Starting phenix.real_space_refine
on Sat May 17 20:10:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tme_41386/05_2025/8tme_41386.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tme_41386/05_2025/8tme_41386.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tme_41386/05_2025/8tme_41386.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tme_41386/05_2025/8tme_41386.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tme_41386/05_2025/8tme_41386.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tme_41386/05_2025/8tme_41386.cif"
  }
  resolution = 3.1
  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=   0.016 sd=   0.043
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Mg      3      5.21       5
     S      59      5.16       5
     C   10474      2.51       5
     N    2626      2.21       5
     O    2962      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 16124
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "L"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 803
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 969
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 2, 'TRANS': 123}
    Chain: "A"
      Number of atoms: 2804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2804
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 13, 'TRANS': 321}
    Chain: "B"
      Number of atoms: 2925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2925
          Classifications: {'peptide': 351}
          Link IDs: {'PTRANS': 15, 'TRANS': 335}
    Chain: "C"
      Number of atoms: 2812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2812
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 13, 'TRANS': 322}
    Chain: "D"
      Number of atoms: 2891
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 347, 2891
          Classifications: {'peptide': 347}
          Link IDs: {'PTRANS': 15, 'TRANS': 331}
    Chain: "E"
      Number of atoms: 2917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2917
          Classifications: {'peptide': 350}
          Link IDs: {'PTRANS': 15, 'TRANS': 334}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 9.41, per 1000 atoms: 0.58
  Number of scatterers: 16124
  At special positions: 0
  Unit cell: (118.548, 148.452, 135.636, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      59     16.00
     Mg      3     11.99
     O    2962      8.00
     N    2626      7.00
     C   10474      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.76
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3742

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 13 sheets defined
      51.5% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.56
  Creating SS restraints...
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.874A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 94
    Processing helix  chain 'A' and resid 46 through 51
      removed outlier: 3.702A  pdb=" N   VAL A  50 " --> pdb=" O   ASP A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 56
      removed outlier: 4.009A  pdb=" N   ASP A  55 " --> pdb=" O   PRO A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 81
      removed outlier: 3.511A  pdb=" N   VAL A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLY A  77 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLU A  78 " --> pdb=" O   GLN A  74 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   PHE A  79 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   PHE A  80 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 91
      removed outlier: 3.558A  pdb=" N   LEU A  87 " --> pdb=" O   HIS A  83 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU A  91 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 157
    Processing helix  chain 'A' and resid 165 through 201
      removed outlier: 3.827A  pdb=" N   GLU A 197 " --> pdb=" O   ASP A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 238
      removed outlier: 3.831A  pdb=" N   VAL A 208 " --> pdb=" O   GLU A 204 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   GLN A 209 " --> pdb=" O   LYS A 205 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   TRP A 226 " --> pdb=" O   ARG A 222 " (cutoff:3.500A)
      Proline residue:  A 227  - end of helix
      removed outlier: 3.849A  pdb=" N   ASP A 238 " --> pdb=" O   SER A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 246
      No H-bonds generated for 'chain 'A' and resid 244 through 246'
    Processing helix  chain 'A' and resid 247 through 282
      removed outlier: 3.665A  pdb=" N   THR A 264 " --> pdb=" O   GLN A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 300
    Processing helix  chain 'A' and resid 301 through 311
      removed outlier: 3.603A  pdb=" N   TYR A 311 " --> pdb=" O   ILE A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 349
      removed outlier: 3.680A  pdb=" N   LYS A 348 " --> pdb=" O   TYR A 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 54
    Processing helix  chain 'B' and resid 69 through 80
    Processing helix  chain 'B' and resid 83 through 92
    Processing helix  chain 'B' and resid 147 through 156
    Processing helix  chain 'B' and resid 165 through 202
      removed outlier: 3.817A  pdb=" N   TYR B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   PHE B 182 " --> pdb=" O   VAL B 178 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL B 183 " --> pdb=" O   ASP B 179 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   ASP B 189 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   ASP B 190 " --> pdb=" O   GLU B 186 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLU B 191 " --> pdb=" O   LYS B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 237
      removed outlier: 3.699A  pdb=" N   VAL B 208 " --> pdb=" O   GLU B 204 " (cutoff:3.500A)
      Proline residue:  B 227  - end of helix
    Processing helix  chain 'B' and resid 244 through 246
      No H-bonds generated for 'chain 'B' and resid 244 through 246'
    Processing helix  chain 'B' and resid 247 through 312
      removed outlier: 3.501A  pdb=" N   PHE B 251 " --> pdb=" O   THR B 247 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLN B 260 " --> pdb=" O   ASP B 256 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASP B 277 " --> pdb=" O   SER B 273 " (cutoff:3.500A)
      Proline residue:  B 303  - end of helix
    Processing helix  chain 'B' and resid 326 through 348
    Processing helix  chain 'C' and resid 69 through 80
      removed outlier: 4.466A  pdb=" N   VAL C  73 " --> pdb=" O   ARG C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 92
    Processing helix  chain 'C' and resid 147 through 157
      removed outlier: 3.859A  pdb=" N   ARG C 151 " --> pdb=" O   PHE C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 202
      removed outlier: 4.332A  pdb=" N   TYR C 171 " --> pdb=" O   ASP C 167 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 238
      Proline residue:  C 227  - end of helix
      removed outlier: 3.750A  pdb=" N   GLU C 230 " --> pdb=" O   TRP C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 311
      removed outlier: 3.965A  pdb=" N   TYR C 255 " --> pdb=" O   PHE C 251 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU C 276 " --> pdb=" O   VAL C 272 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ASP C 277 " --> pdb=" O   SER C 273 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASN C 288 " --> pdb=" O   SER C 284 " (cutoff:3.500A)
      Proline residue:  C 303  - end of helix
    Processing helix  chain 'C' and resid 325 through 348
      removed outlier: 3.938A  pdb=" N   VAL C 329 " --> pdb=" O   TRP C 325 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   LYS C 348 " --> pdb=" O   TYR C 344 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 56
      removed outlier: 3.749A  pdb=" N   VAL D  50 " --> pdb=" O   VAL D  47 " (cutoff:3.500A)
      Proline residue:  D  52  - end of helix
      removed outlier: 3.577A  pdb=" N   SER D  56 " --> pdb=" O   PHE D  53 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 69 through 81
      removed outlier: 3.711A  pdb=" N   VAL D  73 " --> pdb=" O   ARG D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 92
      removed outlier: 3.686A  pdb=" N   LEU D  91 " --> pdb=" O   LEU D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 147 through 157
      removed outlier: 3.668A  pdb=" N   ARG D 151 " --> pdb=" O   PHE D 147 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 165 through 202
      removed outlier: 3.688A  pdb=" N   LEU D 169 " --> pdb=" O   ARG D 165 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ASP D 190 " --> pdb=" O   GLU D 186 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLU D 191 " --> pdb=" O   LYS D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 205 through 238
      removed outlier: 4.513A  pdb=" N   GLN D 209 " --> pdb=" O   LYS D 205 " (cutoff:3.500A)
      Proline residue:  D 227  - end of helix
    Processing helix  chain 'D' and resid 247 through 312
      removed outlier: 3.509A  pdb=" N   PHE D 251 " --> pdb=" O   THR D 247 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   LEU D 276 " --> pdb=" O   VAL D 272 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ASP D 277 " --> pdb=" O   SER D 273 " (cutoff:3.500A)
      Proline residue:  D 303  - end of helix
      removed outlier: 3.523A  pdb=" N   TYR D 311 " --> pdb=" O   ILE D 307 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 325 through 345
      removed outlier: 3.542A  pdb=" N   VAL D 329 " --> pdb=" O   TRP D 325 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   TYR D 344 " --> pdb=" O   ILE D 340 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE D 345 " --> pdb=" O   MET D 341 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 50 through 54
    Processing helix  chain 'E' and resid 69 through 80
      removed outlier: 3.667A  pdb=" N   VAL E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 83 through 91
      removed outlier: 3.745A  pdb=" N   LEU E  87 " --> pdb=" O   HIS E  83 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   GLU E  88 " --> pdb=" O   PRO E  84 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   ASP E  89 " --> pdb=" O   LEU E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 147 through 156
    Processing helix  chain 'E' and resid 165 through 202
      removed outlier: 3.622A  pdb=" N   LEU E 169 " --> pdb=" O   ARG E 165 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 206 through 237
      removed outlier: 3.791A  pdb=" N   ARG E 210 " --> pdb=" O   GLU E 206 " (cutoff:3.500A)
      Proline residue:  E 227  - end of helix
      removed outlier: 3.877A  pdb=" N   GLU E 230 " --> pdb=" O   TRP E 226 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 247 through 313
      removed outlier: 4.200A  pdb=" N   LEU E 276 " --> pdb=" O   VAL E 272 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   ASP E 277 " --> pdb=" O   SER E 273 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   SER E 281 " --> pdb=" O   ASP E 277 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   VAL E 290 " --> pdb=" O   LYS E 286 " (cutoff:3.500A)
      Proline residue:  E 303  - end of helix
    Processing helix  chain 'E' and resid 325 through 346
    Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 8
      removed outlier: 3.718A  pdb=" N   ASP L  71 " --> pdb=" O   SER L  68 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 11 through 14
      removed outlier: 6.610A  pdb=" N   LEU L  12 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 11 through 14
      removed outlier: 6.610A  pdb=" N   LEU L  12 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA5, first strand: chain 'H' and resid 14 through 15
      removed outlier: 3.749A  pdb=" N   SER H  36 " --> pdb=" O   SER H 102 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 14 through 15
      removed outlier: 6.676A  pdb=" N   CYS H  99 " --> pdb=" O   TRP H 119 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   TRP H 119 " --> pdb=" O   CYS H  99 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ARG H 101 " --> pdb=" O   ASP H 117 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 39 through 44
      removed outlier: 3.753A  pdb=" N   CYS A 135 " --> pdb=" O   THR A 132 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 44
    Processing sheet with id=AA9, first strand: chain 'C' and resid 39 through 40
      removed outlier: 3.505A  pdb=" N   ASN C  33 " --> pdb=" O   ARG C  40 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 39 through 40
      removed outlier: 3.505A  pdb=" N   ASN C  33 " --> pdb=" O   ARG C  40 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   THR C  60 " --> pdb=" O   VAL C 136 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   MET C 138 " --> pdb=" O   THR C  60 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   ILE C  62 " --> pdb=" O   MET C 138 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE C 139 " --> pdb=" O   SER C 128 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   SER C 128 " --> pdb=" O   PHE C 139 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU C 123 " --> pdb=" O   THR C 114 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   THR C 114 " --> pdb=" O   GLU C 123 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 39 through 44
      removed outlier: 3.672A  pdb=" N   ARG D  40 " --> pdb=" O   ASN D  33 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ASN D  33 " --> pdb=" O   ARG D  40 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   PHE D  42 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   VAL D  31 " --> pdb=" O   PHE D  42 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   THR D  44 " --> pdb=" O   ILE D  29 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ILE D  29 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLU D  28 " --> pdb=" O   THR D  65 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ILE D 130 " --> pdb=" O   LEU D 137 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   PHE D 139 " --> pdb=" O   SER D 128 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   SER D 128 " --> pdb=" O   PHE D 139 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 114 through 116
      removed outlier: 3.578A  pdb=" N   GLU D 123 " --> pdb=" O   THR D 114 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ASP D 116 " --> pdb=" O   GLU D 121 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU D 121 " --> pdb=" O   ASP D 116 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 41 through 44
      removed outlier: 3.746A  pdb=" N   VAL E  31 " --> pdb=" O   PHE E  42 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   GLU E 121 " --> pdb=" O   ASP E 116 " (cutoff:3.500A)

    959 hydrogen bonds defined for protein.
    2763 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: 4.90

  Time building geometry restraints manager: 4.33 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 5056
        1.34 -     1.46: 3561
        1.46 -     1.58: 7762
        1.58 -     1.70: 0
        1.70 -     1.83: 109
  Bond restraints: 16488
  Sorted by residual:
  bond pdb=" CG  PRO C 227 "
       pdb=" CD  PRO C 227 "
    ideal  model  delta    sigma   weight residual
    1.503  1.403  0.100 3.40e-02 8.65e+02 8.73e+00
  bond pdb=" CB  MET E 291 "
       pdb=" CG  MET E 291 "
    ideal  model  delta    sigma   weight residual
    1.520  1.475  0.045 3.00e-02 1.11e+03 2.24e+00
  bond pdb=" CB  PRO C 227 "
       pdb=" CG  PRO C 227 "
    ideal  model  delta    sigma   weight residual
    1.492  1.564 -0.072 5.00e-02 4.00e+02 2.09e+00
  bond pdb=" CG  MET E 291 "
       pdb=" SD  MET E 291 "
    ideal  model  delta    sigma   weight residual
    1.803  1.768  0.035 2.50e-02 1.60e+03 1.95e+00
  bond pdb=" CG1 ILE B 154 "
       pdb=" CD1 ILE B 154 "
    ideal  model  delta    sigma   weight residual
    1.513  1.469  0.044 3.90e-02 6.57e+02 1.30e+00
  ... (remaining 16483 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 21771
        1.68 -     3.36: 456
        3.36 -     5.05: 98
        5.05 -     6.73: 22
        6.73 -     8.41: 9
  Bond angle restraints: 22356
  Sorted by residual:
  angle pdb=" N   VAL C 146 "
        pdb=" CA  VAL C 146 "
        pdb=" C   VAL C 146 "
      ideal   model   delta    sigma   weight residual
     112.29  107.25    5.04 9.40e-01 1.13e+00 2.88e+01
  angle pdb=" N   PRO C 227 "
        pdb=" CD  PRO C 227 "
        pdb=" CG  PRO C 227 "
      ideal   model   delta    sigma   weight residual
     103.20   95.56    7.64 1.50e+00 4.44e-01 2.59e+01
  angle pdb=" C   LEU A 235 "
        pdb=" N   TYR A 236 "
        pdb=" CA  TYR A 236 "
      ideal   model   delta    sigma   weight residual
     122.53  114.12    8.41 1.92e+00 2.71e-01 1.92e+01
  angle pdb=" CA  PRO C 227 "
        pdb=" N   PRO C 227 "
        pdb=" CD  PRO C 227 "
      ideal   model   delta    sigma   weight residual
     112.00  106.34    5.66 1.40e+00 5.10e-01 1.63e+01
  angle pdb=" N   ARG H  70 "
        pdb=" CA  ARG H  70 "
        pdb=" C   ARG H  70 "
      ideal   model   delta    sigma   weight residual
     114.56  109.50    5.06 1.27e+00 6.20e-01 1.59e+01
  ... (remaining 22351 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 8775
       17.96 -    35.92: 924
       35.92 -    53.88: 157
       53.88 -    71.84: 42
       71.84 -    89.80: 15
  Dihedral angle restraints: 9913
    sinusoidal: 4124
      harmonic: 5789
  Sorted by residual:
  dihedral pdb=" CA  LYS A 349 "
           pdb=" C   LYS A 349 "
           pdb=" N   TRP A 350 "
           pdb=" CA  TRP A 350 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.71   23.29     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  ASP C  46 "
           pdb=" C   ASP C  46 "
           pdb=" N   VAL C  47 "
           pdb=" CA  VAL C  47 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.81  -22.19     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  ILE E 300 "
           pdb=" C   ILE E 300 "
           pdb=" N   PHE E 301 "
           pdb=" CA  PHE E 301 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.62  -19.38     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 9910 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 2055
       0.056 -    0.112: 434
       0.112 -    0.169: 47
       0.169 -    0.225: 4
       0.225 -    0.281: 1
  Chirality restraints: 2541
  Sorted by residual:
  chirality pdb=" CA  ASP C 148 "
            pdb=" N   ASP C 148 "
            pdb=" C   ASP C 148 "
            pdb=" CB  ASP C 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" CA  ASP D 148 "
            pdb=" N   ASP D 148 "
            pdb=" C   ASP D 148 "
            pdb=" CB  ASP D 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.95e-01
  chirality pdb=" CB  VAL C  47 "
            pdb=" CA  VAL C  47 "
            pdb=" CG1 VAL C  47 "
            pdb=" CG2 VAL C  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.06e-01
  ... (remaining 2538 not shown)

  Planarity restraints: 2796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 350 "    0.031 2.00e-02 2.50e+03   2.18e-02 1.19e+01
        pdb=" CG  TRP B 350 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 350 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 350 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 350 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 350 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 350 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 350 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 350 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 350 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 327 "    0.041 5.00e-02 4.00e+02   6.08e-02 5.91e+00
        pdb=" N   PRO C 328 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO C 328 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C 328 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C 226 "    0.039 5.00e-02 4.00e+02   5.68e-02 5.17e+00
        pdb=" N   PRO C 227 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO C 227 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C 227 "    0.032 5.00e-02 4.00e+02
  ... (remaining 2793 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 596
        2.72 -     3.26: 16536
        3.26 -     3.81: 26750
        3.81 -     4.35: 32006
        4.35 -     4.90: 54332
  Nonbonded interactions: 130220
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 288 "
            pdb=" OG1 THR C 287 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" OH  TYR A 115 "
            pdb=" OE1 GLU A 191 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   LYS E 111 "
            pdb=" OH  TYR E 181 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OD1 ASP C 270 "
            pdb=" NH2 ARG D 269 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" NE2 GLN E 140 "
            pdb=" OD1 ASP E 145 "
     model   vdw
     2.248 3.120
  ... (remaining 130215 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 16 through 350)
  selection = (chain 'C' and resid 16 through 350)
  selection = (chain 'D' and resid 16 through 350)
  selection = (chain 'E' and resid 16 through 350)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.49 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.110
  Set scattering table:                    0.120
  Process input model:                     34.980
  Find NCS groups from input model:        0.620
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
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      :  0.004   0.100  16490  Z= 0.175
  Angle     :  0.647   8.412  22360  Z= 0.346
  Chirality :  0.045   0.281   2541
  Planarity :  0.005   0.061   2796
  Dihedral  : 15.246  89.805   6165
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.70 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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:  0.91 (0.20), residues: 1938
  helix:  2.20 (0.17), residues: 927
  sheet:  0.27 (0.28), residues: 370
  loop : -1.65 (0.24), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP B 350 
 HIS   0.014   0.001   HIS A 257 
 PHE   0.022   0.001   PHE A 147 
 TYR   0.020   0.002   TYR B 236 
 ARG   0.009   0.000   ARG L  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14482 (  951)
  hydrogen bonds       : angle       6.37694 ( 2763)
  SS BOND              : bond        0.00129 (    2)
  SS BOND              : angle       0.58658 (    4)
  covalent geometry    : bond        0.00409 (16488)
  covalent geometry    : angle       0.64748 (22356)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  384 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 384
  time to evaluate  : 1.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   15 VAL cc_start: 0.7962 (t) cc_final: 0.7714 (p)
REVERT: H   16 GLN cc_start: 0.7502 (mm-40) cc_final: 0.7145 (mm110)
REVERT: H   70 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7136 (ttp80)
REVERT: H  126 THR cc_start: 0.8187 (m) cc_final: 0.7877 (p)
REVERT: A   28 GLU cc_start: 0.6796 (pt0) cc_final: 0.6515 (pt0)
REVERT: A  116 ASP cc_start: 0.6688 (t70) cc_final: 0.6428 (t0)
REVERT: B  118 ASN cc_start: 0.6086 (m-40) cc_final: 0.5751 (m110)
REVERT: B  306 PHE cc_start: 0.7990 (t80) cc_final: 0.7762 (t80)
REVERT: D   42 PHE cc_start: 0.7907 (p90) cc_final: 0.7616 (p90)
REVERT: E  179 ASP cc_start: 0.7065 (m-30) cc_final: 0.6838 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 384
  average time/residue: 0.2858
  time to fit residues: 161.1841
Evaluate side-chains
  345 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 345
  time to evaluate  : 1.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 162 optimal weight:    2.9990
   chunk 145 optimal weight:    4.9990
   chunk 80 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 98 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0670
   chunk 150 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 91 optimal weight:    6.9990
   chunk 112 optimal weight:    0.9990
   chunk 174 optimal weight:    1.9990
   overall best weight:    0.6720

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

Flipped N/Q/H residues before XYZ refinement:
** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 140 GLN
** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.169922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.140190 restraints weight = 27927.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3751 rms_B_bonded: 2.74
r_work: 0.3489 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3490
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3490 r_free = 0.3490    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3488 r_free = 0.3488    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3488
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.0958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16490  Z= 0.176
  Angle     :  0.628   8.823  22360  Z= 0.333
  Chirality :  0.045   0.229   2541
  Planarity :  0.005   0.050   2796
  Dihedral  :  4.593  21.469   2164
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.59 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  9.70 %
    Favored  : 89.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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:  0.96 (0.19), residues: 1938
  helix:  2.18 (0.17), residues: 931
  sheet:  0.28 (0.27), residues: 374
  loop : -1.56 (0.24), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 350 
 HIS   0.011   0.001   HIS A 257 
 PHE   0.027   0.002   PHE D 147 
 TYR   0.020   0.002   TYR A  19 
 ARG   0.007   0.000   ARG B 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05814 (  951)
  hydrogen bonds       : angle       5.08044 ( 2763)
  SS BOND              : bond        0.00238 (    2)
  SS BOND              : angle       1.22607 (    4)
  covalent geometry    : bond        0.00399 (16488)
  covalent geometry    : angle       0.62794 (22356)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  375 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 357
  time to evaluate  : 1.744 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   15 VAL cc_start: 0.7987 (t) cc_final: 0.7683 (p)
REVERT: H   16 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7407 (mm110)
REVERT: H   28 SER cc_start: 0.8665 (m) cc_final: 0.8210 (p)
REVERT: H   70 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7746 (ttp80)
REVERT: H  126 THR cc_start: 0.8337 (m) cc_final: 0.8042 (p)
REVERT: A   22 LYS cc_start: 0.7909 (pttm) cc_final: 0.7688 (ptpp)
REVERT: A   28 GLU cc_start: 0.7337 (pt0) cc_final: 0.7096 (mt-10)
REVERT: A  116 ASP cc_start: 0.7254 (t70) cc_final: 0.6768 (t0)
REVERT: B  118 ASN cc_start: 0.6325 (m-40) cc_final: 0.5929 (m110)
REVERT: B  154 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8481 (mp)
REVERT: B  306 PHE cc_start: 0.7969 (t80) cc_final: 0.7756 (t80)
REVERT: C  138 MET cc_start: 0.5765 (tmm) cc_final: 0.5234 (tpt)
REVERT: D   42 PHE cc_start: 0.7928 (p90) cc_final: 0.7498 (p90)
REVERT: D  136 VAL cc_start: 0.7874 (p) cc_final: 0.7513 (m)
REVERT: E  134 ASN cc_start: 0.7699 (m-40) cc_final: 0.7481 (m-40)
REVERT: E  179 ASP cc_start: 0.7634 (m-30) cc_final: 0.7424 (m-30)
REVERT: E  222 ARG cc_start: 0.7691 (ptm-80) cc_final: 0.7261 (ttp80)
REVERT: E  324 LYS cc_start: 0.7883 (tmtt) cc_final: 0.7251 (tmtt)
  outliers start: 18
  outliers final: 11
  residues processed: 364
  average time/residue: 0.2881
  time to fit residues: 153.5129
Evaluate side-chains
  348 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 336
  time to evaluate  : 1.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain C residue  130 ILE
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 VAL
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  226 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 130 optimal weight:    7.9990
   chunk 93 optimal weight:    0.4980
   chunk 189 optimal weight:    0.7980
   chunk 169 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 168 optimal weight:    0.9980
   chunk 90 optimal weight:    6.9990
   chunk 100 optimal weight:    2.9990
   chunk 151 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C  63 ASN
** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.167167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.137143 restraints weight = 27899.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 2.67
r_work: 0.3469 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3471
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3471
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.1238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16490  Z= 0.189
  Angle     :  0.616   7.353  22360  Z= 0.327
  Chirality :  0.045   0.179   2541
  Planarity :  0.005   0.057   2796
  Dihedral  :  4.634  21.401   2164
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.59 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 12.34 %
    Favored  : 85.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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:  0.90 (0.19), residues: 1938
  helix:  2.15 (0.17), residues: 932
  sheet:  0.18 (0.27), residues: 373
  loop : -1.56 (0.24), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 350 
 HIS   0.011   0.001   HIS A 257 
 PHE   0.024   0.002   PHE D 147 
 TYR   0.024   0.002   TYR B 236 
 ARG   0.006   0.000   ARG L  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05748 (  951)
  hydrogen bonds       : angle       4.86555 ( 2763)
  SS BOND              : bond        0.00224 (    2)
  SS BOND              : angle       1.19112 (    4)
  covalent geometry    : bond        0.00440 (16488)
  covalent geometry    : angle       0.61551 (22356)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  390 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 353
  time to evaluate  : 1.884 
Fit side-chains
   revert: symmetry clash
REVERT: H   15 VAL cc_start: 0.7984 (t) cc_final: 0.7662 (p)
REVERT: H   16 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7425 (mm110)
REVERT: H   28 SER cc_start: 0.8611 (m) cc_final: 0.8170 (p)
REVERT: H   70 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7682 (ttp-170)
REVERT: H  126 THR cc_start: 0.8327 (m) cc_final: 0.8031 (p)
REVERT: A   28 GLU cc_start: 0.7346 (pt0) cc_final: 0.7103 (mt-10)
REVERT: A  116 ASP cc_start: 0.7215 (t70) cc_final: 0.6710 (t0)
REVERT: A  121 GLU cc_start: 0.7123 (mp0) cc_final: 0.6563 (mp0)
REVERT: A  138 MET cc_start: 0.8182 (ttm) cc_final: 0.7967 (ttm)
REVERT: A  178 VAL cc_start: 0.8324 (m) cc_final: 0.8068 (t)
REVERT: B  118 ASN cc_start: 0.6224 (m-40) cc_final: 0.5571 (m110)
REVERT: B  154 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8477 (mp)
REVERT: C  138 MET cc_start: 0.5615 (tmm) cc_final: 0.5123 (tpt)
REVERT: C  191 GLU cc_start: 0.7790 (tp30) cc_final: 0.7590 (tp30)
REVERT: C  230 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6736 (tp30)
REVERT: C  295 THR cc_start: 0.8038 (m) cc_final: 0.7707 (m)
REVERT: D   42 PHE cc_start: 0.7969 (p90) cc_final: 0.7461 (p90)
REVERT: D   80 PHE cc_start: 0.6910 (m-80) cc_final: 0.6697 (m-80)
REVERT: D  110 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7474 (mt)
REVERT: E  179 ASP cc_start: 0.7671 (m-30) cc_final: 0.7469 (m-30)
REVERT: E  222 ARG cc_start: 0.7746 (ptm-80) cc_final: 0.7335 (ttp80)
REVERT: E  324 LYS cc_start: 0.7887 (tmtt) cc_final: 0.7680 (tmtt)
  outliers start: 37
  outliers final: 24
  residues processed: 368
  average time/residue: 0.2887
  time to fit residues: 156.9931
Evaluate side-chains
  365 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 338
  time to evaluate  : 1.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain C residue   69 ARG
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  130 ILE
Chi-restraints excluded: chain C residue  230 GLU
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 VAL
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  226 TRP
Chi-restraints excluded: chain E residue  291 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 129 optimal weight:    6.9990
   chunk 88 optimal weight:    4.9990
   chunk 97 optimal weight:    4.9990
   chunk 115 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 189 optimal weight:    0.4980
   chunk 145 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  94 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.166839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.136942 restraints weight = 27882.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 2.69
r_work: 0.3471 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3471
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3471
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  16490  Z= 0.180
  Angle     :  0.604   7.991  22360  Z= 0.321
  Chirality :  0.044   0.153   2541
  Planarity :  0.005   0.063   2796
  Dihedral  :  4.603  21.866   2164
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.80 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.26 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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:  0.88 (0.19), residues: 1938
  helix:  2.18 (0.17), residues: 931
  sheet:  0.07 (0.27), residues: 373
  loop : -1.57 (0.24), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 350 
 HIS   0.009   0.001   HIS A 257 
 PHE   0.026   0.001   PHE D 147 
 TYR   0.028   0.002   TYR B 236 
 ARG   0.006   0.000   ARG L  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05612 (  951)
  hydrogen bonds       : angle       4.71609 ( 2763)
  SS BOND              : bond        0.00243 (    2)
  SS BOND              : angle       0.97899 (    4)
  covalent geometry    : bond        0.00416 (16488)
  covalent geometry    : angle       0.60405 (22356)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  411 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 364
  time to evaluate  : 1.713 
Fit side-chains
   revert: symmetry clash
REVERT: H   15 VAL cc_start: 0.8002 (t) cc_final: 0.7703 (p)
REVERT: H   16 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7419 (mm110)
REVERT: H   28 SER cc_start: 0.8564 (m) cc_final: 0.8131 (p)
REVERT: H   94 THR cc_start: 0.8369 (t) cc_final: 0.7927 (m)
REVERT: H  126 THR cc_start: 0.8253 (m) cc_final: 0.7869 (p)
REVERT: A   28 GLU cc_start: 0.7358 (pt0) cc_final: 0.7133 (mt-10)
REVERT: A  116 ASP cc_start: 0.7098 (t70) cc_final: 0.6607 (t0)
REVERT: A  121 GLU cc_start: 0.7177 (mp0) cc_final: 0.6557 (mp0)
REVERT: A  178 VAL cc_start: 0.8294 (m) cc_final: 0.8046 (t)
REVERT: B  118 ASN cc_start: 0.6115 (m-40) cc_final: 0.5550 (m110)
REVERT: B  154 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8476 (mp)
REVERT: C  138 MET cc_start: 0.5841 (tmm) cc_final: 0.5497 (tpt)
REVERT: C  230 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6774 (tp30)
REVERT: C  295 THR cc_start: 0.8071 (m) cc_final: 0.7758 (m)
REVERT: D  110 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7445 (mt)
REVERT: D  136 VAL cc_start: 0.7867 (t) cc_final: 0.7485 (m)
REVERT: E  179 ASP cc_start: 0.7671 (m-30) cc_final: 0.7468 (m-30)
REVERT: E  222 ARG cc_start: 0.7715 (ptm-80) cc_final: 0.7295 (ttp80)
REVERT: E  324 LYS cc_start: 0.7864 (tmtt) cc_final: 0.7626 (tmtt)
  outliers start: 47
  outliers final: 32
  residues processed: 385
  average time/residue: 0.2756
  time to fit residues: 159.5296
Evaluate side-chains
  376 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 341
  time to evaluate  : 1.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain C residue   69 ARG
Chi-restraints excluded: chain C residue  130 ILE
Chi-restraints excluded: chain C residue  230 GLU
Chi-restraints excluded: chain C residue  267 THR
Chi-restraints excluded: chain C residue  282 SER
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 VAL
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue  134 ASN
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  226 TRP
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  291 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 157 optimal weight:    3.9990
   chunk 165 optimal weight:    0.0670
   chunk 154 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 159 optimal weight:    4.9990
   chunk 161 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0970
   overall best weight:    0.5316

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

Flipped N/Q/H residues before XYZ refinement:
** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.167636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.137852 restraints weight = 28175.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 2.67
r_work: 0.3484 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3484
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3484 r_free = 0.3484    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3484 r_free = 0.3484    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3484
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  16490  Z= 0.154
  Angle     :  0.589   8.063  22360  Z= 0.313
  Chirality :  0.044   0.178   2541
  Planarity :  0.004   0.065   2796
  Dihedral  :  4.511  21.924   2164
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.44 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.08 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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:  0.96 (0.20), residues: 1938
  helix:  2.25 (0.17), residues: 932
  sheet:  0.12 (0.26), residues: 390
  loop : -1.60 (0.25), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 350 
 HIS   0.006   0.001   HIS A 257 
 PHE   0.032   0.001   PHE C  27 
 TYR   0.020   0.001   TYR B 236 
 ARG   0.006   0.000   ARG L  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05404 (  951)
  hydrogen bonds       : angle       4.60579 ( 2763)
  SS BOND              : bond        0.00228 (    2)
  SS BOND              : angle       0.86772 (    4)
  covalent geometry    : bond        0.00345 (16488)
  covalent geometry    : angle       0.58892 (22356)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  401 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 352
  time to evaluate  : 1.851 
Fit side-chains
   revert: symmetry clash
REVERT: L   86 THR cc_start: 0.8537 (m) cc_final: 0.8336 (t)
REVERT: H   15 VAL cc_start: 0.7995 (t) cc_final: 0.7693 (p)
REVERT: H   16 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7395 (mm-40)
REVERT: H   28 SER cc_start: 0.8530 (m) cc_final: 0.8083 (p)
REVERT: H   94 THR cc_start: 0.8410 (t) cc_final: 0.8007 (m)
REVERT: H  126 THR cc_start: 0.8260 (m) cc_final: 0.7894 (p)
REVERT: A   28 GLU cc_start: 0.7382 (pt0) cc_final: 0.7141 (mt-10)
REVERT: A  116 ASP cc_start: 0.7138 (t70) cc_final: 0.6631 (t0)
REVERT: A  121 GLU cc_start: 0.7188 (mp0) cc_final: 0.6600 (mp0)
REVERT: B  118 ASN cc_start: 0.6050 (m-40) cc_final: 0.5638 (m110)
REVERT: C  138 MET cc_start: 0.5822 (tmm) cc_final: 0.5573 (tpt)
REVERT: C  230 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6777 (tp30)
REVERT: C  295 THR cc_start: 0.8023 (m) cc_final: 0.7710 (m)
REVERT: D  110 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7467 (mt)
REVERT: D  136 VAL cc_start: 0.7856 (t) cc_final: 0.7419 (m)
REVERT: D  163 LYS cc_start: 0.8805 (mptt) cc_final: 0.8504 (mptt)
REVERT: E  179 ASP cc_start: 0.7624 (m-30) cc_final: 0.7409 (m-30)
REVERT: E  222 ARG cc_start: 0.7711 (ptm-80) cc_final: 0.7287 (ttp80)
REVERT: E  324 LYS cc_start: 0.7620 (tmtt) cc_final: 0.7418 (tmtt)
  outliers start: 49
  outliers final: 33
  residues processed: 376
  average time/residue: 0.2606
  time to fit residues: 146.5665
Evaluate side-chains
  374 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 339
  time to evaluate  : 2.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  145 ASP
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain C residue  130 ILE
Chi-restraints excluded: chain C residue  230 GLU
Chi-restraints excluded: chain C residue  267 THR
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 VAL
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  134 ASN
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  226 TRP
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  291 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 177 optimal weight:    0.9990
   chunk 155 optimal weight:    0.9990
   chunk 159 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 127 optimal weight:    0.0370
   chunk 184 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 187 optimal weight:    1.9990
   chunk 185 optimal weight:    0.9990
   chunk 163 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   overall best weight:    0.8064

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

Flipped N/Q/H residues before XYZ refinement:
A  74 GLN
** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.166232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.136632 restraints weight = 28009.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 2.68
r_work: 0.3472 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  16490  Z= 0.187
  Angle     :  0.611   8.746  22360  Z= 0.325
  Chirality :  0.045   0.173   2541
  Planarity :  0.005   0.072   2796
  Dihedral  :  4.552  21.972   2164
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.64 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.80 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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:  0.85 (0.19), residues: 1938
  helix:  2.17 (0.17), residues: 939
  sheet: -0.01 (0.26), residues: 385
  loop : -1.64 (0.24), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 350 
 HIS   0.010   0.001   HIS A 257 
 PHE   0.028   0.002   PHE D 147 
 TYR   0.021   0.002   TYR B 236 
 ARG   0.008   0.000   ARG L  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05537 (  951)
  hydrogen bonds       : angle       4.60013 ( 2763)
  SS BOND              : bond        0.00235 (    2)
  SS BOND              : angle       0.86822 (    4)
  covalent geometry    : bond        0.00436 (16488)
  covalent geometry    : angle       0.61124 (22356)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  399 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 342
  time to evaluate  : 1.923 
Fit side-chains
   revert: symmetry clash
REVERT: H   16 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7402 (mm-40)
REVERT: H   28 SER cc_start: 0.8529 (m) cc_final: 0.8087 (p)
REVERT: H   94 THR cc_start: 0.8423 (t) cc_final: 0.8005 (m)
REVERT: H  126 THR cc_start: 0.8258 (m) cc_final: 0.7872 (p)
REVERT: A   28 GLU cc_start: 0.7371 (pt0) cc_final: 0.7143 (mt-10)
REVERT: A  116 ASP cc_start: 0.7075 (t70) cc_final: 0.6496 (t0)
REVERT: A  121 GLU cc_start: 0.7165 (mp0) cc_final: 0.6697 (mp0)
REVERT: A  313 MET cc_start: 0.5533 (mtt) cc_final: 0.5220 (mtm)
REVERT: B  118 ASN cc_start: 0.6102 (m-40) cc_final: 0.5719 (m110)
REVERT: C   69 ARG cc_start: 0.5062 (OUTLIER) cc_final: 0.4860 (ptm160)
REVERT: C  138 MET cc_start: 0.5967 (tmm) cc_final: 0.5706 (tpt)
REVERT: C  230 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6759 (tp30)
REVERT: C  295 THR cc_start: 0.8100 (m) cc_final: 0.7829 (m)
REVERT: D  110 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7436 (mt)
REVERT: D  136 VAL cc_start: 0.7832 (t) cc_final: 0.7380 (m)
REVERT: D  163 LYS cc_start: 0.8821 (mptt) cc_final: 0.8487 (mptt)
REVERT: E  324 LYS cc_start: 0.7599 (tmtt) cc_final: 0.7389 (tmtt)
  outliers start: 57
  outliers final: 38
  residues processed: 370
  average time/residue: 0.2733
  time to fit residues: 149.8162
Evaluate side-chains
  378 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 337
  time to evaluate  : 1.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain C residue   69 ARG
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  130 ILE
Chi-restraints excluded: chain C residue  230 GLU
Chi-restraints excluded: chain C residue  267 THR
Chi-restraints excluded: chain C residue  282 SER
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain D residue   92 ASN
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 VAL
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  134 ASN
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  226 TRP
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  291 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 170 optimal weight:    2.9990
   chunk 183 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0980
   chunk 75 optimal weight:    2.9990
   chunk 102 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 117 optimal weight:    0.8980
   chunk 175 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.166775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.137272 restraints weight = 28122.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 2.57
r_work: 0.3488 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  16490  Z= 0.161
  Angle     :  0.599   8.839  22360  Z= 0.319
  Chirality :  0.044   0.169   2541
  Planarity :  0.005   0.065   2796
  Dihedral  :  4.500  21.944   2164
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.44 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 18.62 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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:  0.89 (0.19), residues: 1938
  helix:  2.21 (0.17), residues: 939
  sheet:  0.06 (0.27), residues: 376
  loop : -1.65 (0.24), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 350 
 HIS   0.007   0.001   HIS A 257 
 PHE   0.026   0.001   PHE D 147 
 TYR   0.026   0.002   TYR A  19 
 ARG   0.008   0.000   ARG L  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05405 (  951)
  hydrogen bonds       : angle       4.53064 ( 2763)
  SS BOND              : bond        0.00185 (    2)
  SS BOND              : angle       0.84914 (    4)
  covalent geometry    : bond        0.00364 (16488)
  covalent geometry    : angle       0.59909 (22356)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  395 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 338
  time to evaluate  : 1.701 
Fit side-chains
   revert: symmetry clash
REVERT: H   16 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7419 (mm-40)
REVERT: H   28 SER cc_start: 0.8531 (m) cc_final: 0.8098 (p)
REVERT: H   94 THR cc_start: 0.8403 (t) cc_final: 0.8052 (m)
REVERT: H  126 THR cc_start: 0.8276 (m) cc_final: 0.7893 (p)
REVERT: A   28 GLU cc_start: 0.7439 (pt0) cc_final: 0.7139 (mt-10)
REVERT: A  116 ASP cc_start: 0.7085 (t70) cc_final: 0.6579 (t0)
REVERT: A  121 GLU cc_start: 0.7181 (mp0) cc_final: 0.6681 (mp0)
REVERT: B  118 ASN cc_start: 0.5994 (m-40) cc_final: 0.5743 (m110)
REVERT: C  138 MET cc_start: 0.5921 (tmm) cc_final: 0.5691 (tpt)
REVERT: C  230 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6750 (tp30)
REVERT: C  295 THR cc_start: 0.8065 (m) cc_final: 0.7765 (m)
REVERT: D  110 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7440 (mt)
REVERT: D  136 VAL cc_start: 0.7836 (t) cc_final: 0.7377 (m)
REVERT: D  163 LYS cc_start: 0.8816 (mptt) cc_final: 0.8520 (mptt)
REVERT: D  331 LEU cc_start: 0.6229 (mt) cc_final: 0.5887 (mp)
REVERT: E  222 ARG cc_start: 0.7701 (ptm-80) cc_final: 0.7252 (ptm-80)
REVERT: E  324 LYS cc_start: 0.7551 (tmtt) cc_final: 0.7325 (tmtt)
  outliers start: 57
  outliers final: 42
  residues processed: 368
  average time/residue: 0.2634
  time to fit residues: 144.6406
Evaluate side-chains
  376 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 332
  time to evaluate  : 1.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  167 ASP
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  130 ILE
Chi-restraints excluded: chain C residue  230 GLU
Chi-restraints excluded: chain C residue  267 THR
Chi-restraints excluded: chain C residue  282 SER
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain D residue   92 ASN
Chi-restraints excluded: chain D residue   99 VAL
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  330 VAL
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  134 ASN
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  291 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 128 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 86 optimal weight:    0.3980
   chunk 99 optimal weight:    4.9990
   chunk 103 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9980
   chunk 153 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0970
   chunk 168 optimal weight:    1.9990
   chunk 117 optimal weight:    0.5980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
L  80 GLN
** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.169178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.139362 restraints weight = 27975.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 2.55
r_work: 0.3498 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  16490  Z= 0.156
  Angle     :  0.596   9.604  22360  Z= 0.316
  Chirality :  0.044   0.166   2541
  Planarity :  0.005   0.065   2796
  Dihedral  :  4.470  21.672   2164
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.39 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 19.01 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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:  0.98 (0.19), residues: 1938
  helix:  2.26 (0.17), residues: 939
  sheet:  0.22 (0.27), residues: 375
  loop : -1.66 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 350 
 HIS   0.007   0.001   HIS A 257 
 PHE   0.025   0.001   PHE D 147 
 TYR   0.022   0.001   TYR D 236 
 ARG   0.008   0.000   ARG L  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05270 (  951)
  hydrogen bonds       : angle       4.47499 ( 2763)
  SS BOND              : bond        0.00148 (    2)
  SS BOND              : angle       0.85846 (    4)
  covalent geometry    : bond        0.00352 (16488)
  covalent geometry    : angle       0.59616 (22356)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  388 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 333
  time to evaluate  : 1.747 
Fit side-chains
   revert: symmetry clash
REVERT: H   16 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7408 (mm-40)
REVERT: H   28 SER cc_start: 0.8516 (m) cc_final: 0.8071 (p)
REVERT: H   94 THR cc_start: 0.8306 (t) cc_final: 0.8034 (m)
REVERT: H  126 THR cc_start: 0.8263 (m) cc_final: 0.7895 (p)
REVERT: A   28 GLU cc_start: 0.7400 (pt0) cc_final: 0.7123 (mt-10)
REVERT: A  116 ASP cc_start: 0.7074 (t70) cc_final: 0.6504 (t0)
REVERT: A  121 GLU cc_start: 0.7183 (mp0) cc_final: 0.6707 (mp0)
REVERT: A  313 MET cc_start: 0.5369 (mtt) cc_final: 0.5111 (mtm)
REVERT: B  118 ASN cc_start: 0.6041 (m-40) cc_final: 0.5797 (m110)
REVERT: C  138 MET cc_start: 0.6007 (tmm) cc_final: 0.5756 (tpt)
REVERT: C  230 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6693 (tp30)
REVERT: C  295 THR cc_start: 0.7983 (m) cc_final: 0.7662 (m)
REVERT: D  110 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7356 (mt)
REVERT: D  136 VAL cc_start: 0.7821 (t) cc_final: 0.7353 (m)
REVERT: D  163 LYS cc_start: 0.8830 (mptt) cc_final: 0.8497 (mptt)
REVERT: D  331 LEU cc_start: 0.6256 (mt) cc_final: 0.5893 (mp)
REVERT: E  222 ARG cc_start: 0.7680 (ptm-80) cc_final: 0.7216 (ptm-80)
REVERT: E  324 LYS cc_start: 0.7526 (tmtt) cc_final: 0.7322 (tmtt)
  outliers start: 55
  outliers final: 43
  residues processed: 362
  average time/residue: 0.2553
  time to fit residues: 138.6209
Evaluate side-chains
  373 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 328
  time to evaluate  : 1.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  167 ASP
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  130 ILE
Chi-restraints excluded: chain C residue  230 GLU
Chi-restraints excluded: chain C residue  267 THR
Chi-restraints excluded: chain C residue  282 SER
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain D residue   92 ASN
Chi-restraints excluded: chain D residue   99 VAL
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 VAL
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  134 ASN
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  278 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 169 optimal weight:    3.9990
   chunk 86 optimal weight:    0.8980
   chunk 136 optimal weight:    6.9990
   chunk 32 optimal weight:    0.0170
   chunk 15 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0030
   chunk 184 optimal weight:    2.9990
   chunk 94 optimal weight:    0.8980
   chunk 153 optimal weight:    1.9990
   chunk 174 optimal weight:    0.5980
   overall best weight:    0.4828

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

Flipped N/Q/H residues before XYZ refinement:
B  92 ASN
** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.172504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.143327 restraints weight = 27987.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 2.64
r_work: 0.3502 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16490  Z= 0.149
  Angle     :  0.597   9.673  22360  Z= 0.316
  Chirality :  0.043   0.162   2541
  Planarity :  0.004   0.065   2796
  Dihedral  :  4.429  21.433   2164
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.28 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.01 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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:  0.99 (0.19), residues: 1938
  helix:  2.28 (0.17), residues: 939
  sheet:  0.22 (0.27), residues: 368
  loop : -1.66 (0.24), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 350 
 HIS   0.006   0.001   HIS A 257 
 PHE   0.028   0.001   PHE D 147 
 TYR   0.022   0.001   TYR D 236 
 ARG   0.008   0.000   ARG L  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05173 (  951)
  hydrogen bonds       : angle       4.43761 ( 2763)
  SS BOND              : bond        0.00161 (    2)
  SS BOND              : angle       0.75758 (    4)
  covalent geometry    : bond        0.00332 (16488)
  covalent geometry    : angle       0.59648 (22356)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  389 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 340
  time to evaluate  : 1.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   16 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7393 (mm-40)
REVERT: H   28 SER cc_start: 0.8496 (m) cc_final: 0.8071 (p)
REVERT: H   94 THR cc_start: 0.8285 (t) cc_final: 0.7986 (m)
REVERT: H  126 THR cc_start: 0.8317 (m) cc_final: 0.7949 (p)
REVERT: A   28 GLU cc_start: 0.7408 (pt0) cc_final: 0.7080 (mt-10)
REVERT: A  116 ASP cc_start: 0.6997 (t70) cc_final: 0.6500 (t0)
REVERT: A  121 GLU cc_start: 0.7203 (mp0) cc_final: 0.6692 (mp0)
REVERT: A  313 MET cc_start: 0.5406 (mtt) cc_final: 0.5080 (mtm)
REVERT: B  256 ASP cc_start: 0.6776 (t0) cc_final: 0.6572 (t0)
REVERT: C  138 MET cc_start: 0.5974 (tmm) cc_final: 0.5737 (tpt)
REVERT: C  230 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6712 (tp30)
REVERT: C  295 THR cc_start: 0.7964 (m) cc_final: 0.7615 (m)
REVERT: D  110 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7347 (mt)
REVERT: D  136 VAL cc_start: 0.7851 (t) cc_final: 0.7372 (m)
REVERT: D  318 MET cc_start: 0.5690 (mtm) cc_final: 0.5254 (mtp)
REVERT: D  320 GLU cc_start: 0.5212 (pm20) cc_final: 0.4987 (pm20)
REVERT: D  331 LEU cc_start: 0.6311 (mt) cc_final: 0.5950 (mp)
  outliers start: 49
  outliers final: 42
  residues processed: 365
  average time/residue: 0.2616
  time to fit residues: 142.7178
Evaluate side-chains
  377 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 333
  time to evaluate  : 1.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  167 ASP
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  130 ILE
Chi-restraints excluded: chain C residue  230 GLU
Chi-restraints excluded: chain C residue  267 THR
Chi-restraints excluded: chain C residue  282 SER
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain D residue   92 ASN
Chi-restraints excluded: chain D residue   99 VAL
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 VAL
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  134 ASN
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  311 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 155 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 124 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 110 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 189 optimal weight:    4.9990
   chunk 165 optimal weight:    0.0060
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
B 118 ASN
** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.171105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.141738 restraints weight = 28145.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 2.60
r_work: 0.3490 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  16490  Z= 0.164
  Angle     :  0.613   9.774  22360  Z= 0.324
  Chirality :  0.044   0.173   2541
  Planarity :  0.005   0.065   2796
  Dihedral  :  4.465  21.447   2164
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.28 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.34 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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:  0.97 (0.19), residues: 1938
  helix:  2.26 (0.17), residues: 939
  sheet:  0.19 (0.27), residues: 377
  loop : -1.67 (0.24), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 350 
 HIS   0.007   0.001   HIS A 257 
 PHE   0.025   0.001   PHE D 147 
 TYR   0.024   0.002   TYR D 236 
 ARG   0.009   0.000   ARG L  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05276 (  951)
  hydrogen bonds       : angle       4.45072 ( 2763)
  SS BOND              : bond        0.00134 (    2)
  SS BOND              : angle       0.72393 (    4)
  covalent geometry    : bond        0.00375 (16488)
  covalent geometry    : angle       0.61260 (22356)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  383 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 335
  time to evaluate  : 2.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   16 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7441 (mm-40)
REVERT: H   28 SER cc_start: 0.8503 (m) cc_final: 0.8074 (p)
REVERT: H   66 SER cc_start: 0.8244 (p) cc_final: 0.7939 (t)
REVERT: H   94 THR cc_start: 0.8332 (t) cc_final: 0.7987 (m)
REVERT: H  126 THR cc_start: 0.8331 (m) cc_final: 0.7964 (p)
REVERT: A   28 GLU cc_start: 0.7383 (pt0) cc_final: 0.7127 (mt-10)
REVERT: A  116 ASP cc_start: 0.7210 (t70) cc_final: 0.6651 (t0)
REVERT: A  121 GLU cc_start: 0.7195 (mp0) cc_final: 0.6729 (mp0)
REVERT: A  191 GLU cc_start: 0.7290 (mm-30) cc_final: 0.7050 (mm-30)
REVERT: A  313 MET cc_start: 0.5474 (mtt) cc_final: 0.5168 (mtm)
REVERT: C  138 MET cc_start: 0.5991 (tmm) cc_final: 0.5738 (tpt)
REVERT: C  230 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6682 (tp30)
REVERT: C  256 ASP cc_start: 0.6807 (OUTLIER) cc_final: 0.6572 (t70)
REVERT: C  295 THR cc_start: 0.7954 (m) cc_final: 0.7624 (m)
REVERT: D  110 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7369 (mt)
REVERT: D  136 VAL cc_start: 0.7855 (t) cc_final: 0.7391 (m)
REVERT: D  331 LEU cc_start: 0.6515 (mt) cc_final: 0.6132 (mp)
REVERT: E  324 LYS cc_start: 0.7294 (tmtt) cc_final: 0.6835 (tmtt)
  outliers start: 48
  outliers final: 44
  residues processed: 363
  average time/residue: 0.2791
  time to fit residues: 153.7166
Evaluate side-chains
  381 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 334
  time to evaluate  : 1.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  167 ASP
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  130 ILE
Chi-restraints excluded: chain C residue  230 GLU
Chi-restraints excluded: chain C residue  256 ASP
Chi-restraints excluded: chain C residue  267 THR
Chi-restraints excluded: chain C residue  282 SER
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain D residue   92 ASN
Chi-restraints excluded: chain D residue   99 VAL
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 VAL
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  194 VAL
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  278 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0370
   chunk 177 optimal weight:    0.9990
   chunk 183 optimal weight:    0.9980
   chunk 87 optimal weight:    0.7980
   chunk 99 optimal weight:    3.9990
   chunk 64 optimal weight:    0.5980
   chunk 95 optimal weight:    6.9990
   chunk 0 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   overall best weight:    0.6860

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

Flipped N/Q/H residues before XYZ refinement:
B 118 ASN
** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.170847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.141473 restraints weight = 27852.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 2.61
r_work: 0.3489 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  16490  Z= 0.171
  Angle     :  0.619  10.295  22360  Z= 0.327
  Chirality :  0.044   0.175   2541
  Planarity :  0.005   0.065   2796
  Dihedral  :  4.508  21.531   2164
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.59 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 19.45 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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:  0.95 (0.19), residues: 1938
  helix:  2.25 (0.17), residues: 939
  sheet:  0.15 (0.27), residues: 368
  loop : -1.66 (0.24), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 350 
 HIS   0.008   0.001   HIS A 257 
 PHE   0.027   0.001   PHE D 147 
 TYR   0.025   0.002   TYR D 171 
 ARG   0.009   0.000   ARG L  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05320 (  951)
  hydrogen bonds       : angle       4.45246 ( 2763)
  SS BOND              : bond        0.00166 (    2)
  SS BOND              : angle       0.74704 (    4)
  covalent geometry    : bond        0.00396 (16488)
  covalent geometry    : angle       0.61859 (22356)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9037.51 seconds
wall clock time: 157 minutes 20.62 seconds (9440.62 seconds total)