Starting phenix.real_space_refine (version: 1.21rc1)
on Thu Aug 10 20:13:25 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/08_2023/8g59_29736_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/08_2023/8g59_29736.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/08_2023/8g59_29736_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/08_2023/8g59_29736_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/08_2023/8g59_29736_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/08_2023/8g59_29736.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/08_2023/8g59_29736.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/08_2023/8g59_29736_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/08_2023/8g59_29736_updated.pdb"
  }
  resolution = 2.64
  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=   0.008 sd=   0.088
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: 5
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    5503      2.51       5
     N    1444      2.21       5
     O    1577      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib"
  Total number of atoms: 8583
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2509
          Classifications: {'peptide': 335}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 5, 'TRANS': 329}
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 81
          Unresolved non-hydrogen dihedrals: 53
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 53
    Chain: "Y"
      Number of atoms: 365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 365
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "S"
      Number of atoms: 1739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1739
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "A"
      Number of atoms: 1739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1739
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 2, 'TRANS': 216}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "R"
      Number of atoms: 2231
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 282, 2220
          Unusual residues: {'YN9': 1}
          Classifications: {'peptide': 281, 'undetermined': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 11, 'TRANS': 269, None: 1}
            Not linked:
              pdbres="THR R 324 "
              pdbres="YN9 R 401 "
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 30
      Conformer: "B"
        Number of residues, atoms: 282, 2220
          Unusual residues: {'YN9': 1}
          Classifications: {'peptide': 281, 'undetermined': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 11, 'TRANS': 269, None: 1}
            Not linked:
              pdbres="THR R 324 "
              pdbres="YN9 R 401 "
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 30
          bond proxies already assigned to first conformer: 2260
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE R 115 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE R 115 " occ=0.50
  Time building chain proxies: 5.78, per 1000 atoms: 0.67
  Number of scatterers: 8583
  At special positions: 0
  Unit cell: (105.456, 121.68, 115.596, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      58     16.00
     F       1      9.00
     O    1577      8.00
     N    1444      7.00
     C    5503      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 111 " - pdb=" SG  CYS R 194 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.23
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2102

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      26 helices and 14 sheets defined
      34.2% alpha, 22.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.32
  Creating SS restraints...
    Processing helix  chain 'B' and resid 7 through 23
    Processing helix  chain 'B' and resid 30 through 36
      removed outlier: 4.655A  pdb=" N   ASN B  36 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 10 through 23
    Processing helix  chain 'Y' and resid 30 through 43
    Processing helix  chain 'Y' and resid 45 through 47
      No H-bonds generated for 'chain 'Y' and resid 45 through 47'
    Processing helix  chain 'Y' and resid 56 through 58
      No H-bonds generated for 'chain 'Y' and resid 56 through 58'
    Processing helix  chain 'S' and resid 29 through 31
      No H-bonds generated for 'chain 'S' and resid 29 through 31'
    Processing helix  chain 'S' and resid 88 through 90
      No H-bonds generated for 'chain 'S' and resid 88 through 90'
    Processing helix  chain 'S' and resid 221 through 223
      No H-bonds generated for 'chain 'S' and resid 221 through 223'
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 3.737A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 52
    Processing helix  chain 'A' and resid 208 through 210
      No H-bonds generated for 'chain 'A' and resid 208 through 210'
    Processing helix  chain 'A' and resid 212 through 215
    Processing helix  chain 'A' and resid 227 through 230
      removed outlier: 3.983A  pdb=" N   TYR A 230 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 227 through 230'
    Processing helix  chain 'A' and resid 242 through 254
    Processing helix  chain 'A' and resid 257 through 259
      No H-bonds generated for 'chain 'A' and resid 257 through 259'
    Processing helix  chain 'A' and resid 271 through 278
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 3.636A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 354
    Processing helix  chain 'R' and resid 43 through 69
    Processing helix  chain 'R' and resid 78 through 100
      removed outlier: 3.956A  pdb=" N   ALA R  91 " --> pdb=" O   LEU R  87 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ILE R  92 " --> pdb=" O   PHE R  88 " (cutoff:3.500A)
      Proline residue:  R  93  - end of helix
    Processing helix  chain 'R' and resid 110 through 141
      removed outlier: 4.695A  pdb=" N  APHE R 115 " --> pdb=" O   CYS R 111 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 153 through 175
      removed outlier: 3.561A  pdb=" N   ALA R 170 " --> pdb=" O   SER R 166 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU R 171 " --> pdb=" O   ALA R 167 " (cutoff:3.500A)
      Proline residue:  R 172  - end of helix
    Processing helix  chain 'R' and resid 201 through 244
      removed outlier: 3.556A  pdb=" N   TRP R 207 " --> pdb=" O   GLY R 203 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL R 209 " --> pdb=" O   ILE R 205 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   VAL R 218 " --> pdb=" O   LEU R 214 " (cutoff:3.500A)
      Proline residue:  R 219  - end of helix
      removed outlier: 3.958A  pdb=" N   ARG R 238 " --> pdb=" O   THR R 234 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL R 243 " --> pdb=" O   LYS R 239 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   SER R 244 " --> pdb=" O   ARG R 240 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 249 through 291
      removed outlier: 3.614A  pdb=" N   LEU R 262 " --> pdb=" O   GLN R 258 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   PHE R 263 " --> pdb=" O   ASP R 259 " (cutoff:3.500A)
      Proline residue:  R 279  - end of helix
    Processing helix  chain 'R' and resid 300 through 320
      removed outlier: 3.903A  pdb=" N   TRP R 305 " --> pdb=" O   SER R 301 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ASN R 313 " --> pdb=" O   PHE R 309 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   SER R 314 " --> pdb=" O   THR R 310 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ALA R 315 " --> pdb=" O   PHE R 311 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
    Processing sheet with id=  A, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.846A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.826A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.165A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.983A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.484A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.133A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.700A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.531A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 327 through 330
      removed outlier: 3.541A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.527A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   CYS S  22 " --> pdb=" O   LEU S  79 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'S' and resid 115 through 117
      removed outlier: 3.572A  pdb=" N   THR S 115 " --> pdb=" O   TYR S  94 " (cutoff:3.500A)
      removed outlier: 5.727A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   ALA S  40 " --> pdb=" O   LEU S  45 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   LEU S  45 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'S' and resid 140 through 142
      removed outlier: 3.559A  pdb=" N   ALA S 211 " --> pdb=" O   SER S 208 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.656A  pdb=" N   LYS S 244 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  K
    Processing sheet with id=  L, first strand: chain 'S' and resid 226 through 231
      removed outlier: 3.624A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'A' and resid 319 through 323
      removed outlier: 6.408A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   HIS A 195 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   LEU A  36 " --> pdb=" O   HIS A 195 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   LYS A 197 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   LEU A  38 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 8.740A  pdb=" N   GLY A  40 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'R' and resid 177 through 182

    383 hydrogen bonds defined for protein.
    1114 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: 2.33

  Time building geometry restraints manager: 3.49 seconds

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

  Histogram of bond lengths:
        1.12 -     1.26: 1365
        1.26 -     1.40: 2177
        1.40 -     1.53: 4857
        1.53 -     1.67: 280
        1.67 -     1.81: 84
  Bond restraints: 8763
  Sorted by residual:
  bond pdb=" C   PHE R 260 "
       pdb=" O   PHE R 260 "
    ideal  model  delta    sigma   weight residual
    1.233  1.117  0.116 1.46e-02 4.69e+03 6.29e+01
  bond pdb=" N   GLN R 258 "
       pdb=" CA  GLN R 258 "
    ideal  model  delta    sigma   weight residual
    1.458  1.383  0.074 1.33e-02 5.65e+03 3.12e+01
  bond pdb=" N   ASP R 259 "
       pdb=" CA  ASP R 259 "
    ideal  model  delta    sigma   weight residual
    1.456  1.393  0.063 1.18e-02 7.18e+03 2.84e+01
  bond pdb=" C   ARG R  36 "
       pdb=" O   ARG R  36 "
    ideal  model  delta    sigma   weight residual
    1.235  1.172  0.063 1.25e-02 6.40e+03 2.54e+01
  bond pdb=" CA  ASP A 346 "
       pdb=" C   ASP A 346 "
    ideal  model  delta    sigma   weight residual
    1.524  1.465  0.059 1.26e-02 6.30e+03 2.20e+01
  ... (remaining 8758 not shown)

  Histogram of bond angle deviations from ideal:
      100.24 -   107.00: 206
      107.00 -   113.77: 4920
      113.77 -   120.53: 3309
      120.53 -   127.30: 3385
      127.30 -   134.06: 90
  Bond angle restraints: 11910
  Sorted by residual:
  angle pdb=" N   PHE R 260 "
        pdb=" CA  PHE R 260 "
        pdb=" C   PHE R 260 "
      ideal   model   delta    sigma   weight residual
     114.04  102.67   11.37 1.24e+00 6.50e-01 8.41e+01
  angle pdb=" C   ALA R  91 "
        pdb=" N   ILE R  92 "
        pdb=" CA  ILE R  92 "
      ideal   model   delta    sigma   weight residual
     120.24  124.87   -4.63 6.30e-01 2.52e+00 5.39e+01
  angle pdb=" N   ILE R  89 "
        pdb=" CA  ILE R  89 "
        pdb=" C   ILE R  89 "
      ideal   model   delta    sigma   weight residual
     110.62  117.17   -6.55 1.02e+00 9.61e-01 4.13e+01
  angle pdb=" N   LEU A 358 "
        pdb=" CA  LEU A 358 "
        pdb=" C   LEU A 358 "
      ideal   model   delta    sigma   weight residual
     111.36  118.33   -6.97 1.09e+00 8.42e-01 4.09e+01
  angle pdb=" C   ASP R 259 "
        pdb=" CA  ASP R 259 "
        pdb=" CB  ASP R 259 "
      ideal   model   delta    sigma   weight residual
     110.94  120.06   -9.12 1.65e+00 3.67e-01 3.05e+01
  ... (remaining 11905 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 4693
       15.94 -    31.87: 361
       31.87 -    47.81: 63
       47.81 -    63.75: 14
       63.75 -    79.68: 8
  Dihedral angle restraints: 5139
    sinusoidal: 1895
      harmonic: 3244
  Sorted by residual:
  dihedral pdb=" C   ASP R 259 "
           pdb=" N   ASP R 259 "
           pdb=" CA  ASP R 259 "
           pdb=" CB  ASP R 259 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -144.58   21.98     0      2.50e+00 1.60e-01 7.73e+01
  dihedral pdb=" N   ASP R 259 "
           pdb=" C   ASP R 259 "
           pdb=" CA  ASP R 259 "
           pdb=" CB  ASP R 259 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  142.49  -19.69     0      2.50e+00 1.60e-01 6.21e+01
  dihedral pdb=" CB  CYS R 111 "
           pdb=" SG  CYS R 111 "
           pdb=" SG  CYS R 194 "
           pdb=" CB  CYS R 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   27.64   65.36     1      1.00e+01 1.00e-02 5.60e+01
  ... (remaining 5136 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.197: 1389
       0.197 -    0.394: 3
       0.394 -    0.591: 0
       0.591 -    0.788: 0
       0.788 -    0.985: 1
  Chirality restraints: 1393
  Sorted by residual:
  chirality pdb=" CA  ASP R 259 "
            pdb=" N   ASP R 259 "
            pdb=" C   ASP R 259 "
            pdb=" CB  ASP R 259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.53    0.99 2.00e-01 2.50e+01 2.43e+01
  chirality pdb=" CA  ARG R 254 "
            pdb=" N   ARG R 254 "
            pdb=" C   ARG R 254 "
            pdb=" CB  ARG R 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" CA  GLN R 258 "
            pdb=" N   GLN R 258 "
            pdb=" C   GLN R 258 "
            pdb=" CB  GLN R 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.91e+00
  ... (remaining 1390 not shown)

  Planarity restraints: 1491
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN R 257 "   -0.028 2.00e-02 2.50e+03   5.65e-02 3.19e+01
        pdb=" C   GLN R 257 "    0.098 2.00e-02 2.50e+03
        pdb=" O   GLN R 257 "   -0.037 2.00e-02 2.50e+03
        pdb=" N   GLN R 258 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "   -0.075 5.00e-02 4.00e+02   1.12e-01 2.01e+01
        pdb=" N   PRO S  75 "    0.194 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "   -0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP R 299 "    0.040 5.00e-02 4.00e+02   6.13e-02 6.01e+00
        pdb=" N   PRO R 300 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO R 300 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R 300 "    0.034 5.00e-02 4.00e+02
  ... (remaining 1488 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 56
        2.52 -     3.12: 6344
        3.12 -     3.71: 13332
        3.71 -     4.31: 19324
        4.31 -     4.90: 32229
  Nonbonded interactions: 71285
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG R 238 "
            pdb=" OD2 ASP R 259 "
     model   vdw
     1.930 2.520
  nonbonded pdb=" O   CYS R  60 "
            pdb=" CD2 LEU R  64 "
     model   vdw
     1.953 3.460
  nonbonded pdb=" O   ALA A  41 "
            pdb=" OG  SER A  44 "
     model   vdw
     2.183 2.440
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.222 2.440
  nonbonded pdb=" O   CYS A 254 "
            pdb=" NZ  LYS A 317 "
     model   vdw
     2.255 2.520
  ... (remaining 71280 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             0.370
  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:          2.270
  Check model and map are aligned:         0.140
  Set scattering table:                    0.080
  Process input model:                     26.720
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
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      :  0.005   0.116   8763  Z= 0.337
  Angle     :  0.759  16.011  11910  Z= 0.436
  Chirality :  0.053   0.985   1393
  Planarity :  0.006   0.112   1491
  Dihedral  : 12.177  79.684   3031
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.85 %
    Favored  : 96.06 %
  Rotamer Outliers :  0.22 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.15 (0.25), residues: 1095
  helix:  0.23 (0.25), residues: 387
  sheet:  0.39 (0.30), residues: 301
  loop : -0.65 (0.30), residues: 407

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 159
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 161
  average time/residue: 1.5221
  time to fit residues: 257.9322
Evaluate side-chains
  134 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 133
  time to evaluate  : 0.982 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 1
  residues processed: 0
  time to fit residues: 1.3316
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 83 optimal weight:    0.0000
   chunk 46 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 56 optimal weight:    0.2980
   chunk 44 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 33 optimal weight:    8.9990
   chunk 52 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN
S 186 GLN
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 357 ASN
** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.1274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8763  Z= 0.174
  Angle     :  0.591  10.731  11910  Z= 0.300
  Chirality :  0.042   0.151   1393
  Planarity :  0.005   0.075   1491
  Dihedral  :  4.855  65.745   1201
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer Outliers :  1.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.40 (0.25), residues: 1095
  helix:  1.01 (0.27), residues: 378
  sheet:  0.53 (0.30), residues: 308
  loop : -0.54 (0.30), residues: 409

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 0.936 
Fit side-chains
  outliers start: 12
  outliers final: 4
  residues processed: 147
  average time/residue: 1.4129
  time to fit residues: 219.1388
Evaluate side-chains
  127 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 123
  time to evaluate  : 0.932 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 1
  residues processed: 3
  average time/residue: 0.2192
  time to fit residues: 2.1683
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    0.2980
   chunk 31 optimal weight:    6.9990
   chunk 83 optimal weight:    0.0040
   chunk 68 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 99 optimal weight:    0.1980
   chunk 34 optimal weight:   20.0000
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.4194

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN
A 188 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8763  Z= 0.143
  Angle     :  0.534  10.068  11910  Z= 0.270
  Chirality :  0.041   0.134   1393
  Planarity :  0.004   0.062   1491
  Dihedral  :  4.433  54.709   1201
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer Outliers :  1.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.75 (0.26), residues: 1095
  helix:  1.48 (0.27), residues: 375
  sheet:  0.57 (0.30), residues: 305
  loop : -0.38 (0.31), residues: 415

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 148
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 5
  residues processed: 154
  average time/residue: 1.3699
  time to fit residues: 223.3676
Evaluate side-chains
  136 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 131
  time to evaluate  : 0.982 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 3
  residues processed: 2
  average time/residue: 0.2164
  time to fit residues: 1.8885
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 51 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 95 optimal weight:    0.1980
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.0388

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN
Y  59 ASN
S  77 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8763  Z= 0.203
  Angle     :  0.564  11.174  11910  Z= 0.285
  Chirality :  0.042   0.142   1393
  Planarity :  0.004   0.058   1491
  Dihedral  :  4.402  51.853   1201
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer Outliers :  1.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.80 (0.26), residues: 1095
  helix:  1.33 (0.27), residues: 380
  sheet:  0.78 (0.30), residues: 301
  loop : -0.33 (0.31), residues: 414

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 142
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 9
  residues processed: 146
  average time/residue: 1.4695
  time to fit residues: 226.1700
Evaluate side-chains
  140 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 131
  time to evaluate  : 1.014 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 4
  residues processed: 5
  average time/residue: 0.4389
  time to fit residues: 3.9591
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 60 optimal weight:   10.0000
   chunk 1 optimal weight:   20.0000
   chunk 79 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 90 optimal weight:    0.1980
   chunk 73 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 54 optimal weight:   10.0000
   chunk 95 optimal weight:    0.8980
   chunk 26 optimal weight:   10.0000
   overall best weight:    2.6184

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN
Y  59 ASN
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.058   8763  Z= 0.399
  Angle     :  0.664  11.565  11910  Z= 0.339
  Chirality :  0.046   0.165   1393
  Planarity :  0.005   0.060   1491
  Dihedral  :  5.020  55.630   1201
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer Outliers :  2.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.25), residues: 1095
  helix:  0.70 (0.26), residues: 389
  sheet:  0.66 (0.31), residues: 288
  loop : -0.26 (0.30), residues: 418

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
  outliers start: 21
  outliers final: 7
  residues processed: 150
  average time/residue: 1.5424
  time to fit residues: 243.5005
Evaluate side-chains
  143 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 136
  time to evaluate  : 0.990 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 3
  residues processed: 4
  average time/residue: 0.1601
  time to fit residues: 2.2493
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 95 optimal weight:    0.8980
   chunk 21 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 106 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0970
   chunk 49 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 102 optimal weight:    0.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
A 204 GLN
R 252 GLN
R 290 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8763  Z= 0.199
  Angle     :  0.566   8.970  11910  Z= 0.291
  Chirality :  0.042   0.150   1393
  Planarity :  0.005   0.058   1491
  Dihedral  :  4.662  54.892   1201
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer Outliers :  1.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.69 (0.26), residues: 1095
  helix:  1.08 (0.27), residues: 383
  sheet:  0.73 (0.30), residues: 299
  loop : -0.23 (0.31), residues: 413

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
  outliers start: 15
  outliers final: 6
  residues processed: 145
  average time/residue: 1.4767
  time to fit residues: 225.5490
Evaluate side-chains
  141 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 135
  time to evaluate  : 0.972 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 3
  residues processed: 3
  average time/residue: 0.6408
  time to fit residues: 3.4648
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 89 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 106 optimal weight:    0.8980
   chunk 66 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0060
   chunk 65 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.5800

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8763  Z= 0.268
  Angle     :  0.599  10.728  11910  Z= 0.308
  Chirality :  0.043   0.155   1393
  Planarity :  0.005   0.058   1491
  Dihedral  :  4.753  55.769   1201
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer Outliers :  1.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: 1095
  helix:  1.04 (0.27), residues: 383
  sheet:  0.74 (0.30), residues: 299
  loop : -0.25 (0.31), residues: 413

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 1.003 
Fit side-chains
  outliers start: 15
  outliers final: 7
  residues processed: 139
  average time/residue: 1.5527
  time to fit residues: 227.1498
Evaluate side-chains
  135 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 128
  time to evaluate  : 0.968 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 5
  residues processed: 2
  average time/residue: 0.9422
  time to fit residues: 3.3665
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 52 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 83 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9990
   chunk 101 optimal weight:    0.7980
   chunk 92 optimal weight:    0.5980
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 175 GLN
B 268 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8763  Z= 0.211
  Angle     :  0.590   8.803  11910  Z= 0.302
  Chirality :  0.042   0.156   1393
  Planarity :  0.005   0.058   1491
  Dihedral  :  4.666  57.725   1201
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer Outliers :  0.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.77 (0.26), residues: 1095
  helix:  1.15 (0.27), residues: 389
  sheet:  0.78 (0.30), residues: 299
  loop : -0.20 (0.32), residues: 407

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 133
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 5
  residues processed: 139
  average time/residue: 1.6120
  time to fit residues: 235.1782
Evaluate side-chains
  133 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 128
  time to evaluate  : 0.937 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 4
  residues processed: 1
  average time/residue: 1.7045
  time to fit residues: 3.0530
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    0.2980
   chunk 101 optimal weight:    0.8980
   chunk 59 optimal weight:    0.2980
   chunk 43 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 89 optimal weight:    0.0980
   chunk 93 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 104 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 175 GLN
B 268 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 194 ASN
** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8763  Z= 0.151
  Angle     :  0.554  11.347  11910  Z= 0.284
  Chirality :  0.041   0.142   1393
  Planarity :  0.005   0.057   1491
  Dihedral  :  4.493  59.322   1201
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer Outliers :  1.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.26), residues: 1095
  helix:  1.56 (0.27), residues: 389
  sheet:  0.76 (0.30), residues: 298
  loop : -0.13 (0.32), residues: 408

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 0.971 
Fit side-chains
  outliers start: 13
  outliers final: 5
  residues processed: 148
  average time/residue: 1.4830
  time to fit residues: 231.3796
Evaluate side-chains
  143 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 138
  time to evaluate  : 0.968 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 4
  residues processed: 1
  average time/residue: 0.2300
  time to fit residues: 1.6180
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 72 optimal weight:    4.9990
   chunk 109 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0020
   chunk 67 optimal weight:    3.9990
   chunk 53 optimal weight:    0.3980
   chunk 69 optimal weight:    0.7980
   chunk 92 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
A 294 ASN
** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8763  Z= 0.166
  Angle     :  0.566  11.591  11910  Z= 0.287
  Chirality :  0.041   0.142   1393
  Planarity :  0.005   0.057   1491
  Dihedral  :  4.436  59.047   1201
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer Outliers :  0.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.26), residues: 1095
  helix:  1.67 (0.27), residues: 389
  sheet:  0.83 (0.30), residues: 298
  loop : -0.08 (0.32), residues: 408

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 141
  time to evaluate  : 0.880 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 146
  average time/residue: 1.4108
  time to fit residues: 217.6207
Evaluate side-chains
  134 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 130
  time to evaluate  : 0.960 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 4
  residues processed: 0
  time to fit residues: 1.3219
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 89 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 175 GLN
B 220 GLN
B 268 ASN
B 340 ASN
Y  59 ASN
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.152634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.117544 restraints weight = 20522.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 2.41
r_work: 0.3492 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3334
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3334 r_free = 0.3334    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3334 r_free = 0.3334    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3334
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.007   0.063   8763  Z= 0.446
  Angle     :  0.721  12.063  11910  Z= 0.368
  Chirality :  0.048   0.164   1393
  Planarity :  0.005   0.068   1491
  Dihedral  :  5.157  62.047   1201
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer Outliers :  1.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.52 (0.25), residues: 1095
  helix:  0.76 (0.26), residues: 390
  sheet:  0.84 (0.30), residues: 311
  loop : -0.34 (0.31), residues: 394
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4274.49 seconds
wall clock time: 76 minutes 7.41 seconds (4567.41 seconds total)