Starting phenix.real_space_refine
on Sun Aug 24 01:41:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tme_41386/08_2025/8tme_41386.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tme_41386/08_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_41386/08_2025/8tme_41386.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tme_41386/08_2025/8tme_41386.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tme_41386/08_2025/8tme_41386.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tme_41386/08_2025/8tme_41386.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.08, per 1000 atoms: 0.25
  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: 1.33
  Conformation dependent library (CDL) restraints added in 713.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.52
  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: 2.59

  Time building geometry restraints manager: 1.80 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:             3.080
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     15.510
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.580
-------------------------------------------------------------------------------
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 : 11.76
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.009   0.000   ARG L  19 
 TYR   0.020   0.002   TYR B 236 
 PHE   0.022   0.001   PHE A 147 
 TRP   0.057   0.002   TRP B 350 
 HIS   0.014   0.001   HIS A 257 

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

*********************** 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  : 0.495 
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: 0.1325
  time to fit residues: 75.2300
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  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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**
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  74 GLN
E  94 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.167272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.136997 restraints weight = 27835.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 2.62
r_work: 0.3465 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3462
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3461 r_free = 0.3461    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3461
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.1019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  16490  Z= 0.225
  Angle     :  0.663   9.717  22360  Z= 0.351
  Chirality :  0.046   0.228   2541
  Planarity :  0.005   0.051   2796
  Dihedral  :  4.727  21.687   2164
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.85 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 10.47 %
    Favored  : 88.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.19), residues: 1938
  helix:  2.05 (0.16), residues: 931
  sheet:  0.18 (0.27), residues: 375
  loop : -1.59 (0.24), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 237 
 TYR   0.022   0.002   TYR H 106 
 PHE   0.028   0.002   PHE D 147 
 TRP   0.019   0.001   TRP B 350 
 HIS   0.013   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 (16488)
  covalent geometry    : angle       0.66323 (22356)
  SS BOND              : bond        0.00231 (    2)
  SS BOND              : angle       1.27014 (    4)
  hydrogen bonds       : bond        0.06129 (  951)
  hydrogen bonds       : angle       5.15561 ( 2763)

*********************** 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
  377 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 358
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   15 VAL cc_start: 0.8035 (t) cc_final: 0.7715 (p)
REVERT: H   16 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7441 (mm110)
REVERT: H   28 SER cc_start: 0.8641 (m) cc_final: 0.8256 (p)
REVERT: H   90 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7408 (mtt-85)
REVERT: H  126 THR cc_start: 0.8336 (m) cc_final: 0.8036 (p)
REVERT: A   28 GLU cc_start: 0.7327 (pt0) cc_final: 0.7103 (mt-10)
REVERT: A  116 ASP cc_start: 0.7311 (t70) cc_final: 0.6829 (t0)
REVERT: A  178 VAL cc_start: 0.8347 (m) cc_final: 0.8075 (t)
REVERT: B  118 ASN cc_start: 0.6290 (m-40) cc_final: 0.5848 (m110)
REVERT: B  120 HIS cc_start: 0.6968 (m-70) cc_final: 0.6501 (m-70)
REVERT: B  154 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8472 (mp)
REVERT: B  306 PHE cc_start: 0.8009 (t80) cc_final: 0.7798 (t80)
REVERT: B  350 TRP cc_start: 0.6281 (t-100) cc_final: 0.5971 (m100)
REVERT: C  138 MET cc_start: 0.5729 (tmm) cc_final: 0.5184 (tpt)
REVERT: D   42 PHE cc_start: 0.7939 (p90) cc_final: 0.7467 (p90)
REVERT: D  136 VAL cc_start: 0.7892 (p) cc_final: 0.7526 (m)
REVERT: E  134 ASN cc_start: 0.7667 (m-40) cc_final: 0.7463 (m-40)
REVERT: E  179 ASP cc_start: 0.7685 (m-30) cc_final: 0.7478 (m-30)
REVERT: E  222 ARG cc_start: 0.7681 (ptm-80) cc_final: 0.7248 (ttp80)
REVERT: E  324 LYS cc_start: 0.7943 (tmtt) cc_final: 0.7329 (tmtt)
  outliers start: 19
  outliers final: 14
  residues processed: 366
  average time/residue: 0.1121
  time to fit residues: 60.5377
Evaluate side-chains
  352 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 336
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain H residue   90 ARG
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  130 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 48 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9980
   chunk 183 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   chunk 162 optimal weight:    0.9980
   chunk 89 optimal weight:    0.0010
   chunk 132 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 146 optimal weight:    6.9990
   overall best weight:    0.6586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.169311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.138872 restraints weight = 28218.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 2.60
r_work: 0.3482 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3483
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3483
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.1230

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= 0.170
  Angle     :  0.607   7.306  22360  Z= 0.323
  Chirality :  0.044   0.185   2541
  Planarity :  0.005   0.056   2796
  Dihedral  :  4.642  21.429   2164
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.70 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.00 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.19), residues: 1938
  helix:  2.17 (0.17), residues: 931
  sheet:  0.15 (0.27), residues: 376
  loop : -1.59 (0.24), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 237 
 TYR   0.025   0.002   TYR B 236 
 PHE   0.021   0.002   PHE D 147 
 TRP   0.015   0.001   TRP B 350 
 HIS   0.008   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (16488)
  covalent geometry    : angle       0.60697 (22356)
  SS BOND              : bond        0.00186 (    2)
  SS BOND              : angle       1.11727 (    4)
  hydrogen bonds       : bond        0.05705 (  951)
  hydrogen bonds       : angle       4.86182 ( 2763)

*********************** 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
  393 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 356
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
REVERT: H   15 VAL cc_start: 0.7998 (t) cc_final: 0.7720 (p)
REVERT: H   16 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7407 (mm110)
REVERT: H   28 SER cc_start: 0.8628 (m) cc_final: 0.8228 (p)
REVERT: H   90 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7409 (mtt-85)
REVERT: H   94 THR cc_start: 0.8379 (t) cc_final: 0.7916 (m)
REVERT: H  126 THR cc_start: 0.8318 (m) cc_final: 0.7955 (p)
REVERT: A   28 GLU cc_start: 0.7316 (pt0) cc_final: 0.7087 (mt-10)
REVERT: A  116 ASP cc_start: 0.7225 (t70) cc_final: 0.6723 (t0)
REVERT: A  121 GLU cc_start: 0.7084 (mp0) cc_final: 0.6522 (mp0)
REVERT: A  138 MET cc_start: 0.8144 (ttm) cc_final: 0.7933 (ttm)
REVERT: A  178 VAL cc_start: 0.8295 (m) cc_final: 0.8038 (t)
REVERT: B  118 ASN cc_start: 0.6236 (m-40) cc_final: 0.5602 (m110)
REVERT: B  120 HIS cc_start: 0.6895 (m-70) cc_final: 0.6457 (m-70)
REVERT: B  154 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8479 (mp)
REVERT: B  306 PHE cc_start: 0.7968 (t80) cc_final: 0.7762 (t80)
REVERT: C  125 GLU cc_start: 0.6608 (pm20) cc_final: 0.6245 (pm20)
REVERT: C  138 MET cc_start: 0.5619 (tmm) cc_final: 0.5124 (tpt)
REVERT: C  230 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6737 (tp30)
REVERT: C  295 THR cc_start: 0.8024 (m) cc_final: 0.7676 (m)
REVERT: D   42 PHE cc_start: 0.7968 (p90) cc_final: 0.7439 (p90)
REVERT: D   80 PHE cc_start: 0.6906 (m-80) cc_final: 0.6705 (m-80)
REVERT: D  110 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7462 (mt)
REVERT: E  179 ASP cc_start: 0.7664 (m-30) cc_final: 0.7456 (m-30)
REVERT: E  222 ARG cc_start: 0.7741 (ptm-80) cc_final: 0.7327 (ttp80)
  outliers start: 37
  outliers final: 22
  residues processed: 371
  average time/residue: 0.1106
  time to fit residues: 61.3597
Evaluate side-chains
  366 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 340
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   90 ARG
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   57 SER
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  154 ILE
Chi-restraints excluded: chain B residue  288 ASN
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  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 91 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 178 optimal weight:    1.9990
   chunk 135 optimal weight:    5.9990
   chunk 149 optimal weight:    0.9990
   chunk 145 optimal weight:    1.9990
   chunk 111 optimal weight:    0.0470
   chunk 96 optimal weight:    0.0970
   chunk 84 optimal weight:    0.5980
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
C  63 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 = 0.4197 r_free = 0.4197 target = 0.169201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.139394 restraints weight = 28072.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 2.69
r_work: 0.3486 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3485
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3485 r_free = 0.3485    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3485 r_free = 0.3485    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3485
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.1398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  16490  Z= 0.154
  Angle     :  0.588   7.476  22360  Z= 0.313
  Chirality :  0.043   0.173   2541
  Planarity :  0.004   0.062   2796
  Dihedral  :  4.548  21.713   2164
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.64 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.10 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.19), residues: 1938
  helix:  2.23 (0.17), residues: 932
  sheet:  0.17 (0.27), residues: 381
  loop : -1.57 (0.24), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  19 
 TYR   0.033   0.002   TYR A 115 
 PHE   0.026   0.001   PHE D 147 
 TRP   0.012   0.001   TRP A 350 
 HIS   0.007   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (16488)
  covalent geometry    : angle       0.58840 (22356)
  SS BOND              : bond        0.00167 (    2)
  SS BOND              : angle       0.95067 (    4)
  hydrogen bonds       : bond        0.05443 (  951)
  hydrogen bonds       : angle       4.69027 ( 2763)

*********************** 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
  407 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 362
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
REVERT: L   86 THR cc_start: 0.8550 (m) cc_final: 0.8344 (t)
REVERT: H   15 VAL cc_start: 0.7995 (t) cc_final: 0.7705 (p)
REVERT: H   16 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7398 (mm-40)
REVERT: H   28 SER cc_start: 0.8589 (m) cc_final: 0.8153 (p)
REVERT: H   70 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7723 (ttp-170)
REVERT: H   90 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7306 (mtt-85)
REVERT: H   94 THR cc_start: 0.8335 (t) cc_final: 0.7917 (m)
REVERT: H  126 THR cc_start: 0.8253 (m) cc_final: 0.7909 (p)
REVERT: A   28 GLU cc_start: 0.7338 (pt0) cc_final: 0.7129 (mt-10)
REVERT: A  116 ASP cc_start: 0.7124 (t70) cc_final: 0.6604 (t0)
REVERT: A  121 GLU cc_start: 0.7162 (mp0) cc_final: 0.6617 (mp0)
REVERT: B  118 ASN cc_start: 0.6128 (m-40) cc_final: 0.5577 (m110)
REVERT: B  120 HIS cc_start: 0.6878 (m-70) cc_final: 0.6458 (m-70)
REVERT: B  306 PHE cc_start: 0.7904 (t80) cc_final: 0.7682 (t80)
REVERT: C  138 MET cc_start: 0.5802 (tmm) cc_final: 0.5502 (tpt)
REVERT: C  230 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6764 (tp30)
REVERT: C  295 THR cc_start: 0.7956 (m) cc_final: 0.7611 (m)
REVERT: D   42 PHE cc_start: 0.7961 (p90) cc_final: 0.7495 (p90)
REVERT: D  110 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7454 (mt)
REVERT: E  179 ASP cc_start: 0.7625 (m-30) cc_final: 0.7417 (m-30)
REVERT: E  222 ARG cc_start: 0.7709 (ptm-80) cc_final: 0.7285 (ttp80)
REVERT: E  324 LYS cc_start: 0.7684 (tmtt) cc_final: 0.7124 (tmtt)
  outliers start: 45
  outliers final: 30
  residues processed: 383
  average time/residue: 0.1083
  time to fit residues: 62.2307
Evaluate side-chains
  375 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 342
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   90 ARG
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  195 LEU
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  282 SER
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  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 86 optimal weight:    2.9990
   chunk 165 optimal weight:    0.0570
   chunk 91 optimal weight:   10.0000
   chunk 16 optimal weight:    0.6980
   chunk 100 optimal weight:    0.8980
   chunk 114 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0870
   chunk 29 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 176 optimal weight:    0.8980
   chunk 169 optimal weight:    2.9990
   overall best weight:    0.4876

-------------------------------------------------------------------------------
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**
E 140 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.171962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.142052 restraints weight = 27903.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 2.63
r_work: 0.3486 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3485
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3485 r_free = 0.3485    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3485 r_free = 0.3485    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3485
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.1538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  16490  Z= 0.148
  Angle     :  0.580   8.010  22360  Z= 0.308
  Chirality :  0.043   0.165   2541
  Planarity :  0.004   0.064   2796
  Dihedral  :  4.458  21.779   2164
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.64 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.58 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.20), residues: 1938
  helix:  2.31 (0.17), residues: 931
  sheet:  0.19 (0.27), residues: 381
  loop : -1.59 (0.24), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  19 
 TYR   0.020   0.001   TYR B 236 
 PHE   0.032   0.001   PHE C  27 
 TRP   0.015   0.001   TRP A 350 
 HIS   0.006   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (16488)
  covalent geometry    : angle       0.57960 (22356)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       0.76799 (    4)
  hydrogen bonds       : bond        0.05272 (  951)
  hydrogen bonds       : angle       4.56085 ( 2763)

*********************** 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
  410 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 358
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
REVERT: L   86 THR cc_start: 0.8550 (m) cc_final: 0.8346 (t)
REVERT: H   15 VAL cc_start: 0.8004 (t) cc_final: 0.7701 (p)
REVERT: H   16 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7570 (mm-40)
REVERT: H   28 SER cc_start: 0.8549 (m) cc_final: 0.8115 (p)
REVERT: H   94 THR cc_start: 0.8421 (t) cc_final: 0.8012 (m)
REVERT: H  126 THR cc_start: 0.8275 (m) cc_final: 0.7917 (p)
REVERT: A   28 GLU cc_start: 0.7352 (pt0) cc_final: 0.7137 (mt-10)
REVERT: A  116 ASP cc_start: 0.7117 (t70) cc_final: 0.6650 (t0)
REVERT: A  121 GLU cc_start: 0.7188 (mp0) cc_final: 0.6584 (mp0)
REVERT: B  118 ASN cc_start: 0.6051 (m-40) cc_final: 0.5631 (m110)
REVERT: B  120 HIS cc_start: 0.6867 (m-70) cc_final: 0.6489 (m-70)
REVERT: B  306 PHE cc_start: 0.7906 (t80) cc_final: 0.7695 (t80)
REVERT: C  138 MET cc_start: 0.5777 (tmm) cc_final: 0.5492 (tpt)
REVERT: C  230 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6805 (tp30)
REVERT: C  295 THR cc_start: 0.8013 (m) cc_final: 0.7673 (m)
REVERT: D  110 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7439 (mt)
REVERT: D  136 VAL cc_start: 0.7837 (t) cc_final: 0.7415 (m)
REVERT: E   49 SER cc_start: 0.6002 (OUTLIER) cc_final: 0.5605 (p)
REVERT: E  179 ASP cc_start: 0.7654 (m-30) cc_final: 0.7452 (m-30)
REVERT: E  222 ARG cc_start: 0.7730 (ptm-80) cc_final: 0.7278 (ttp80)
  outliers start: 52
  outliers final: 34
  residues processed: 385
  average time/residue: 0.1054
  time to fit residues: 61.1644
Evaluate side-chains
  384 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 347
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   73 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   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  195 LEU
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  247 THR
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  282 SER
Chi-restraints excluded: chain C residue  300 ILE
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  283 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 VAL
Chi-restraints excluded: chain E residue   49 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 77 optimal weight:    0.0870
   chunk 104 optimal weight:    9.9990
   chunk 138 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 168 optimal weight:    1.9990
   chunk 181 optimal weight:    0.0870
   chunk 26 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 136 optimal weight:    0.6980
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.5536

-------------------------------------------------------------------------------
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 = 0.4199 r_free = 0.4199 target = 0.169421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.139484 restraints weight = 27913.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 2.64
r_work: 0.3489 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  16490  Z= 0.155
  Angle     :  0.587   8.474  22360  Z= 0.312
  Chirality :  0.044   0.162   2541
  Planarity :  0.005   0.071   2796
  Dihedral  :  4.449  21.821   2164
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.54 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 17.58 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.19), residues: 1938
  helix:  2.27 (0.17), residues: 932
  sheet:  0.16 (0.26), residues: 382
  loop : -1.60 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG L  19 
 TYR   0.023   0.002   TYR A 115 
 PHE   0.029   0.001   PHE D 147 
 TRP   0.017   0.001   TRP A 350 
 HIS   0.007   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (16488)
  covalent geometry    : angle       0.58685 (22356)
  SS BOND              : bond        0.00153 (    2)
  SS BOND              : angle       0.81909 (    4)
  hydrogen bonds       : bond        0.05267 (  951)
  hydrogen bonds       : angle       4.51154 ( 2763)

*********************** 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: 54
    poor density    : 345
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
REVERT: L   86 THR cc_start: 0.8545 (m) cc_final: 0.8338 (t)
REVERT: H   15 VAL cc_start: 0.7995 (t) cc_final: 0.7679 (p)
REVERT: H   16 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7591 (mm-40)
REVERT: H   28 SER cc_start: 0.8537 (m) cc_final: 0.8112 (p)
REVERT: H   94 THR cc_start: 0.8403 (t) cc_final: 0.7989 (m)
REVERT: H  126 THR cc_start: 0.8334 (m) cc_final: 0.7972 (p)
REVERT: A   28 GLU cc_start: 0.7322 (pt0) cc_final: 0.7120 (mt-10)
REVERT: A  116 ASP cc_start: 0.7080 (t70) cc_final: 0.6560 (t0)
REVERT: A  121 GLU cc_start: 0.7204 (mp0) cc_final: 0.6735 (mp0)
REVERT: B  118 ASN cc_start: 0.6068 (m-40) cc_final: 0.5673 (m110)
REVERT: B  120 HIS cc_start: 0.6865 (m-70) cc_final: 0.6523 (m-70)
REVERT: C   69 ARG cc_start: 0.5114 (OUTLIER) cc_final: 0.4885 (ptm160)
REVERT: C  138 MET cc_start: 0.5877 (tmm) cc_final: 0.5645 (tpt)
REVERT: C  230 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6698 (tp30)
REVERT: C  295 THR cc_start: 0.8009 (m) cc_final: 0.7677 (m)
REVERT: D   80 PHE cc_start: 0.7125 (m-80) cc_final: 0.6851 (m-80)
REVERT: D  110 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7473 (mt)
REVERT: D  136 VAL cc_start: 0.7834 (t) cc_final: 0.7374 (m)
REVERT: E  179 ASP cc_start: 0.7664 (m-30) cc_final: 0.7461 (m-30)
REVERT: E  222 ARG cc_start: 0.7747 (ptm-80) cc_final: 0.7377 (ptm-80)
  outliers start: 54
  outliers final: 38
  residues processed: 371
  average time/residue: 0.1229
  time to fit residues: 68.8225
Evaluate side-chains
  380 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 339
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   73 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   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  195 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  246 GLU
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   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  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 49 optimal weight:    0.8980
   chunk 138 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 162 optimal weight:    0.0470
   chunk 160 optimal weight:    1.9990
   chunk 158 optimal weight:    6.9990
   chunk 119 optimal weight:    2.9990
   chunk 156 optimal weight:    5.9990
   chunk 155 optimal weight:    0.9980
   chunk 126 optimal weight:    2.9990
   overall best weight:    0.7880

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

Flipped N/Q/H residues before XYZ refinement:
A 120 HIS
** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  63 ASN
E 140 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.167781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.137631 restraints weight = 27739.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 2.55
r_work: 0.3494 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.1660

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= 0.183
  Angle     :  0.611   9.001  22360  Z= 0.323
  Chirality :  0.044   0.169   2541
  Planarity :  0.005   0.065   2796
  Dihedral  :  4.508  21.968   2164
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.64 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 18.18 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.19), residues: 1938
  helix:  2.19 (0.17), residues: 939
  sheet:  0.10 (0.26), residues: 395
  loop : -1.66 (0.25), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG L  19 
 TYR   0.026   0.002   TYR A  19 
 PHE   0.027   0.002   PHE D 147 
 TRP   0.017   0.001   TRP A 350 
 HIS   0.009   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (16488)
  covalent geometry    : angle       0.61091 (22356)
  SS BOND              : bond        0.00163 (    2)
  SS BOND              : angle       0.74427 (    4)
  hydrogen bonds       : bond        0.05439 (  951)
  hydrogen bonds       : angle       4.52488 ( 2763)

*********************** 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
  401 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 344
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
REVERT: H   16 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7384 (mm-40)
REVERT: H   28 SER cc_start: 0.8546 (m) cc_final: 0.8092 (p)
REVERT: H   94 THR cc_start: 0.8401 (t) cc_final: 0.7963 (m)
REVERT: H  126 THR cc_start: 0.8236 (m) cc_final: 0.7840 (p)
REVERT: A   28 GLU cc_start: 0.7383 (pt0) cc_final: 0.7139 (mt-10)
REVERT: A  116 ASP cc_start: 0.7111 (t70) cc_final: 0.6637 (t0)
REVERT: A  121 GLU cc_start: 0.7127 (mp0) cc_final: 0.6631 (mp0)
REVERT: B  118 ASN cc_start: 0.6021 (m-40) cc_final: 0.5738 (m110)
REVERT: B  120 HIS cc_start: 0.6890 (m-70) cc_final: 0.6536 (m-70)
REVERT: C  138 MET cc_start: 0.5870 (tmm) cc_final: 0.5646 (tpt)
REVERT: C  230 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6672 (tp30)
REVERT: C  295 THR cc_start: 0.8068 (m) cc_final: 0.7779 (m)
REVERT: D   80 PHE cc_start: 0.7244 (m-80) cc_final: 0.6933 (m-80)
REVERT: D  110 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7413 (mt)
REVERT: D  136 VAL cc_start: 0.7809 (t) cc_final: 0.7338 (m)
REVERT: E  179 ASP cc_start: 0.7684 (m-30) cc_final: 0.7465 (m-30)
REVERT: E  222 ARG cc_start: 0.7778 (ptm-80) cc_final: 0.7463 (ptm-80)
  outliers start: 57
  outliers final: 44
  residues processed: 373
  average time/residue: 0.1167
  time to fit residues: 65.9578
Evaluate side-chains
  381 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 335
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
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   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  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   90 ILE
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  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  226 TRP
Chi-restraints excluded: chain E residue  270 ASP
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 162 optimal weight:    0.0170
   chunk 56 optimal weight:    0.0070
   chunk 102 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 121 optimal weight:    1.9990
   chunk 126 optimal weight:    0.0270
   chunk 61 optimal weight:    0.6980
   chunk 94 optimal weight:    0.5980
   chunk 82 optimal weight:    0.4980
   chunk 7 optimal weight:    1.9990
   chunk 164 optimal weight:    5.9990
   overall best weight:    0.2294

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

Flipped N/Q/H residues before XYZ refinement:
L  80 GLN
A  74 GLN
C 288 ASN
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.172476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.143123 restraints weight = 28085.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 2.52
r_work: 0.3541 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16490  Z= 0.129
  Angle     :  0.579   9.167  22360  Z= 0.307
  Chirality :  0.043   0.161   2541
  Planarity :  0.004   0.066   2796
  Dihedral  :  4.315  21.251   2164
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.97 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 20.28 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.20), residues: 1938
  helix:  2.36 (0.17), residues: 940
  sheet:  0.32 (0.27), residues: 365
  loop : -1.61 (0.24), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  19 
 TYR   0.023   0.001   TYR D 171 
 PHE   0.024   0.001   PHE D 147 
 TRP   0.020   0.001   TRP A 350 
 HIS   0.002   0.001   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (16488)
  covalent geometry    : angle       0.57848 (22356)
  SS BOND              : bond        0.00192 (    2)
  SS BOND              : angle       0.81504 (    4)
  hydrogen bonds       : bond        0.04873 (  951)
  hydrogen bonds       : angle       4.33540 ( 2763)

*********************** 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
  380 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 347
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
REVERT: H   28 SER cc_start: 0.8489 (m) cc_final: 0.8069 (p)
REVERT: H   94 THR cc_start: 0.8287 (t) cc_final: 0.8023 (m)
REVERT: H   96 VAL cc_start: 0.8547 (p) cc_final: 0.8249 (t)
REVERT: H  126 THR cc_start: 0.8322 (m) cc_final: 0.7962 (p)
REVERT: A   74 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6593 (tt0)
REVERT: A  116 ASP cc_start: 0.6982 (t70) cc_final: 0.6609 (t0)
REVERT: A  121 GLU cc_start: 0.7127 (mp0) cc_final: 0.6497 (mp0)
REVERT: A  318 MET cc_start: 0.6920 (ppp) cc_final: 0.6719 (ppp)
REVERT: B  120 HIS cc_start: 0.6813 (m-70) cc_final: 0.6485 (m-70)
REVERT: C  138 MET cc_start: 0.5935 (tmm) cc_final: 0.5719 (tpt)
REVERT: C  230 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6861 (tp30)
REVERT: C  295 THR cc_start: 0.7933 (m) cc_final: 0.7586 (m)
REVERT: D   80 PHE cc_start: 0.7164 (m-80) cc_final: 0.6871 (m-80)
REVERT: D  110 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7336 (mt)
REVERT: D  136 VAL cc_start: 0.7771 (t) cc_final: 0.7260 (m)
REVERT: D  331 LEU cc_start: 0.6433 (mt) cc_final: 0.6091 (mp)
REVERT: E   49 SER cc_start: 0.5900 (OUTLIER) cc_final: 0.5420 (p)
REVERT: E  179 ASP cc_start: 0.7528 (m-30) cc_final: 0.7309 (m-30)
REVERT: E  222 ARG cc_start: 0.7664 (ptm-80) cc_final: 0.7333 (ptm-80)
  outliers start: 33
  outliers final: 24
  residues processed: 364
  average time/residue: 0.1194
  time to fit residues: 65.8353
Evaluate side-chains
  360 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 332
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   74 GLN
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  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  246 GLU
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  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   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  330 VAL
Chi-restraints excluded: chain E residue   49 SER
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  278 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 175 optimal weight:    0.7980
   chunk 91 optimal weight:    8.9990
   chunk 26 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 109 optimal weight:    0.9980
   chunk 153 optimal weight:    1.9990
   chunk 119 optimal weight:    0.5980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
H  16 GLN
A  74 GLN
B  92 ASN
B 118 ASN
** B 260 GLN ** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.169146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.139651 restraints weight = 28004.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 2.64
r_work: 0.3488 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  16490  Z= 0.189
  Angle     :  0.629   9.727  22360  Z= 0.332
  Chirality :  0.045   0.175   2541
  Planarity :  0.005   0.065   2796
  Dihedral  :  4.446  21.449   2164
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.33 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 19.89 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.20), residues: 1938
  helix:  2.27 (0.17), residues: 940
  sheet:  0.29 (0.26), residues: 382
  loop : -1.68 (0.24), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG L  19 
 TYR   0.028   0.002   TYR A  19 
 PHE   0.033   0.002   PHE D 147 
 TRP   0.019   0.001   TRP A 350 
 HIS   0.009   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (16488)
  covalent geometry    : angle       0.62862 (22356)
  SS BOND              : bond        0.00110 (    2)
  SS BOND              : angle       0.66705 (    4)
  hydrogen bonds       : bond        0.05280 (  951)
  hydrogen bonds       : angle       4.43175 ( 2763)

*********************** 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
  384 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 341
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
REVERT: H   16 GLN cc_start: 0.7888 (mm110) cc_final: 0.7618 (mm-40)
REVERT: H   28 SER cc_start: 0.8512 (m) cc_final: 0.8068 (p)
REVERT: H   94 THR cc_start: 0.8351 (t) cc_final: 0.8012 (m)
REVERT: H  126 THR cc_start: 0.8324 (m) cc_final: 0.7944 (p)
REVERT: A   74 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6794 (tt0)
REVERT: A  116 ASP cc_start: 0.7141 (t70) cc_final: 0.6621 (t0)
REVERT: A  121 GLU cc_start: 0.7237 (mp0) cc_final: 0.6771 (mp0)
REVERT: A  191 GLU cc_start: 0.7824 (tp30) cc_final: 0.7577 (tp30)
REVERT: B  120 HIS cc_start: 0.6898 (m-70) cc_final: 0.6537 (m-70)
REVERT: C  138 MET cc_start: 0.5998 (tmm) cc_final: 0.5762 (tpt)
REVERT: C  175 ASP cc_start: 0.7371 (t70) cc_final: 0.7166 (t0)
REVERT: C  230 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6803 (tp30)
REVERT: C  291 MET cc_start: 0.7448 (tpt) cc_final: 0.7035 (tpp)
REVERT: C  295 THR cc_start: 0.7987 (m) cc_final: 0.7692 (m)
REVERT: D   80 PHE cc_start: 0.7092 (m-80) cc_final: 0.6772 (m-80)
REVERT: D  110 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7359 (mt)
REVERT: D  163 LYS cc_start: 0.8843 (mptt) cc_final: 0.8511 (mptt)
  outliers start: 43
  outliers final: 36
  residues processed: 364
  average time/residue: 0.1177
  time to fit residues: 65.2709
Evaluate side-chains
  378 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 339
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   74 GLN
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  291 MET
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain C residue   90 ILE
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  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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 142 optimal weight:    3.9990
   chunk 190 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   chunk 154 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 164 optimal weight:    1.9990
   chunk 132 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 169 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B 118 ASN
** B 260 GLN ** 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 = 0.4188 r_free = 0.4188 target = 0.170999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.141738 restraints weight = 27808.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 2.66
r_work: 0.3479 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  16490  Z= 0.199
  Angle     :  0.645  10.720  22360  Z= 0.340
  Chirality :  0.045   0.183   2541
  Planarity :  0.005   0.066   2796
  Dihedral  :  4.557  22.077   2164
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.64 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 20.11 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.19), residues: 1938
  helix:  2.17 (0.17), residues: 940
  sheet:  0.13 (0.27), residues: 378
  loop : -1.72 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  19 
 TYR   0.026   0.002   TYR D 171 
 PHE   0.028   0.002   PHE D 147 
 TRP   0.020   0.001   TRP B 350 
 HIS   0.010   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (16488)
  covalent geometry    : angle       0.64490 (22356)
  SS BOND              : bond        0.00148 (    2)
  SS BOND              : angle       0.80630 (    4)
  hydrogen bonds       : bond        0.05464 (  951)
  hydrogen bonds       : angle       4.50080 ( 2763)

********************** 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
  378 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 335
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   16 GLN cc_start: 0.7834 (mm110) cc_final: 0.7566 (mm110)
REVERT: H   28 SER cc_start: 0.8523 (m) cc_final: 0.8074 (p)
REVERT: H   94 THR cc_start: 0.8388 (t) cc_final: 0.7988 (m)
REVERT: H  126 THR cc_start: 0.8321 (m) cc_final: 0.7914 (p)
REVERT: A  116 ASP cc_start: 0.7120 (t70) cc_final: 0.6616 (t0)
REVERT: A  121 GLU cc_start: 0.7200 (mp0) cc_final: 0.6735 (mp0)
REVERT: A  191 GLU cc_start: 0.7758 (tp30) cc_final: 0.7490 (tp30)
REVERT: B  120 HIS cc_start: 0.6929 (m-70) cc_final: 0.6560 (m-70)
REVERT: C  138 MET cc_start: 0.6028 (tmm) cc_final: 0.5784 (tpt)
REVERT: C  175 ASP cc_start: 0.7387 (t70) cc_final: 0.7180 (t0)
REVERT: C  230 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6793 (tp30)
REVERT: C  295 THR cc_start: 0.8050 (m) cc_final: 0.7769 (m)
REVERT: D   80 PHE cc_start: 0.7126 (m-80) cc_final: 0.6845 (m-80)
REVERT: D  110 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7349 (mt)
REVERT: D  136 VAL cc_start: 0.7809 (t) cc_final: 0.7271 (m)
REVERT: D  331 LEU cc_start: 0.6298 (mt) cc_final: 0.5963 (mp)
  outliers start: 43
  outliers final: 37
  residues processed: 360
  average time/residue: 0.1196
  time to fit residues: 65.4454
Evaluate side-chains
  373 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 334
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
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   15 VAL
Chi-restraints excluded: chain A residue   20 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  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   90 ILE
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 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  146 VAL
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  248 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 3 optimal weight:    0.2980
   chunk 88 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 21 optimal weight:    0.4980
   chunk 29 optimal weight:    0.0020
   chunk 173 optimal weight:    2.9990
   chunk 139 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
A  74 GLN
B 118 ASN
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.172235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.142892 restraints weight = 27831.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3761 rms_B_bonded: 2.58
r_work: 0.3506 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16490  Z= 0.148
  Angle     :  0.608  10.572  22360  Z= 0.320
  Chirality :  0.044   0.165   2541
  Planarity :  0.004   0.066   2796
  Dihedral  :  4.463  21.650   2164
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.49 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 20.61 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.20), residues: 1938
  helix:  2.29 (0.17), residues: 939
  sheet:  0.16 (0.27), residues: 362
  loop : -1.64 (0.24), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG L  19 
 TYR   0.025   0.002   TYR D 171 
 PHE   0.028   0.001   PHE D 147 
 TRP   0.020   0.001   TRP A 350 
 HIS   0.006   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (16488)
  covalent geometry    : angle       0.60847 (22356)
  SS BOND              : bond        0.00166 (    2)
  SS BOND              : angle       0.69542 (    4)
  hydrogen bonds       : bond        0.05148 (  951)
  hydrogen bonds       : angle       4.39917 ( 2763)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4350.62 seconds
wall clock time: 75 minutes 8.53 seconds (4508.53 seconds total)