Starting phenix.real_space_refine
on Thu Mar 13 12:11:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xgu_38332/03_2025/8xgu_38332.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xgu_38332/03_2025/8xgu_38332.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xgu_38332/03_2025/8xgu_38332.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xgu_38332/03_2025/8xgu_38332.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xgu_38332/03_2025/8xgu_38332.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xgu_38332/03_2025/8xgu_38332.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    5603      2.51       5
     N    1521      2.21       5
     O    1613      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8799
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2231
          Classifications: {'peptide': 287}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 269}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1697
          Classifications: {'peptide': 213}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 2, 'TRANS': 210}
          Chain breaks: 3
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 2580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2580
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "G"
      Number of atoms: 431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 431
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "S"
      Number of atoms: 1772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1772
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "E"
      Number of atoms: 87
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 87
          Unusual residues: {'ACE': 1, 'XZA': 1}
          Classifications: {'peptide': 8, 'undetermined': 2}
          Modifications used: {'PEPT-D': 1}
          Link IDs: {'ACE_C-N': 1, 'CIS': 2, 'TRANS': 4, None: 2}
            Not linked:
              pdbres="PHE E   6 "
              pdbres="XZA E   7 "
            Not linked:
              pdbres="XZA E   7 "
              pdbres="LEU E   8 "
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Planarities with less than four sites: {'NMM:plan-2': 1, 'HZP:plan-1': 1, 'XZA:plan-1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.78, per 1000 atoms: 0.66
  Number of scatterers: 8799
  At special positions: 0
  Unit cell: (93.5, 122.4, 128.35, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      62     16.00
     O    1613      8.00
     N    1521      7.00
     C    5603      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 115 " - pdb=" SG  CYS A 191 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.04

  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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.64
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DTY E   2 "
      Input volumes are d-peptide like
        pdb=" CB  NMM E   9 "
        pdb=" CB  TRP E  10 "
  Number of C-beta restraints generated:  2112

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 17 sheets defined
      36.8% alpha, 19.3% 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 40 through 45
    Processing helix  chain 'A' and resid 45 through 70
      removed outlier: 4.040A  pdb=" N   PHE A  49 " --> pdb=" O   VAL A  45 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   ALA A  51 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 101
      Proline residue:  A  97  - end of helix
    Processing helix  chain 'A' and resid 111 through 146
      removed outlier: 3.514A  pdb=" N   CYS A 115 " --> pdb=" O   GLY A 111 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLN A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   THR A 134 " --> pdb=" O   CYS A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 175
    Processing helix  chain 'A' and resid 176 through 179
    Processing helix  chain 'A' and resid 197 through 234
      Proline residue:  A 216  - end of helix
      removed outlier: 3.623A  pdb=" N   VAL A 234 " --> pdb=" O   HIS A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 276
      removed outlier: 3.635A  pdb=" N   LEU A 250 " --> pdb=" O   GLN A 246 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   ALA A 256 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   ALA A 259 " --> pdb=" O   GLY A 255 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   LYS A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   SER A 262 " --> pdb=" O   ARG A 258 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   TRP A 276 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 289
      removed outlier: 3.903A  pdb=" N   LEU A 288 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 325
      removed outlier: 3.767A  pdb=" N   SER A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
      Proline residue:  A 320  - end of helix
    Processing helix  chain 'A' and resid 327 through 335
    Processing helix  chain 'C' and resid 6 through 31
    Processing helix  chain 'C' and resid 47 through 52
    Processing helix  chain 'C' and resid 207 through 216
      removed outlier: 3.570A  pdb=" N   LYS C 210 " --> pdb=" O   GLU C 207 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ILE C 212 " --> pdb=" O   LYS C 209 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   HIS C 213 " --> pdb=" O   LYS C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 242 through 255
    Processing helix  chain 'C' and resid 270 through 279
      removed outlier: 3.814A  pdb=" N   PHE C 274 " --> pdb=" O   LYS C 270 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   LYS C 279 " --> pdb=" O   GLU C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 286
    Processing helix  chain 'C' and resid 295 through 309
    Processing helix  chain 'C' and resid 329 through 351
      removed outlier: 3.868A  pdb=" N   VAL C 335 " --> pdb=" O   ASN C 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 26
      removed outlier: 3.511A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.524A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 23
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.709A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.600A  pdb=" N   PHE S  32 " --> pdb=" O   PHE S  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 4.185A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 185 through 191
      removed outlier: 7.033A  pdb=" N   LYS C  35 " --> pdb=" O   ALA C 220 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   ILE C 222 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   LEU C  37 " --> pdb=" O   ILE C 222 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   CYS C 224 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.042A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLY B 330 " --> pdb=" O   CYS B 317 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.906A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.853A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 7.023A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 4.067A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.712A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.635A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 6 through 7
      removed outlier: 3.651A  pdb=" N   THR S  69 " --> pdb=" O   GLN S  82 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.164A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 50 through 51
    Processing sheet with id=AB3, first strand: chain 'S' and resid 38 through 39
    Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141
    Processing sheet with id=AB5, first strand: chain 'S' and resid 147 through 148
      removed outlier: 6.536A  pdb=" N   VAL S 147 " --> pdb=" O   GLU S 246 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'S' and resid 174 through 175
    Processing sheet with id=AB7, first strand: chain 'S' and resid 185 through 186
    Processing sheet with id=AB8, first strand: chain 'S' and resid 189 through 190

    412 hydrogen bonds defined for protein.
    1158 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: 2.78

  Time building geometry restraints manager: 3.01 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1406
        1.30 -     1.43: 2458
        1.43 -     1.56: 5024
        1.56 -     1.69: 12
        1.69 -     1.83: 88
  Bond restraints: 8988
  Sorted by residual:
  bond pdb=" C   NMM E   9 "
       pdb=" N   TRP E  10 "
    ideal  model  delta    sigma   weight residual
    1.329  1.512 -0.183 1.40e-02 5.10e+03 1.72e+02
  bond pdb=" C   ASN E   4 "
       pdb=" N   THR E   5 "
    ideal  model  delta    sigma   weight residual
    1.329  1.510 -0.181 1.40e-02 5.10e+03 1.68e+02
  bond pdb=" C   HZP E   3 "
       pdb=" N   ASN E   4 "
    ideal  model  delta    sigma   weight residual
    1.329  1.492 -0.163 1.40e-02 5.10e+03 1.36e+02
  bond pdb=" C   LEU E   8 "
       pdb=" N   NMM E   9 "
    ideal  model  delta    sigma   weight residual
    1.329  1.483 -0.154 1.40e-02 5.10e+03 1.21e+02
  bond pdb=" C   THR E   5 "
       pdb=" N   PHE E   6 "
    ideal  model  delta    sigma   weight residual
    1.329  1.468 -0.139 1.40e-02 5.10e+03 9.80e+01
  ... (remaining 8983 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 11771
        1.52 -     3.03: 311
        3.03 -     4.55: 65
        4.55 -     6.06: 33
        6.06 -     7.58: 6
  Bond angle restraints: 12186
  Sorted by residual:
  angle pdb=" CA  ASN E   4 "
        pdb=" CB  ASN E   4 "
        pdb=" CG  ASN E   4 "
      ideal   model   delta    sigma   weight residual
     112.60  118.60   -6.00 1.00e+00 1.00e+00 3.60e+01
  angle pdb=" CA  ASN E   4 "
        pdb=" C   ASN E   4 "
        pdb=" N   THR E   5 "
      ideal   model   delta    sigma   weight residual
     116.20  123.50   -7.30 2.00e+00 2.50e-01 1.33e+01
  angle pdb=" C   ARG S 191 "
        pdb=" N   MET S 192 "
        pdb=" CA  MET S 192 "
      ideal   model   delta    sigma   weight residual
     121.54  127.88   -6.34 1.91e+00 2.74e-01 1.10e+01
  angle pdb=" O   ASN E   4 "
        pdb=" C   ASN E   4 "
        pdb=" N   THR E   5 "
      ideal   model   delta    sigma   weight residual
     123.00  117.82    5.18 1.60e+00 3.91e-01 1.05e+01
  angle pdb=" C   LEU A  47 "
        pdb=" N   PHE A  48 "
        pdb=" CA  PHE A  48 "
      ideal   model   delta    sigma   weight residual
     121.54  127.52   -5.98 1.91e+00 2.74e-01 9.79e+00
  ... (remaining 12181 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.23: 4802
       16.23 -    32.46: 397
       32.46 -    48.69: 83
       48.69 -    64.92: 13
       64.92 -    81.15: 10
  Dihedral angle restraints: 5305
    sinusoidal: 2028
      harmonic: 3277
  Sorted by residual:
  dihedral pdb=" CA  PHE A  48 "
           pdb=" C   PHE A  48 "
           pdb=" N   PHE A  49 "
           pdb=" CA  PHE A  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.86   21.14     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  SER A 184 "
           pdb=" C   SER A 184 "
           pdb=" N   PRO A 185 "
           pdb=" CA  PRO A 185 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.74  -20.26     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  GLU A 252 "
           pdb=" C   GLU A 252 "
           pdb=" N   ARG A 253 "
           pdb=" CA  ARG A 253 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.79   18.21     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 5302 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.045: 1377
       1.045 -    2.090: 0
       2.090 -    3.135: 0
       3.135 -    4.180: 0
       4.180 -    5.225: 3
  Chirality restraints: 1380
  Sorted by residual:
  chirality pdb=" CB  THR E   5 "
            pdb=" CA  THR E   5 "
            pdb=" OG1 THR E   5 "
            pdb=" CG2 THR E   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55   -2.67    5.22 2.00e-01 2.50e+01 6.82e+02
  chirality pdb=" CA  TRP E  10 "
            pdb=" N   TRP E  10 "
            pdb=" C   TRP E  10 "
            pdb=" CB  TRP E  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.27    4.78 2.00e-01 2.50e+01 5.71e+02
  chirality pdb=" CA  NMM E   9 "
            pdb=" N   NMM E   9 "
            pdb=" C   NMM E   9 "
            pdb=" CB  NMM E   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.10    4.61 2.00e-01 2.50e+01 5.30e+02
  ... (remaining 1377 not shown)

  Planarity restraints: 1541
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  48 "    0.013 2.00e-02 2.50e+03   2.67e-02 7.11e+00
        pdb=" C   PHE A  48 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   PHE A  48 "    0.017 2.00e-02 2.50e+03
        pdb=" N   PHE A  49 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 186 "   -0.041 5.00e-02 4.00e+02   6.30e-02 6.34e+00
        pdb=" N   PRO A 187 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 187 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 187 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 211 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.68e+00
        pdb=" C   ALA A 211 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ALA A 211 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LEU A 212 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1538 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 142
        2.67 -     3.23: 8350
        3.23 -     3.78: 13524
        3.78 -     4.34: 17830
        4.34 -     4.90: 30201
  Nonbonded interactions: 70047
  Sorted by model distance:
  nonbonded pdb=" O   ARG S  67 "
            pdb=" OG1 THR S  84 "
     model   vdw
     2.111 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" OG1 THR B  29 "
            pdb=" OE1 GLN B  32 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" OG  SER A 192 "
            pdb=" OE1 GLU A 193 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" OH  TYR A 213 "
            pdb=" O   ALA A 273 "
     model   vdw
     2.188 3.040
  ... (remaining 70042 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:             2.190
  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:          0.420
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     24.340
  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:             0.010
  Load rotamer database and sin/cos tables:13.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
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      :  0.008   0.195   8988  Z= 0.560
  Angle     :  0.662   7.581  12186  Z= 0.351
  Chirality :  0.232   5.225   1380
  Planarity :  0.004   0.063   1541
  Dihedral  : 13.143  81.153   3184
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.54 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.28 %
    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: -0.32 (0.26), residues: 1105
  helix:  1.62 (0.28), residues: 374
  sheet: -0.82 (0.30), residues: 289
  loop : -1.35 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  43 
 HIS   0.004   0.001   HIS A 181 
 PHE   0.012   0.001   PHE A 195 
 TYR   0.021   0.001   TYR A 313 
 ARG   0.004   0.000   ARG C 242 

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 188
  time to evaluate  : 1.034 
Fit side-chains
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: A   43 TRP cc_start: 0.8194 (p-90) cc_final: 0.7964 (p-90)
REVERT: A  193 GLU cc_start: 0.8375 (mp0) cc_final: 0.8152 (OUTLIER)
REVERT: A  295 HIS cc_start: 0.8356 (t70) cc_final: 0.8129 (t70)
REVERT: C  306 GLN cc_start: 0.8659 (mm110) cc_final: 0.8263 (mm110)
REVERT: B   59 TYR cc_start: 0.8493 (m-80) cc_final: 0.8223 (m-80)
REVERT: B  175 GLN cc_start: 0.8300 (mm110) cc_final: 0.8095 (mm-40)
REVERT: B  259 GLN cc_start: 0.8382 (pt0) cc_final: 0.8151 (pt0)
REVERT: B  262 MET cc_start: 0.8568 (mmt) cc_final: 0.8103 (mpp)
REVERT: G   21 MET cc_start: 0.8942 (tmm) cc_final: 0.8718 (tmm)
REVERT: E    5 THR cc_start: 0.6941 (OUTLIER) cc_final: 0.6653 (p)
  outliers start: 2
  outliers final: 2
  residues processed: 190
  average time/residue: 1.1669
  time to fit residues: 237.0237
Evaluate side-chains
  145 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 143
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain E residue    5 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    0.4980
   chunk 87 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.1980
   chunk 64 optimal weight:    3.9990
   chunk 100 optimal weight:   20.0000
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 208 ASN
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 294 ASN
B 110 ASN
B 340 ASN
** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 186 GLN
E   4 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.111437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.079857 restraints weight = 16540.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 3.41
r_work: 0.3003 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.1150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8988  Z= 0.209
  Angle     :  0.697  12.233  12186  Z= 0.347
  Chirality :  0.050   0.701   1380
  Planarity :  0.005   0.057   1541
  Dihedral  :  5.693  70.264   1241
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 12.88 %
    Favored  : 85.94 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.28 %
    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: -0.30 (0.26), residues: 1105
  helix:  1.48 (0.27), residues: 387
  sheet: -0.76 (0.30), residues: 288
  loop : -1.31 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  43 
 HIS   0.003   0.001   HIS A 181 
 PHE   0.012   0.001   PHE E   6 
 TYR   0.033   0.001   TYR A 313 
 ARG   0.008   0.001   ARG S 160 

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 160
  time to evaluate  : 1.028 
Fit side-chains
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: A  114 MET cc_start: 0.6930 (mmp) cc_final: 0.6346 (tpp)
REVERT: A  193 GLU cc_start: 0.8645 (mp0) cc_final: 0.8280 (pp20)
REVERT: A  295 HIS cc_start: 0.8494 (t70) cc_final: 0.8248 (t70)
REVERT: C  306 GLN cc_start: 0.8840 (mm110) cc_final: 0.8428 (mm110)
REVERT: C  313 ARG cc_start: 0.8979 (ttm110) cc_final: 0.8745 (ptp-110)
REVERT: B   19 ARG cc_start: 0.7999 (ppt90) cc_final: 0.7653 (ppt170)
REVERT: B  130 GLU cc_start: 0.8374 (mp0) cc_final: 0.8069 (mp0)
REVERT: B  259 GLN cc_start: 0.8444 (pt0) cc_final: 0.8204 (pt0)
REVERT: B  262 MET cc_start: 0.9022 (mmt) cc_final: 0.8706 (tpp)
REVERT: S   83 MET cc_start: 0.8276 (mmt) cc_final: 0.7918 (mmt)
  outliers start: 11
  outliers final: 4
  residues processed: 165
  average time/residue: 1.3066
  time to fit residues: 228.8795
Evaluate side-chains
  147 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 143
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue  307 PHE
Chi-restraints excluded: chain B residue   33 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 106 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.109186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.077687 restraints weight = 16944.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 3.40
r_work: 0.2966 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8988  Z= 0.287
  Angle     :  0.699  11.789  12186  Z= 0.352
  Chirality :  0.048   0.560   1380
  Planarity :  0.005   0.057   1541
  Dihedral  :  5.291  60.450   1237
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.38 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.26), residues: 1105
  helix:  1.44 (0.27), residues: 389
  sheet: -0.72 (0.30), residues: 289
  loop : -1.34 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A  43 
 HIS   0.004   0.001   HIS A 329 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.015   0.001   TYR A 313 
 ARG   0.007   0.000   ARG B  42 

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: A  193 GLU cc_start: 0.8643 (mp0) cc_final: 0.8281 (pp20)
REVERT: A  295 HIS cc_start: 0.8510 (t70) cc_final: 0.8273 (t70)
REVERT: C  313 ARG cc_start: 0.8964 (ttm110) cc_final: 0.8750 (ptp-110)
REVERT: B  130 GLU cc_start: 0.8478 (mp0) cc_final: 0.8083 (mp0)
REVERT: B  259 GLN cc_start: 0.8486 (pt0) cc_final: 0.8183 (pt0)
REVERT: B  262 MET cc_start: 0.9049 (mmt) cc_final: 0.8680 (tpp)
REVERT: G   18 GLN cc_start: 0.7800 (tp40) cc_final: 0.7582 (tp40)
REVERT: G   21 MET cc_start: 0.8902 (tmm) cc_final: 0.8612 (tmt)
REVERT: G   22 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7691 (tm-30)
  outliers start: 17
  outliers final: 8
  residues processed: 156
  average time/residue: 1.4382
  time to fit residues: 238.8531
Evaluate side-chains
  149 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue  307 PHE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 110 optimal weight:    8.9990
   chunk 46 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 15 optimal weight:    5.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 181 HIS
** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
** S 142 GLN ** 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 = 0.3694 r_free = 0.3694 target = 0.111434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.079755 restraints weight = 16248.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 3.28
r_work: 0.3043 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.1604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8988  Z= 0.213
  Angle     :  0.679  11.991  12186  Z= 0.340
  Chirality :  0.047   0.547   1380
  Planarity :  0.004   0.057   1541
  Dihedral  :  5.011  54.075   1237
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 19.31 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.28 %
    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: -0.28 (0.26), residues: 1105
  helix:  1.50 (0.27), residues: 389
  sheet: -0.71 (0.30), residues: 289
  loop : -1.35 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A  43 
 HIS   0.002   0.001   HIS A 181 
 PHE   0.011   0.001   PHE E   6 
 TYR   0.014   0.001   TYR A 313 
 ARG   0.010   0.000   ARG S 160 

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 147
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: A  114 MET cc_start: 0.6934 (mmp) cc_final: 0.6462 (tpp)
REVERT: A  295 HIS cc_start: 0.8409 (t70) cc_final: 0.8161 (t70)
REVERT: B   19 ARG cc_start: 0.8300 (tmm160) cc_final: 0.8082 (tmm160)
REVERT: B  130 GLU cc_start: 0.8575 (mp0) cc_final: 0.8363 (mp0)
REVERT: B  259 GLN cc_start: 0.8494 (pt0) cc_final: 0.8221 (pt0)
REVERT: B  262 MET cc_start: 0.8989 (mmt) cc_final: 0.8685 (tpp)
REVERT: G   18 GLN cc_start: 0.7913 (tp40) cc_final: 0.7639 (tp40)
REVERT: G   21 MET cc_start: 0.8936 (tmm) cc_final: 0.8696 (tmt)
REVERT: G   22 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7779 (tm-30)
REVERT: G   47 GLU cc_start: 0.8627 (mp0) cc_final: 0.8129 (tm-30)
REVERT: S  144 THR cc_start: 0.7435 (OUTLIER) cc_final: 0.7131 (p)
  outliers start: 15
  outliers final: 6
  residues processed: 155
  average time/residue: 1.2739
  time to fit residues: 209.7678
Evaluate side-chains
  145 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 138
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain C residue  307 PHE
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 15 optimal weight:   10.0000
   chunk 101 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 67 optimal weight:    0.3980
   chunk 107 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0060
   chunk 14 optimal weight:   10.0000
   chunk 100 optimal weight:    9.9990
   chunk 58 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
A 208 ASN
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 142 GLN ** 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 = 0.3710 r_free = 0.3710 target = 0.112778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.081475 restraints weight = 16171.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 3.25
r_work: 0.3072 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8988  Z= 0.181
  Angle     :  0.688  12.065  12186  Z= 0.343
  Chirality :  0.047   0.536   1380
  Planarity :  0.005   0.055   1541
  Dihedral  :  4.771  52.316   1237
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 20.06 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.28 %
    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: -0.22 (0.26), residues: 1105
  helix:  1.53 (0.27), residues: 387
  sheet: -0.60 (0.30), residues: 288
  loop : -1.33 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A  43 
 HIS   0.002   0.000   HIS A 329 
 PHE   0.015   0.001   PHE E   6 
 TYR   0.029   0.001   TYR A 190 
 ARG   0.011   0.001   ARG S 160 

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: A  114 MET cc_start: 0.6918 (mmp) cc_final: 0.6424 (tpp)
REVERT: A  295 HIS cc_start: 0.8423 (t70) cc_final: 0.8186 (t70)
REVERT: B   19 ARG cc_start: 0.8329 (tmm160) cc_final: 0.7850 (tmm160)
REVERT: B   20 ASP cc_start: 0.9176 (OUTLIER) cc_final: 0.8517 (m-30)
REVERT: B  130 GLU cc_start: 0.8569 (mp0) cc_final: 0.8366 (mp0)
REVERT: B  259 GLN cc_start: 0.8456 (pt0) cc_final: 0.8217 (pt0)
REVERT: B  262 MET cc_start: 0.8950 (mmt) cc_final: 0.8670 (tpp)
REVERT: G   18 GLN cc_start: 0.7883 (tp40) cc_final: 0.7584 (tp40)
REVERT: G   21 MET cc_start: 0.9013 (tmm) cc_final: 0.8771 (tmt)
REVERT: G   22 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7722 (tm-30)
REVERT: G   47 GLU cc_start: 0.8610 (mp0) cc_final: 0.8133 (tm-30)
REVERT: S  144 THR cc_start: 0.7423 (OUTLIER) cc_final: 0.7130 (p)
REVERT: S  218 ARG cc_start: 0.8242 (mmp80) cc_final: 0.7943 (mmp80)
  outliers start: 17
  outliers final: 7
  residues processed: 167
  average time/residue: 1.2213
  time to fit residues: 217.3363
Evaluate side-chains
  154 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 145
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain C residue  307 PHE
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 49 optimal weight:    0.3980
   chunk 58 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 109 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
** S 142 GLN ** 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 = 0.3707 r_free = 0.3707 target = 0.112429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.081011 restraints weight = 16148.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 3.26
r_work: 0.3060 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8988  Z= 0.193
  Angle     :  0.700  12.284  12186  Z= 0.346
  Chirality :  0.048   0.548   1380
  Planarity :  0.004   0.055   1541
  Dihedral  :  4.673  50.836   1237
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 21.24 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.28 %
    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 (0.26), residues: 1105
  helix:  1.53 (0.28), residues: 387
  sheet: -0.51 (0.31), residues: 281
  loop : -1.31 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A  43 
 HIS   0.003   0.001   HIS C 188 
 PHE   0.015   0.001   PHE E   6 
 TYR   0.023   0.001   TYR A 190 
 ARG   0.011   0.000   ARG S 160 

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 148
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: A  114 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6435 (tpp)
REVERT: A  295 HIS cc_start: 0.8411 (t70) cc_final: 0.8168 (t70)
REVERT: B   19 ARG cc_start: 0.8364 (tmm160) cc_final: 0.8071 (tmm160)
REVERT: B  130 GLU cc_start: 0.8593 (mp0) cc_final: 0.8276 (mp0)
REVERT: G   18 GLN cc_start: 0.7871 (tp40) cc_final: 0.7572 (tp40)
REVERT: G   21 MET cc_start: 0.8889 (tmm) cc_final: 0.8563 (tmt)
REVERT: G   22 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7644 (tm-30)
REVERT: G   47 GLU cc_start: 0.8595 (mp0) cc_final: 0.8128 (tm-30)
REVERT: S  144 THR cc_start: 0.7505 (OUTLIER) cc_final: 0.7246 (p)
  outliers start: 18
  outliers final: 7
  residues processed: 158
  average time/residue: 1.3320
  time to fit residues: 223.7730
Evaluate side-chains
  150 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 141
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 66 optimal weight:    0.4980
   chunk 96 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 101 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 208 ASN
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 142 GLN ** 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 = 0.3645 r_free = 0.3645 target = 0.110406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.078878 restraints weight = 16713.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 3.38
r_work: 0.2989 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8988  Z= 0.238
  Angle     :  0.726  12.361  12186  Z= 0.360
  Chirality :  0.049   0.540   1380
  Planarity :  0.005   0.058   1541
  Dihedral  :  4.746  49.863   1237
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 22.42 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.28 %
    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: -0.23 (0.26), residues: 1105
  helix:  1.51 (0.28), residues: 387
  sheet: -0.56 (0.30), residues: 286
  loop : -1.38 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A  43 
 HIS   0.002   0.001   HIS S 232 
 PHE   0.012   0.001   PHE E   6 
 TYR   0.025   0.001   TYR A 190 
 ARG   0.011   0.000   ARG S 160 

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 1.074 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: A  114 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6431 (tpp)
REVERT: A  295 HIS cc_start: 0.8522 (t70) cc_final: 0.8290 (t70)
REVERT: B  130 GLU cc_start: 0.8505 (mp0) cc_final: 0.8262 (mp0)
REVERT: G   18 GLN cc_start: 0.7742 (tp40) cc_final: 0.7522 (tp40)
REVERT: G   21 MET cc_start: 0.8830 (tmm) cc_final: 0.8486 (tmt)
REVERT: G   22 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7532 (tm-30)
REVERT: G   47 GLU cc_start: 0.8607 (mp0) cc_final: 0.8053 (tm-30)
REVERT: S   83 MET cc_start: 0.8474 (mmt) cc_final: 0.8058 (tpp)
REVERT: S  144 THR cc_start: 0.7392 (OUTLIER) cc_final: 0.7139 (p)
REVERT: S  218 ARG cc_start: 0.8113 (mmp80) cc_final: 0.7872 (mmp80)
REVERT: E    5 THR cc_start: 0.8185 (m) cc_final: 0.7984 (p)
  outliers start: 20
  outliers final: 6
  residues processed: 151
  average time/residue: 1.2637
  time to fit residues: 203.2488
Evaluate side-chains
  144 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 136
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 100 optimal weight:    9.9990
   chunk 92 optimal weight:    0.0770
   chunk 16 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0870
   chunk 91 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.8120

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

Flipped N/Q/H residues before XYZ refinement:
A 208 ASN
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
** S 142 GLN ** 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 = 0.3657 r_free = 0.3657 target = 0.111252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.079834 restraints weight = 16721.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 3.37
r_work: 0.2993 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8988  Z= 0.202
  Angle     :  0.744  12.317  12186  Z= 0.366
  Chirality :  0.048   0.526   1380
  Planarity :  0.005   0.061   1541
  Dihedral  :  4.691  49.146   1237
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 23.18 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.28 %
    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: -0.22 (0.26), residues: 1105
  helix:  1.51 (0.28), residues: 387
  sheet: -0.50 (0.31), residues: 278
  loop : -1.39 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP A  43 
 HIS   0.001   0.000   HIS A 295 
 PHE   0.009   0.001   PHE E   6 
 TYR   0.028   0.001   TYR A 190 
 ARG   0.013   0.001   ARG S 160 

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: A  114 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.6383 (tpp)
REVERT: A  295 HIS cc_start: 0.8504 (t70) cc_final: 0.8285 (t70)
REVERT: B  130 GLU cc_start: 0.8500 (mp0) cc_final: 0.8283 (mp0)
REVERT: G   13 ARG cc_start: 0.8593 (pmt170) cc_final: 0.8210 (pmt170)
REVERT: G   17 GLU cc_start: 0.9406 (tp30) cc_final: 0.8966 (pt0)
REVERT: G   18 GLN cc_start: 0.7713 (tp40) cc_final: 0.7415 (tp40)
REVERT: G   21 MET cc_start: 0.8825 (tmm) cc_final: 0.8438 (tmt)
REVERT: G   22 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7598 (tm-30)
REVERT: S   83 MET cc_start: 0.8485 (mmt) cc_final: 0.8175 (tpp)
REVERT: S  144 THR cc_start: 0.7372 (OUTLIER) cc_final: 0.7144 (p)
REVERT: S  218 ARG cc_start: 0.8133 (mmp80) cc_final: 0.7858 (mmp80)
REVERT: E    5 THR cc_start: 0.8230 (m) cc_final: 0.8003 (p)
  outliers start: 18
  outliers final: 10
  residues processed: 154
  average time/residue: 1.3744
  time to fit residues: 225.5277
Evaluate side-chains
  150 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 19 optimal weight:    0.0070
   chunk 91 optimal weight:   10.0000
   chunk 66 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 107 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9980
   chunk 109 optimal weight:    0.7980
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
A 208 ASN
** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 188 HIS
** S 142 GLN ** 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 = 0.3668 r_free = 0.3668 target = 0.112088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.080433 restraints weight = 16563.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 3.39
r_work: 0.3016 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8988  Z= 0.198
  Angle     :  0.764  12.273  12186  Z= 0.372
  Chirality :  0.048   0.522   1380
  Planarity :  0.005   0.064   1541
  Dihedral  :  4.652  48.643   1237
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 24.14 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.28 %
    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: -0.26 (0.26), residues: 1105
  helix:  1.44 (0.28), residues: 387
  sheet: -0.53 (0.31), residues: 280
  loop : -1.36 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A  43 
 HIS   0.002   0.000   HIS A 329 
 PHE   0.009   0.001   PHE B 292 
 TYR   0.027   0.001   TYR A 190 
 ARG   0.014   0.001   ARG S 160 

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: A  114 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6373 (tpp)
REVERT: A  295 HIS cc_start: 0.8511 (t70) cc_final: 0.8292 (t70)
REVERT: B   19 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7739 (ttp80)
REVERT: B   61 MET cc_start: 0.9101 (pp-130) cc_final: 0.8822 (pp-130)
REVERT: B  130 GLU cc_start: 0.8461 (mp0) cc_final: 0.8259 (mp0)
REVERT: B  215 GLU cc_start: 0.8657 (mp0) cc_final: 0.8363 (pm20)
REVERT: G   13 ARG cc_start: 0.8584 (pmt170) cc_final: 0.8364 (pmm-80)
REVERT: G   18 GLN cc_start: 0.7755 (tp40) cc_final: 0.7529 (tp40)
REVERT: G   21 MET cc_start: 0.8828 (tmm) cc_final: 0.8448 (tmt)
REVERT: G   22 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7601 (tm-30)
REVERT: S  144 THR cc_start: 0.7440 (OUTLIER) cc_final: 0.7219 (p)
REVERT: S  218 ARG cc_start: 0.8140 (mmp80) cc_final: 0.7862 (mmp80)
  outliers start: 11
  outliers final: 7
  residues processed: 152
  average time/residue: 1.3073
  time to fit residues: 211.1745
Evaluate side-chains
  143 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 134
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 37 optimal weight:    8.9990
   chunk 71 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0170
   chunk 66 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 99 optimal weight:    6.9990
   chunk 57 optimal weight:    0.8980
   chunk 98 optimal weight:    0.4980
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
A 208 ASN
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 142 GLN ** 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 = 0.3671 r_free = 0.3671 target = 0.112386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.080774 restraints weight = 16560.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 3.39
r_work: 0.3020 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8988  Z= 0.198
  Angle     :  0.780  12.310  12186  Z= 0.379
  Chirality :  0.048   0.519   1380
  Planarity :  0.005   0.066   1541
  Dihedral  :  4.613  48.445   1237
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 24.68 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.28 %
    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: -0.26 (0.26), residues: 1105
  helix:  1.44 (0.28), residues: 387
  sheet: -0.54 (0.31), residues: 279
  loop : -1.35 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A  43 
 HIS   0.003   0.001   HIS C 188 
 PHE   0.018   0.001   PHE S  68 
 TYR   0.026   0.001   TYR A 190 
 ARG   0.015   0.001   ARG S 160 

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: A  114 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6353 (tpp)
REVERT: A  295 HIS cc_start: 0.8508 (t70) cc_final: 0.8282 (t70)
REVERT: C  313 ARG cc_start: 0.8994 (ptp-110) cc_final: 0.8792 (ptp-110)
REVERT: B   19 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7742 (ttp80)
REVERT: B  217 MET cc_start: 0.8087 (ptm) cc_final: 0.7855 (ppp)
REVERT: G   13 ARG cc_start: 0.8585 (pmt170) cc_final: 0.7787 (pmm-80)
REVERT: G   17 GLU cc_start: 0.9411 (tp30) cc_final: 0.9011 (pm20)
REVERT: G   18 GLN cc_start: 0.7738 (tp40) cc_final: 0.7417 (tp40)
REVERT: G   21 MET cc_start: 0.8838 (tmm) cc_final: 0.8441 (tmt)
REVERT: G   22 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7543 (tm-30)
REVERT: S  144 THR cc_start: 0.7430 (OUTLIER) cc_final: 0.7207 (p)
REVERT: S  218 ARG cc_start: 0.8150 (mmp80) cc_final: 0.7687 (mmp80)
  outliers start: 11
  outliers final: 8
  residues processed: 145
  average time/residue: 1.3051
  time to fit residues: 200.8387
Evaluate side-chains
  144 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   chunk 92 optimal weight:    0.0050
   chunk 25 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 105 optimal weight:    2.9990
   chunk 63 optimal weight:    0.4980
   chunk 102 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
A 208 ASN
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 188 HIS
** S 142 GLN ** 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 = 0.3678 r_free = 0.3678 target = 0.112878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.081346 restraints weight = 16642.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 3.41
r_work: 0.3032 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8988  Z= 0.197
  Angle     :  0.789  12.319  12186  Z= 0.380
  Chirality :  0.048   0.514   1380
  Planarity :  0.004   0.066   1541
  Dihedral  :  4.601  48.323   1237
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 24.57 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.28 %
    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: -0.23 (0.26), residues: 1105
  helix:  1.45 (0.28), residues: 387
  sheet: -0.55 (0.31), residues: 279
  loop : -1.30 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP A  43 
 HIS   0.002   0.000   HIS A 181 
 PHE   0.021   0.001   PHE S  68 
 TYR   0.027   0.001   TYR C 290 
 ARG   0.015   0.000   ARG S 160 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6513.46 seconds
wall clock time: 113 minutes 20.10 seconds (6800.10 seconds total)