Starting phenix.real_space_refine
on Mon Jun 16 17:29:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tml_41393/06_2025/8tml_41393.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tml_41393/06_2025/8tml_41393.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tml_41393/06_2025/8tml_41393.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tml_41393/06_2025/8tml_41393.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tml_41393/06_2025/8tml_41393.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tml_41393/06_2025/8tml_41393.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.038
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1577 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Mg      4      5.21       5
     S      65      5.16       5
     C   11503      2.51       5
     N    2895      2.21       5
     O    3292      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17759
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "H"
      Number of atoms: 950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 950
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 2, 'TRANS': 120}
    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: "G"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 794
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
    Chain: "F"
      Number of atoms: 950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 950
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 2, 'TRANS': 120}
    Chain: "A"
      Number of atoms: 2805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2805
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 13, 'TRANS': 321}
    Chain: "B"
      Number of atoms: 2909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2909
          Classifications: {'peptide': 349}
          Link IDs: {'PTRANS': 15, 'TRANS': 333}
    Chain: "C"
      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: "D"
      Number of atoms: 2935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2935
          Classifications: {'peptide': 352}
          Link IDs: {'PTRANS': 15, 'TRANS': 336}
    Chain: "E"
      Number of atoms: 2805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2805
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 13, 'TRANS': 321}
    Chain: "B"
      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}
    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: 12.45, per 1000 atoms: 0.70
  Number of scatterers: 17759
  At special positions: 0
  Unit cell: (122.245, 142.442, 140.316, 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      65     16.00
     Mg      4     11.99
     O    3292      8.00
     N    2895      7.00
     C   11503      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  24 " - pdb=" SG  CYS G  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  96 " 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: 4.32
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4132

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 17 sheets defined
      49.1% alpha, 21.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.85
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 31
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'F' and resid 28 through 32
      removed outlier: 3.697A  pdb=" N   TYR F  31 " --> pdb=" O   ASN F  28 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   TYR F  32 " --> pdb=" O   VAL F  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 28 through 32'
    Processing helix  chain 'F' and resid 87 through 91
      removed outlier: 3.798A  pdb=" N   THR F  91 " --> pdb=" O   ALA F  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 56
      removed outlier: 3.667A  pdb=" N   VAL A  50 " --> pdb=" O   VAL A  47 " (cutoff:3.500A)
      Proline residue:  A  52  - end of helix
    Processing helix  chain 'A' and resid 69 through 81
      removed outlier: 3.794A  pdb=" N   VAL A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 92
      removed outlier: 3.683A  pdb=" N   LEU A  91 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 156
    Processing helix  chain 'A' and resid 165 through 202
      removed outlier: 4.097A  pdb=" N   LEU A 169 " --> pdb=" O   ARG A 165 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU A 170 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 239
      Proline residue:  A 227  - end of helix
      removed outlier: 3.504A  pdb=" N   VAL A 239 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 276
      removed outlier: 4.251A  pdb=" N   LEU A 276 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 282
    Processing helix  chain 'A' and resid 285 through 312
      removed outlier: 3.521A  pdb=" N   GLU A 289 " --> pdb=" O   ASN A 285 " (cutoff:3.500A)
      Proline residue:  A 303  - end of helix
    Processing helix  chain 'A' and resid 325 through 345
      removed outlier: 3.564A  pdb=" N   VAL A 329 " --> pdb=" O   TRP A 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 56
      removed outlier: 3.825A  pdb=" N   ASP B  55 " --> pdb=" O   PRO B  52 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   SER B  56 " --> pdb=" O   PHE B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 80
      removed outlier: 3.504A  pdb=" N   VAL B  73 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 92
    Processing helix  chain 'B' and resid 147 through 156
    Processing helix  chain 'B' and resid 160 through 164
    Processing helix  chain 'B' and resid 165 through 202
      removed outlier: 3.506A  pdb=" N   LEU B 169 " --> pdb=" O   ARG B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 238
      removed outlier: 3.594A  pdb=" N   VAL B 208 " --> pdb=" O   GLU B 204 " (cutoff:3.500A)
      Proline residue:  B 227  - end of helix
      removed outlier: 4.297A  pdb=" N   ASP B 238 " --> pdb=" O   SER B 234 " (cutoff:3.500A)
    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 300
      removed outlier: 3.547A  pdb=" N   LEU B 276 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   ASP B 277 " --> pdb=" O   SER B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 311
      removed outlier: 3.563A  pdb=" N   THR B 305 " --> pdb=" O   PHE B 301 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   PHE B 306 " --> pdb=" O   MET B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 348
    Processing helix  chain 'C' and resid 51 through 56
      removed outlier: 3.605A  pdb=" N   ARG C  54 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASP C  55 " --> pdb=" O   PRO C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 80
      removed outlier: 3.591A  pdb=" N   VAL C  73 " --> pdb=" O   ARG C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 92
      removed outlier: 3.785A  pdb=" N   ASP C  89 " --> pdb=" O   LEU C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 156
    Processing helix  chain 'C' and resid 165 through 202
      removed outlier: 3.540A  pdb=" N   LEU C 169 " --> pdb=" O   ARG C 165 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL C 194 " --> pdb=" O   ASP C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 237
      Proline residue:  C 227  - end of helix
      removed outlier: 3.734A  pdb=" N   GLU C 230 " --> pdb=" O   TRP C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 246
      No H-bonds generated for 'chain 'C' and resid 244 through 246'
    Processing helix  chain 'C' and resid 247 through 282
      removed outlier: 3.904A  pdb=" N   PHE C 251 " --> pdb=" O   THR C 247 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ARG C 252 " --> pdb=" O   VAL C 248 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   VAL C 278 " --> pdb=" O   GLY C 274 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   TYR C 279 " --> pdb=" O   LEU C 275 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   SER C 282 " --> pdb=" O   VAL C 278 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 283 through 312
      removed outlier: 3.748A  pdb=" N   ILE C 300 " --> pdb=" O   ILE C 296 " (cutoff:3.500A)
      Proline residue:  C 303  - end of helix
    Processing helix  chain 'C' and resid 318 through 323
      removed outlier: 3.916A  pdb=" N   ARG C 322 " --> pdb=" O   MET C 318 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   TRP C 323 " --> pdb=" O   PRO C 319 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 318 through 323'
    Processing helix  chain 'C' and resid 325 through 348
      removed outlier: 3.832A  pdb=" N   LYS C 348 " --> pdb=" O   TYR C 344 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 46 through 56
      Proline residue:  D  52  - end of helix
      removed outlier: 3.937A  pdb=" N   ASP D  55 " --> pdb=" O   PRO D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 69 through 81
      removed outlier: 3.546A  pdb=" N   VAL D  73 " --> pdb=" O   ARG D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 92
    Processing helix  chain 'D' and resid 147 through 157
    Processing helix  chain 'D' and resid 165 through 202
    Processing helix  chain 'D' and resid 205 through 238
      removed outlier: 4.027A  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 240 through 244
      removed outlier: 3.754A  pdb=" N   GLU D 244 " --> pdb=" O   PRO D 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 247 through 311
      removed outlier: 3.563A  pdb=" N   PHE D 251 " --> pdb=" O   THR D 247 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ARG D 252 " --> pdb=" O   VAL D 248 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ASP D 253 " --> pdb=" O   PRO D 249 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   VAL D 254 " --> pdb=" O   TYR D 250 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASP D 277 " --> pdb=" O   SER D 273 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   VAL D 290 " --> pdb=" O   LYS D 286 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ILE D 300 " --> pdb=" O   ILE D 296 " (cutoff:3.500A)
      Proline residue:  D 303  - end of helix
      removed outlier: 3.804A  pdb=" N   TYR D 311 " --> pdb=" O   ILE D 307 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 325 through 349
    Processing helix  chain 'E' and resid 46 through 51
      removed outlier: 4.345A  pdb=" N   VAL E  50 " --> pdb=" O   ASP E  46 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   LEU E  51 " --> pdb=" O   VAL E  47 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 46 through 51'
    Processing helix  chain 'E' and resid 52 through 56
      removed outlier: 4.447A  pdb=" N   ASP E  55 " --> pdb=" O   PRO E  52 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   SER E  56 " --> pdb=" O   PHE E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 52 through 56'
    Processing helix  chain 'E' and resid 69 through 80
      removed outlier: 3.696A  pdb=" N   VAL E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 83 through 92
    Processing helix  chain 'E' and resid 147 through 157
    Processing helix  chain 'E' and resid 165 through 202
      removed outlier: 3.906A  pdb=" N   TYR E 181 " --> pdb=" O   LEU E 177 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   PHE E 182 " --> pdb=" O   VAL E 178 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL E 183 " --> pdb=" O   ASP E 179 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLU E 197 " --> pdb=" O   ASP E 193 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 204 through 239
      Proline residue:  E 227  - end of helix
      removed outlier: 3.661A  pdb=" N   ASP E 238 " --> pdb=" O   SER E 234 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   VAL E 239 " --> pdb=" O   LEU E 235 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 247 through 311
      Proline residue:  E 303  - end of helix
      removed outlier: 3.559A  pdb=" N   TYR E 311 " --> pdb=" O   ILE E 307 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 325 through 349
      removed outlier: 4.113A  pdb=" N   PHE E 345 " --> pdb=" O   MET E 341 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LYS E 346 " --> pdb=" O   VAL E 342 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LYS E 347 " --> pdb=" O   VAL E 343 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LYS E 348 " --> pdb=" O   TYR E 344 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 60
      removed outlier: 6.637A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   SER H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   ILE H  34 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   SER H  33 " --> pdb=" O   SER H  99 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   TYR H 115 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   TYR H 100 " --> pdb=" O   MET H 113 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   MET H 113 " --> pdb=" O   TYR H 100 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   TYR H 102 " --> pdb=" O   ASN H 111 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   ASN H 111 " --> pdb=" O   TYR H 102 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 60
      removed outlier: 6.637A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   SER H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   ILE H  34 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   SER H  33 " --> pdb=" O   SER H  99 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 14
      removed outlier: 3.663A  pdb=" N   TYR L  87 " --> pdb=" O   THR L 103 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 14
      removed outlier: 3.663A  pdb=" N   TYR L  87 " --> pdb=" O   THR L 103 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 5 through 8
    Processing sheet with id=AA8, first strand: chain 'G' and resid 11 through 13
      removed outlier: 6.437A  pdb=" N   LEU G  12 " --> pdb=" O   GLU G 106 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   VAL G  34 " --> pdb=" O   TYR G  50 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   TYR G  50 " --> pdb=" O   VAL G  34 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   TRP G  36 " --> pdb=" O   LEU G  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 11 through 13
      removed outlier: 6.437A  pdb=" N   LEU G  12 " --> pdb=" O   GLU G 106 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR G  98 " --> pdb=" O   GLN G  91 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'F' and resid 58 through 60
      removed outlier: 6.573A  pdb=" N   TRP F  36 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   SER F  50 " --> pdb=" O   ILE F  34 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ILE F  34 " --> pdb=" O   SER F  50 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   SER F  33 " --> pdb=" O   SER F  99 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLY F 110 " --> pdb=" O   TYR F 102 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 58 through 60
      removed outlier: 6.573A  pdb=" N   TRP F  36 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   SER F  50 " --> pdb=" O   ILE F  34 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ILE F  34 " --> pdb=" O   SER F  50 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   SER F  33 " --> pdb=" O   SER F  99 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 40 through 43
      removed outlier: 3.527A  pdb=" N   VAL A 109 " --> pdb=" O   LYS A  98 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LYS A  98 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 41 through 44
      removed outlier: 4.427A  pdb=" N   GLU B 121 " --> pdb=" O   ASP B 116 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ASP B 116 " --> pdb=" O   GLU B 121 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 41
      removed outlier: 4.899A  pdb=" N   GLU C 121 " --> pdb=" O   ASP C 116 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ASP C 116 " --> pdb=" O   GLU C 121 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL C 127 " --> pdb=" O   LEU C 110 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL C 106 " --> pdb=" O   LEU C 131 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 39 through 44
      removed outlier: 6.562A  pdb=" N   THR D  60 " --> pdb=" O   VAL D 136 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   MET D 138 " --> pdb=" O   THR D  60 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ILE D  62 " --> pdb=" O   MET D 138 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   GLN D 140 " --> pdb=" O   ILE D  62 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   ILE D  64 " --> pdb=" O   GLN D 140 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   GLU D 121 " --> pdb=" O   ASP D 116 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASP D 116 " --> pdb=" O   GLU D 121 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LYS D  98 " --> pdb=" O   VAL D 109 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 39 through 41
      removed outlier: 3.798A  pdb=" N   PHE E 139 " --> pdb=" O   SER E 128 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   SER E 128 " --> pdb=" O   PHE E 139 " (cutoff:3.500A)

    1080 hydrogen bonds defined for protein.
    3072 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: 6.07

  Time building geometry restraints manager: 5.13 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: 5593
        1.34 -     1.46: 4189
        1.46 -     1.58: 8263
        1.58 -     1.70: 0
        1.70 -     1.82: 117
  Bond restraints: 18162
  Sorted by residual:
  bond pdb=" CD  LYS C 292 "
       pdb=" CE  LYS C 292 "
    ideal  model  delta    sigma   weight residual
    1.520  1.460  0.060 3.00e-02 1.11e+03 3.98e+00
  bond pdb=" CB  PRO A  59 "
       pdb=" CG  PRO A  59 "
    ideal  model  delta    sigma   weight residual
    1.492  1.565 -0.073 5.00e-02 4.00e+02 2.16e+00
  bond pdb=" CG  LEU D 184 "
       pdb=" CD1 LEU D 184 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 1.99e+00
  bond pdb=" N   LYS C 349 "
       pdb=" CA  LYS C 349 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.29e-02 6.01e+03 1.53e+00
  bond pdb=" CB  VAL A 290 "
       pdb=" CG2 VAL A 290 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.43e+00
  ... (remaining 18157 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 24301
        2.40 -     4.79: 287
        4.79 -     7.19: 42
        7.19 -     9.58: 2
        9.58 -    11.98: 1
  Bond angle restraints: 24633
  Sorted by residual:
  angle pdb=" CA  PRO A  59 "
        pdb=" N   PRO A  59 "
        pdb=" CD  PRO A  59 "
      ideal   model   delta    sigma   weight residual
     112.00  105.65    6.35 1.40e+00 5.10e-01 2.06e+01
  angle pdb=" CB  MET A 291 "
        pdb=" CG  MET A 291 "
        pdb=" SD  MET A 291 "
      ideal   model   delta    sigma   weight residual
     112.70  100.72   11.98 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" C   LYS D 117 "
        pdb=" N   ASN D 118 "
        pdb=" CA  ASN D 118 "
      ideal   model   delta    sigma   weight residual
     121.54  128.51   -6.97 1.91e+00 2.74e-01 1.33e+01
  angle pdb=" C   SER L  51 "
        pdb=" N   ALA L  52 "
        pdb=" CA  ALA L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  128.12   -6.58 1.91e+00 2.74e-01 1.19e+01
  angle pdb=" C   THR E 211 "
        pdb=" N   HIS E 212 "
        pdb=" CA  HIS E 212 "
      ideal   model   delta    sigma   weight residual
     121.14  115.13    6.01 1.75e+00 3.27e-01 1.18e+01
  ... (remaining 24628 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 9736
       17.97 -    35.94: 956
       35.94 -    53.91: 145
       53.91 -    71.88: 30
       71.88 -    89.85: 13
  Dihedral angle restraints: 10880
    sinusoidal: 4473
      harmonic: 6407
  Sorted by residual:
  dihedral pdb=" CB  CYS G  24 "
           pdb=" SG  CYS G  24 "
           pdb=" SG  CYS G  89 "
           pdb=" CB  CYS G  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  169.68  -76.68     1      1.00e+01 1.00e-02 7.39e+01
  dihedral pdb=" CA  CYS G  89 "
           pdb=" C   CYS G  89 "
           pdb=" N   GLN G  90 "
           pdb=" CA  GLN G  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.16   23.84     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  PRO B 240 "
           pdb=" C   PRO B 240 "
           pdb=" N   PRO B 241 "
           pdb=" CA  PRO B 241 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.54  -21.46     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 10877 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 2034
       0.046 -    0.092: 602
       0.092 -    0.138: 135
       0.138 -    0.183: 16
       0.183 -    0.229: 1
  Chirality restraints: 2788
  Sorted by residual:
  chirality pdb=" CB  VAL B 265 "
            pdb=" CA  VAL B 265 "
            pdb=" CG1 VAL B 265 "
            pdb=" CG2 VAL B 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CB  ILE E  64 "
            pdb=" CA  ILE E  64 "
            pdb=" CG1 ILE E  64 "
            pdb=" CG2 ILE E  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.40e-01
  chirality pdb=" CA  GLU B 266 "
            pdb=" N   GLU B 266 "
            pdb=" C   GLU B 266 "
            pdb=" CB  GLU B 266 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.84e-01
  ... (remaining 2785 not shown)

  Planarity restraints: 3083
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  58 "   -0.053 5.00e-02 4.00e+02   7.73e-02 9.55e+00
        pdb=" N   PRO A  59 "    0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO A  59 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A  59 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 292 "   -0.011 2.00e-02 2.50e+03   2.28e-02 5.19e+00
        pdb=" C   LYS B 292 "    0.039 2.00e-02 2.50e+03
        pdb=" O   LYS B 292 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   VAL B 293 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 263 "    0.010 2.00e-02 2.50e+03   2.06e-02 4.25e+00
        pdb=" C   ASP B 263 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ASP B 263 "    0.013 2.00e-02 2.50e+03
        pdb=" N   THR B 264 "    0.012 2.00e-02 2.50e+03
  ... (remaining 3080 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 844
        2.72 -     3.27: 18587
        3.27 -     3.81: 29798
        3.81 -     4.36: 35213
        4.36 -     4.90: 60966
  Nonbonded interactions: 145408
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 288 "
            pdb=" OG1 THR C 287 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" O   GLU A 204 "
            pdb=" OG1 THR A 207 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" OE1 GLN D 260 "
            pdb=" NH2 ARG E  96 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" NE2 GLN A 140 "
            pdb=" OD2 ASP A 145 "
     model   vdw
     2.226 3.120
  nonbonded pdb=" NH1 ARG A 216 "
            pdb=" OD1 ASP E 193 "
     model   vdw
     2.237 3.120
  ... (remaining 145403 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' and resid 17 through 350)
  selection = (chain 'B' and resid 17 through 350)
  selection = (chain 'C' and resid 17 through 350)
  selection = (chain 'D' and resid 17 through 350)
  selection = (chain 'E' and resid 17 through 350)
}
ncs_group {
  reference = chain 'F'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'G'
  selection = (chain 'L' and resid 2 through 107)
}

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:             61.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.130
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.730
  Check model and map are aligned:         0.130
  Set scattering table:                    0.160
  Process input model:                     42.440
  Find NCS groups from input model:        0.880
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  109.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
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   0.073  18166  Z= 0.182
  Angle     :  0.668  11.976  24641  Z= 0.360
  Chirality :  0.045   0.229   2788
  Planarity :  0.005   0.077   3083
  Dihedral  : 14.467  89.853   6736
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.30 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.18), residues: 2147
  helix:  1.60 (0.16), residues: 940
  sheet:  0.32 (0.24), residues: 471
  loop : -1.70 (0.22), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A  61 
 HIS   0.009   0.001   HIS E 212 
 PHE   0.019   0.002   PHE G  99 
 TYR   0.015   0.001   TYR D 236 
 ARG   0.008   0.000   ARG A 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13084 ( 1048)
  hydrogen bonds       : angle       6.23281 ( 3072)
  SS BOND              : bond        0.00501 (    4)
  SS BOND              : angle       1.34861 (    8)
  covalent geometry    : bond        0.00416 (18162)
  covalent geometry    : angle       0.66736 (24633)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  414 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 413
  time to evaluate  : 1.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   92 SER cc_start: 0.8702 (p) cc_final: 0.8427 (p)
REVERT: A  121 GLU cc_start: 0.6012 (pm20) cc_final: 0.5743 (pm20)
REVERT: A  129 LEU cc_start: 0.7915 (mm) cc_final: 0.7653 (mt)
REVERT: A  151 ARG cc_start: 0.6300 (ttm170) cc_final: 0.5857 (ttp-170)
REVERT: A  155 ARG cc_start: 0.6072 (ttm110) cc_final: 0.5680 (ttm110)
REVERT: A  181 TYR cc_start: 0.6794 (m-80) cc_final: 0.6464 (m-80)
REVERT: A  193 ASP cc_start: 0.6921 (t0) cc_final: 0.6589 (t0)
REVERT: A  214 LEU cc_start: 0.8256 (tp) cc_final: 0.7973 (tp)
REVERT: A  291 MET cc_start: 0.7610 (mmm) cc_final: 0.7132 (mmt)
REVERT: B  121 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6570 (mt-10)
REVERT: B  198 GLU cc_start: 0.6851 (tp30) cc_final: 0.6604 (tp30)
REVERT: C  112 MET cc_start: 0.8150 (mtp) cc_final: 0.7822 (mtp)
REVERT: C  186 GLU cc_start: 0.7087 (tt0) cc_final: 0.6587 (tt0)
REVERT: C  263 ASP cc_start: 0.7555 (m-30) cc_final: 0.7341 (m-30)
REVERT: C  313 MET cc_start: 0.4985 (tpp) cc_final: 0.4605 (tpp)
REVERT: C  341 MET cc_start: 0.4917 (mmt) cc_final: 0.4572 (mmp)
REVERT: D  220 GLU cc_start: 0.7243 (tt0) cc_final: 0.7027 (mt-10)
REVERT: D  259 ILE cc_start: 0.8462 (mm) cc_final: 0.7879 (mm)
REVERT: E  164 LYS cc_start: 0.7465 (mttt) cc_final: 0.7098 (mtpt)
  outliers start: 1
  outliers final: 0
  residues processed: 413
  average time/residue: 0.2996
  time to fit residues: 186.5551
Evaluate side-chains
  365 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 365
  time to evaluate  : 1.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 179 optimal weight:    4.9990
   chunk 160 optimal weight:    0.1980
   chunk 89 optimal weight:    0.9990
   chunk 54 optimal weight:    7.9990
   chunk 108 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 166 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9980
   chunk 123 optimal weight:    0.6980
   chunk 192 optimal weight:    0.4980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  90 GLN
F  39 GLN
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 120 HIS
B 157 ASN
** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  63 ASN
E 212 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.193723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.151153 restraints weight = 20718.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.64
r_work: 0.3187 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3176
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.0877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  18166  Z= 0.173
  Angle     :  0.618   9.335  24641  Z= 0.325
  Chirality :  0.044   0.221   2788
  Planarity :  0.005   0.053   3083
  Dihedral  :  4.706  21.568   2400
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  8.93 %
    Favored  : 89.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.18), residues: 2147
  helix:  2.02 (0.16), residues: 949
  sheet:  0.43 (0.24), residues: 446
  loop : -1.58 (0.22), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A  61 
 HIS   0.015   0.001   HIS E 212 
 PHE   0.023   0.002   PHE B 306 
 TYR   0.021   0.001   TYR E 344 
 ARG   0.006   0.001   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05751 ( 1048)
  hydrogen bonds       : angle       4.97919 ( 3072)
  SS BOND              : bond        0.00406 (    4)
  SS BOND              : angle       1.12694 (    8)
  covalent geometry    : bond        0.00393 (18162)
  covalent geometry    : angle       0.61765 (24633)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  398 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 372
  time to evaluate  : 1.877 
Fit side-chains
   revert: symmetry clash
REVERT: H   21 SER cc_start: 0.8991 (t) cc_final: 0.8740 (m)
REVERT: L   25 ARG cc_start: 0.8096 (mtp-110) cc_final: 0.7687 (mtp-110)
REVERT: L   90 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8173 (tt0)
REVERT: A  111 LYS cc_start: 0.7321 (mtpp) cc_final: 0.7097 (mtpp)
REVERT: A  121 GLU cc_start: 0.6214 (pm20) cc_final: 0.5841 (pm20)
REVERT: A  151 ARG cc_start: 0.6637 (ttm170) cc_final: 0.6406 (ttp-170)
REVERT: A  202 ARG cc_start: 0.6050 (mtm180) cc_final: 0.5797 (ptt180)
REVERT: A  214 LEU cc_start: 0.8334 (tp) cc_final: 0.7950 (tp)
REVERT: A  296 ILE cc_start: 0.7757 (pt) cc_final: 0.7467 (pt)
REVERT: B  157 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8092 (t0)
REVERT: B  198 GLU cc_start: 0.7119 (tp30) cc_final: 0.6822 (tp30)
REVERT: B  291 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7009 (mtp)
REVERT: B  318 MET cc_start: 0.3494 (tmm) cc_final: 0.1750 (mmm)
REVERT: C  112 MET cc_start: 0.8507 (mtp) cc_final: 0.8138 (mtp)
REVERT: C  186 GLU cc_start: 0.7472 (tt0) cc_final: 0.7019 (tt0)
REVERT: C  292 LYS cc_start: 0.7561 (mmtp) cc_final: 0.7149 (mmtp)
REVERT: C  313 MET cc_start: 0.4794 (tpp) cc_final: 0.4574 (tpp)
REVERT: C  341 MET cc_start: 0.4825 (mmt) cc_final: 0.4478 (mmp)
REVERT: D  190 ASP cc_start: 0.7428 (m-30) cc_final: 0.6956 (m-30)
REVERT: D  193 ASP cc_start: 0.6258 (t0) cc_final: 0.6029 (t0)
REVERT: D  196 GLU cc_start: 0.7751 (tt0) cc_final: 0.7475 (tt0)
REVERT: D  220 GLU cc_start: 0.8010 (tt0) cc_final: 0.7690 (mt-10)
REVERT: E   40 ARG cc_start: 0.4908 (tpt90) cc_final: 0.4586 (tpt90)
REVERT: E  134 ASN cc_start: 0.6877 (p0) cc_final: 0.6532 (p0)
REVERT: E  164 LYS cc_start: 0.7185 (mttt) cc_final: 0.6633 (mtpt)
  outliers start: 26
  outliers final: 19
  residues processed: 378
  average time/residue: 0.2913
  time to fit residues: 167.1007
Evaluate side-chains
  382 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 360
  time to evaluate  : 2.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   28 ASN
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   59 SER
Chi-restraints excluded: chain L residue   10 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue   92 SER
Chi-restraints excluded: chain A residue  189 ASP
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain B residue   46 ASP
Chi-restraints excluded: chain B residue  135 CYS
Chi-restraints excluded: chain B residue  157 ASN
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  233 SER
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain E residue  219 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 157 optimal weight:    0.3980
   chunk 94 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 199 optimal weight:    3.9990
   chunk 167 optimal weight:    0.9980
   chunk 177 optimal weight:    0.9980
   chunk 149 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0870
   chunk 121 optimal weight:    0.0170
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  80 GLN
G  39 GLN
F  39 GLN
A  63 ASN
A 209 GLN
B 260 GLN
** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.193626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.149582 restraints weight = 20762.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.49
r_work: 0.3218 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3214
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3214
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.1152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18166  Z= 0.150
  Angle     :  0.582   9.764  24641  Z= 0.305
  Chirality :  0.043   0.313   2788
  Planarity :  0.004   0.049   3083
  Dihedral  :  4.551  21.601   2400
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.84 %
    Favored  : 86.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.18), residues: 2147
  helix:  2.17 (0.16), residues: 953
  sheet:  0.46 (0.24), residues: 444
  loop : -1.59 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  61 
 HIS   0.006   0.001   HIS D 257 
 PHE   0.021   0.001   PHE B 306 
 TYR   0.023   0.001   TYR C  19 
 ARG   0.007   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05353 ( 1048)
  hydrogen bonds       : angle       4.71913 ( 3072)
  SS BOND              : bond        0.00447 (    4)
  SS BOND              : angle       0.89937 (    8)
  covalent geometry    : bond        0.00336 (18162)
  covalent geometry    : angle       0.58163 (24633)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  399 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 362
  time to evaluate  : 1.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   21 SER cc_start: 0.8974 (t) cc_final: 0.8754 (m)
REVERT: H   37 VAL cc_start: 0.8785 (p) cc_final: 0.8436 (t)
REVERT: H   83 MET cc_start: 0.8168 (mtm) cc_final: 0.7837 (mtt)
REVERT: A  121 GLU cc_start: 0.6207 (pm20) cc_final: 0.5833 (pm20)
REVERT: A  151 ARG cc_start: 0.6519 (ttm170) cc_final: 0.6253 (ttp-170)
REVERT: A  191 GLU cc_start: 0.7876 (tt0) cc_final: 0.7561 (tt0)
REVERT: A  202 ARG cc_start: 0.6122 (mtm180) cc_final: 0.5878 (ptt180)
REVERT: A  209 GLN cc_start: 0.6815 (OUTLIER) cc_final: 0.6514 (tp-100)
REVERT: A  222 ARG cc_start: 0.6969 (ttm-80) cc_final: 0.6139 (ttm-80)
REVERT: B  121 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7186 (pt0)
REVERT: B  156 TYR cc_start: 0.7368 (m-80) cc_final: 0.6648 (m-80)
REVERT: B  157 ASN cc_start: 0.8371 (t0) cc_final: 0.7948 (t0)
REVERT: B  163 LYS cc_start: 0.7793 (mmmt) cc_final: 0.7320 (mmtp)
REVERT: B  198 GLU cc_start: 0.7082 (tp30) cc_final: 0.6771 (tp30)
REVERT: B  247 THR cc_start: 0.7857 (OUTLIER) cc_final: 0.7642 (p)
REVERT: B  252 ARG cc_start: 0.7487 (tpt-90) cc_final: 0.6542 (mmm160)
REVERT: B  266 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7521 (tt0)
REVERT: B  318 MET cc_start: 0.3375 (tmm) cc_final: 0.1582 (mmm)
REVERT: C  112 MET cc_start: 0.8512 (mtp) cc_final: 0.8109 (mtp)
REVERT: C  292 LYS cc_start: 0.7410 (mmtp) cc_final: 0.6963 (mmtp)
REVERT: C  313 MET cc_start: 0.4461 (tpp) cc_final: 0.4181 (tpp)
REVERT: C  341 MET cc_start: 0.4867 (mmt) cc_final: 0.4560 (mmp)
REVERT: D  190 ASP cc_start: 0.7334 (m-30) cc_final: 0.6852 (m-30)
REVERT: D  193 ASP cc_start: 0.6210 (t0) cc_final: 0.5977 (t0)
REVERT: D  220 GLU cc_start: 0.7957 (tt0) cc_final: 0.7594 (mt-10)
REVERT: D  289 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7584 (tp30)
REVERT: E   53 PHE cc_start: 0.5784 (t80) cc_final: 0.5394 (t80)
REVERT: E  134 ASN cc_start: 0.6818 (p0) cc_final: 0.6452 (p0)
REVERT: E  164 LYS cc_start: 0.7077 (mttt) cc_final: 0.6512 (mtpt)
  outliers start: 37
  outliers final: 23
  residues processed: 376
  average time/residue: 0.3003
  time to fit residues: 171.1077
Evaluate side-chains
  376 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 349
  time to evaluate  : 2.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   28 ASN
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue   92 SER
Chi-restraints excluded: chain F residue  106 SER
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  189 ASP
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  135 CYS
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  266 GLU
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  233 SER
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  289 GLU
Chi-restraints excluded: chain E residue  219 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0070
   chunk 27 optimal weight:    0.3980
   chunk 110 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 150 optimal weight:    1.9990
   chunk 114 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  90 GLN
G  90 GLN
A 209 GLN
B  94 HIS
** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.193427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.149243 restraints weight = 20743.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 2.61
r_work: 0.3196 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.1315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  18166  Z= 0.172
  Angle     :  0.585   9.239  24641  Z= 0.306
  Chirality :  0.044   0.253   2788
  Planarity :  0.004   0.044   3083
  Dihedral  :  4.545  21.784   2400
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.85 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.18), residues: 2147
  helix:  2.15 (0.16), residues: 954
  sheet:  0.42 (0.24), residues: 452
  loop : -1.64 (0.22), residues: 741

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 350 
 HIS   0.007   0.001   HIS D 257 
 PHE   0.019   0.001   PHE C  27 
 TYR   0.016   0.001   TYR B 311 
 ARG   0.007   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05334 ( 1048)
  hydrogen bonds       : angle       4.67031 ( 3072)
  SS BOND              : bond        0.00543 (    4)
  SS BOND              : angle       0.98082 (    8)
  covalent geometry    : bond        0.00400 (18162)
  covalent geometry    : angle       0.58441 (24633)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  417 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 371
  time to evaluate  : 1.878 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   21 SER cc_start: 0.8988 (t) cc_final: 0.8769 (m)
REVERT: H   37 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8463 (t)
REVERT: F   39 GLN cc_start: 0.6164 (tt0) cc_final: 0.5541 (tt0)
REVERT: A   87 LEU cc_start: 0.7716 (tp) cc_final: 0.7498 (tp)
REVERT: A  129 LEU cc_start: 0.7160 (mt) cc_final: 0.6691 (mm)
REVERT: A  151 ARG cc_start: 0.6559 (ttm170) cc_final: 0.6345 (ttp-170)
REVERT: A  202 ARG cc_start: 0.6203 (mtm180) cc_final: 0.5930 (ptt180)
REVERT: A  300 ILE cc_start: 0.7941 (mt) cc_final: 0.7732 (mt)
REVERT: B  157 ASN cc_start: 0.8494 (t0) cc_final: 0.7945 (t0)
REVERT: B  163 LYS cc_start: 0.7884 (mmmt) cc_final: 0.7496 (mmtp)
REVERT: B  202 ARG cc_start: 0.6660 (mmm-85) cc_final: 0.6456 (mtm110)
REVERT: B  247 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7667 (p)
REVERT: B  252 ARG cc_start: 0.7461 (tpt-90) cc_final: 0.6546 (mmm160)
REVERT: B  318 MET cc_start: 0.3358 (tmm) cc_final: 0.1644 (mmm)
REVERT: C  112 MET cc_start: 0.8518 (mtp) cc_final: 0.8162 (mtp)
REVERT: C  191 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7349 (mm-30)
REVERT: C  292 LYS cc_start: 0.7443 (mmtp) cc_final: 0.7036 (mmtp)
REVERT: C  341 MET cc_start: 0.5072 (mmt) cc_final: 0.4761 (mmp)
REVERT: D  190 ASP cc_start: 0.7388 (m-30) cc_final: 0.6908 (m-30)
REVERT: D  220 GLU cc_start: 0.7930 (tt0) cc_final: 0.7588 (mt-10)
REVERT: D  289 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7629 (tp30)
REVERT: E  134 ASN cc_start: 0.6798 (p0) cc_final: 0.6430 (p0)
REVERT: E  164 LYS cc_start: 0.7152 (mttt) cc_final: 0.6534 (mtpt)
REVERT: E  195 LEU cc_start: 0.6988 (mt) cc_final: 0.6738 (mt)
  outliers start: 46
  outliers final: 32
  residues processed: 392
  average time/residue: 0.2877
  time to fit residues: 170.6568
Evaluate side-chains
  393 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 357
  time to evaluate  : 2.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   28 ASN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   59 SER
Chi-restraints excluded: chain H residue  118 GLN
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue   92 SER
Chi-restraints excluded: chain F residue   91 THR
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  189 ASP
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain B residue  135 CYS
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  160 ILE
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  243 ILE
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  233 SER
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  289 GLU
Chi-restraints excluded: chain E residue   74 GLN
Chi-restraints excluded: chain E residue  219 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 87 optimal weight:    0.5980
   chunk 205 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9980
   chunk 148 optimal weight:    1.9990
   chunk 207 optimal weight:    0.2980
   chunk 135 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 127 optimal weight:    0.1980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  90 GLN
** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.195127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.151979 restraints weight = 21010.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 2.70
r_work: 0.3203 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3194
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3194
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  18166  Z= 0.144
  Angle     :  0.560   9.435  24641  Z= 0.295
  Chirality :  0.042   0.151   2788
  Planarity :  0.004   0.048   3083
  Dihedral  :  4.447  21.511   2400
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.25 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.18), residues: 2147
  helix:  2.26 (0.16), residues: 955
  sheet:  0.46 (0.24), residues: 447
  loop : -1.59 (0.22), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 350 
 HIS   0.006   0.001   HIS D 257 
 PHE   0.022   0.001   PHE E  53 
 TYR   0.031   0.001   TYR C  19 
 ARG   0.007   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05057 ( 1048)
  hydrogen bonds       : angle       4.55874 ( 3072)
  SS BOND              : bond        0.00570 (    4)
  SS BOND              : angle       0.88096 (    8)
  covalent geometry    : bond        0.00324 (18162)
  covalent geometry    : angle       0.55972 (24633)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  401 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 357
  time to evaluate  : 1.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   21 SER cc_start: 0.8981 (t) cc_final: 0.8759 (m)
REVERT: H   37 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8514 (t)
REVERT: L   25 ARG cc_start: 0.8055 (mtp-110) cc_final: 0.7698 (mtp-110)
REVERT: L   90 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8022 (tt0)
REVERT: G   90 GLN cc_start: 0.6888 (mt0) cc_final: 0.6626 (mt0)
REVERT: F   39 GLN cc_start: 0.6181 (tt0) cc_final: 0.5583 (tt0)
REVERT: A   38 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7003 (mm-30)
REVERT: A   87 LEU cc_start: 0.7707 (tp) cc_final: 0.7459 (tp)
REVERT: A  121 GLU cc_start: 0.6242 (pm20) cc_final: 0.5836 (pm20)
REVERT: A  151 ARG cc_start: 0.6578 (ttm170) cc_final: 0.6371 (ttp-170)
REVERT: A  214 LEU cc_start: 0.8433 (tp) cc_final: 0.8133 (tp)
REVERT: A  222 ARG cc_start: 0.7042 (ttm-80) cc_final: 0.6443 (tpp80)
REVERT: A  259 ILE cc_start: 0.8527 (mm) cc_final: 0.8310 (mm)
REVERT: B  121 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7328 (tt0)
REVERT: B  157 ASN cc_start: 0.8473 (t0) cc_final: 0.7883 (t0)
REVERT: B  163 LYS cc_start: 0.7835 (mmmt) cc_final: 0.7557 (mmtm)
REVERT: B  318 MET cc_start: 0.3318 (tmm) cc_final: 0.1625 (mmm)
REVERT: C  112 MET cc_start: 0.8556 (mtp) cc_final: 0.8253 (mtp)
REVERT: C  191 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7345 (mm-30)
REVERT: C  292 LYS cc_start: 0.7490 (mmtp) cc_final: 0.7090 (mmtp)
REVERT: C  341 MET cc_start: 0.5098 (mmt) cc_final: 0.4788 (mmp)
REVERT: D   10 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7730 (tttp)
REVERT: D  190 ASP cc_start: 0.7387 (m-30) cc_final: 0.6888 (m-30)
REVERT: D  220 GLU cc_start: 0.8014 (tt0) cc_final: 0.7667 (mt-10)
REVERT: E   53 PHE cc_start: 0.5977 (t80) cc_final: 0.5749 (t80)
REVERT: E   74 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.6847 (tp-100)
REVERT: E  134 ASN cc_start: 0.6849 (p0) cc_final: 0.6492 (p0)
REVERT: E  164 LYS cc_start: 0.7156 (mttt) cc_final: 0.6520 (mtpt)
REVERT: E  195 LEU cc_start: 0.6993 (mt) cc_final: 0.6738 (mt)
  outliers start: 44
  outliers final: 28
  residues processed: 378
  average time/residue: 0.2889
  time to fit residues: 165.6057
Evaluate side-chains
  382 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 348
  time to evaluate  : 2.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   59 SER
Chi-restraints excluded: chain H residue  118 GLN
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue   92 SER
Chi-restraints excluded: chain F residue   91 THR
Chi-restraints excluded: chain A residue   38 GLU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  189 ASP
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain B residue  135 CYS
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  243 ILE
Chi-restraints excluded: chain D residue   10 LYS
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  233 SER
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain E residue   64 ILE
Chi-restraints excluded: chain E residue   74 GLN
Chi-restraints excluded: chain E residue  219 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0040
   chunk 61 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 105 optimal weight:    1.9990
   chunk 137 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 65 optimal weight:    0.4980
   chunk 87 optimal weight:    0.5980
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  90 GLN
A 217 ASN
** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.192755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.148902 restraints weight = 20755.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 2.49
r_work: 0.3194 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.1536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  18166  Z= 0.159
  Angle     :  0.575   9.308  24641  Z= 0.301
  Chirality :  0.043   0.322   2788
  Planarity :  0.004   0.048   3083
  Dihedral  :  4.448  22.269   2400
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.01 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.18), residues: 2147
  helix:  2.23 (0.16), residues: 958
  sheet:  0.44 (0.24), residues: 452
  loop : -1.61 (0.22), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP D 226 
 HIS   0.006   0.001   HIS D 257 
 PHE   0.016   0.001   PHE C  27 
 TYR   0.018   0.001   TYR C  19 
 ARG   0.007   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05086 ( 1048)
  hydrogen bonds       : angle       4.54479 ( 3072)
  SS BOND              : bond        0.00574 (    4)
  SS BOND              : angle       1.05208 (    8)
  covalent geometry    : bond        0.00366 (18162)
  covalent geometry    : angle       0.57482 (24633)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  422 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 365
  time to evaluate  : 2.001 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   21 SER cc_start: 0.9008 (t) cc_final: 0.8761 (m)
REVERT: H   37 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8528 (t)
REVERT: H   76 LYS cc_start: 0.7899 (ptmm) cc_final: 0.7606 (ptpt)
REVERT: L   90 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7963 (tt0)
REVERT: G   90 GLN cc_start: 0.6723 (mt0) cc_final: 0.6384 (mt0)
REVERT: F   39 GLN cc_start: 0.6134 (tt0) cc_final: 0.5557 (tt0)
REVERT: A   38 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6801 (mm-30)
REVERT: A   87 LEU cc_start: 0.7699 (tp) cc_final: 0.7481 (tp)
REVERT: A  121 GLU cc_start: 0.6235 (pm20) cc_final: 0.5835 (pm20)
REVERT: A  222 ARG cc_start: 0.7074 (ttm-80) cc_final: 0.6299 (tpp80)
REVERT: A  259 ILE cc_start: 0.8529 (mm) cc_final: 0.8300 (mm)
REVERT: B  157 ASN cc_start: 0.8519 (t0) cc_final: 0.8073 (t0)
REVERT: B  163 LYS cc_start: 0.7792 (mmmt) cc_final: 0.7517 (mmtm)
REVERT: B  266 GLU cc_start: 0.7826 (tt0) cc_final: 0.7610 (tt0)
REVERT: B  318 MET cc_start: 0.3269 (tmm) cc_final: 0.1605 (mmm)
REVERT: C  112 MET cc_start: 0.8548 (mtp) cc_final: 0.8249 (mtp)
REVERT: C  191 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7256 (mm-30)
REVERT: C  313 MET cc_start: 0.4150 (tpp) cc_final: 0.3938 (tpp)
REVERT: C  341 MET cc_start: 0.5060 (mmt) cc_final: 0.4731 (mmp)
REVERT: D   10 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7866 (tttp)
REVERT: D  190 ASP cc_start: 0.7394 (m-30) cc_final: 0.6878 (m-30)
REVERT: D  220 GLU cc_start: 0.8062 (tt0) cc_final: 0.7732 (mt-10)
REVERT: E   40 ARG cc_start: 0.4220 (tpt90) cc_final: 0.4014 (tpt90)
REVERT: E   74 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6766 (tp-100)
REVERT: E  134 ASN cc_start: 0.6841 (p0) cc_final: 0.6493 (p0)
REVERT: E  164 LYS cc_start: 0.7127 (mttt) cc_final: 0.6486 (mtpt)
REVERT: E  195 LEU cc_start: 0.7015 (mt) cc_final: 0.6760 (mt)
  outliers start: 57
  outliers final: 40
  residues processed: 395
  average time/residue: 0.2876
  time to fit residues: 172.9515
Evaluate side-chains
  398 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 352
  time to evaluate  : 2.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   59 SER
Chi-restraints excluded: chain H residue  118 GLN
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   54 SER
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue   92 SER
Chi-restraints excluded: chain F residue   91 THR
Chi-restraints excluded: chain A residue   38 GLU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  189 ASP
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  135 CYS
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  243 ILE
Chi-restraints excluded: chain D residue   10 LYS
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   55 ASP
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  233 SER
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain E residue   64 ILE
Chi-restraints excluded: chain E residue   74 GLN
Chi-restraints excluded: chain E residue  204 GLU
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  278 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 166 optimal weight:    0.6980
   chunk 21 optimal weight:    0.1980
   chunk 81 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 16 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   chunk 125 optimal weight:    0.4980
   chunk 27 optimal weight:    0.1980
   chunk 127 optimal weight:    0.4980
   chunk 85 optimal weight:    0.9990
   chunk 183 optimal weight:    5.9990
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  90 GLN
** G  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 217 ASN
B 157 ASN
** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  33 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.193758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.151190 restraints weight = 20660.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 2.65
r_work: 0.3185 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3166
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3166
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  18166  Z= 0.135
  Angle     :  0.558   9.356  24641  Z= 0.292
  Chirality :  0.043   0.305   2788
  Planarity :  0.004   0.045   3083
  Dihedral  :  4.360  22.012   2400
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.21 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.18), residues: 2147
  helix:  2.33 (0.16), residues: 958
  sheet:  0.46 (0.24), residues: 447
  loop : -1.57 (0.22), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP D 226 
 HIS   0.005   0.001   HIS D 257 
 PHE   0.021   0.001   PHE E 301 
 TYR   0.015   0.001   TYR A  23 
 ARG   0.008   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04853 ( 1048)
  hydrogen bonds       : angle       4.45380 ( 3072)
  SS BOND              : bond        0.00614 (    4)
  SS BOND              : angle       1.01287 (    8)
  covalent geometry    : bond        0.00298 (18162)
  covalent geometry    : angle       0.55735 (24633)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  409 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 356
  time to evaluate  : 2.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   21 SER cc_start: 0.8998 (t) cc_final: 0.8755 (m)
REVERT: H   37 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8555 (t)
REVERT: H   76 LYS cc_start: 0.7900 (ptmm) cc_final: 0.7601 (ptpt)
REVERT: L   25 ARG cc_start: 0.8124 (mtp-110) cc_final: 0.7786 (mtp-110)
REVERT: L   90 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7934 (tt0)
REVERT: G   90 GLN cc_start: 0.6730 (mt0) cc_final: 0.6342 (mt0)
REVERT: F   39 GLN cc_start: 0.6133 (tt0) cc_final: 0.5700 (tt0)
REVERT: A   38 GLU cc_start: 0.7119 (tp30) cc_final: 0.6849 (mm-30)
REVERT: A   87 LEU cc_start: 0.7651 (tp) cc_final: 0.7420 (tp)
REVERT: A  121 GLU cc_start: 0.6244 (pm20) cc_final: 0.5857 (pm20)
REVERT: A  222 ARG cc_start: 0.7096 (ttm-80) cc_final: 0.6345 (tpp80)
REVERT: A  318 MET cc_start: 0.5565 (tmm) cc_final: 0.4688 (mmm)
REVERT: B  157 ASN cc_start: 0.8482 (t0) cc_final: 0.8100 (t0)
REVERT: B  266 GLU cc_start: 0.7871 (tt0) cc_final: 0.7589 (tt0)
REVERT: B  313 MET cc_start: 0.5707 (OUTLIER) cc_final: 0.5451 (mmm)
REVERT: B  318 MET cc_start: 0.3221 (tmm) cc_final: 0.1589 (mmm)
REVERT: C  112 MET cc_start: 0.8550 (mtp) cc_final: 0.8251 (mtp)
REVERT: C  191 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7385 (mm-30)
REVERT: C  313 MET cc_start: 0.4287 (tpp) cc_final: 0.4063 (tpp)
REVERT: C  341 MET cc_start: 0.5165 (mmt) cc_final: 0.4841 (mmp)
REVERT: D   10 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7777 (tttp)
REVERT: D   50 VAL cc_start: 0.9233 (OUTLIER) cc_final: 0.8999 (m)
REVERT: D  190 ASP cc_start: 0.7431 (m-30) cc_final: 0.6944 (m-30)
REVERT: D  220 GLU cc_start: 0.8098 (tt0) cc_final: 0.7788 (mt-10)
REVERT: E   74 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.6768 (tp-100)
REVERT: E  134 ASN cc_start: 0.6853 (p0) cc_final: 0.6537 (p0)
REVERT: E  164 LYS cc_start: 0.7174 (mttt) cc_final: 0.6534 (mtpt)
REVERT: E  195 LEU cc_start: 0.7095 (mt) cc_final: 0.6864 (mt)
REVERT: E  280 LEU cc_start: 0.8386 (tp) cc_final: 0.8142 (tp)
  outliers start: 53
  outliers final: 38
  residues processed: 385
  average time/residue: 0.2977
  time to fit residues: 174.0940
Evaluate side-chains
  393 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 348
  time to evaluate  : 2.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   28 ASN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   59 SER
Chi-restraints excluded: chain H residue  118 GLN
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   54 SER
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue   92 SER
Chi-restraints excluded: chain F residue   50 SER
Chi-restraints excluded: chain F residue   91 THR
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  189 ASP
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain B residue  135 CYS
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  243 ILE
Chi-restraints excluded: chain D residue   10 LYS
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  233 SER
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain E residue   64 ILE
Chi-restraints excluded: chain E residue   74 GLN
Chi-restraints excluded: chain E residue  204 GLU
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  278 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 122 optimal weight:    0.7980
   chunk 123 optimal weight:    0.8980
   chunk 121 optimal weight:    0.3980
   chunk 104 optimal weight:    0.5980
   chunk 93 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0870
   chunk 47 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 158 optimal weight:    0.9980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  90 GLN
** G  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.194387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.151541 restraints weight = 20663.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 2.78
r_work: 0.3189 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  18166  Z= 0.153
  Angle     :  0.571   9.404  24641  Z= 0.299
  Chirality :  0.043   0.164   2788
  Planarity :  0.004   0.044   3083
  Dihedral  :  4.405  21.899   2400
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 17.36 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.18), residues: 2147
  helix:  2.27 (0.16), residues: 958
  sheet:  0.45 (0.24), residues: 447
  loop : -1.57 (0.22), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.001   TRP D 226 
 HIS   0.005   0.001   HIS D 257 
 PHE   0.017   0.001   PHE E 301 
 TYR   0.020   0.001   TYR B 311 
 ARG   0.007   0.000   ARG A 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04942 ( 1048)
  hydrogen bonds       : angle       4.46427 ( 3072)
  SS BOND              : bond        0.00410 (    4)
  SS BOND              : angle       1.79746 (    8)
  covalent geometry    : bond        0.00353 (18162)
  covalent geometry    : angle       0.57039 (24633)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  414 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 356
  time to evaluate  : 2.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   21 SER cc_start: 0.9012 (t) cc_final: 0.8765 (m)
REVERT: H   37 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8532 (t)
REVERT: H   76 LYS cc_start: 0.7906 (ptmm) cc_final: 0.7612 (ptpt)
REVERT: L   28 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8039 (mm-40)
REVERT: G   90 GLN cc_start: 0.6700 (mt0) cc_final: 0.6287 (mt0)
REVERT: F   39 GLN cc_start: 0.6071 (tt0) cc_final: 0.5619 (tt0)
REVERT: F   82 GLN cc_start: 0.6432 (tm-30) cc_final: 0.6156 (tm-30)
REVERT: A   38 GLU cc_start: 0.7138 (tp30) cc_final: 0.6862 (mm-30)
REVERT: A   87 LEU cc_start: 0.7708 (tp) cc_final: 0.7481 (tp)
REVERT: A  259 ILE cc_start: 0.8449 (mm) cc_final: 0.8220 (mm)
REVERT: A  301 PHE cc_start: 0.7210 (m-80) cc_final: 0.6866 (m-80)
REVERT: B  157 ASN cc_start: 0.8410 (t0) cc_final: 0.8087 (t0)
REVERT: B  266 GLU cc_start: 0.7838 (tt0) cc_final: 0.7477 (tt0)
REVERT: B  313 MET cc_start: 0.5684 (OUTLIER) cc_final: 0.5451 (mmm)
REVERT: B  318 MET cc_start: 0.2787 (tmm) cc_final: 0.1468 (mmm)
REVERT: C  112 MET cc_start: 0.8534 (mtp) cc_final: 0.8263 (mtp)
REVERT: C  191 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7323 (mm-30)
REVERT: C  313 MET cc_start: 0.4310 (tpp) cc_final: 0.4069 (tpp)
REVERT: C  341 MET cc_start: 0.5135 (mmt) cc_final: 0.4811 (mmp)
REVERT: D   10 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7955 (tttp)
REVERT: D   50 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.9014 (m)
REVERT: D  190 ASP cc_start: 0.7418 (m-30) cc_final: 0.6974 (m-30)
REVERT: D  220 GLU cc_start: 0.8040 (tt0) cc_final: 0.7723 (mt-10)
REVERT: D  226 TRP cc_start: 0.9133 (m-10) cc_final: 0.8804 (m-10)
REVERT: E   74 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6770 (tp-100)
REVERT: E  134 ASN cc_start: 0.6878 (p0) cc_final: 0.6555 (p0)
REVERT: E  164 LYS cc_start: 0.7140 (mttt) cc_final: 0.6492 (mtpt)
REVERT: E  195 LEU cc_start: 0.6992 (mt) cc_final: 0.6760 (mt)
REVERT: E  280 LEU cc_start: 0.8348 (tp) cc_final: 0.8118 (tp)
  outliers start: 58
  outliers final: 45
  residues processed: 388
  average time/residue: 0.2818
  time to fit residues: 168.1954
Evaluate side-chains
  401 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 349
  time to evaluate  : 2.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   28 ASN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   59 SER
Chi-restraints excluded: chain H residue  118 GLN
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   54 SER
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue    3 ILE
Chi-restraints excluded: chain G residue   92 SER
Chi-restraints excluded: chain F residue   50 SER
Chi-restraints excluded: chain F residue   91 THR
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  189 ASP
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  135 CYS
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  243 ILE
Chi-restraints excluded: chain D residue   10 LYS
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   55 ASP
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  233 SER
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain E residue   64 ILE
Chi-restraints excluded: chain E residue   74 GLN
Chi-restraints excluded: chain E residue  204 GLU
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  278 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 173 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 193 optimal weight:    7.9990
   chunk 36 optimal weight:    0.1980
   chunk 3 optimal weight:    1.9990
   chunk 179 optimal weight:    3.9990
   chunk 4 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 197 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  90 GLN
** G  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.192855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.149666 restraints weight = 20761.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.71
r_work: 0.3188 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  18166  Z= 0.155
  Angle     :  0.576   9.342  24641  Z= 0.301
  Chirality :  0.043   0.156   2788
  Planarity :  0.004   0.044   3083
  Dihedral  :  4.403  21.901   2400
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 17.31 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.18), residues: 2147
  helix:  2.25 (0.16), residues: 958
  sheet:  0.44 (0.24), residues: 447
  loop : -1.57 (0.22), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP D 226 
 HIS   0.005   0.001   HIS D 257 
 PHE   0.012   0.001   PHE C 147 
 TYR   0.019   0.001   TYR B 311 
 ARG   0.008   0.000   ARG A 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04935 ( 1048)
  hydrogen bonds       : angle       4.45106 ( 3072)
  SS BOND              : bond        0.00566 (    4)
  SS BOND              : angle       1.72544 (    8)
  covalent geometry    : bond        0.00357 (18162)
  covalent geometry    : angle       0.57538 (24633)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  416 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 356
  time to evaluate  : 2.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   21 SER cc_start: 0.9010 (t) cc_final: 0.8764 (m)
REVERT: H   37 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8538 (t)
REVERT: H   76 LYS cc_start: 0.7908 (ptmm) cc_final: 0.7612 (ptpt)
REVERT: L   28 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8070 (mm-40)
REVERT: L   90 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7820 (tt0)
REVERT: G   90 GLN cc_start: 0.6715 (mt0) cc_final: 0.6319 (mt0)
REVERT: F   39 GLN cc_start: 0.6102 (tt0) cc_final: 0.5665 (tt0)
REVERT: F   82 GLN cc_start: 0.6422 (tm-30) cc_final: 0.6140 (tm-30)
REVERT: A   38 GLU cc_start: 0.7125 (tp30) cc_final: 0.6840 (mm-30)
REVERT: A   87 LEU cc_start: 0.7687 (tp) cc_final: 0.7476 (tp)
REVERT: A  109 VAL cc_start: 0.7774 (OUTLIER) cc_final: 0.7568 (m)
REVERT: A  222 ARG cc_start: 0.6960 (ttm-80) cc_final: 0.6139 (ttm-80)
REVERT: A  259 ILE cc_start: 0.8500 (mm) cc_final: 0.8291 (mm)
REVERT: A  301 PHE cc_start: 0.7239 (m-80) cc_final: 0.6883 (m-80)
REVERT: A  318 MET cc_start: 0.5991 (tmm) cc_final: 0.5197 (mmm)
REVERT: B  157 ASN cc_start: 0.8406 (t0) cc_final: 0.8102 (t0)
REVERT: B  266 GLU cc_start: 0.7820 (tt0) cc_final: 0.7350 (tt0)
REVERT: B  313 MET cc_start: 0.5693 (OUTLIER) cc_final: 0.5462 (mmm)
REVERT: B  318 MET cc_start: 0.2768 (tmm) cc_final: 0.1452 (mmm)
REVERT: C  112 MET cc_start: 0.8529 (mtp) cc_final: 0.8256 (mtp)
REVERT: C  191 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7339 (mm-30)
REVERT: C  313 MET cc_start: 0.4230 (tpp) cc_final: 0.3996 (tpp)
REVERT: C  341 MET cc_start: 0.5127 (mmt) cc_final: 0.4813 (mmp)
REVERT: D   10 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.8037 (tttp)
REVERT: D   50 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.9023 (m)
REVERT: D  190 ASP cc_start: 0.7465 (m-30) cc_final: 0.6958 (m-30)
REVERT: D  220 GLU cc_start: 0.8089 (tt0) cc_final: 0.7771 (mt-10)
REVERT: D  226 TRP cc_start: 0.9112 (m-10) cc_final: 0.8701 (m-10)
REVERT: E   74 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.6704 (tp-100)
REVERT: E  125 GLU cc_start: 0.7843 (tp30) cc_final: 0.6981 (tm-30)
REVERT: E  134 ASN cc_start: 0.6887 (p0) cc_final: 0.6566 (p0)
REVERT: E  164 LYS cc_start: 0.7141 (mttt) cc_final: 0.6492 (mtpt)
REVERT: E  195 LEU cc_start: 0.6978 (mt) cc_final: 0.6685 (mt)
REVERT: E  280 LEU cc_start: 0.8346 (tp) cc_final: 0.8126 (tp)
  outliers start: 60
  outliers final: 47
  residues processed: 391
  average time/residue: 0.3527
  time to fit residues: 210.2020
Evaluate side-chains
  407 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 351
  time to evaluate  : 2.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   28 ASN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   59 SER
Chi-restraints excluded: chain H residue  118 GLN
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   54 SER
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue    3 ILE
Chi-restraints excluded: chain G residue   92 SER
Chi-restraints excluded: chain F residue   50 SER
Chi-restraints excluded: chain F residue   91 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  189 ASP
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  135 CYS
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  243 ILE
Chi-restraints excluded: chain D residue   10 LYS
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   55 ASP
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  233 SER
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  290 VAL
Chi-restraints excluded: chain E residue   64 ILE
Chi-restraints excluded: chain E residue   74 GLN
Chi-restraints excluded: chain E residue  204 GLU
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  278 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 119 optimal weight:    0.1980
   chunk 88 optimal weight:    0.7980
   chunk 184 optimal weight:    3.9990
   chunk 205 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 198 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 190 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  90 GLN
** G  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.191735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.149282 restraints weight = 20718.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 2.76
r_work: 0.3170 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3155
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3155 r_free = 0.3155    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3155 r_free = 0.3155    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3155
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  18166  Z= 0.172
  Angle     :  0.596   9.648  24641  Z= 0.310
  Chirality :  0.043   0.159   2788
  Planarity :  0.004   0.044   3083
  Dihedral  :  4.457  21.881   2400
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.71 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.18), residues: 2147
  helix:  2.19 (0.16), residues: 958
  sheet:  0.41 (0.24), residues: 456
  loop : -1.64 (0.22), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP D 226 
 HIS   0.005   0.001   HIS D 257 
 PHE   0.016   0.001   PHE E 113 
 TYR   0.019   0.001   TYR B 311 
 ARG   0.010   0.000   ARG D 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05058 ( 1048)
  hydrogen bonds       : angle       4.50377 ( 3072)
  SS BOND              : bond        0.00418 (    4)
  SS BOND              : angle       1.60679 (    8)
  covalent geometry    : bond        0.00405 (18162)
  covalent geometry    : angle       0.59550 (24633)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  420 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 359
  time to evaluate  : 2.210 
Fit side-chains
   revert: symmetry clash
REVERT: H   21 SER cc_start: 0.9013 (t) cc_final: 0.8784 (m)
REVERT: H   37 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8535 (t)
REVERT: H   76 LYS cc_start: 0.7916 (ptmm) cc_final: 0.7616 (ptpt)
REVERT: L   28 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8145 (mm-40)
REVERT: L   90 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7849 (tt0)
REVERT: G   90 GLN cc_start: 0.6811 (mt0) cc_final: 0.6385 (mt0)
REVERT: F   39 GLN cc_start: 0.6245 (tt0) cc_final: 0.5737 (tt0)
REVERT: F   82 GLN cc_start: 0.6446 (tm-30) cc_final: 0.6151 (tm-30)
REVERT: A   38 GLU cc_start: 0.7052 (tp30) cc_final: 0.6741 (mm-30)
REVERT: A   87 LEU cc_start: 0.7676 (tp) cc_final: 0.7450 (tp)
REVERT: A  109 VAL cc_start: 0.7772 (OUTLIER) cc_final: 0.7565 (m)
REVERT: A  155 ARG cc_start: 0.5745 (ttm110) cc_final: 0.5310 (ttm110)
REVERT: A  222 ARG cc_start: 0.7052 (ttm-80) cc_final: 0.6132 (ttm-80)
REVERT: A  259 ILE cc_start: 0.8516 (mm) cc_final: 0.8302 (mm)
REVERT: A  301 PHE cc_start: 0.7188 (m-80) cc_final: 0.6836 (m-80)
REVERT: A  318 MET cc_start: 0.5859 (tmm) cc_final: 0.4961 (mmm)
REVERT: B   54 ARG cc_start: 0.7242 (ttm170) cc_final: 0.6885 (ttm170)
REVERT: B  157 ASN cc_start: 0.8386 (t0) cc_final: 0.8098 (t0)
REVERT: B  266 GLU cc_start: 0.7832 (tt0) cc_final: 0.7364 (tt0)
REVERT: B  313 MET cc_start: 0.5779 (OUTLIER) cc_final: 0.5454 (mmm)
REVERT: B  318 MET cc_start: 0.2788 (tmm) cc_final: 0.1446 (mmm)
REVERT: C  112 MET cc_start: 0.8551 (mtp) cc_final: 0.8284 (mtp)
REVERT: C  191 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7369 (mm-30)
REVERT: C  313 MET cc_start: 0.4294 (tpp) cc_final: 0.4045 (tpp)
REVERT: C  341 MET cc_start: 0.5120 (mmt) cc_final: 0.4814 (mmp)
REVERT: D   10 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8150 (tttp)
REVERT: D   50 VAL cc_start: 0.9291 (OUTLIER) cc_final: 0.9076 (m)
REVERT: D  190 ASP cc_start: 0.7505 (m-30) cc_final: 0.6994 (m-30)
REVERT: D  220 GLU cc_start: 0.8113 (tt0) cc_final: 0.7787 (mt-10)
REVERT: D  226 TRP cc_start: 0.9120 (m-10) cc_final: 0.8730 (m-10)
REVERT: D  236 TYR cc_start: 0.8102 (t80) cc_final: 0.7600 (t80)
REVERT: E   74 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6774 (tp-100)
REVERT: E  125 GLU cc_start: 0.7828 (tp30) cc_final: 0.6890 (tm-30)
REVERT: E  134 ASN cc_start: 0.6889 (p0) cc_final: 0.6571 (p0)
REVERT: E  164 LYS cc_start: 0.7125 (mttt) cc_final: 0.6475 (mtpt)
REVERT: E  195 LEU cc_start: 0.6938 (mt) cc_final: 0.6717 (mt)
REVERT: E  280 LEU cc_start: 0.8371 (tp) cc_final: 0.8146 (tp)
  outliers start: 61
  outliers final: 49
  residues processed: 392
  average time/residue: 0.3608
  time to fit residues: 220.4965
Evaluate side-chains
  413 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 355
  time to evaluate  : 2.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   28 ASN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   59 SER
Chi-restraints excluded: chain H residue  118 GLN
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   54 SER
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue    3 ILE
Chi-restraints excluded: chain G residue   92 SER
Chi-restraints excluded: chain F residue   50 SER
Chi-restraints excluded: chain F residue   91 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  189 ASP
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  135 CYS
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  243 ILE
Chi-restraints excluded: chain D residue   10 LYS
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   22 LYS
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   55 ASP
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  233 SER
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  290 VAL
Chi-restraints excluded: chain E residue   64 ILE
Chi-restraints excluded: chain E residue   74 GLN
Chi-restraints excluded: chain E residue  204 GLU
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  278 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 189 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0970
   chunk 44 optimal weight:    0.0570
   chunk 92 optimal weight:    0.6980
   chunk 32 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 108 optimal weight:    4.9990
   chunk 20 optimal weight:    0.4980
   chunk 36 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 174 optimal weight:    0.9980
   overall best weight:    0.4296

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

Flipped N/Q/H residues before XYZ refinement:
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  90 GLN
** G  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.193211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.150789 restraints weight = 20678.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.88
r_work: 0.3176 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3156
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3156
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  18166  Z= 0.142
  Angle     :  0.581   9.450  24641  Z= 0.303
  Chirality :  0.043   0.181   2788
  Planarity :  0.004   0.043   3083
  Dihedral  :  4.404  21.842   2400
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 17.81 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.18), residues: 2147
  helix:  2.25 (0.16), residues: 958
  sheet:  0.43 (0.24), residues: 447
  loop : -1.57 (0.22), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP D 226 
 HIS   0.005   0.001   HIS D 257 
 PHE   0.012   0.001   PHE C 147 
 TYR   0.019   0.001   TYR B 311 
 ARG   0.009   0.000   ARG D 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04866 ( 1048)
  hydrogen bonds       : angle       4.45522 ( 3072)
  SS BOND              : bond        0.00401 (    4)
  SS BOND              : angle       1.50341 (    8)
  covalent geometry    : bond        0.00322 (18162)
  covalent geometry    : angle       0.58021 (24633)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10154.55 seconds
wall clock time: 177 minutes 18.32 seconds (10638.32 seconds total)