Starting phenix.real_space_refine
on Wed Mar  4 03:44:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y65_33634/03_2026/7y65_33634_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y65_33634/03_2026/7y65_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y65_33634/03_2026/7y65_33634_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y65_33634/03_2026/7y65_33634_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y65_33634/03_2026/7y65_33634.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y65_33634/03_2026/7y65_33634.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'MEA:plan-2': 1, 'ZAL:plan-1': 1, 'ALC:plan-1': 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: 2.03, per 1000 atoms: 0.23
  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: 0.72
  Conformation dependent library (CDL) restraints added in 329.1 milliseconds
  

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  ZAL L   4 "
      Input residue name is d-peptide
        pdb=" CB  DAR L   6 "
  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: 0.30
  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: 1.38

  Time building geometry restraints manager: 0.96 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:             1.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.920
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.070
-------------------------------------------------------------------------------
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 : 8.56
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.012   0.001   ARG S  98 
 TYR   0.008   0.001   TYR S 101 
 PHE   0.034   0.001   PHE D  44 
 TRP   0.020   0.001   TRP D 255 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8909)
  covalent geometry    : angle       0.59133 (12065)
  SS BOND              : bond        0.00605 (    2)
  SS BOND              : angle       1.21684 (    4)
  hydrogen bonds       : bond        0.13023 (  390)
  hydrogen bonds       : angle       5.43349 ( 1116)
  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  : 0.231 
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: 0.6990 (mmm)
  outliers start: 8
  outliers final: 3
  residues processed: 133
  average time/residue: 0.0788
  time to fit residues: 15.0689
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  : 0.192 
-------------------------------------------------------------------------------
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 108 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    8.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 292 ASN
D 308 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.183673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.146429 restraints weight = 11207.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 2.14
r_work: 0.3671 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3539 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8912  Z= 0.191
  Angle     :  0.647   8.282  12069  Z= 0.341
  Chirality :  0.045   0.245   1370
  Planarity :  0.005   0.053   1515
  Dihedral  :  6.437  86.001   1216
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  8.06 %
    Favored  : 90.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.25), residues: 1084
  helix:  1.93 (0.27), residues: 367
  sheet:  0.24 (0.32), residues: 261
  loop : -1.36 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG S  98 
 TYR   0.023   0.002   TYR B 105 
 PHE   0.019   0.002   PHE A 196 
 TRP   0.018   0.002   TRP B 332 
 HIS   0.011   0.002   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 8909)
  covalent geometry    : angle       0.64622 (12065)
  SS BOND              : bond        0.00391 (    2)
  SS BOND              : angle       1.81964 (    4)
  hydrogen bonds       : bond        0.05779 (  390)
  hydrogen bonds       : angle       4.78431 ( 1116)
  Misc. bond           : bond        0.00145 (    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
  116 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A  304 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7370 (tt0)
REVERT: A  309 ASP cc_start: 0.6838 (m-30) cc_final: 0.6577 (m-30)
REVERT: D  192 TYR cc_start: 0.6520 (m-80) cc_final: 0.6267 (m-80)
REVERT: D  199 GLU cc_start: 0.6169 (tt0) cc_final: 0.5885 (tt0)
  outliers start: 12
  outliers final: 7
  residues processed: 115
  average time/residue: 0.0788
  time to fit residues: 13.1287
Evaluate side-chains
  101 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 57 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   chunk 103 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.4336 r_free = 0.4336 target = 0.188612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.155060 restraints weight = 11170.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 2.09
r_work: 0.3732 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3603 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.2375

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= 0.126
  Angle     :  0.551   8.431  12069  Z= 0.289
  Chirality :  0.042   0.250   1370
  Planarity :  0.004   0.047   1515
  Dihedral  :  5.830  77.239   1214
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 11.35 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.26), residues: 1084
  helix:  2.13 (0.27), residues: 366
  sheet:  0.28 (0.32), residues: 269
  loop : -1.31 (0.27), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  34 
 TYR   0.017   0.001   TYR D 174 
 PHE   0.011   0.001   PHE D  75 
 TRP   0.042   0.002   TRP B 332 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8909)
  covalent geometry    : angle       0.55041 (12065)
  SS BOND              : bond        0.00493 (    2)
  SS BOND              : angle       1.10104 (    4)
  hydrogen bonds       : bond        0.04690 (  390)
  hydrogen bonds       : angle       4.51922 ( 1116)
  Misc. bond           : bond        0.00070 (    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
  114 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  276 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7251 (mp0)
REVERT: A  309 ASP cc_start: 0.6929 (m-30) cc_final: 0.6643 (m-30)
REVERT: B  338 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7841 (mt)
REVERT: S   47 TRP cc_start: 0.5756 (t60) cc_final: 0.5538 (t60)
REVERT: D  192 TYR cc_start: 0.6377 (m-80) cc_final: 0.6133 (m-80)
REVERT: D  199 GLU cc_start: 0.6247 (tt0) cc_final: 0.6041 (tt0)
REVERT: D  280 LYS cc_start: 0.8288 (mmtp) cc_final: 0.8044 (mmtm)
  outliers start: 15
  outliers final: 8
  residues processed: 110
  average time/residue: 0.0856
  time to fit residues: 13.4201
Evaluate side-chains
  105 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue  228 ASP
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  268 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 56 optimal weight:   20.0000
   chunk 6 optimal weight:    0.5980
   chunk 42 optimal weight:    8.9990
   chunk 93 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 85 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 16 optimal weight:    7.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 255 ASN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.187943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.153836 restraints weight = 11312.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 2.03
r_work: 0.3722 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3594 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8912  Z= 0.122
  Angle     :  0.544   7.562  12069  Z= 0.284
  Chirality :  0.042   0.268   1370
  Planarity :  0.004   0.047   1515
  Dihedral  :  5.642  76.645   1214
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.04 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.26), residues: 1084
  helix:  2.19 (0.27), residues: 366
  sheet:  0.32 (0.32), residues: 277
  loop : -1.25 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  34 
 TYR   0.010   0.001   TYR B  59 
 PHE   0.012   0.001   PHE S 177 
 TRP   0.027   0.001   TRP B 332 
 HIS   0.004   0.001   HIS S 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8909)
  covalent geometry    : angle       0.54368 (12065)
  SS BOND              : bond        0.00630 (    2)
  SS BOND              : angle       1.38472 (    4)
  hydrogen bonds       : bond        0.04530 (  390)
  hydrogen bonds       : angle       4.47157 ( 1116)
  Misc. bond           : bond        0.00069 (    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
  119 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A  276 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7211 (mp0)
REVERT: B  338 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7795 (mt)
REVERT: D  290 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7094 (m-80)
  outliers start: 20
  outliers final: 13
  residues processed: 112
  average time/residue: 0.0899
  time to fit residues: 14.1806
Evaluate side-chains
  107 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  262 MET
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  186 VAL
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 93 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 106 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 46 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 25 optimal weight:   20.0000
   chunk 18 optimal weight:    0.0670
   chunk 16 optimal weight:    7.9990
   chunk 100 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   overall best weight:    1.8124

-------------------------------------------------------------------------------
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
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.184428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.149826 restraints weight = 11304.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 2.03
r_work: 0.3676 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3546 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8912  Z= 0.161
  Angle     :  0.589   7.514  12069  Z= 0.308
  Chirality :  0.043   0.293   1370
  Planarity :  0.004   0.048   1515
  Dihedral  :  5.747  77.336   1214
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 14.85 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.26), residues: 1084
  helix:  2.14 (0.27), residues: 366
  sheet:  0.20 (0.32), residues: 277
  loop : -1.29 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.014   0.002   TYR D 174 
 PHE   0.015   0.002   PHE A 196 
 TRP   0.028   0.001   TRP B 332 
 HIS   0.004   0.001   HIS S 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 8909)
  covalent geometry    : angle       0.58866 (12065)
  SS BOND              : bond        0.00605 (    2)
  SS BOND              : angle       1.54527 (    4)
  hydrogen bonds       : bond        0.05176 (  390)
  hydrogen bonds       : angle       4.56295 ( 1116)
  Misc. bond           : bond        0.00078 (    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
  124 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8276 (ttp-170) cc_final: 0.7967 (ttm170)
REVERT: A  276 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7142 (mp0)
REVERT: A  309 ASP cc_start: 0.6970 (m-30) cc_final: 0.6718 (m-30)
REVERT: B  105 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.7455 (t80)
REVERT: B  215 GLU cc_start: 0.7149 (mp0) cc_final: 0.6942 (mp0)
REVERT: B  284 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8287 (mp)
REVERT: B  338 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7869 (mt)
REVERT: D   85 SER cc_start: 0.7171 (t) cc_final: 0.6921 (t)
REVERT: D  290 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.7154 (m-80)
  outliers start: 24
  outliers final: 15
  residues processed: 117
  average time/residue: 0.0871
  time to fit residues: 14.3597
Evaluate side-chains
  114 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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  105 TYR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  262 MET
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 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   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  290 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 39 optimal weight:    0.1980
   chunk 55 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   chunk 96 optimal weight:    1.9990
   chunk 92 optimal weight:    7.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A  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 = 0.4308 r_free = 0.4308 target = 0.185719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.151459 restraints weight = 11294.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3927 rms_B_bonded: 1.99
r_work: 0.3690 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3563 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8912  Z= 0.131
  Angle     :  0.577  14.535  12069  Z= 0.296
  Chirality :  0.043   0.310   1370
  Planarity :  0.004   0.048   1515
  Dihedral  :  5.673  76.459   1214
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.26), residues: 1084
  helix:  2.14 (0.27), residues: 366
  sheet:  0.22 (0.31), residues: 278
  loop : -1.23 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  34 
 TYR   0.010   0.001   TYR B  59 
 PHE   0.011   0.001   PHE S 177 
 TRP   0.024   0.001   TRP S  47 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8909)
  covalent geometry    : angle       0.57623 (12065)
  SS BOND              : bond        0.00626 (    2)
  SS BOND              : angle       1.35121 (    4)
  hydrogen bonds       : bond        0.04735 (  390)
  hydrogen bonds       : angle       4.49309 ( 1116)
  Misc. bond           : bond        0.00068 (    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
  122 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6042 (mp)
REVERT: A  276 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7156 (mp0)
REVERT: B  215 GLU cc_start: 0.7161 (mp0) cc_final: 0.6902 (mp0)
REVERT: B  234 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.7644 (t80)
REVERT: B  262 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8057 (mtt)
REVERT: B  284 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8280 (mp)
REVERT: B  338 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7860 (mt)
REVERT: D   85 SER cc_start: 0.7175 (t) cc_final: 0.6920 (t)
REVERT: D  104 PHE cc_start: 0.5627 (OUTLIER) cc_final: 0.5166 (t80)
REVERT: D  290 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7245 (m-80)
  outliers start: 25
  outliers final: 13
  residues processed: 115
  average time/residue: 0.0891
  time to fit residues: 14.4830
Evaluate side-chains
  115 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  262 MET
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 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  104 PHE
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  191 ASP
Chi-restraints excluded: chain D residue  193 SER
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 50 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 56 optimal weight:   20.0000
   chunk 108 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 99 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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 = 0.180032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.141991 restraints weight = 11257.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 2.38
r_work: 0.3589 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3457 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.3488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   8912  Z= 0.184
  Angle     :  0.643  12.774  12069  Z= 0.330
  Chirality :  0.045   0.341   1370
  Planarity :  0.004   0.049   1515
  Dihedral  :  5.859  77.975   1214
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 15.69 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.26), residues: 1084
  helix:  1.93 (0.28), residues: 369
  sheet:  0.13 (0.32), residues: 274
  loop : -1.26 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.015   0.002   TYR B  59 
 PHE   0.016   0.002   PHE A 196 
 TRP   0.028   0.002   TRP B 332 
 HIS   0.005   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 8909)
  covalent geometry    : angle       0.64207 (12065)
  SS BOND              : bond        0.00624 (    2)
  SS BOND              : angle       1.66747 (    4)
  hydrogen bonds       : bond        0.05576 (  390)
  hydrogen bonds       : angle       4.64169 ( 1116)
  Misc. bond           : bond        0.00089 (    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
  132 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 100
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8204 (ttp-170) cc_final: 0.7925 (ttm170)
REVERT: A   23 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6018 (mp)
REVERT: A  276 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7022 (mp0)
REVERT: B  105 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7672 (t80)
REVERT: B  234 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7602 (t80)
REVERT: B  262 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8238 (mtt)
REVERT: B  284 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8299 (mp)
REVERT: B  338 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7936 (mp)
REVERT: S   64 VAL cc_start: 0.5839 (m) cc_final: 0.5504 (p)
REVERT: S  109 ASP cc_start: 0.6539 (OUTLIER) cc_final: 0.6189 (m-30)
REVERT: D   85 SER cc_start: 0.7234 (t) cc_final: 0.6968 (t)
REVERT: D  104 PHE cc_start: 0.5753 (OUTLIER) cc_final: 0.5217 (t80)
REVERT: D  290 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7385 (m-80)
  outliers start: 32
  outliers final: 16
  residues processed: 122
  average time/residue: 0.0992
  time to fit residues: 16.7734
Evaluate side-chains
  120 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
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   47 THR
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  262 MET
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 C residue   30 VAL
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue  104 PHE
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  193 SER
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 46 optimal weight:   10.0000
   chunk 59 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   chunk 74 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 = 0.4252 r_free = 0.4252 target = 0.182520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.145219 restraints weight = 11205.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3843 rms_B_bonded: 2.28
r_work: 0.3622 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3490 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8912  Z= 0.127
  Angle     :  0.580  11.625  12069  Z= 0.297
  Chirality :  0.043   0.338   1370
  Planarity :  0.004   0.049   1515
  Dihedral  :  5.539  75.838   1212
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.54 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.26), residues: 1084
  helix:  2.08 (0.28), residues: 367
  sheet:  0.18 (0.32), residues: 278
  loop : -1.25 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  34 
 TYR   0.010   0.001   TYR B  59 
 PHE   0.012   0.001   PHE S 177 
 TRP   0.025   0.001   TRP B 332 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8909)
  covalent geometry    : angle       0.57954 (12065)
  SS BOND              : bond        0.00630 (    2)
  SS BOND              : angle       1.27274 (    4)
  hydrogen bonds       : bond        0.04609 (  390)
  hydrogen bonds       : angle       4.50392 ( 1116)
  Misc. bond           : bond        0.00050 (    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
  123 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.5926 (mp)
REVERT: A  228 SER cc_start: 0.6651 (t) cc_final: 0.6401 (t)
REVERT: A  276 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7051 (mp0)
REVERT: B  105 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.7381 (t80)
REVERT: B  234 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7683 (t80)
REVERT: B  262 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8224 (mtt)
REVERT: B  338 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7914 (mt)
REVERT: S   64 VAL cc_start: 0.5859 (m) cc_final: 0.5541 (p)
REVERT: S  109 ASP cc_start: 0.6452 (OUTLIER) cc_final: 0.6221 (m-30)
REVERT: D   85 SER cc_start: 0.7151 (t) cc_final: 0.6885 (t)
REVERT: D  104 PHE cc_start: 0.5720 (OUTLIER) cc_final: 0.5203 (t80)
REVERT: D  290 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7329 (m-80)
  outliers start: 24
  outliers final: 11
  residues processed: 114
  average time/residue: 0.0922
  time to fit residues: 14.8190
Evaluate side-chains
  117 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
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  259 GLN
Chi-restraints excluded: chain B residue  262 MET
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 S residue  109 ASP
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue  104 PHE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 67 optimal weight:    0.1980
   chunk 30 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   chunk 78 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.181538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.143804 restraints weight = 11207.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 2.29
r_work: 0.3598 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3466 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.3637

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= 0.152
  Angle     :  0.605  10.935  12069  Z= 0.312
  Chirality :  0.044   0.334   1370
  Planarity :  0.004   0.049   1515
  Dihedral  :  5.577  76.653   1212
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.86 %
    Favored  : 80.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.26), residues: 1084
  helix:  1.96 (0.27), residues: 374
  sheet:  0.15 (0.32), residues: 273
  loop : -1.25 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  34 
 TYR   0.013   0.002   TYR B  59 
 PHE   0.013   0.002   PHE A 196 
 TRP   0.025   0.001   TRP B 332 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 8909)
  covalent geometry    : angle       0.60423 (12065)
  SS BOND              : bond        0.00533 (    2)
  SS BOND              : angle       1.35636 (    4)
  hydrogen bonds       : bond        0.04998 (  390)
  hydrogen bonds       : angle       4.55319 ( 1116)
  Misc. bond           : bond        0.00067 (    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
  122 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8198 (ttp-170) cc_final: 0.7911 (ttm170)
REVERT: A   23 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.5984 (mp)
REVERT: A  228 SER cc_start: 0.6665 (t) cc_final: 0.6402 (t)
REVERT: A  276 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7051 (mp0)
REVERT: B  105 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7427 (t80)
REVERT: B  234 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7709 (t80)
REVERT: B  262 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8282 (mtt)
REVERT: B  284 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8282 (mp)
REVERT: B  338 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7894 (mt)
REVERT: S   64 VAL cc_start: 0.5913 (m) cc_final: 0.5577 (p)
REVERT: S  109 ASP cc_start: 0.6481 (OUTLIER) cc_final: 0.6195 (m-30)
REVERT: D   85 SER cc_start: 0.7233 (t) cc_final: 0.6967 (t)
REVERT: D  104 PHE cc_start: 0.5742 (OUTLIER) cc_final: 0.5204 (t80)
REVERT: D  290 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7351 (m-80)
  outliers start: 23
  outliers final: 12
  residues processed: 115
  average time/residue: 0.0903
  time to fit residues: 14.5966
Evaluate side-chains
  119 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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  259 GLN
Chi-restraints excluded: chain B residue  262 MET
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 S residue  109 ASP
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue  104 PHE
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  193 SER
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 28 optimal weight:    7.9990
   chunk 57 optimal weight:    7.9990
   chunk 95 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9980
   chunk 99 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
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**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.182044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.144000 restraints weight = 11167.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 2.33
r_work: 0.3595 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3462 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.3760

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= 0.153
  Angle     :  0.615  10.559  12069  Z= 0.318
  Chirality :  0.044   0.332   1370
  Planarity :  0.004   0.049   1515
  Dihedral  :  5.581  76.471   1212
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.18 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.26), residues: 1084
  helix:  1.87 (0.27), residues: 377
  sheet:  0.17 (0.32), residues: 278
  loop : -1.23 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  34 
 TYR   0.013   0.002   TYR B  59 
 PHE   0.013   0.002   PHE A 196 
 TRP   0.028   0.001   TRP B 332 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 8909)
  covalent geometry    : angle       0.61447 (12065)
  SS BOND              : bond        0.00562 (    2)
  SS BOND              : angle       1.42247 (    4)
  hydrogen bonds       : bond        0.05025 (  390)
  hydrogen bonds       : angle       4.57447 ( 1116)
  Misc. bond           : bond        0.00070 (    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
  123 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8216 (ttp-170) cc_final: 0.7931 (ttm170)
REVERT: A   23 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.5979 (mp)
REVERT: A  228 SER cc_start: 0.6671 (t) cc_final: 0.6423 (t)
REVERT: A  276 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7091 (mp0)
REVERT: B  105 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7526 (t80)
REVERT: B  234 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.7704 (t80)
REVERT: B  262 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8233 (mtt)
REVERT: B  332 TRP cc_start: 0.7407 (m100) cc_final: 0.6936 (m-10)
REVERT: B  338 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7921 (mp)
REVERT: S   64 VAL cc_start: 0.6040 (m) cc_final: 0.5693 (p)
REVERT: S  109 ASP cc_start: 0.6524 (OUTLIER) cc_final: 0.6219 (m-30)
REVERT: D   85 SER cc_start: 0.7243 (t) cc_final: 0.6988 (t)
REVERT: D  104 PHE cc_start: 0.5768 (OUTLIER) cc_final: 0.5206 (t80)
REVERT: D  185 LYS cc_start: 0.7506 (tptp) cc_final: 0.6155 (tppt)
REVERT: D  290 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7403 (m-80)
  outliers start: 25
  outliers final: 15
  residues processed: 115
  average time/residue: 0.0861
  time to fit residues: 13.9783
Evaluate side-chains
  122 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
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 A residue  332 VAL
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  259 GLN
Chi-restraints excluded: chain B residue  262 MET
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 S residue  109 ASP
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue  104 PHE
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  193 SER
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 81 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0570
   chunk 105 optimal weight:    2.9990
   chunk 92 optimal weight:    0.3980
   chunk 93 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 48 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    1.0900

-------------------------------------------------------------------------------
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**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.181834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.144131 restraints weight = 11133.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3839 rms_B_bonded: 2.41
r_work: 0.3612 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3479 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8912  Z= 0.127
  Angle     :  0.584  10.347  12069  Z= 0.300
  Chirality :  0.043   0.316   1370
  Planarity :  0.004   0.049   1515
  Dihedral  :  5.483  75.746   1212
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.50 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.26), residues: 1084
  helix:  2.04 (0.28), residues: 374
  sheet:  0.23 (0.32), residues: 272
  loop : -1.26 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG S 160 
 TYR   0.010   0.001   TYR B  59 
 PHE   0.012   0.001   PHE S 177 
 TRP   0.026   0.001   TRP B 332 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8909)
  covalent geometry    : angle       0.58366 (12065)
  SS BOND              : bond        0.00535 (    2)
  SS BOND              : angle       1.22900 (    4)
  hydrogen bonds       : bond        0.04517 (  390)
  hydrogen bonds       : angle       4.48500 ( 1116)
  Misc. bond           : bond        0.00054 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2463.97 seconds
wall clock time: 42 minutes 46.55 seconds (2566.55 seconds total)