Starting phenix.real_space_refine
on Mon May 12 00:10:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ihi_35445/05_2025/8ihi_35445.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ihi_35445/05_2025/8ihi_35445.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ihi_35445/05_2025/8ihi_35445.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ihi_35445/05_2025/8ihi_35445.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ihi_35445/05_2025/8ihi_35445.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ihi_35445/05_2025/8ihi_35445.cif"
  }
  resolution = 3.11
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.077
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    5545      2.51       5
     N    1472      2.21       5
     O    1591      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8665
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1695
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 216}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 30
    Chain: "S"
      Number of atoms: 1706
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1706
          Classifications: {'peptide': 226}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 10, 'TRANS': 215}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      Number of atoms: 2477
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2477
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 129
          Unresolved non-hydrogen angles: 156
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 91
    Chain: "C"
      Number of atoms: 376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 376
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "R"
      Number of atoms: 2381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2381
          Classifications: {'peptide': 292}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 281}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "R"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 30
          Unusual residues: {'NAG': 1, 'P9X': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.33, per 1000 atoms: 0.62
  Number of scatterers: 8665
  At special positions: 0
  Unit cell: (89.1, 117.81, 135.63, 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      57     16.00
     O    1591      8.00
     N    1472      7.00
     C    5545      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.86
    Simple disulfide: pdb=" SG  CYS R  18 " - pdb=" SG  CYS R 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  19 " - pdb=" SG  CYS R 266 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 100 " - pdb=" SG  CYS R 177 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG R 601 " - " ASN R  17 "
  Time building additional restraints: 2.14
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2118

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 15 sheets defined
      36.4% alpha, 20.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.517A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.718A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.550A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   CYS A 214 " --> pdb=" O   TRP A 211 " (cutoff:3.500A)
    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
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 4.293A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.726A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.523A  pdb=" N   LYS A 349 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASP A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 62 through 65
      removed outlier: 3.973A  pdb=" N   LYS S  65 " --> pdb=" O   ASP S  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 62 through 65'
    Processing helix  chain 'B' and resid 3 through 25
      removed outlier: 3.534A  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 9 through 24
      removed outlier: 3.545A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU C  22 " --> pdb=" O   GLN C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.581A  pdb=" N   ASP C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'R' and resid 24 through 55
      removed outlier: 3.842A  pdb=" N   LYS R  28 " --> pdb=" O   ASP R  24 " (cutoff:3.500A)
      Proline residue:  R  31  - end of helix
      removed outlier: 3.520A  pdb=" N   LEU R  36 " --> pdb=" O   PRO R  32 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLU R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   PHE R  38 " --> pdb=" O   LEU R  34 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   LEU R  43 " --> pdb=" O   ILE R  39 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 78
      removed outlier: 3.548A  pdb=" N   ILE R  78 " --> pdb=" O   PHE R  74 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 79 through 89
      removed outlier: 3.529A  pdb=" N   ASN R  86 " --> pdb=" O   PHE R  82 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 97 through 128
      removed outlier: 3.863A  pdb=" N   LEU R 107 " --> pdb=" O   MET R 103 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ARG R 111 " --> pdb=" O   LEU R 107 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   VAL R 121 " --> pdb=" O   PHE R 117 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 134 through 139
      removed outlier: 3.798A  pdb=" N   ILE R 139 " --> pdb=" O   LEU R 136 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 158
    Processing helix  chain 'R' and resid 159 through 163
    Processing helix  chain 'R' and resid 187 through 218
      removed outlier: 4.064A  pdb=" N   PHE R 197 " --> pdb=" O   PHE R 193 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU R 199 " --> pdb=" O   LEU R 195 " (cutoff:3.500A)
      Proline residue:  R 200  - end of helix
    Processing helix  chain 'R' and resid 223 through 261
      removed outlier: 3.536A  pdb=" N   PHE R 232 " --> pdb=" O   ARG R 228 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   MET R 234 " --> pdb=" O   ILE R 230 " (cutoff:3.500A)
      Proline residue:  R 246  - end of helix
    Processing helix  chain 'R' and resid 269 through 281
      removed outlier: 3.615A  pdb=" N   LEU R 274 " --> pdb=" O   ARG R 270 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 282 through 295
      removed outlier: 3.827A  pdb=" N   ASN R 286 " --> pdb=" O   PHE R 282 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   SER R 287 " --> pdb=" O   THR R 283 " (cutoff:3.500A)
      Proline residue:  R 291  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.683A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.582A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'S' and resid 6 through 7
      removed outlier: 3.715A  pdb=" N   SER S   7 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'S' and resid 58 through 60
      removed outlier: 3.538A  pdb=" N   VAL S  97 " --> pdb=" O   HIS S  35 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'S' and resid 45 through 46
      removed outlier: 3.582A  pdb=" N   ALA S  92 " --> pdb=" O   LEU S 117 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'S' and resid 155 through 160
    Processing sheet with id=AA6, first strand: chain 'S' and resid 194 through 195
      removed outlier: 5.383A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   TYR S 227 " --> pdb=" O   THR S 243 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.720A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.738A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.616A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.079A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.781A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.815A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.132A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.465A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.559A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 10 through 12
      removed outlier: 3.962A  pdb=" N   ILE R 182 " --> pdb=" O   CYS R  19 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'R' and resid 169 through 171
      removed outlier: 3.584A  pdb=" N   ILE R 169 " --> pdb=" O   LEU R 176 " (cutoff:3.500A)

    404 hydrogen bonds defined for protein.
    1131 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.75

  Time building geometry restraints manager: 2.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2784
        1.34 -     1.46: 2206
        1.46 -     1.58: 3792
        1.58 -     1.70: 0
        1.70 -     1.82: 79
  Bond restraints: 8861
  Sorted by residual:
  bond pdb=" C5  P9X R 602 "
       pdb=" O2  P9X R 602 "
    ideal  model  delta    sigma   weight residual
    1.250  1.306 -0.056 2.00e-02 2.50e+03 7.81e+00
  bond pdb=" C4  P9X R 602 "
       pdb=" C5  P9X R 602 "
    ideal  model  delta    sigma   weight residual
    1.530  1.476  0.054 2.00e-02 2.50e+03 7.34e+00
  bond pdb=" CA  LYS R 165 "
       pdb=" C   LYS R 165 "
    ideal  model  delta    sigma   weight residual
    1.523  1.494  0.029 1.24e-02 6.50e+03 5.43e+00
  bond pdb=" N   LYS R 165 "
       pdb=" CA  LYS R 165 "
    ideal  model  delta    sigma   weight residual
    1.455  1.432  0.024 1.22e-02 6.72e+03 3.83e+00
  bond pdb=" CB  PRO S 151 "
       pdb=" CG  PRO S 151 "
    ideal  model  delta    sigma   weight residual
    1.492  1.569 -0.077 5.00e-02 4.00e+02 2.40e+00
  ... (remaining 8856 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 11912
        2.16 -     4.33: 106
        4.33 -     6.49: 15
        6.49 -     8.65: 3
        8.65 -    10.81: 2
  Bond angle restraints: 12038
  Sorted by residual:
  angle pdb=" CB  MET R 167 "
        pdb=" CG  MET R 167 "
        pdb=" SD  MET R 167 "
      ideal   model   delta    sigma   weight residual
     112.70  123.51  -10.81 3.00e+00 1.11e-01 1.30e+01
  angle pdb=" CA  PRO S 151 "
        pdb=" N   PRO S 151 "
        pdb=" CD  PRO S 151 "
      ideal   model   delta    sigma   weight residual
     112.00  107.01    4.99 1.40e+00 5.10e-01 1.27e+01
  angle pdb=" C   ASP R  97 "
        pdb=" N   ILE R  98 "
        pdb=" CA  ILE R  98 "
      ideal   model   delta    sigma   weight residual
     120.33  122.69   -2.36 8.00e-01 1.56e+00 8.73e+00
  angle pdb=" CA  LEU A 283 "
        pdb=" CB  LEU A 283 "
        pdb=" CG  LEU A 283 "
      ideal   model   delta    sigma   weight residual
     116.30  125.82   -9.52 3.50e+00 8.16e-02 7.41e+00
  angle pdb=" CA  LEU R  47 "
        pdb=" CB  LEU R  47 "
        pdb=" CG  LEU R  47 "
      ideal   model   delta    sigma   weight residual
     116.30  124.60   -8.30 3.50e+00 8.16e-02 5.62e+00
  ... (remaining 12033 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 4497
       17.92 -    35.84: 543
       35.84 -    53.77: 138
       53.77 -    71.69: 29
       71.69 -    89.61: 5
  Dihedral angle restraints: 5212
    sinusoidal: 1936
      harmonic: 3276
  Sorted by residual:
  dihedral pdb=" CB  CYS R 100 "
           pdb=" SG  CYS R 100 "
           pdb=" SG  CYS R 177 "
           pdb=" CB  CYS R 177 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -138.25   52.25     1      1.00e+01 1.00e-02 3.72e+01
  dihedral pdb=" CA  PHE R 117 "
           pdb=" C   PHE R 117 "
           pdb=" N   LEU R 118 "
           pdb=" CA  LEU R 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.66   24.34     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CB  CYS R  19 "
           pdb=" SG  CYS R  19 "
           pdb=" SG  CYS R 266 "
           pdb=" CB  CYS R 266 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -55.41  -30.59     1      1.00e+01 1.00e-02 1.34e+01
  ... (remaining 5209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 804
       0.027 -    0.054: 360
       0.054 -    0.080: 120
       0.080 -    0.107: 67
       0.107 -    0.134: 27
  Chirality restraints: 1378
  Sorted by residual:
  chirality pdb=" CA  VAL S 147 "
            pdb=" N   VAL S 147 "
            pdb=" C   VAL S 147 "
            pdb=" CB  VAL S 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.50e-01
  chirality pdb=" CA  ASP S  90 "
            pdb=" N   ASP S  90 "
            pdb=" C   ASP S  90 "
            pdb=" CB  ASP S  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.04e-01
  ... (remaining 1375 not shown)

  Planarity restraints: 1523
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR S 150 "   -0.082 5.00e-02 4.00e+02   1.22e-01 2.39e+01
        pdb=" N   PRO S 151 "    0.211 5.00e-02 4.00e+02
        pdb=" CA  PRO S 151 "   -0.065 5.00e-02 4.00e+02
        pdb=" CD  PRO S 151 "   -0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R  31 "    0.038 5.00e-02 4.00e+02   5.77e-02 5.32e+00
        pdb=" N   PRO R  32 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO R  32 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO R  32 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  52 "   -0.032 5.00e-02 4.00e+02   4.84e-02 3.75e+00
        pdb=" N   PRO C  53 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO C  53 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C  53 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1520 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1386
        2.76 -     3.29: 7952
        3.29 -     3.83: 13782
        3.83 -     4.36: 16840
        4.36 -     4.90: 29890
  Nonbonded interactions: 69850
  Sorted by model distance:
  nonbonded pdb=" O   LEU R 280 "
            pdb=" OG1 THR R 283 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   GLY R 262 "
            pdb=" OH  TYR R 269 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   LEU R 257 "
            pdb=" OG  SER R 261 "
     model   vdw
     2.264 3.040
  ... (remaining 69845 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.810
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
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      :  0.009   0.831   8866  Z= 0.460
  Angle     :  0.538  10.813  12049  Z= 0.276
  Chirality :  0.040   0.134   1378
  Planarity :  0.005   0.122   1522
  Dihedral  : 16.775  89.608   3082
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  : 25.98 %
    Favored  : 73.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.25), residues: 1115
  helix:  0.14 (0.28), residues: 352
  sheet: -0.02 (0.31), residues: 269
  loop : -0.92 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 152 
 HIS   0.002   0.000   HIS R 189 
 PHE   0.026   0.001   PHE R  38 
 TYR   0.021   0.001   TYR S 235 
 ARG   0.005   0.000   ARG S  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00076 (    1)
  link_NAG-ASN         : angle       0.80151 (    3)
  hydrogen bonds       : bond        0.27149 (  404)
  hydrogen bonds       : angle       8.26752 ( 1131)
  SS BOND              : bond        0.41533 (    4)
  SS BOND              : angle       3.10052 (    8)
  covalent geometry    : bond        0.00287 ( 8861)
  covalent geometry    : angle       0.53199 (12038)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 144
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
REVERT: S   69 THR cc_start: 0.8404 (t) cc_final: 0.8071 (m)
REVERT: S   87 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7526 (mtm-85)
REVERT: C   42 GLU cc_start: 0.7684 (mp0) cc_final: 0.7262 (mp0)
  outliers start: 2
  outliers final: 2
  residues processed: 145
  average time/residue: 0.2105
  time to fit residues: 42.3435
Evaluate side-chains
  136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 134
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain R residue  272 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 83 optimal weight:    6.9990
   chunk 46 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 86 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:   10.0000
   chunk 99 optimal weight:    0.9980
   overall best weight:    3.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.147457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.114017 restraints weight = 11209.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.40
r_work: 0.3308 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8866  Z= 0.215
  Angle     :  0.616   7.902  12049  Z= 0.324
  Chirality :  0.044   0.185   1378
  Planarity :  0.005   0.082   1522
  Dihedral  :  5.356  59.881   1259
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 24.30 %
    Favored  : 72.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.25), residues: 1115
  helix:  1.07 (0.27), residues: 360
  sheet:  0.04 (0.32), residues: 262
  loop : -0.91 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP S  47 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.015   0.002   PHE R 232 
 TYR   0.024   0.002   TYR S 235 
 ARG   0.005   0.001   ARG S  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00066 (    1)
  link_NAG-ASN         : angle       1.83063 (    3)
  hydrogen bonds       : bond        0.05558 (  404)
  hydrogen bonds       : angle       4.95140 ( 1131)
  SS BOND              : bond        0.00312 (    4)
  SS BOND              : angle       0.90291 (    8)
  covalent geometry    : bond        0.00511 ( 8861)
  covalent geometry    : angle       0.61526 (12038)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 135
  time to evaluate  : 0.920 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7426 (mtm110) cc_final: 0.7070 (ttp-110)
REVERT: A  197 LYS cc_start: 0.8888 (mmtm) cc_final: 0.8429 (mtmt)
REVERT: A  244 HIS cc_start: 0.7259 (m90) cc_final: 0.6920 (m90)
REVERT: S   67 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7560 (mtm180)
REVERT: S  202 ARG cc_start: 0.8370 (mtm110) cc_final: 0.8105 (mtm110)
REVERT: B  234 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8673 (m-80)
  outliers start: 25
  outliers final: 15
  residues processed: 155
  average time/residue: 0.2384
  time to fit residues: 50.0682
Evaluate side-chains
  138 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  186 GLN
Chi-restraints excluded: chain S residue  189 ILE
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  268 VAL
Chi-restraints excluded: chain R residue  284 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 108 optimal weight:    0.9980
   chunk 2 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.150006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.116316 restraints weight = 11385.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.47
r_work: 0.3341 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8866  Z= 0.146
  Angle     :  0.548   9.782  12049  Z= 0.285
  Chirality :  0.043   0.189   1378
  Planarity :  0.004   0.065   1522
  Dihedral  :  4.781  43.944   1256
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 25.42 %
    Favored  : 70.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.25), residues: 1115
  helix:  1.58 (0.27), residues: 360
  sheet:  0.06 (0.32), residues: 263
  loop : -0.94 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP S  47 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.016   0.002   PHE R  38 
 TYR   0.023   0.001   TYR S 235 
 ARG   0.003   0.000   ARG S  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00058 (    1)
  link_NAG-ASN         : angle       1.79969 (    3)
  hydrogen bonds       : bond        0.04549 (  404)
  hydrogen bonds       : angle       4.49166 ( 1131)
  SS BOND              : bond        0.00353 (    4)
  SS BOND              : angle       0.71022 (    8)
  covalent geometry    : bond        0.00343 ( 8861)
  covalent geometry    : angle       0.54721 (12038)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 131
  time to evaluate  : 1.035 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7382 (mtm110) cc_final: 0.7051 (ttp-110)
REVERT: S   13 GLN cc_start: 0.7873 (pm20) cc_final: 0.7625 (pm20)
REVERT: S   67 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7593 (mtm180)
REVERT: S  202 ARG cc_start: 0.8352 (mtm110) cc_final: 0.8073 (mtm110)
REVERT: B  234 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8694 (m-80)
REVERT: R   14 ASP cc_start: 0.7321 (m-30) cc_final: 0.6500 (t0)
REVERT: R  165 LYS cc_start: 0.7327 (mmtt) cc_final: 0.6598 (mtmt)
REVERT: R  217 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7502 (tt0)
REVERT: R  285 MET cc_start: 0.7712 (tpt) cc_final: 0.7420 (tpt)
  outliers start: 33
  outliers final: 18
  residues processed: 158
  average time/residue: 0.2347
  time to fit residues: 50.4913
Evaluate side-chains
  141 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  186 GLN
Chi-restraints excluded: chain S residue  189 ILE
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue  179 SER
Chi-restraints excluded: chain R residue  217 GLN
Chi-restraints excluded: chain R residue  221 ASP
Chi-restraints excluded: chain R residue  263 THR
Chi-restraints excluded: chain R residue  268 VAL
Chi-restraints excluded: chain R residue  284 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 53 optimal weight:    0.2980
   chunk 92 optimal weight:    1.9990
   chunk 93 optimal weight:    0.4980
   chunk 63 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 70 optimal weight:    0.9980
   chunk 99 optimal weight:    7.9990
   chunk 77 optimal weight:    8.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.153440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.119347 restraints weight = 11319.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.51
r_work: 0.3363 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8866  Z= 0.112
  Angle     :  0.520   8.314  12049  Z= 0.267
  Chirality :  0.041   0.144   1378
  Planarity :  0.004   0.055   1522
  Dihedral  :  4.289  24.075   1256
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 26.09 %
    Favored  : 70.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.26), residues: 1115
  helix:  1.92 (0.28), residues: 360
  sheet:  0.15 (0.32), residues: 270
  loop : -0.96 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.022   0.001   PHE R  38 
 TYR   0.024   0.001   TYR S 235 
 ARG   0.003   0.000   ARG R 270 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00038 (    1)
  link_NAG-ASN         : angle       1.97793 (    3)
  hydrogen bonds       : bond        0.03839 (  404)
  hydrogen bonds       : angle       4.21511 ( 1131)
  SS BOND              : bond        0.00239 (    4)
  SS BOND              : angle       0.53634 (    8)
  covalent geometry    : bond        0.00255 ( 8861)
  covalent geometry    : angle       0.51936 (12038)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 139
  time to evaluate  : 0.918 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8285 (t0) cc_final: 0.7974 (m-30)
REVERT: A   24 ARG cc_start: 0.7331 (mtm110) cc_final: 0.7033 (ttp-110)
REVERT: A  197 LYS cc_start: 0.8844 (mmtm) cc_final: 0.8475 (mtmt)
REVERT: A  244 HIS cc_start: 0.7350 (m90) cc_final: 0.7100 (m90)
REVERT: B  234 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8680 (m-80)
REVERT: R   14 ASP cc_start: 0.7350 (m-30) cc_final: 0.6499 (t0)
REVERT: R  165 LYS cc_start: 0.7288 (mmtt) cc_final: 0.6593 (mtmt)
REVERT: R  167 MET cc_start: 0.6163 (tpp) cc_final: 0.5814 (tpp)
REVERT: R  190 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6778 (mm-30)
REVERT: R  217 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7481 (tt0)
REVERT: R  285 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7579 (tpt)
  outliers start: 31
  outliers final: 16
  residues processed: 161
  average time/residue: 0.2132
  time to fit residues: 46.3148
Evaluate side-chains
  145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue  179 SER
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  217 GLN
Chi-restraints excluded: chain R residue  221 ASP
Chi-restraints excluded: chain R residue  263 THR
Chi-restraints excluded: chain R residue  268 VAL
Chi-restraints excluded: chain R residue  285 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 34 optimal weight:    0.0070
   chunk 66 optimal weight:    7.9990
   chunk 55 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 12 optimal weight:    7.9990
   chunk 101 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 77 optimal weight:    9.9990
   chunk 3 optimal weight:    0.9980
   chunk 78 optimal weight:   20.0000
   overall best weight:    1.8004

-------------------------------------------------------------------------------
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 322 HIS
S 186 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.152429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.118218 restraints weight = 11282.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.50
r_work: 0.3346 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8866  Z= 0.139
  Angle     :  0.533   6.866  12049  Z= 0.276
  Chirality :  0.042   0.159   1378
  Planarity :  0.004   0.050   1522
  Dihedral  :  4.235  20.875   1256
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 26.20 %
    Favored  : 69.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.26), residues: 1115
  helix:  2.03 (0.28), residues: 361
  sheet:  0.14 (0.32), residues: 268
  loop : -1.00 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.023   0.001   PHE R  38 
 TYR   0.027   0.001   TYR S 235 
 ARG   0.002   0.000   ARG R 270 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00022 (    1)
  link_NAG-ASN         : angle       2.09278 (    3)
  hydrogen bonds       : bond        0.03919 (  404)
  hydrogen bonds       : angle       4.16666 ( 1131)
  SS BOND              : bond        0.00274 (    4)
  SS BOND              : angle       0.57095 (    8)
  covalent geometry    : bond        0.00330 ( 8861)
  covalent geometry    : angle       0.53154 (12038)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 128
  time to evaluate  : 0.918 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8310 (t0) cc_final: 0.7998 (m-30)
REVERT: A   24 ARG cc_start: 0.7372 (mtm110) cc_final: 0.7039 (ttp-110)
REVERT: A  197 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8495 (mtmt)
REVERT: B  234 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8619 (m-80)
REVERT: R   14 ASP cc_start: 0.7298 (m-30) cc_final: 0.6415 (t0)
REVERT: R  165 LYS cc_start: 0.7310 (mmtt) cc_final: 0.6630 (mtmt)
REVERT: R  167 MET cc_start: 0.6234 (tpp) cc_final: 0.6008 (tpp)
REVERT: R  217 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7530 (tt0)
REVERT: R  285 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7549 (tpt)
  outliers start: 35
  outliers final: 22
  residues processed: 153
  average time/residue: 0.2143
  time to fit residues: 45.5712
Evaluate side-chains
  148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  189 ILE
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue  217 GLN
Chi-restraints excluded: chain R residue  221 ASP
Chi-restraints excluded: chain R residue  263 THR
Chi-restraints excluded: chain R residue  268 VAL
Chi-restraints excluded: chain R residue  285 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 109 optimal weight:    3.9990
   chunk 108 optimal weight:    0.8980
   chunk 75 optimal weight:    6.9990
   chunk 85 optimal weight:    0.5980
   chunk 52 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 76 optimal weight:   40.0000
   chunk 24 optimal weight:    0.1980
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 188 HIS
A 322 HIS
S 186 GLN
** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.155371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.121256 restraints weight = 11190.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 2.50
r_work: 0.3383 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8866  Z= 0.100
  Angle     :  0.507   8.597  12049  Z= 0.261
  Chirality :  0.041   0.140   1378
  Planarity :  0.004   0.049   1522
  Dihedral  :  3.949  19.296   1256
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 26.76 %
    Favored  : 69.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.26), residues: 1115
  helix:  2.20 (0.28), residues: 361
  sheet:  0.26 (0.32), residues: 269
  loop : -0.92 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP S  47 
 HIS   0.002   0.000   HIS A 188 
 PHE   0.025   0.001   PHE R  38 
 TYR   0.019   0.001   TYR S 235 
 ARG   0.004   0.000   ARG R 270 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00113 (    1)
  link_NAG-ASN         : angle       1.95261 (    3)
  hydrogen bonds       : bond        0.03425 (  404)
  hydrogen bonds       : angle       4.00856 ( 1131)
  SS BOND              : bond        0.00219 (    4)
  SS BOND              : angle       0.49001 (    8)
  covalent geometry    : bond        0.00223 ( 8861)
  covalent geometry    : angle       0.50591 (12038)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 1.056 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8254 (t0) cc_final: 0.7953 (m-30)
REVERT: A   24 ARG cc_start: 0.7394 (mtm110) cc_final: 0.7156 (ttp-110)
REVERT: A  197 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8499 (mtmt)
REVERT: B  234 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8647 (m-80)
REVERT: R   14 ASP cc_start: 0.7308 (m-30) cc_final: 0.6417 (t0)
REVERT: R  165 LYS cc_start: 0.7424 (mmtt) cc_final: 0.6687 (mtmt)
REVERT: R  190 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6620 (mp0)
REVERT: R  217 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7598 (tt0)
REVERT: R  285 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7580 (tpt)
  outliers start: 30
  outliers final: 14
  residues processed: 154
  average time/residue: 0.2042
  time to fit residues: 44.3977
Evaluate side-chains
  144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue  179 SER
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  217 GLN
Chi-restraints excluded: chain R residue  221 ASP
Chi-restraints excluded: chain R residue  263 THR
Chi-restraints excluded: chain R residue  285 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 62 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9980
   chunk 92 optimal weight:    4.9990
   chunk 78 optimal weight:    5.9990
   chunk 34 optimal weight:    0.5980
   chunk 73 optimal weight:   10.0000
   chunk 86 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 188 HIS
A 322 HIS
B 176 GLN
** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.152963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.118675 restraints weight = 11358.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.51
r_work: 0.3349 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8866  Z= 0.146
  Angle     :  0.541   7.674  12049  Z= 0.278
  Chirality :  0.042   0.137   1378
  Planarity :  0.004   0.047   1522
  Dihedral  :  4.179  20.037   1256
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 27.20 %
    Favored  : 69.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.26), residues: 1115
  helix:  2.18 (0.28), residues: 360
  sheet:  0.23 (0.32), residues: 267
  loop : -0.97 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  82 
 HIS   0.002   0.001   HIS C  44 
 PHE   0.025   0.001   PHE R  38 
 TYR   0.024   0.001   TYR S 235 
 ARG   0.004   0.000   ARG R 270 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00011 (    1)
  link_NAG-ASN         : angle       1.93827 (    3)
  hydrogen bonds       : bond        0.03770 (  404)
  hydrogen bonds       : angle       4.05265 ( 1131)
  SS BOND              : bond        0.00231 (    4)
  SS BOND              : angle       0.48617 (    8)
  covalent geometry    : bond        0.00347 ( 8861)
  covalent geometry    : angle       0.53991 (12038)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 1.023 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8352 (t0) cc_final: 0.8053 (m-30)
REVERT: A   24 ARG cc_start: 0.7396 (mtm110) cc_final: 0.7088 (ttp-110)
REVERT: A  197 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8378 (mtmt)
REVERT: B  234 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8614 (m-80)
REVERT: R   14 ASP cc_start: 0.7345 (m-30) cc_final: 0.6401 (t0)
REVERT: R  165 LYS cc_start: 0.7440 (mmtt) cc_final: 0.6743 (mtmt)
REVERT: R  190 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6760 (mm-30)
REVERT: R  217 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7635 (tt0)
  outliers start: 32
  outliers final: 21
  residues processed: 154
  average time/residue: 0.2039
  time to fit residues: 43.5161
Evaluate side-chains
  153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  217 GLN
Chi-restraints excluded: chain R residue  221 ASP
Chi-restraints excluded: chain R residue  263 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 80 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 3 optimal weight:    8.9990
   chunk 105 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 38 optimal weight:    7.9990
   chunk 54 optimal weight:    7.9990
   chunk 46 optimal weight:    6.9990
   chunk 50 optimal weight:    0.7980
   chunk 98 optimal weight:   10.0000
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 188 HIS
A 322 HIS
** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.155421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.121299 restraints weight = 11354.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 2.51
r_work: 0.3382 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8866  Z= 0.104
  Angle     :  0.523   8.860  12049  Z= 0.268
  Chirality :  0.041   0.136   1378
  Planarity :  0.004   0.047   1522
  Dihedral  :  3.979  18.512   1256
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 27.87 %
    Favored  : 69.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.26), residues: 1115
  helix:  2.33 (0.28), residues: 360
  sheet:  0.28 (0.32), residues: 267
  loop : -0.94 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP S  47 
 HIS   0.002   0.000   HIS C  44 
 PHE   0.027   0.001   PHE R  38 
 TYR   0.021   0.001   TYR S 235 
 ARG   0.003   0.000   ARG R 270 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00120 (    1)
  link_NAG-ASN         : angle       1.81149 (    3)
  hydrogen bonds       : bond        0.03378 (  404)
  hydrogen bonds       : angle       3.95433 ( 1131)
  SS BOND              : bond        0.00204 (    4)
  SS BOND              : angle       0.47222 (    8)
  covalent geometry    : bond        0.00237 ( 8861)
  covalent geometry    : angle       0.52212 (12038)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.924 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8264 (t0) cc_final: 0.8005 (m-30)
REVERT: A   24 ARG cc_start: 0.7406 (mtm110) cc_final: 0.7178 (ttp-110)
REVERT: A  197 LYS cc_start: 0.8795 (mmtm) cc_final: 0.8460 (mtmt)
REVERT: S   18 ARG cc_start: 0.7695 (tpp80) cc_final: 0.7270 (tpt170)
REVERT: S   65 LYS cc_start: 0.8411 (tptt) cc_final: 0.7713 (tppt)
REVERT: B  234 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8648 (m-80)
REVERT: R   14 ASP cc_start: 0.7314 (m-30) cc_final: 0.6337 (t0)
REVERT: R  165 LYS cc_start: 0.7447 (mmtt) cc_final: 0.6732 (mtmt)
REVERT: R  167 MET cc_start: 0.5697 (tpp) cc_final: 0.5402 (tpp)
REVERT: R  190 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6615 (mp0)
  outliers start: 25
  outliers final: 18
  residues processed: 148
  average time/residue: 0.1945
  time to fit residues: 40.9187
Evaluate side-chains
  143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain S residue  237 LEU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  221 ASP
Chi-restraints excluded: chain R residue  263 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 100 optimal weight:    0.4980
   chunk 94 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   chunk 39 optimal weight:    8.9990
   chunk 52 optimal weight:    8.9990
   chunk 58 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 18 optimal weight:    7.9990
   chunk 89 optimal weight:    5.9990
   overall best weight:    2.0988

-------------------------------------------------------------------------------
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 188 HIS
A 322 HIS
S 186 GLN
** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.152644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.118524 restraints weight = 11312.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.49
r_work: 0.3351 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8866  Z= 0.154
  Angle     :  0.553   8.339  12049  Z= 0.285
  Chirality :  0.042   0.155   1378
  Planarity :  0.004   0.050   1522
  Dihedral  :  4.168  19.146   1256
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 27.42 %
    Favored  : 69.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.26), residues: 1115
  helix:  2.19 (0.28), residues: 361
  sheet:  0.26 (0.32), residues: 267
  loop : -0.94 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP S  47 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.026   0.001   PHE R  38 
 TYR   0.023   0.001   TYR S 235 
 ARG   0.004   0.000   ARG S 180 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00028 (    1)
  link_NAG-ASN         : angle       1.78403 (    3)
  hydrogen bonds       : bond        0.03755 (  404)
  hydrogen bonds       : angle       4.01636 ( 1131)
  SS BOND              : bond        0.00233 (    4)
  SS BOND              : angle       0.49112 (    8)
  covalent geometry    : bond        0.00372 ( 8861)
  covalent geometry    : angle       0.55191 (12038)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 0.991 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8332 (t0) cc_final: 0.8057 (m-30)
REVERT: A   24 ARG cc_start: 0.7412 (mtm110) cc_final: 0.7164 (ttp-110)
REVERT: S   18 ARG cc_start: 0.7705 (tpp80) cc_final: 0.7289 (tpt170)
REVERT: B  234 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8623 (m-80)
REVERT: R   14 ASP cc_start: 0.7326 (m-30) cc_final: 0.6276 (t0)
REVERT: R  165 LYS cc_start: 0.7511 (mmtt) cc_final: 0.6795 (mtmt)
REVERT: R  190 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6790 (mm-30)
REVERT: R  217 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7636 (tt0)
  outliers start: 27
  outliers final: 21
  residues processed: 150
  average time/residue: 0.2279
  time to fit residues: 46.9265
Evaluate side-chains
  150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain S residue  237 LEU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  217 GLN
Chi-restraints excluded: chain R residue  221 ASP
Chi-restraints excluded: chain R residue  263 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 100 optimal weight:    0.8980
   chunk 12 optimal weight:    0.3980
   chunk 72 optimal weight:    0.9990
   chunk 87 optimal weight:    5.9990
   chunk 97 optimal weight:   20.0000
   chunk 79 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9990
   chunk 63 optimal weight:    8.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 322 HIS
** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.155571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.121366 restraints weight = 11318.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.52
r_work: 0.3390 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8866  Z= 0.102
  Angle     :  0.522   8.398  12049  Z= 0.267
  Chirality :  0.041   0.134   1378
  Planarity :  0.004   0.047   1522
  Dihedral  :  3.960  17.409   1256
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 28.21 %
    Favored  : 69.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.26), residues: 1115
  helix:  2.37 (0.28), residues: 361
  sheet:  0.15 (0.31), residues: 281
  loop : -0.84 (0.29), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 188 
 HIS   0.002   0.000   HIS A 322 
 PHE   0.027   0.001   PHE R  38 
 TYR   0.020   0.001   TYR S 235 
 ARG   0.010   0.000   ARG C  27 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00153 (    1)
  link_NAG-ASN         : angle       1.61130 (    3)
  hydrogen bonds       : bond        0.03322 (  404)
  hydrogen bonds       : angle       3.94313 ( 1131)
  SS BOND              : bond        0.00195 (    4)
  SS BOND              : angle       0.50399 (    8)
  covalent geometry    : bond        0.00230 ( 8861)
  covalent geometry    : angle       0.52104 (12038)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.982 
Fit side-chains
REVERT: S   18 ARG cc_start: 0.7637 (tpp80) cc_final: 0.7215 (tpt170)
REVERT: B  234 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8614 (m-80)
REVERT: R   14 ASP cc_start: 0.7167 (m-30) cc_final: 0.6216 (t0)
REVERT: R  165 LYS cc_start: 0.7461 (mmtt) cc_final: 0.6825 (mtmt)
REVERT: R  190 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6533 (mp0)
  outliers start: 21
  outliers final: 19
  residues processed: 142
  average time/residue: 0.2029
  time to fit residues: 40.2348
Evaluate side-chains
  145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain S residue  237 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  221 ASP
Chi-restraints excluded: chain R residue  263 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 64 optimal weight:    0.2980
   chunk 72 optimal weight:    7.9990
   chunk 40 optimal weight:    9.9990
   chunk 18 optimal weight:    7.9990
   chunk 76 optimal weight:   40.0000
   chunk 52 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0770
   chunk 109 optimal weight:    0.0470
   chunk 92 optimal weight:    4.9990
   chunk 2 optimal weight:    7.9990
   overall best weight:    1.2840

-------------------------------------------------------------------------------
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 322 HIS
** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.154210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.120213 restraints weight = 11340.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 2.50
r_work: 0.3375 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8866  Z= 0.117
  Angle     :  0.526   8.298  12049  Z= 0.271
  Chirality :  0.041   0.139   1378
  Planarity :  0.004   0.050   1522
  Dihedral  :  3.982  16.853   1256
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 28.32 %
    Favored  : 68.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.26), residues: 1115
  helix:  2.42 (0.28), residues: 360
  sheet:  0.23 (0.32), residues: 269
  loop : -0.89 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP S  47 
 HIS   0.002   0.000   HIS B  91 
 PHE   0.027   0.001   PHE R  38 
 TYR   0.020   0.001   TYR S 235 
 ARG   0.003   0.000   ARG R 270 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00101 (    1)
  link_NAG-ASN         : angle       1.58301 (    3)
  hydrogen bonds       : bond        0.03436 (  404)
  hydrogen bonds       : angle       3.93293 ( 1131)
  SS BOND              : bond        0.00198 (    4)
  SS BOND              : angle       0.45599 (    8)
  covalent geometry    : bond        0.00276 ( 8861)
  covalent geometry    : angle       0.52571 (12038)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5051.54 seconds
wall clock time: 87 minutes 52.41 seconds (5272.41 seconds total)