Starting phenix.real_space_refine
on Fri Feb 14 21:08:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y67_33636/02_2025/7y67_33636_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y67_33636/02_2025/7y67_33636.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y67_33636/02_2025/7y67_33636.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y67_33636/02_2025/7y67_33636.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y67_33636/02_2025/7y67_33636_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y67_33636/02_2025/7y67_33636_neut.cif"
  }
  resolution = 2.8
  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=   0.002 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2047 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      59      5.16       5
     C    5675      2.51       5
     N    1514      2.21       5
     O    1641      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8889
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1803
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2611
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "D"
      Number of atoms: 2197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2197
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 11, 'TRANS': 266}
          Chain breaks: 1
    Chain: "S"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1777
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 53
          Classifications: {'peptide': 5}
          Link IDs: {'PTRANS': 1, 'TRANS': 3}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'ZAL:plan-1': 1, 'MEA:plan-2': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "L"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1, 'PEPT-D': 1}
  Time building chain proxies: 5.82, per 1000 atoms: 0.65
  Number of scatterers: 8889
  At special positions: 0
  Unit cell: (95.2, 123.25, 132.6, 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      59     16.00
     O    1641      8.00
     N    1514      7.00
     C    5675      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 109 " - pdb=" SG  CYS D 188 " 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=0, symmetry=0
  Time building additional restraints: 2.40
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DAR L   6 "
      Input volumes are d-peptide like
        pdb=" CB  ZAL L   4 "
  Number of C-beta restraints generated:  2120

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 13 sheets defined
      37.7% alpha, 21.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 30
      removed outlier: 3.734A  pdb=" N   LYS A  10 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ALA A  30 " --> pdb=" O   ASP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 215
      removed outlier: 4.488A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 278
      removed outlier: 3.857A  pdb=" N   PHE A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 4.165A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.605A  pdb=" N   PHE A 334 " --> pdb=" O   LYS A 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 25
      removed outlier: 3.736A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 23
    Processing helix  chain 'C' and resid 29 through 45
      removed outlier: 3.653A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 48
      No H-bonds generated for 'chain 'C' and resid 46 through 48'
    Processing helix  chain 'C' and resid 55 through 59
      removed outlier: 3.562A  pdb=" N   ASN C  59 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 65
      removed outlier: 3.650A  pdb=" N   ILE D  38 " --> pdb=" O   ARG D  34 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU D  39 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLU D  65 " --> pdb=" O   VAL D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 71 through 88
      removed outlier: 3.784A  pdb=" N   PHE D  75 " --> pdb=" O   ASN D  71 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ASN D  77 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU D  78 " --> pdb=" O   TRP D  74 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ALA D  88 " --> pdb=" O   LEU D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 88 through 98
      removed outlier: 3.795A  pdb=" N   LEU D  92 " --> pdb=" O   ALA D  88 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLN D  98 " --> pdb=" O   THR D  94 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 110
    Processing helix  chain 'D' and resid 117 through 139
      removed outlier: 3.749A  pdb=" N   TYR D 121 " --> pdb=" O   LEU D 117 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   SER D 123 " --> pdb=" O   ASN D 119 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 147
      removed outlier: 3.778A  pdb=" N   CYS D 144 " --> pdb=" O   LYS D 140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 149 through 174
      removed outlier: 3.679A  pdb=" N   ALA D 153 " --> pdb=" O   GLY D 149 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ALA D 164 " --> pdb=" O   ALA D 160 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LEU D 165 " --> pdb=" O   TRP D 161 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LEU D 166 " --> pdb=" O   GLY D 162 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LEU D 167 " --> pdb=" O   LEU D 163 " (cutoff:3.500A)
      Proline residue:  D 170  - end of helix
    Processing helix  chain 'D' and resid 196 through 231
      Proline residue:  D 214  - end of helix
    Processing helix  chain 'D' and resid 238 through 268
      removed outlier: 3.503A  pdb=" N   LYS D 242 " --> pdb=" O   THR D 238 " (cutoff:3.500A)
      Proline residue:  D 257  - end of helix
      removed outlier: 3.591A  pdb=" N   MET D 264 " --> pdb=" O   VAL D 260 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 272 through 288
      removed outlier: 4.560A  pdb=" N   SER D 283 " --> pdb=" O   LYS D 279 " (cutoff:3.500A)
      removed outlier: 5.145A  pdb=" N   LEU D 284 " --> pdb=" O   LYS D 280 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 289 through 303
      removed outlier: 3.946A  pdb=" N   CYS D 293 " --> pdb=" O   ALA D 289 " (cutoff:3.500A)
      Proline residue:  D 297  - end of helix
      removed outlier: 3.933A  pdb=" N   TYR D 300 " --> pdb=" O   ASN D 296 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 306 through 314
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.565A  pdb=" N   SER S  31 " --> pdb=" O   ALA S  28 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 62 through 65
      removed outlier: 3.520A  pdb=" N   LYS S  65 " --> pdb=" O   ASP S  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 62 through 65'
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 4.137A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.655A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.282A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.875A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.573A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.875A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.897A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.958A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 7.243A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.551A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 175 through 178
      removed outlier: 4.568A  pdb=" N   VAL D 190 " --> pdb=" O   LYS L   2 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LYS L   2 " --> pdb=" O   VAL D 190 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 6.834A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.072A  pdb=" N   VAL S 147 " --> pdb=" O   GLU S 246 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
      removed outlier: 5.968A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.477A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 160

    414 hydrogen bonds defined for protein.
    1176 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: 2.40

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2858
        1.35 -     1.47: 2244
        1.47 -     1.58: 3891
        1.58 -     1.70: 1
        1.70 -     1.82: 83
  Bond restraints: 9077
  Sorted by residual:
  bond pdb=" C   MEA L   1 "
       pdb=" N   LYS L   2 "
    ideal  model  delta    sigma   weight residual
    1.329  1.390 -0.061 1.40e-02 5.10e+03 1.92e+01
  bond pdb=" N   ARG A 208 "
       pdb=" CA  ARG A 208 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.30e-02 5.92e+03 7.66e+00
  bond pdb=" CB  PRO S  75 "
       pdb=" CG  PRO S  75 "
    ideal  model  delta    sigma   weight residual
    1.492  1.597 -0.105 5.00e-02 4.00e+02 4.39e+00
  bond pdb=" CE1 HIS D 100 "
       pdb=" NE2 HIS D 100 "
    ideal  model  delta    sigma   weight residual
    1.321  1.338 -0.017 1.00e-02 1.00e+04 2.81e+00
  bond pdb=" N   LYS D 279 "
       pdb=" CA  LYS D 279 "
    ideal  model  delta    sigma   weight residual
    1.458  1.479 -0.021 1.30e-02 5.92e+03 2.60e+00
  ... (remaining 9072 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.86: 12279
        4.86 -     9.73: 17
        9.73 -    14.59: 0
       14.59 -    19.46: 0
       19.46 -    24.32: 3
  Bond angle restraints: 12299
  Sorted by residual:
  angle pdb=" O   MEA L   1 "
        pdb=" C   MEA L   1 "
        pdb=" N   LYS L   2 "
      ideal   model   delta    sigma   weight residual
     123.00   99.93   23.07 1.60e+00 3.91e-01 2.08e+02
  angle pdb=" CA  MEA L   1 "
        pdb=" C   MEA L   1 "
        pdb=" N   LYS L   2 "
      ideal   model   delta    sigma   weight residual
     116.20  140.52  -24.32 2.00e+00 2.50e-01 1.48e+02
  angle pdb=" C   MEA L   1 "
        pdb=" N   LYS L   2 "
        pdb=" CA  LYS L   2 "
      ideal   model   delta    sigma   weight residual
     121.70  142.91  -21.21 1.80e+00 3.09e-01 1.39e+02
  angle pdb=" CA  PRO S  75 "
        pdb=" N   PRO S  75 "
        pdb=" CD  PRO S  75 "
      ideal   model   delta    sigma   weight residual
     112.00  104.63    7.37 1.40e+00 5.10e-01 2.77e+01
  angle pdb=" N   LYS D 279 "
        pdb=" CA  LYS D 279 "
        pdb=" C   LYS D 279 "
      ideal   model   delta    sigma   weight residual
     112.23  106.24    5.99 1.26e+00 6.30e-01 2.26e+01
  ... (remaining 12294 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.34: 5130
       25.34 -    50.67: 218
       50.67 -    76.01: 14
       76.01 -   101.35: 5
      101.35 -   126.68: 1
  Dihedral angle restraints: 5368
    sinusoidal: 2086
      harmonic: 3282
  Sorted by residual:
  dihedral pdb=" CD  DAR L   6 "
           pdb=" NE  DAR L   6 "
           pdb=" CZ  DAR L   6 "
           pdb=" NH1 DAR L   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00 -126.68  126.68     1      1.00e+01 1.00e-02 1.53e+02
  dihedral pdb=" CA  ZAL L   4 "
           pdb=" C   ZAL L   4 "
           pdb=" N   TRP L   5 "
           pdb=" CA  TRP L   5 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.08  -28.92     0      5.00e+00 4.00e-02 3.35e+01
  dihedral pdb=" CA  TRP B 297 "
           pdb=" C   TRP B 297 "
           pdb=" N   ASP B 298 "
           pdb=" CA  ASP B 298 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.00   17.00     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 5365 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 853
       0.030 -    0.059: 338
       0.059 -    0.089: 128
       0.089 -    0.119: 67
       0.119 -    0.148: 16
  Chirality restraints: 1402
  Sorted by residual:
  chirality pdb=" CA  HIS D 100 "
            pdb=" N   HIS D 100 "
            pdb=" C   HIS D 100 "
            pdb=" CB  HIS D 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.50e-01
  chirality pdb=" CA  ILE A 265 "
            pdb=" N   ILE A 265 "
            pdb=" C   ILE A 265 "
            pdb=" CB  ILE A 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.66e-01
  chirality pdb=" C1  ZAL L   4 "
            pdb=" CB  ZAL L   4 "
            pdb=" C2  ZAL L   4 "
            pdb=" C6  ZAL L   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.73    0.13 2.00e-01 2.50e+01 4.45e-01
  ... (remaining 1399 not shown)

  Planarity restraints: 1548
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  DAR L   6 "   -0.905 9.50e-02 1.11e+02   4.06e-01 9.95e+01
        pdb=" NE  DAR L   6 "    0.052 2.00e-02 2.50e+03
        pdb=" CZ  DAR L   6 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 DAR L   6 "   -0.024 2.00e-02 2.50e+03
        pdb=" NH2 DAR L   6 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "    0.078 5.00e-02 4.00e+02   1.14e-01 2.09e+01
        pdb=" N   PRO S  75 "   -0.198 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "    0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MEA L   1 "   -0.022 2.00e-02 2.50e+03   3.50e-02 1.22e+01
        pdb=" C   MEA L   1 "    0.060 2.00e-02 2.50e+03
        pdb=" O   MEA L   1 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LYS L   2 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 1545 not shown)

  Histogram of nonbonded interaction distances:
        1.33 -     2.04: 2
        2.04 -     2.76: 1178
        2.76 -     3.47: 11769
        3.47 -     4.19: 19275
        4.19 -     4.90: 35114
  Nonbonded interactions: 67338
  Sorted by model distance:
  nonbonded pdb=" C   TRP L   5 "
            pdb=" N   DAR L   6 "
     model   vdw
     1.329 3.350
  nonbonded pdb=" O   THR A 327 "
            pdb=" OD1 ASP A 328 "
     model   vdw
     1.877 3.040
  nonbonded pdb=" O   ZAL L   4 "
            pdb=" O   TRP L   5 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   TRP L   5 "
            pdb=" N   DAR L   6 "
     model   vdw
     2.248 3.120
  ... (remaining 67333 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     23.160
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.105   9077  Z= 0.199
  Angle     :  0.691  24.323  12299  Z= 0.388
  Chirality :  0.042   0.148   1402
  Planarity :  0.011   0.406   1548
  Dihedral  : 13.096 126.683   3242
  Min Nonbonded Distance : 1.329

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.21 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.25), residues: 1114
  helix:  2.03 (0.28), residues: 367
  sheet:  0.71 (0.31), residues: 296
  loop : -1.25 (0.25), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L   5 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.017   0.001   PHE S 177 
 TYR   0.018   0.001   TYR D 300 
 ARG   0.007   0.000   ARG D 200 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 213
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.7670 (tp) cc_final: 0.7431 (tp)
REVERT: A   25 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6417 (tm-30)
REVERT: A   26 ASP cc_start: 0.6825 (m-30) cc_final: 0.6336 (m-30)
REVERT: A   33 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6639 (mm-30)
REVERT: A  197 LYS cc_start: 0.7350 (tppt) cc_final: 0.6909 (tptp)
REVERT: A  248 LYS cc_start: 0.7453 (ttpp) cc_final: 0.7105 (mtpp)
REVERT: A  252 SER cc_start: 0.7869 (m) cc_final: 0.7645 (m)
REVERT: A  261 ASP cc_start: 0.6431 (t0) cc_final: 0.6159 (t0)
REVERT: B  212 ASP cc_start: 0.7003 (t70) cc_final: 0.6750 (t0)
REVERT: B  217 MET cc_start: 0.6469 (ppp) cc_final: 0.6085 (ppp)
REVERT: B  237 ASN cc_start: 0.7553 (t0) cc_final: 0.7343 (t0)
REVERT: B  331 SER cc_start: 0.8069 (p) cc_final: 0.7802 (p)
REVERT: D  282 ASP cc_start: 0.7911 (t70) cc_final: 0.7541 (t70)
REVERT: S   21 SER cc_start: 0.8323 (m) cc_final: 0.8028 (p)
REVERT: S  119 VAL cc_start: 0.8728 (t) cc_final: 0.8411 (p)
REVERT: S  193 SER cc_start: 0.7595 (m) cc_final: 0.7336 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 214
  average time/residue: 1.1805
  time to fit residues: 270.4257
Evaluate side-chains
  173 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0970
   chunk 46 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0980
   chunk 44 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0670
   chunk 33 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 64 optimal weight:    0.4980
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.3116

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 125 ASN
B 340 ASN
C  59 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.135387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.113996 restraints weight = 13196.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.01
r_work: 0.3418 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.1093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9077  Z= 0.146
  Angle     :  0.514   6.332  12299  Z= 0.268
  Chirality :  0.041   0.136   1402
  Planarity :  0.004   0.062   1548
  Dihedral  :  6.682 177.797   1235
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 12.99 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.25), residues: 1114
  helix:  2.05 (0.27), residues: 382
  sheet:  0.64 (0.31), residues: 290
  loop : -1.24 (0.25), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 211 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.016   0.001   PHE B 234 
 TYR   0.016   0.001   TYR S 190 
 ARG   0.008   0.000   ARG S  98 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 177
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A   23 LEU cc_start: 0.7864 (tp) cc_final: 0.7628 (tp)
REVERT: A   25 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7092 (tm-30)
REVERT: A   26 ASP cc_start: 0.7598 (m-30) cc_final: 0.7189 (m-30)
REVERT: A  229 ASP cc_start: 0.7635 (m-30) cc_final: 0.7351 (t0)
REVERT: A  248 LYS cc_start: 0.7896 (ttpp) cc_final: 0.7495 (mtpp)
REVERT: A  261 ASP cc_start: 0.7288 (t0) cc_final: 0.6965 (t0)
REVERT: B  187 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8313 (t)
REVERT: B  212 ASP cc_start: 0.7565 (t70) cc_final: 0.7241 (t0)
REVERT: B  217 MET cc_start: 0.7701 (ppp) cc_final: 0.7186 (ppp)
REVERT: B  237 ASN cc_start: 0.7856 (t0) cc_final: 0.7589 (t0)
REVERT: D  253 ILE cc_start: 0.8186 (mt) cc_final: 0.7980 (pt)
REVERT: D  263 ILE cc_start: 0.8119 (tp) cc_final: 0.7877 (tp)
REVERT: D  282 ASP cc_start: 0.8223 (t70) cc_final: 0.7837 (t70)
REVERT: S    6 GLU cc_start: 0.7871 (mp0) cc_final: 0.7418 (mp0)
REVERT: S   21 SER cc_start: 0.8584 (m) cc_final: 0.8242 (p)
REVERT: S  119 VAL cc_start: 0.8769 (t) cc_final: 0.8493 (p)
REVERT: S  154 SER cc_start: 0.8442 (p) cc_final: 0.8181 (m)
REVERT: S  192 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8047 (ttp)
  outliers start: 16
  outliers final: 8
  residues processed: 187
  average time/residue: 1.1665
  time to fit residues: 233.0826
Evaluate side-chains
  183 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 173
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 LYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 106 optimal weight:    0.0050
   chunk 0 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 95 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.9398

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
B  54 HIS
B  75 GLN
B 125 ASN
C  44 HIS
C  59 ASN
D 145 GLN
S  35 HIS
S 142 GLN
S 186 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.130275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.108195 restraints weight = 13149.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.04
r_work: 0.3329 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   9077  Z= 0.236
  Angle     :  0.562   6.715  12299  Z= 0.295
  Chirality :  0.042   0.136   1402
  Planarity :  0.004   0.052   1548
  Dihedral  :  6.666 178.257   1235
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 13.93 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.25), residues: 1114
  helix:  2.02 (0.27), residues: 382
  sheet:  0.69 (0.31), residues: 294
  loop : -1.33 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP S  47 
 HIS   0.006   0.001   HIS B  62 
 PHE   0.017   0.002   PHE A 189 
 TYR   0.022   0.002   TYR D 300 
 ARG   0.010   0.001   ARG S  98 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 191
  time to evaluate  : 0.930 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7298 (tm-30)
REVERT: A   26 ASP cc_start: 0.7729 (m-30) cc_final: 0.7372 (m-30)
REVERT: A   33 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7351 (mm-30)
REVERT: A  240 MET cc_start: 0.6511 (mmp) cc_final: 0.5938 (mmp)
REVERT: A  248 LYS cc_start: 0.7856 (ttpp) cc_final: 0.7579 (mtpp)
REVERT: A  261 ASP cc_start: 0.7341 (t0) cc_final: 0.7052 (t0)
REVERT: A  304 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7986 (tt0)
REVERT: B   52 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7864 (mtp85)
REVERT: B  129 ARG cc_start: 0.6450 (tpm170) cc_final: 0.6080 (tpt90)
REVERT: B  187 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8308 (t)
REVERT: B  212 ASP cc_start: 0.7626 (t70) cc_final: 0.7289 (t70)
REVERT: B  217 MET cc_start: 0.7753 (ppp) cc_final: 0.7188 (ppp)
REVERT: B  228 ASP cc_start: 0.7863 (m-30) cc_final: 0.7534 (p0)
REVERT: B  254 ASP cc_start: 0.7736 (t70) cc_final: 0.7284 (t0)
REVERT: B  303 ASP cc_start: 0.7703 (m-30) cc_final: 0.7492 (m-30)
REVERT: D   82 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6955 (t70)
REVERT: D  236 ARG cc_start: 0.8503 (ttp-110) cc_final: 0.8280 (ttp-110)
REVERT: D  282 ASP cc_start: 0.8391 (t70) cc_final: 0.8016 (t70)
REVERT: S   21 SER cc_start: 0.8585 (m) cc_final: 0.8252 (p)
REVERT: S  119 VAL cc_start: 0.8866 (t) cc_final: 0.8523 (p)
REVERT: S  154 SER cc_start: 0.8487 (p) cc_final: 0.8257 (m)
REVERT: S  192 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8098 (ttp)
  outliers start: 29
  outliers final: 11
  residues processed: 207
  average time/residue: 1.1264
  time to fit residues: 249.3981
Evaluate side-chains
  201 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 186
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   82 ASP
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain D residue  265 MET
Chi-restraints excluded: chain D residue  287 SER
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  192 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0060
   chunk 82 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
B  75 GLN
B 237 ASN
C  59 ASN
D 145 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.130822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.108986 restraints weight = 13039.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.01
r_work: 0.3344 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9077  Z= 0.186
  Angle     :  0.517   8.224  12299  Z= 0.272
  Chirality :  0.041   0.130   1402
  Planarity :  0.004   0.046   1548
  Dihedral  :  6.597 178.779   1235
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 17.88 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.25), residues: 1114
  helix:  2.29 (0.27), residues: 375
  sheet:  0.65 (0.31), residues: 290
  loop : -1.31 (0.25), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP S  47 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.016   0.001   TYR D 300 
 ARG   0.004   0.000   ARG B  68 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 185
  time to evaluate  : 1.016 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7426 (tm-30)
REVERT: A  197 LYS cc_start: 0.8155 (tppp) cc_final: 0.7794 (mmmm)
REVERT: A  229 ASP cc_start: 0.7701 (m-30) cc_final: 0.7452 (t0)
REVERT: A  240 MET cc_start: 0.6521 (mmp) cc_final: 0.5982 (mmp)
REVERT: A  248 LYS cc_start: 0.7842 (ttpp) cc_final: 0.7603 (mtpp)
REVERT: A  261 ASP cc_start: 0.7338 (t0) cc_final: 0.7032 (t0)
REVERT: A  304 GLN cc_start: 0.8312 (tm-30) cc_final: 0.8001 (tt0)
REVERT: B   52 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7851 (mtp85)
REVERT: B  187 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8312 (t)
REVERT: B  212 ASP cc_start: 0.7635 (t70) cc_final: 0.7329 (t70)
REVERT: B  217 MET cc_start: 0.7792 (ppp) cc_final: 0.7273 (ppp)
REVERT: B  228 ASP cc_start: 0.7820 (m-30) cc_final: 0.7553 (p0)
REVERT: B  254 ASP cc_start: 0.7723 (t70) cc_final: 0.7295 (t0)
REVERT: B  303 ASP cc_start: 0.7700 (m-30) cc_final: 0.7487 (m-30)
REVERT: D   41 LEU cc_start: 0.8225 (tp) cc_final: 0.7977 (mm)
REVERT: D   82 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6952 (t70)
REVERT: D  236 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.8286 (ttp-110)
REVERT: D  263 ILE cc_start: 0.8136 (tp) cc_final: 0.7918 (tp)
REVERT: D  282 ASP cc_start: 0.8404 (t70) cc_final: 0.8039 (t70)
REVERT: S   21 SER cc_start: 0.8561 (m) cc_final: 0.8252 (p)
REVERT: S  119 VAL cc_start: 0.8858 (t) cc_final: 0.8510 (p)
REVERT: S  154 SER cc_start: 0.8502 (p) cc_final: 0.8274 (m)
REVERT: S  192 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8132 (ttp)
  outliers start: 29
  outliers final: 13
  residues processed: 197
  average time/residue: 1.1524
  time to fit residues: 242.8605
Evaluate side-chains
  196 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 179
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   82 ASP
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  265 MET
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  210 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0980
   chunk 14 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 93 optimal weight:    0.4980
   chunk 1 optimal weight:    0.9980
   chunk 104 optimal weight:    0.0570
   chunk 74 optimal weight:    0.0170
   chunk 42 optimal weight:    5.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.2936

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
B  75 GLN
B 268 ASN
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 145 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.133874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.112088 restraints weight = 13057.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.03
r_work: 0.3382 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9077  Z= 0.127
  Angle     :  0.481  10.543  12299  Z= 0.251
  Chirality :  0.040   0.140   1402
  Planarity :  0.003   0.044   1548
  Dihedral  :  6.451 179.978   1235
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.54 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.25), residues: 1114
  helix:  2.43 (0.27), residues: 374
  sheet:  0.71 (0.31), residues: 288
  loop : -1.28 (0.25), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP S 176 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.014   0.001   TYR D 300 
 ARG   0.011   0.000   ARG S  98 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 192
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7415 (tm-30)
REVERT: A  229 ASP cc_start: 0.7630 (m-30) cc_final: 0.7327 (t0)
REVERT: A  240 MET cc_start: 0.6537 (mmp) cc_final: 0.6001 (mmp)
REVERT: A  248 LYS cc_start: 0.7857 (ttpp) cc_final: 0.7635 (mtpp)
REVERT: A  261 ASP cc_start: 0.7287 (t0) cc_final: 0.6976 (t0)
REVERT: A  304 GLN cc_start: 0.8283 (tm-30) cc_final: 0.8036 (tt0)
REVERT: B  129 ARG cc_start: 0.6197 (tpm170) cc_final: 0.5848 (tpt-90)
REVERT: B  187 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8275 (t)
REVERT: B  212 ASP cc_start: 0.7607 (t70) cc_final: 0.7347 (t70)
REVERT: B  217 MET cc_start: 0.7803 (ppp) cc_final: 0.7276 (ppp)
REVERT: B  254 ASP cc_start: 0.7724 (t70) cc_final: 0.7309 (t0)
REVERT: B  303 ASP cc_start: 0.7639 (m-30) cc_final: 0.7426 (m-30)
REVERT: D   82 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6946 (t70)
REVERT: D  236 ARG cc_start: 0.8546 (ttp-110) cc_final: 0.8325 (ttp-110)
REVERT: D  263 ILE cc_start: 0.8142 (tp) cc_final: 0.7898 (tp)
REVERT: D  282 ASP cc_start: 0.8359 (t70) cc_final: 0.8022 (t70)
REVERT: S   21 SER cc_start: 0.8595 (m) cc_final: 0.8294 (p)
REVERT: S  119 VAL cc_start: 0.8860 (t) cc_final: 0.8517 (p)
REVERT: S  154 SER cc_start: 0.8462 (p) cc_final: 0.8228 (m)
REVERT: S  192 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8071 (ttp)
  outliers start: 26
  outliers final: 12
  residues processed: 202
  average time/residue: 1.1670
  time to fit residues: 253.3258
Evaluate side-chains
  202 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 187
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   82 ASP
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  280 LYS
Chi-restraints excluded: chain D residue  287 SER
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  210 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 68 optimal weight:    0.0050
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.1398

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
B  75 GLN
B 237 ASN
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.130023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.108053 restraints weight = 13031.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 2.02
r_work: 0.3306 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   9077  Z= 0.268
  Angle     :  0.579  12.134  12299  Z= 0.302
  Chirality :  0.043   0.132   1402
  Planarity :  0.004   0.073   1548
  Dihedral  :  6.663 179.972   1235
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 20.37 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.64 (0.25), residues: 1114
  helix:  2.23 (0.27), residues: 376
  sheet:  0.61 (0.31), residues: 301
  loop : -1.39 (0.25), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP S  47 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.018   0.002   PHE A 189 
 TYR   0.014   0.002   TYR D 300 
 ARG   0.005   0.000   ARG B  68 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 185
  time to evaluate  : 0.986 
Fit side-chains
REVERT: A  229 ASP cc_start: 0.7717 (m-30) cc_final: 0.7361 (t0)
REVERT: A  240 MET cc_start: 0.6533 (mmp) cc_final: 0.6074 (mmp)
REVERT: A  248 LYS cc_start: 0.7838 (ttpp) cc_final: 0.7629 (mtpp)
REVERT: A  261 ASP cc_start: 0.7412 (t0) cc_final: 0.7108 (t0)
REVERT: A  280 LYS cc_start: 0.7493 (mppt) cc_final: 0.7198 (mppt)
REVERT: A  304 GLN cc_start: 0.8337 (tm-30) cc_final: 0.8011 (tt0)
REVERT: B  129 ARG cc_start: 0.6721 (tpm170) cc_final: 0.6324 (mtp180)
REVERT: B  187 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8329 (t)
REVERT: B  212 ASP cc_start: 0.7595 (t70) cc_final: 0.7295 (t70)
REVERT: B  217 MET cc_start: 0.7757 (ppp) cc_final: 0.7179 (ppp)
REVERT: B  254 ASP cc_start: 0.7799 (t70) cc_final: 0.7318 (t0)
REVERT: B  271 CYS cc_start: 0.7085 (m) cc_final: 0.6691 (p)
REVERT: B  303 ASP cc_start: 0.7762 (m-30) cc_final: 0.7536 (m-30)
REVERT: D   82 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6943 (t70)
REVERT: D  136 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8256 (tp)
REVERT: D  236 ARG cc_start: 0.8494 (ttp-110) cc_final: 0.8239 (ttp-110)
REVERT: D  263 ILE cc_start: 0.8119 (tp) cc_final: 0.7897 (tp)
REVERT: D  282 ASP cc_start: 0.8493 (t70) cc_final: 0.8136 (t70)
REVERT: S   21 SER cc_start: 0.8578 (m) cc_final: 0.8267 (p)
REVERT: S  119 VAL cc_start: 0.8848 (t) cc_final: 0.8488 (p)
REVERT: S  154 SER cc_start: 0.8456 (p) cc_final: 0.8226 (m)
REVERT: S  192 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8135 (ttp)
  outliers start: 29
  outliers final: 13
  residues processed: 196
  average time/residue: 1.2254
  time to fit residues: 256.5801
Evaluate side-chains
  197 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 180
  time to evaluate  : 1.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   82 ASP
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  271 SER
Chi-restraints excluded: chain D residue  280 LYS
Chi-restraints excluded: chain D residue  287 SER
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  192 MET
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 30 optimal weight:    0.5980
   chunk 88 optimal weight:    0.0870
   chunk 20 optimal weight:    0.0970
   chunk 105 optimal weight:    0.5980
   chunk 106 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0670
   chunk 45 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 104 optimal weight:    0.8980
   chunk 56 optimal weight:   20.0000
   overall best weight:    0.2894

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
B  75 GLN
B 237 ASN
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  35 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.133097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.111469 restraints weight = 13187.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 2.04
r_work: 0.3371 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9077  Z= 0.129
  Angle     :  0.493  13.378  12299  Z= 0.253
  Chirality :  0.041   0.141   1402
  Planarity :  0.003   0.033   1548
  Dihedral  :  6.440 179.410   1235
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 20.79 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.25), residues: 1114
  helix:  2.32 (0.27), residues: 382
  sheet:  0.68 (0.31), residues: 293
  loop : -1.40 (0.25), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP S 176 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.013   0.001   TYR S 190 
 ARG   0.005   0.000   ARG B  48 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 187
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A  229 ASP cc_start: 0.7658 (m-30) cc_final: 0.7340 (t0)
REVERT: A  240 MET cc_start: 0.6566 (mmp) cc_final: 0.6065 (mmp)
REVERT: A  248 LYS cc_start: 0.7780 (ttpp) cc_final: 0.7565 (mtpp)
REVERT: A  261 ASP cc_start: 0.7346 (t0) cc_final: 0.7048 (t0)
REVERT: A  280 LYS cc_start: 0.7464 (mppt) cc_final: 0.7176 (mppt)
REVERT: A  304 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7972 (tt0)
REVERT: B  130 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7556 (mt-10)
REVERT: B  187 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8246 (t)
REVERT: B  212 ASP cc_start: 0.7606 (t70) cc_final: 0.7315 (t70)
REVERT: B  217 MET cc_start: 0.7807 (ppp) cc_final: 0.7210 (ppp)
REVERT: B  254 ASP cc_start: 0.7768 (t70) cc_final: 0.7283 (t0)
REVERT: B  303 ASP cc_start: 0.7646 (m-30) cc_final: 0.7422 (m-30)
REVERT: D   82 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6900 (t70)
REVERT: D  236 ARG cc_start: 0.8522 (ttp-110) cc_final: 0.8303 (ttp-110)
REVERT: D  263 ILE cc_start: 0.8086 (tp) cc_final: 0.7859 (tp)
REVERT: D  282 ASP cc_start: 0.8395 (t70) cc_final: 0.7991 (t70)
REVERT: S   21 SER cc_start: 0.8603 (m) cc_final: 0.8294 (p)
REVERT: S  119 VAL cc_start: 0.8859 (t) cc_final: 0.8513 (p)
REVERT: S  177 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6512 (p90)
REVERT: S  192 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8118 (ttp)
  outliers start: 26
  outliers final: 15
  residues processed: 200
  average time/residue: 1.1677
  time to fit residues: 249.6154
Evaluate side-chains
  198 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 179
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   82 ASP
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  271 SER
Chi-restraints excluded: chain D residue  280 LYS
Chi-restraints excluded: chain D residue  287 SER
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  177 PHE
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  210 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 12 optimal weight:    0.0470
   chunk 54 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0070
   chunk 19 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9990
   chunk 80 optimal weight:    0.2980
   chunk 58 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.4096

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
B  75 GLN
B 125 ASN
B 237 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.132033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.110423 restraints weight = 13274.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.05
r_work: 0.3362 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9077  Z= 0.137
  Angle     :  0.493  13.289  12299  Z= 0.254
  Chirality :  0.040   0.136   1402
  Planarity :  0.003   0.032   1548
  Dihedral  :  6.366 178.965   1235
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 21.52 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.25), residues: 1114
  helix:  2.36 (0.27), residues: 382
  sheet:  0.72 (0.31), residues: 294
  loop : -1.37 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP S 176 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.012   0.001   TYR D 300 
 ARG   0.004   0.000   ARG B  48 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 182
  time to evaluate  : 0.957 
Fit side-chains
REVERT: A  229 ASP cc_start: 0.7653 (m-30) cc_final: 0.7325 (t0)
REVERT: A  240 MET cc_start: 0.6587 (mmp) cc_final: 0.6067 (mmp)
REVERT: A  248 LYS cc_start: 0.7793 (ttpp) cc_final: 0.7567 (mtpp)
REVERT: A  261 ASP cc_start: 0.7343 (t0) cc_final: 0.7043 (t0)
REVERT: A  280 LYS cc_start: 0.7472 (mppt) cc_final: 0.7204 (mppt)
REVERT: A  289 GLU cc_start: 0.7941 (mp0) cc_final: 0.7716 (mp0)
REVERT: A  304 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7988 (tt0)
REVERT: B  129 ARG cc_start: 0.7695 (mtp180) cc_final: 0.7294 (tpm170)
REVERT: B  187 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8296 (t)
REVERT: B  212 ASP cc_start: 0.7640 (t70) cc_final: 0.7342 (t70)
REVERT: B  217 MET cc_start: 0.7804 (ppp) cc_final: 0.7253 (ppp)
REVERT: B  254 ASP cc_start: 0.7767 (t70) cc_final: 0.7280 (t0)
REVERT: B  271 CYS cc_start: 0.7017 (m) cc_final: 0.6306 (p)
REVERT: B  303 ASP cc_start: 0.7681 (m-30) cc_final: 0.7444 (m-30)
REVERT: D   82 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6918 (t70)
REVERT: D  236 ARG cc_start: 0.8507 (ttp-110) cc_final: 0.8281 (ttp-110)
REVERT: D  263 ILE cc_start: 0.8076 (tp) cc_final: 0.7832 (tp)
REVERT: D  282 ASP cc_start: 0.8436 (t70) cc_final: 0.8036 (t70)
REVERT: S   21 SER cc_start: 0.8597 (m) cc_final: 0.8275 (p)
REVERT: S  119 VAL cc_start: 0.8855 (t) cc_final: 0.8501 (p)
REVERT: S  154 SER cc_start: 0.8412 (p) cc_final: 0.8183 (m)
REVERT: S  177 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6512 (p90)
REVERT: S  192 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8136 (ttp)
  outliers start: 23
  outliers final: 15
  residues processed: 195
  average time/residue: 1.1536
  time to fit residues: 240.4103
Evaluate side-chains
  198 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 179
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   82 ASP
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  233 ARG
Chi-restraints excluded: chain D residue  280 LYS
Chi-restraints excluded: chain D residue  287 SER
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  177 PHE
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  210 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 83 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 100 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 98 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 86 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 340 ASN
C  59 ASN
D 145 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.130589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.109120 restraints weight = 13169.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 2.03
r_work: 0.3341 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9077  Z= 0.176
  Angle     :  0.518  13.542  12299  Z= 0.268
  Chirality :  0.041   0.134   1402
  Planarity :  0.003   0.033   1548
  Dihedral  :  6.411 178.411   1235
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 21.93 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.25), residues: 1114
  helix:  2.32 (0.27), residues: 382
  sheet:  0.73 (0.31), residues: 294
  loop : -1.42 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP S  47 
 HIS   0.006   0.001   HIS A 188 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.023   0.002   TYR S 227 
 ARG   0.004   0.000   ARG B  68 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 187
  time to evaluate  : 1.047 
Fit side-chains
REVERT: A  229 ASP cc_start: 0.7661 (m-30) cc_final: 0.7327 (t0)
REVERT: A  240 MET cc_start: 0.6605 (mmp) cc_final: 0.6059 (mmp)
REVERT: A  248 LYS cc_start: 0.7813 (ttpp) cc_final: 0.7594 (mtpp)
REVERT: A  261 ASP cc_start: 0.7351 (t0) cc_final: 0.7057 (t0)
REVERT: A  280 LYS cc_start: 0.7447 (mppt) cc_final: 0.7192 (mppt)
REVERT: A  289 GLU cc_start: 0.7940 (mp0) cc_final: 0.7714 (mp0)
REVERT: A  304 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7991 (tt0)
REVERT: B  129 ARG cc_start: 0.7790 (mtp180) cc_final: 0.7163 (tpm170)
REVERT: B  130 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7695 (mt-10)
REVERT: B  187 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8311 (t)
REVERT: B  212 ASP cc_start: 0.7629 (t70) cc_final: 0.7338 (t70)
REVERT: B  217 MET cc_start: 0.7773 (ppp) cc_final: 0.7213 (ppp)
REVERT: B  254 ASP cc_start: 0.7784 (t70) cc_final: 0.7291 (t0)
REVERT: B  271 CYS cc_start: 0.7062 (m) cc_final: 0.6409 (p)
REVERT: B  303 ASP cc_start: 0.7713 (m-30) cc_final: 0.7501 (m-30)
REVERT: D   82 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6938 (t70)
REVERT: D  236 ARG cc_start: 0.8498 (ttp-110) cc_final: 0.8265 (ttp-110)
REVERT: D  263 ILE cc_start: 0.8080 (tp) cc_final: 0.7847 (tp)
REVERT: D  282 ASP cc_start: 0.8450 (t70) cc_final: 0.8049 (t70)
REVERT: S    6 GLU cc_start: 0.7852 (mp0) cc_final: 0.7629 (mp0)
REVERT: S   21 SER cc_start: 0.8608 (m) cc_final: 0.8285 (p)
REVERT: S  119 VAL cc_start: 0.8861 (t) cc_final: 0.8497 (p)
REVERT: S  154 SER cc_start: 0.8431 (p) cc_final: 0.8195 (m)
REVERT: S  177 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6552 (p90)
REVERT: S  192 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8146 (ttp)
  outliers start: 20
  outliers final: 11
  residues processed: 198
  average time/residue: 1.1727
  time to fit residues: 247.7805
Evaluate side-chains
  202 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 187
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   82 ASP
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  280 LYS
Chi-restraints excluded: chain D residue  287 SER
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  177 PHE
Chi-restraints excluded: chain S residue  192 MET
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 74 optimal weight:    0.0020
   chunk 99 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 54 optimal weight:    0.5980
   chunk 22 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.8792

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
D 145 GLN
S 142 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.130381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.108674 restraints weight = 13113.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.03
r_work: 0.3319 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9077  Z= 0.214
  Angle     :  0.550  13.823  12299  Z= 0.283
  Chirality :  0.042   0.138   1402
  Planarity :  0.003   0.034   1548
  Dihedral  :  6.530 178.201   1235
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 22.45 %
    Favored  : 75.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.25), residues: 1114
  helix:  2.30 (0.27), residues: 382
  sheet:  0.68 (0.31), residues: 300
  loop : -1.45 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 255 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.017   0.002   PHE A 189 
 TYR   0.012   0.002   TYR D 258 
 ARG   0.005   0.000   ARG B  68 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 187
  time to evaluate  : 1.056 
Fit side-chains
REVERT: A  229 ASP cc_start: 0.7698 (m-30) cc_final: 0.7359 (t0)
REVERT: A  240 MET cc_start: 0.6676 (mmp) cc_final: 0.6117 (mmp)
REVERT: A  248 LYS cc_start: 0.7820 (ttpp) cc_final: 0.7609 (mtpp)
REVERT: A  261 ASP cc_start: 0.7414 (t0) cc_final: 0.7112 (t0)
REVERT: A  280 LYS cc_start: 0.7455 (mppt) cc_final: 0.7192 (mppt)
REVERT: A  289 GLU cc_start: 0.7962 (mp0) cc_final: 0.7737 (mp0)
REVERT: A  304 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7999 (tt0)
REVERT: B  130 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7749 (mt-10)
REVERT: B  212 ASP cc_start: 0.7617 (t70) cc_final: 0.7321 (t70)
REVERT: B  217 MET cc_start: 0.7788 (ppp) cc_final: 0.7179 (ppp)
REVERT: B  254 ASP cc_start: 0.7812 (t70) cc_final: 0.7321 (t0)
REVERT: B  271 CYS cc_start: 0.7120 (m) cc_final: 0.6528 (p)
REVERT: B  303 ASP cc_start: 0.7705 (m-30) cc_final: 0.7498 (m-30)
REVERT: D   82 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6933 (t70)
REVERT: D  136 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8233 (tp)
REVERT: D  190 VAL cc_start: 0.8464 (m) cc_final: 0.8214 (t)
REVERT: D  236 ARG cc_start: 0.8488 (ttp-110) cc_final: 0.8248 (ttp-110)
REVERT: D  263 ILE cc_start: 0.8084 (tp) cc_final: 0.7858 (tp)
REVERT: D  282 ASP cc_start: 0.8469 (t70) cc_final: 0.8080 (t70)
REVERT: S   21 SER cc_start: 0.8606 (m) cc_final: 0.8303 (p)
REVERT: S  119 VAL cc_start: 0.8858 (t) cc_final: 0.8486 (p)
REVERT: S  177 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.6707 (p90)
REVERT: S  192 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8202 (ttp)
  outliers start: 20
  outliers final: 13
  residues processed: 195
  average time/residue: 1.2006
  time to fit residues: 249.9479
Evaluate side-chains
  201 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 184
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   82 ASP
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  280 LYS
Chi-restraints excluded: chain D residue  287 SER
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  177 PHE
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  224 VAL
Chi-restraints excluded: chain S residue  243 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 18 optimal weight:    0.2980
   chunk 45 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   chunk 79 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 110 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
D 145 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.129790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.108165 restraints weight = 13102.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 2.03
r_work: 0.3312 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9077  Z= 0.227
  Angle     :  0.562  13.794  12299  Z= 0.289
  Chirality :  0.042   0.138   1402
  Planarity :  0.003   0.042   1548
  Dihedral  :  6.567 178.083   1235
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 22.77 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.25), residues: 1114
  helix:  2.26 (0.27), residues: 383
  sheet:  0.67 (0.31), residues: 298
  loop : -1.50 (0.24), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 255 
 HIS   0.006   0.001   HIS A 188 
 PHE   0.017   0.002   PHE A 189 
 TYR   0.012   0.002   TYR D 300 
 ARG   0.008   0.000   ARG B 137 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7725.96 seconds
wall clock time: 136 minutes 31.65 seconds (8191.65 seconds total)