3.751A  pdb=" N   ILE D  38 " --> pdb=" O   ARG D  34 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   LEU D  39 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLU D  65 " --> pdb=" O   VAL D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 69 through 88
      removed outlier: 3.986A  pdb=" N   ILE D  73 " --> pdb=" O   THR D  69 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   TRP D  74 " --> pdb=" O   ILE D  70 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   PHE D  75 " --> pdb=" O   ASN D  71 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ASN D  77 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU D  78 " --> pdb=" O   TRP D  74 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA D  88 " --> pdb=" O   LEU D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 88 through 98
      removed outlier: 4.000A  pdb=" N   LEU D  92 " --> pdb=" O   ALA D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 139
      removed outlier: 4.242A  pdb=" N   ALA D 108 " --> pdb=" O   PHE D 104 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   CYS D 109 " --> pdb=" O   GLY D 105 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER D 110 " --> pdb=" O   GLY D 106 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   ILE D 111 " --> pdb=" O   ALA D 107 " (cutoff:3.500A)
      Proline residue:  D 113  - end of helix
      removed outlier: 4.237A  pdb=" N   ILE D 116 " --> pdb=" O   LEU D 112 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   TYR D 121 " --> pdb=" O   LEU D 117 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE D 135 " --> pdb=" O   SER D 131 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 142 through 147
      removed outlier: 3.505A  pdb=" N   ASN D 146 " --> pdb=" O   ILE D 142 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 149 through 174
      removed outlier: 3.854A  pdb=" N   ALA D 153 " --> pdb=" O   GLY D 149 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ALA D 164 " --> pdb=" O   ALA D 160 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   LEU D 165 " --> pdb=" O   TRP D 161 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   LEU D 166 " --> pdb=" O   GLY D 162 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   LEU D 167 " --> pdb=" O   LEU D 163 " (cutoff:3.500A)
      Proline residue:  D 170  - end of helix
    Processing helix  chain 'D' and resid 195 through 230
      Proline residue:  D 214  - end of helix
    Processing helix  chain 'D' and resid 238 through 268
      removed outlier: 3.712A  pdb=" N   LYS D 242 " --> pdb=" O   THR D 238 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA D 246 " --> pdb=" O   LYS D 242 " (cutoff:3.500A)
      Proline residue:  D 257  - end of helix
      removed outlier: 3.556A  pdb=" N   MET D 264 " --> pdb=" O   VAL D 260 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 272 through 303
      removed outlier: 3.512A  pdb=" N   LEU D 276 " --> pdb=" O   SER D 272 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   SER D 283 " --> pdb=" O   LYS D 279 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   LEU D 284 " --> pdb=" O   LYS D 280 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   ASN D 292 " --> pdb=" O   PHE D 288 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   CYS D 293 " --> pdb=" O   ALA D 289 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   CYS D 294 " --> pdb=" O   TYR D 290 " (cutoff:3.500A)
      Proline residue:  D 297  - end of helix
      removed outlier: 3.959A  pdb=" N   TYR D 300 " --> pdb=" O   ASN D 296 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 306 through 314
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.473A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.894A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.435A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.908A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.605A  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: 6.808A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.757A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.108A  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: 7.128A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.474A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.777A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.626A  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: 3.647A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.676A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU B 308 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 5
      removed outlier: 3.590A  pdb=" N   GLN S   3 " --> pdb=" O   SER S  25 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   SER S  25 " --> pdb=" O   GLN S   3 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60
      removed outlier: 4.868A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 69 through 73
    Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160
    Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195
      removed outlier: 6.703A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   THR S 243 " --> pdb=" O   TYR S 227 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 175 through 180
      removed outlier: 3.765A  pdb=" N   VAL D 176 " --> pdb=" O   GLY D 189 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LYS D 185 " --> pdb=" O   GLU D 180 " (cutoff:3.500A)

    390 hydrogen bonds defined for protein.
    1116 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: 2.21

  Time building geometry restraints manager: 2.67 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2788
        1.35 -     1.46: 2186
        1.46 -     1.58: 3851
        1.58 -     1.70: 0
        1.70 -     1.82: 84
  Bond restraints: 8909
  Sorted by residual:
  bond pdb=" N   HIS D 194 "
       pdb=" CA  HIS D 194 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.08e-02 8.57e+03 6.14e+00
  bond pdb=" N   PHE D 211 "
       pdb=" CA  PHE D 211 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.25e-02 6.40e+03 6.10e+00
  bond pdb=" N   LYS D 279 "
       pdb=" CA  LYS D 279 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.23e-02 6.61e+03 5.78e+00
  bond pdb=" N   SER D 193 "
       pdb=" CA  SER D 193 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.030 1.29e-02 6.01e+03 5.46e+00
  bond pdb=" N   ARG D 178 "
       pdb=" CA  ARG D 178 "
    ideal  model  delta    sigma   weight residual
    1.455  1.483 -0.027 1.23e-02 6.61e+03 4.99e+00
  ... (remaining 8904 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 11711
        1.53 -     3.06: 290
        3.06 -     4.59: 47
        4.59 -     6.12: 14
        6.12 -     7.65: 3
  Bond angle restraints: 12065
  Sorted by residual:
  angle pdb=" CA  PRO D 297 "
        pdb=" N   PRO D 297 "
        pdb=" CD  PRO D 297 "
      ideal   model   delta    sigma   weight residual
     112.00  105.51    6.49 1.40e+00 5.10e-01 2.15e+01
  angle pdb=" CA  VAL D 190 "
        pdb=" C   VAL D 190 "
        pdb=" O   VAL D 190 "
      ideal   model   delta    sigma   weight residual
     121.97  118.23    3.74 9.80e-01 1.04e+00 1.46e+01
  angle pdb=" C   GLY D 210 "
        pdb=" N   PHE D 211 "
        pdb=" CA  PHE D 211 "
      ideal   model   delta    sigma   weight residual
     122.79  116.90    5.89 1.70e+00 3.46e-01 1.20e+01
  angle pdb=" C   ARG D 206 "
        pdb=" CA  ARG D 206 "
        pdb=" CB  ARG D 206 "
      ideal   model   delta    sigma   weight residual
     110.85  105.45    5.40 1.70e+00 3.46e-01 1.01e+01
  angle pdb=" N   ASP D 195 "
        pdb=" CA  ASP D 195 "
        pdb=" C   ASP D 195 "
      ideal   model   delta    sigma   weight residual
     113.20  108.95    4.25 1.36e+00 5.41e-01 9.77e+00
  ... (remaining 12060 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.29: 4895
       22.29 -    44.58: 329
       44.58 -    66.86: 27
       66.86 -    89.15: 7
       89.15 -   111.44: 6
  Dihedral angle restraints: 5264
    sinusoidal: 2053
      harmonic: 3211
  Sorted by residual:
  dihedral pdb=" CA  PRO D 183 "
           pdb=" C   PRO D 183 "
           pdb=" N   PRO D 184 "
           pdb=" CA  PRO D 184 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.96  -26.04     0      5.00e+00 4.00e-02 2.71e+01
  dihedral pdb=" CG  ALC L   5 "
           pdb=" CD2 ALC L   5 "
           pdb=" CE2 ALC L   5 "
           pdb=" CZ  ALC L   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.58  -55.86  111.44     1      3.00e+01 1.11e-03 1.46e+01
  dihedral pdb=" CD1 ALC L   5 "
           pdb=" CE1 ALC L   5 "
           pdb=" CZ  ALC L   5 "
           pdb=" CE2 ALC L   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.37  -55.44  110.81     1      3.00e+01 1.11e-03 1.45e+01
  ... (remaining 5261 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.032: 1369
       1.032 -    2.064: 0
       2.064 -    3.096: 0
       3.096 -    4.128: 0
       4.128 -    5.160: 1
  Chirality restraints: 1370
  Sorted by residual:
  chirality pdb=" CG  ALC L   5 "
            pdb=" CB  ALC L   5 "
            pdb=" CD1 ALC L   5 "
            pdb=" CD2 ALC L   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52    2.64   -5.16 2.00e-01 2.50e+01 6.66e+02
  chirality pdb=" CB  VAL A 201 "
            pdb=" CA  VAL A 201 "
            pdb=" CG1 VAL A 201 "
            pdb=" CG2 VAL A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 8.56e-01
  chirality pdb=" CA  PRO D 297 "
            pdb=" N   PRO D 297 "
            pdb=" C   PRO D 297 "
            pdb=" CB  PRO D 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.17 2.00e-01 2.50e+01 7.56e-01
  ... (remaining 1367 not shown)

  Planarity restraints: 1515
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D 296 "    0.061 5.00e-02 4.00e+02   8.85e-02 1.25e+01
        pdb=" N   PRO D 297 "   -0.153 5.00e-02 4.00e+02
        pdb=" CA  PRO D 297 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO D 297 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  DAR L   6 "   -0.233 9.50e-02 1.11e+02   1.05e-01 6.71e+00
        pdb=" NE  DAR L   6 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  DAR L   6 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 DAR L   6 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 DAR L   6 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  38 "   -0.043 5.00e-02 4.00e+02   6.36e-02 6.47e+00
        pdb=" N   PRO B  39 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO B  39 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B  39 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1512 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 396
        2.73 -     3.27: 8385
        3.27 -     3.81: 13860
        3.81 -     4.36: 15930
        4.36 -     4.90: 28735
  Nonbonded interactions: 67306
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" O   GLY D  51 "
            pdb=" ND2 ASN D  55 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" NE2 HIS S  35 "
            pdb=" OH  TYR S 101 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.287 3.040
  ... (remaining 67301 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:             0.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     21.600
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6728
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.093   8912  Z= 0.186
  Angle     :  0.592   7.651  12069  Z= 0.342
  Chirality :  0.146   5.160   1370
  Planarity :  0.005   0.105   1515
  Dihedral  : 14.435 111.440   3182
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.23 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  0.32 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.35 (0.26), residues: 1084
  helix:  1.89 (0.27), residues: 358
  sheet:  0.49 (0.34), residues: 242
  loop : -1.21 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D 255 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.034   0.001   PHE D  44 
 TYR   0.008   0.001   TYR S 101 
 ARG   0.012   0.001   ARG S  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13023 (  390)
  hydrogen bonds       : angle       5.43349 ( 1116)
  SS BOND              : bond        0.00605 (    2)
  SS BOND              : angle       1.21684 (    4)
  covalent geometry    : bond        0.00293 ( 8909)
  covalent geometry    : angle       0.59133 (12065)
  Misc. bond           : bond        0.09318 (    1)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 127
  time to evaluate  : 1.019 
Fit side-chains
REVERT: A  304 GLN cc_start: 0.6967 (tm-30) cc_final: 0.6673 (tm-30)
REVERT: A  309 ASP cc_start: 0.6235 (m-30) cc_final: 0.5984 (m-30)
REVERT: B  262 MET cc_start: 0.7306 (tpp) cc_final: 0.6989 (mmm)
  outliers start: 8
  outliers final: 3
  residues processed: 133
  average time/residue: 0.1904
  time to fit residues: 36.0485
Evaluate side-chains
  93 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  191 ASP
Chi-restraints excluded: chain D residue  194 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.0070
   chunk 82 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   chunk 55 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 85 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 63 optimal weight:    0.5980
   chunk 98 optimal weight:    2.9990
   overall best weight:    1.9002

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 308 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.186668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.150848 restraints weight = 11286.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3911 rms_B_bonded: 2.24
r_work: 0.3677 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8912  Z= 0.183
  Angle     :  0.631   8.135  12069  Z= 0.332
  Chirality :  0.045   0.243   1370
  Planarity :  0.005   0.055   1515
  Dihedral  :  6.431  89.961   1216
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  7.74 %
    Favored  : 90.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.31 (0.25), residues: 1084
  helix:  1.96 (0.27), residues: 367
  sheet:  0.22 (0.33), residues: 258
  loop : -1.29 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 332 
 HIS   0.010   0.002   HIS B  54 
 PHE   0.018   0.002   PHE A 196 
 TYR   0.021   0.002   TYR B 105 
 ARG   0.005   0.001   ARG S  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05670 (  390)
  hydrogen bonds       : angle       4.75698 ( 1116)
  SS BOND              : bond        0.00595 (    2)
  SS BOND              : angle       1.82553 (    4)
  covalent geometry    : bond        0.00419 ( 8909)
  covalent geometry    : angle       0.63072 (12065)
  Misc. bond           : bond        0.00177 (    1)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.981 
Fit side-chains
REVERT: A  309 ASP cc_start: 0.6722 (m-30) cc_final: 0.6470 (m-30)
REVERT: D  193 SER cc_start: 0.7221 (OUTLIER) cc_final: 0.6994 (p)
  outliers start: 12
  outliers final: 7
  residues processed: 114
  average time/residue: 0.1955
  time to fit residues: 32.2234
Evaluate side-chains
  104 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  191 ASP
Chi-restraints excluded: chain D residue  193 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 70 optimal weight:    0.0070
   chunk 51 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   chunk 59 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.2804

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 ASN
B 268 ASN
** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 194 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.188093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.153068 restraints weight = 11278.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3944 rms_B_bonded: 2.03
r_work: 0.3735 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3611 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8912  Z= 0.136
  Angle     :  0.560   8.407  12069  Z= 0.294
  Chirality :  0.043   0.250   1370
  Planarity :  0.004   0.048   1515
  Dihedral  :  5.888  79.141   1214
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 10.71 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.42 (0.26), residues: 1084
  helix:  2.08 (0.27), residues: 366
  sheet:  0.29 (0.32), residues: 269
  loop : -1.28 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP B 332 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.011   0.001   PHE D  75 
 TYR   0.013   0.001   TYR D 174 
 ARG   0.003   0.000   ARG D  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04906 (  390)
  hydrogen bonds       : angle       4.56345 ( 1116)
  SS BOND              : bond        0.00525 (    2)
  SS BOND              : angle       1.21725 (    4)
  covalent geometry    : bond        0.00302 ( 8909)
  covalent geometry    : angle       0.55996 (12065)
  Misc. bond           : bond        0.00087 (    1)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   47 TRP cc_start: 0.5771 (t60) cc_final: 0.5235 (t60)
REVERT: D  280 LYS cc_start: 0.8306 (mmtp) cc_final: 0.8050 (mmtm)
  outliers start: 16
  outliers final: 10
  residues processed: 113
  average time/residue: 0.1891
  time to fit residues: 30.6474
Evaluate side-chains
  103 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  191 ASP
Chi-restraints excluded: chain D residue  268 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 56 optimal weight:   20.0000
   chunk 89 optimal weight:    0.7980
   chunk 66 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 80 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 18 optimal weight:    7.9990
   chunk 33 optimal weight:    0.4980
   chunk 15 optimal weight:    5.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.186779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.152291 restraints weight = 11316.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 1.97
r_work: 0.3715 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3591 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8912  Z= 0.130
  Angle     :  0.551   7.559  12069  Z= 0.289
  Chirality :  0.042   0.260   1370
  Planarity :  0.004   0.047   1515
  Dihedral  :  5.743  77.385   1214
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 12.62 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.50 (0.26), residues: 1084
  helix:  2.14 (0.27), residues: 366
  sheet:  0.27 (0.32), residues: 277
  loop : -1.21 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP B 332 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.012   0.002   PHE A 196 
 TYR   0.010   0.001   TYR S 175 
 ARG   0.003   0.000   ARG D  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04729 (  390)
  hydrogen bonds       : angle       4.51692 ( 1116)
  SS BOND              : bond        0.00672 (    2)
  SS BOND              : angle       1.60803 (    4)
  covalent geometry    : bond        0.00293 ( 8909)
  covalent geometry    : angle       0.55032 (12065)
  Misc. bond           : bond        0.00063 (    1)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
REVERT: A  276 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7217 (mp0)
REVERT: B  338 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7863 (mt)
REVERT: D   85 SER cc_start: 0.7319 (t) cc_final: 0.7059 (t)
REVERT: D  290 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7157 (m-80)
  outliers start: 19
  outliers final: 10
  residues processed: 113
  average time/residue: 0.2061
  time to fit residues: 32.6500
Evaluate side-chains
  107 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  191 ASP
Chi-restraints excluded: chain D residue  290 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 41 optimal weight:    8.9990
   chunk 61 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 56 optimal weight:   20.0000
   chunk 49 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 59 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   chunk 102 optimal weight:    0.8980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 ASN
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.183576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.148672 restraints weight = 11244.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3899 rms_B_bonded: 2.13
r_work: 0.3655 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3526 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8912  Z= 0.158
  Angle     :  0.585   8.037  12069  Z= 0.307
  Chirality :  0.044   0.284   1370
  Planarity :  0.004   0.048   1515
  Dihedral  :  5.829  77.686   1214
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 14.95 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.36 (0.26), residues: 1084
  helix:  2.07 (0.27), residues: 366
  sheet:  0.14 (0.31), residues: 280
  loop : -1.30 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 332 
 HIS   0.005   0.001   HIS S 167 
 PHE   0.016   0.002   PHE A 196 
 TYR   0.016   0.002   TYR D 174 
 ARG   0.003   0.000   ARG D  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05242 (  390)
  hydrogen bonds       : angle       4.59809 ( 1116)
  SS BOND              : bond        0.00583 (    2)
  SS BOND              : angle       1.58603 (    4)
  covalent geometry    : bond        0.00365 ( 8909)
  covalent geometry    : angle       0.58441 (12065)
  Misc. bond           : bond        0.00071 (    1)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7128 (mp0)
REVERT: A  309 ASP cc_start: 0.6925 (m-30) cc_final: 0.6649 (m-30)
REVERT: B  215 GLU cc_start: 0.7046 (mp0) cc_final: 0.6753 (mp0)
REVERT: B  262 MET cc_start: 0.8371 (tpp) cc_final: 0.8047 (mtt)
REVERT: B  284 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8253 (mp)
REVERT: B  338 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7912 (mp)
REVERT: D   85 SER cc_start: 0.7190 (t) cc_final: 0.6938 (t)
REVERT: D  290 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.7253 (m-80)
  outliers start: 24
  outliers final: 16
  residues processed: 120
  average time/residue: 0.2125
  time to fit residues: 35.1173
Evaluate side-chains
  115 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   91 ILE
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  191 ASP
Chi-restraints excluded: chain D residue  267 PHE
Chi-restraints excluded: chain D residue  290 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 100 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 60 optimal weight:    6.9990
   chunk 64 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   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  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 ASN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.183799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.149450 restraints weight = 11201.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 1.94
r_work: 0.3698 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3573 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8912  Z= 0.126
  Angle     :  0.570  14.262  12069  Z= 0.293
  Chirality :  0.042   0.305   1370
  Planarity :  0.004   0.049   1515
  Dihedral  :  5.681  76.193   1214
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 15.27 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.26), residues: 1084
  helix:  2.12 (0.28), residues: 366
  sheet:  0.21 (0.31), residues: 279
  loop : -1.29 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 332 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.011   0.001   PHE S 177 
 TYR   0.016   0.001   TYR D 174 
 ARG   0.003   0.000   ARG D  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04648 (  390)
  hydrogen bonds       : angle       4.51499 ( 1116)
  SS BOND              : bond        0.00561 (    2)
  SS BOND              : angle       1.32988 (    4)
  covalent geometry    : bond        0.00282 ( 8909)
  covalent geometry    : angle       0.56954 (12065)
  Misc. bond           : bond        0.00047 (    1)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.5876 (mp)
REVERT: A  276 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7153 (mp0)
REVERT: A  309 ASP cc_start: 0.6935 (m-30) cc_final: 0.6689 (m-30)
REVERT: B  105 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7304 (t80)
REVERT: B  234 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7671 (t80)
REVERT: B  262 MET cc_start: 0.8410 (tpp) cc_final: 0.8095 (mtt)
REVERT: B  284 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8218 (mp)
REVERT: B  338 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7893 (mt)
REVERT: D   85 SER cc_start: 0.7194 (t) cc_final: 0.6956 (t)
REVERT: D  104 PHE cc_start: 0.5730 (t80) cc_final: 0.5379 (t80)
REVERT: D  290 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7337 (m-80)
  outliers start: 25
  outliers final: 12
  residues processed: 117
  average time/residue: 0.2191
  time to fit residues: 35.4161
Evaluate side-chains
  114 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  191 ASP
Chi-restraints excluded: chain D residue  267 PHE
Chi-restraints excluded: chain D residue  290 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 58 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0670
   chunk 64 optimal weight:    4.9990
   chunk 90 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   overall best weight:    1.3722

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 ASN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.183224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.148930 restraints weight = 11358.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3913 rms_B_bonded: 2.26
r_work: 0.3671 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3546 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8912  Z= 0.140
  Angle     :  0.596  12.939  12069  Z= 0.306
  Chirality :  0.043   0.333   1370
  Planarity :  0.004   0.049   1515
  Dihedral  :  5.689  76.289   1214
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.12 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.37 (0.26), residues: 1084
  helix:  2.00 (0.28), residues: 367
  sheet:  0.14 (0.31), residues: 285
  loop : -1.24 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 332 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.012   0.002   PHE A 196 
 TYR   0.016   0.002   TYR D 174 
 ARG   0.003   0.000   ARG D  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04821 (  390)
  hydrogen bonds       : angle       4.53694 ( 1116)
  SS BOND              : bond        0.00554 (    2)
  SS BOND              : angle       1.34612 (    4)
  covalent geometry    : bond        0.00323 ( 8909)
  covalent geometry    : angle       0.59557 (12065)
  Misc. bond           : bond        0.00056 (    1)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6005 (mp)
REVERT: A  276 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7183 (mp0)
REVERT: A  309 ASP cc_start: 0.6944 (m-30) cc_final: 0.6669 (m-30)
REVERT: B  105 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.7436 (t80)
REVERT: B  234 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7704 (t80)
REVERT: B  262 MET cc_start: 0.8447 (tpp) cc_final: 0.8143 (mtt)
REVERT: B  338 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7893 (mt)
REVERT: D   85 SER cc_start: 0.7213 (t) cc_final: 0.6978 (t)
REVERT: D  290 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7374 (m-80)
  outliers start: 27
  outliers final: 13
  residues processed: 115
  average time/residue: 0.2029
  time to fit residues: 32.8941
Evaluate side-chains
  114 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  267 PHE
Chi-restraints excluded: chain D residue  290 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 23 optimal weight:    7.9990
   chunk 63 optimal weight:    4.9990
   chunk 78 optimal weight:    0.0370
   chunk 93 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 46 optimal weight:   10.0000
   chunk 79 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.9464

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 ASN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.180077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.142270 restraints weight = 11307.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3814 rms_B_bonded: 2.40
r_work: 0.3578 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3443 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8912  Z= 0.170
  Angle     :  0.629  11.605  12069  Z= 0.324
  Chirality :  0.044   0.349   1370
  Planarity :  0.004   0.049   1515
  Dihedral  :  5.721  77.211   1212
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.33 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.21 (0.26), residues: 1084
  helix:  1.78 (0.28), residues: 370
  sheet:  0.09 (0.32), residues: 279
  loop : -1.28 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 332 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.014   0.002   PHE A 196 
 TYR   0.018   0.002   TYR D 174 
 ARG   0.003   0.000   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05350 (  390)
  hydrogen bonds       : angle       4.64138 ( 1116)
  SS BOND              : bond        0.00598 (    2)
  SS BOND              : angle       1.67877 (    4)
  covalent geometry    : bond        0.00403 ( 8909)
  covalent geometry    : angle       0.62793 (12065)
  Misc. bond           : bond        0.00070 (    1)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.5991 (mp)
REVERT: A  276 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7057 (mp0)
REVERT: A  309 ASP cc_start: 0.6804 (m-30) cc_final: 0.6476 (m-30)
REVERT: B  105 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7578 (t80)
REVERT: B  234 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7700 (t80)
REVERT: B  284 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8307 (mp)
REVERT: B  338 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7955 (mp)
REVERT: S   64 VAL cc_start: 0.6016 (m) cc_final: 0.5717 (p)
REVERT: D   85 SER cc_start: 0.7240 (t) cc_final: 0.6981 (t)
REVERT: D  290 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7349 (m-80)
  outliers start: 26
  outliers final: 15
  residues processed: 117
  average time/residue: 0.1985
  time to fit residues: 32.4993
Evaluate side-chains
  116 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  267 PHE
Chi-restraints excluded: chain D residue  290 TYR
Chi-restraints excluded: chain D residue  295 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 88 optimal weight:    0.4980
   chunk 78 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 96 optimal weight:    0.0670
   chunk 42 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
A 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.187023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.152192 restraints weight = 11253.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3935 rms_B_bonded: 2.05
r_work: 0.3710 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3582 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.3608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8912  Z= 0.110
  Angle     :  0.569  11.191  12069  Z= 0.291
  Chirality :  0.042   0.341   1370
  Planarity :  0.003   0.049   1515
  Dihedral  :  5.444  74.874   1212
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.18 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.26), residues: 1084
  helix:  1.94 (0.28), residues: 375
  sheet:  0.25 (0.32), residues: 272
  loop : -1.22 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 332 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.012   0.001   PHE S 177 
 TYR   0.017   0.001   TYR D 174 
 ARG   0.004   0.000   ARG D  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04087 (  390)
  hydrogen bonds       : angle       4.44007 ( 1116)
  SS BOND              : bond        0.00538 (    2)
  SS BOND              : angle       1.06269 (    4)
  covalent geometry    : bond        0.00244 ( 8909)
  covalent geometry    : angle       0.56835 (12065)
  Misc. bond           : bond        0.00030 (    1)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.5828 (mp)
REVERT: A  276 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7212 (mp0)
REVERT: A  309 ASP cc_start: 0.6911 (m-30) cc_final: 0.6621 (m-30)
REVERT: B  105 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.7130 (t80)
REVERT: B  234 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7800 (t80)
REVERT: B  338 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7936 (mt)
REVERT: D   85 SER cc_start: 0.7178 (t) cc_final: 0.6942 (t)
REVERT: D  104 PHE cc_start: 0.5680 (t80) cc_final: 0.5402 (t80)
REVERT: D  290 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7375 (m-80)
  outliers start: 19
  outliers final: 11
  residues processed: 110
  average time/residue: 0.1949
  time to fit residues: 30.2347
Evaluate side-chains
  109 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  267 PHE
Chi-restraints excluded: chain D residue  290 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0270
   chunk 63 optimal weight:    6.9990
   chunk 79 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0470
   chunk 21 optimal weight:    0.9990
   chunk 71 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 17 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.7940

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** 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 = 0.4318 r_free = 0.4318 target = 0.186804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.152504 restraints weight = 11171.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 2.16
r_work: 0.3691 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8912  Z= 0.118
  Angle     :  0.576  10.807  12069  Z= 0.295
  Chirality :  0.042   0.348   1370
  Planarity :  0.003   0.048   1515
  Dihedral  :  5.398  74.835   1212
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.60 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.26), residues: 1084
  helix:  1.97 (0.28), residues: 375
  sheet:  0.31 (0.32), residues: 275
  loop : -1.19 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 332 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.012   0.001   PHE S 177 
 TYR   0.017   0.001   TYR D 174 
 ARG   0.003   0.000   ARG S 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04206 (  390)
  hydrogen bonds       : angle       4.40762 ( 1116)
  SS BOND              : bond        0.00513 (    2)
  SS BOND              : angle       1.19801 (    4)
  covalent geometry    : bond        0.00269 ( 8909)
  covalent geometry    : angle       0.57612 (12065)
  Misc. bond           : bond        0.00043 (    1)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8097 (ttp-170) cc_final: 0.7788 (ttm170)
REVERT: A   23 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.5879 (mp)
REVERT: A  276 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7172 (mp0)
REVERT: A  309 ASP cc_start: 0.6795 (m-30) cc_final: 0.6513 (m-30)
REVERT: B  105 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7147 (t80)
REVERT: B  234 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7694 (t80)
REVERT: B  338 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7813 (mt)
REVERT: S  195 LEU cc_start: 0.8674 (tp) cc_final: 0.8473 (tp)
REVERT: D   85 SER cc_start: 0.7214 (t) cc_final: 0.6994 (t)
REVERT: D  104 PHE cc_start: 0.5543 (t80) cc_final: 0.5279 (t80)
REVERT: D  290 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7275 (m-80)
  outliers start: 17
  outliers final: 10
  residues processed: 103
  average time/residue: 0.2136
  time to fit residues: 30.7276
Evaluate side-chains
  106 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  290 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0020
   chunk 10 optimal weight:    0.0030
   chunk 45 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0270
   chunk 57 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   chunk 108 optimal weight:   10.0000
   chunk 20 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** 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 = 0.4349 r_free = 0.4349 target = 0.190004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.155835 restraints weight = 11214.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 1.96
r_work: 0.3760 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3628 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8912  Z= 0.102
  Angle     :  0.548  10.508  12069  Z= 0.279
  Chirality :  0.041   0.330   1370
  Planarity :  0.003   0.049   1515
  Dihedral  :  5.273  76.791   1212
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 18.24 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.59 (0.26), residues: 1084
  helix:  2.09 (0.28), residues: 375
  sheet:  0.41 (0.32), residues: 270
  loop : -1.15 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 332 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.013   0.001   PHE S 177 
 TYR   0.017   0.001   TYR D 174 
 ARG   0.003   0.000   ARG S 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03627 (  390)
  hydrogen bonds       : angle       4.27204 ( 1116)
  SS BOND              : bond        0.00493 (    2)
  SS BOND              : angle       1.04042 (    4)
  covalent geometry    : bond        0.00224 ( 8909)
  covalent geometry    : angle       0.54781 (12065)
  Misc. bond           : bond        0.00029 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4898.82 seconds
wall clock time: 85 minutes 26.46 seconds (5126.46 seconds total)