Starting phenix.real_space_refine
on Sat Jun 14 23:32:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tmf_41387/06_2025/8tmf_41387.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tmf_41387/06_2025/8tmf_41387.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/8tmf_41387/06_2025/8tmf_41387.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tmf_41387/06_2025/8tmf_41387.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tmf_41387/06_2025/8tmf_41387.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tmf_41387/06_2025/8tmf_41387.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=   0.037
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 793 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      2      5.21       5
     S      59      5.16       5
     C   10481      2.51       5
     N    2623      2.21       5
     O    2962      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 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: 16127
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "L"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 803
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 983
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 983
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 2, 'TRANS': 125}
    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: 2925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2925
          Classifications: {'peptide': 351}
          Link IDs: {'PTRANS': 15, 'TRANS': 335}
    Chain: "C"
      Number of atoms: 2805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2805
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 13, 'TRANS': 321}
    Chain: "D"
      Number of atoms: 2879
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2879
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 15, 'TRANS': 330}
    Chain: "E"
      Number of atoms: 2925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2925
          Classifications: {'peptide': 351}
          Link IDs: {'PTRANS': 15, 'TRANS': 335}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 10.42, per 1000 atoms: 0.65
  Number of scatterers: 16127
  At special positions: 0
  Unit cell: (119.616, 144.18, 139.908, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      59     16.00
     Mg      2     11.99
     O    2962      8.00
     N    2623      7.00
     C   10481      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.03
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3744

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 11 sheets defined
      53.3% alpha, 16.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.57
  Creating SS restraints...
    Processing helix  chain 'H' and resid 31 through 34
      removed outlier: 3.501A  pdb=" N   TYR H  34 " --> pdb=" O   ASN H  31 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 31 through 34'
    Processing helix  chain 'H' and resid 65 through 68
    Processing helix  chain 'H' and resid 90 through 94
    Processing helix  chain 'A' and resid 46 through 54
      removed outlier: 3.556A  pdb=" N   SER A  49 " --> pdb=" O   ASP A  46 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A  51 " --> pdb=" O   GLU A  48 " (cutoff:3.500A)
      Proline residue:  A  52  - end of helix
    Processing helix  chain 'A' and resid 69 through 80
      removed outlier: 4.103A  pdb=" N   VAL A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 92
      removed outlier: 3.580A  pdb=" N   LEU A  87 " --> pdb=" O   HIS A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 157
    Processing helix  chain 'A' and resid 160 through 164
      removed outlier: 3.527A  pdb=" N   LYS A 164 " --> pdb=" O   ILE A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 201
      removed outlier: 3.592A  pdb=" N   LEU A 169 " --> pdb=" O   ARG A 165 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLU A 201 " --> pdb=" O   GLU A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 238
      removed outlier: 3.930A  pdb=" N   VAL A 208 " --> pdb=" O   GLU A 204 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   GLN A 209 " --> pdb=" O   LYS A 205 " (cutoff:3.500A)
      Proline residue:  A 227  - end of helix
      removed outlier: 4.128A  pdb=" N   ASP A 238 " --> pdb=" O   SER A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 246
      No H-bonds generated for 'chain 'A' and resid 244 through 246'
    Processing helix  chain 'A' and resid 247 through 281
    Processing helix  chain 'A' and resid 283 through 300
      removed outlier: 3.536A  pdb=" N   ILE A 300 " --> pdb=" O   ILE A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 312
    Processing helix  chain 'A' and resid 326 through 347
      removed outlier: 4.086A  pdb=" N   VAL A 330 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 350
      No H-bonds generated for 'chain 'A' and resid 348 through 350'
    Processing helix  chain 'B' and resid 46 through 56
      removed outlier: 3.575A  pdb=" N   SER B  49 " --> pdb=" O   ASP B  46 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LEU B  51 " --> pdb=" O   GLU B  48 " (cutoff:3.500A)
      Proline residue:  B  52  - end of helix
      removed outlier: 3.714A  pdb=" N   ASP B  55 " --> pdb=" O   PRO B  52 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   SER B  56 " --> pdb=" O   PHE B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 81
      removed outlier: 3.798A  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 157
    Processing helix  chain 'B' and resid 165 through 200
      removed outlier: 3.551A  pdb=" N   LEU B 169 " --> pdb=" O   ARG B 165 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 238
      Proline residue:  B 227  - end of helix
    Processing helix  chain 'B' and resid 247 through 311
      Proline residue:  B 303  - end of helix
    Processing helix  chain 'B' and resid 322 through 325
    Processing helix  chain 'B' and resid 326 through 348
    Processing helix  chain 'C' and resid 69 through 81
      removed outlier: 4.269A  pdb=" N   VAL C  73 " --> pdb=" O   ARG C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 91
      removed outlier: 3.842A  pdb=" N   LEU C  91 " --> pdb=" O   LEU C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 156
    Processing helix  chain 'C' and resid 166 through 202
    Processing helix  chain 'C' and resid 204 through 236
      removed outlier: 4.343A  pdb=" N   VAL C 208 " --> pdb=" O   GLU C 204 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   GLN C 209 " --> pdb=" O   LYS C 205 " (cutoff:3.500A)
      Proline residue:  C 227  - end of helix
      removed outlier: 3.566A  pdb=" N   TYR C 236 " --> pdb=" O   LEU C 232 " (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 311
      removed outlier: 3.521A  pdb=" N   PHE C 251 " --> pdb=" O   THR C 247 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ASP C 277 " --> pdb=" O   SER C 273 " (cutoff:3.500A)
      Proline residue:  C 303  - end of helix
    Processing helix  chain 'C' and resid 325 through 348
    Processing helix  chain 'D' and resid 46 through 51
      removed outlier: 3.937A  pdb=" N   VAL D  50 " --> pdb=" O   ASP D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 69 through 80
      removed outlier: 4.025A  pdb=" N   VAL D  73 " --> pdb=" O   ARG D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 91
    Processing helix  chain 'D' and resid 147 through 157
    Processing helix  chain 'D' and resid 165 through 202
      removed outlier: 3.519A  pdb=" N   LEU D 169 " --> pdb=" O   ARG D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 238
      removed outlier: 4.301A  pdb=" N   VAL D 208 " --> pdb=" O   GLU D 204 " (cutoff:3.500A)
      removed outlier: 4.270A  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 244 through 246
      No H-bonds generated for 'chain 'D' and resid 244 through 246'
    Processing helix  chain 'D' and resid 247 through 311
      removed outlier: 4.091A  pdb=" N   LEU D 276 " --> pdb=" O   VAL D 272 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   ASP D 277 " --> pdb=" O   SER D 273 " (cutoff:3.500A)
      Proline residue:  D 303  - end of helix
    Processing helix  chain 'D' and resid 326 through 348
      removed outlier: 4.082A  pdb=" N   VAL D 330 " --> pdb=" O   GLY D 326 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LEU D 331 " --> pdb=" O   TYR D 327 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 54
      removed outlier: 3.743A  pdb=" N   SER E  49 " --> pdb=" O   ASP E  46 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   LEU E  51 " --> pdb=" O   GLU E  48 " (cutoff:3.500A)
      Proline residue:  E  52  - end of helix
    Processing helix  chain 'E' and resid 69 through 81
      removed outlier: 3.763A  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 156
    Processing helix  chain 'E' and resid 160 through 164
      removed outlier: 3.889A  pdb=" N   LYS E 164 " --> pdb=" O   ILE E 161 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 165 through 202
      removed outlier: 3.609A  pdb=" N   LEU E 169 " --> pdb=" O   ARG E 165 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 204 through 237
      removed outlier: 3.792A  pdb=" N   VAL E 208 " --> pdb=" O   GLU E 204 " (cutoff:3.500A)
      Proline residue:  E 227  - end of helix
      removed outlier: 3.782A  pdb=" N   GLU E 230 " --> pdb=" O   TRP E 226 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 244 through 246
      No H-bonds generated for 'chain 'E' and resid 244 through 246'
    Processing helix  chain 'E' and resid 247 through 311
      removed outlier: 4.066A  pdb=" N   LEU E 276 " --> pdb=" O   VAL E 272 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   ASP E 277 " --> pdb=" O   SER E 273 " (cutoff:3.500A)
      Proline residue:  E 303  - end of helix
      removed outlier: 3.588A  pdb=" N   TYR E 311 " --> pdb=" O   ILE E 307 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 325 through 349
    Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 8
      removed outlier: 3.541A  pdb=" N   THR L  23 " --> pdb=" O   SER L   8 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 11 through 13
      removed outlier: 6.864A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.969A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 11 through 13
      removed outlier: 3.571A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 6 through 10
      removed outlier: 3.799A  pdb=" N   THR H  81 " --> pdb=" O   ASP H  76 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 61 through 63
      removed outlier: 7.094A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   SER H  36 " --> pdb=" O   SER H 102 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   CYS H  99 " --> pdb=" O   TRP H 119 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   TRP H 119 " --> pdb=" O   CYS H  99 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   ARG H 101 " --> pdb=" O   ASP H 117 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 61 through 63
      removed outlier: 7.094A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   SER H  36 " --> pdb=" O   SER H 102 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 40 through 44
    Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 44
      removed outlier: 6.570A  pdb=" N   THR B  60 " --> pdb=" O   VAL B 136 " (cutoff:3.500A)
      removed outlier: 7.682A  pdb=" N   MET B 138 " --> pdb=" O   THR B  60 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ILE B  62 " --> pdb=" O   MET B 138 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   GLN B 140 " --> pdb=" O   ILE B  62 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE B  64 " --> pdb=" O   GLN B 140 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   GLU B 121 " --> pdb=" O   ASP B 116 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE B 107 " --> pdb=" O   GLU B 100 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 39 through 41
      removed outlier: 3.575A  pdb=" N   TRP C  61 " --> pdb=" O   MET C  32 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   THR C  60 " --> pdb=" O   VAL C 136 " (cutoff:3.500A)
      removed outlier: 8.925A  pdb=" N   MET C 138 " --> pdb=" O   THR C  60 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ILE C  62 " --> pdb=" O   MET C 138 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   GLN C 140 " --> pdb=" O   ILE C  62 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   ILE C  64 " --> pdb=" O   GLN C 140 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   SER C 128 " --> pdb=" O   PHE C 139 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLU C 125 " --> pdb=" O   MET C 112 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL C 127 " --> pdb=" O   LEU C 110 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ILE C 108 " --> pdb=" O   LEU C 129 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU C 131 " --> pdb=" O   VAL C 106 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL C 106 " --> pdb=" O   LEU C 131 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 42 through 43
      removed outlier: 3.525A  pdb=" N   PHE D  42 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLU D  28 " --> pdb=" O   THR D  65 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLU D 121 " --> pdb=" O   ASP D 116 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 28 through 30
      removed outlier: 3.643A  pdb=" N   ILE E 130 " --> pdb=" O   LEU E 137 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   GLU E 121 " --> pdb=" O   ASP E 116 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ASP E 116 " --> pdb=" O   GLU E 121 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   THR E 114 " --> pdb=" O   GLU E 123 " (cutoff:3.500A)

    986 hydrogen bonds defined for protein.
    2850 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: 5.06

  Time building geometry restraints manager: 4.77 seconds

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

  Histogram of bond lengths:
        1.05 -     1.21: 1
        1.21 -     1.36: 5123
        1.36 -     1.51: 4629
        1.51 -     1.66: 6630
        1.66 -     1.81: 109
  Bond restraints: 16492
  Sorted by residual:
  bond pdb=" CG  PRO C  59 "
       pdb=" CD  PRO C  59 "
    ideal  model  delta    sigma   weight residual
    1.503  1.055  0.448 3.40e-02 8.65e+02 1.74e+02
  bond pdb=" N   PRO C  59 "
       pdb=" CD  PRO C  59 "
    ideal  model  delta    sigma   weight residual
    1.473  1.526 -0.053 1.40e-02 5.10e+03 1.42e+01
  bond pdb=" CB  PRO C  59 "
       pdb=" CG  PRO C  59 "
    ideal  model  delta    sigma   weight residual
    1.492  1.311  0.181 5.00e-02 4.00e+02 1.31e+01
  bond pdb=" CB  PRO D 319 "
       pdb=" CG  PRO D 319 "
    ideal  model  delta    sigma   weight residual
    1.492  1.578 -0.086 5.00e-02 4.00e+02 2.95e+00
  bond pdb=" CG  PRO D 319 "
       pdb=" CD  PRO D 319 "
    ideal  model  delta    sigma   weight residual
    1.503  1.446  0.057 3.40e-02 8.65e+02 2.81e+00
  ... (remaining 16487 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.30: 22343
        6.30 -    12.59: 17
       12.59 -    18.89: 0
       18.89 -    25.18: 1
       25.18 -    31.48: 2
  Bond angle restraints: 22363
  Sorted by residual:
  angle pdb=" N   PRO C  59 "
        pdb=" CD  PRO C  59 "
        pdb=" CG  PRO C  59 "
      ideal   model   delta    sigma   weight residual
     103.20   75.89   27.31 1.50e+00 4.44e-01 3.31e+02
  angle pdb=" CA  PRO C  59 "
        pdb=" CB  PRO C  59 "
        pdb=" CG  PRO C  59 "
      ideal   model   delta    sigma   weight residual
     104.50   81.99   22.51 1.90e+00 2.77e-01 1.40e+02
  angle pdb=" CB  PRO C  59 "
        pdb=" CG  PRO C  59 "
        pdb=" CD  PRO C  59 "
      ideal   model   delta    sigma   weight residual
     106.10  137.58  -31.48 3.20e+00 9.77e-02 9.68e+01
  angle pdb=" N   GLY D 326 "
        pdb=" CA  GLY D 326 "
        pdb=" C   GLY D 326 "
      ideal   model   delta    sigma   weight residual
     111.67  118.73   -7.06 9.20e-01 1.18e+00 5.89e+01
  angle pdb=" CA  PRO C  59 "
        pdb=" N   PRO C  59 "
        pdb=" CD  PRO C  59 "
      ideal   model   delta    sigma   weight residual
     112.00  101.76   10.24 1.40e+00 5.10e-01 5.35e+01
  ... (remaining 22358 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 8725
       17.56 -    35.12: 979
       35.12 -    52.69: 167
       52.69 -    70.25: 26
       70.25 -    87.81: 17
  Dihedral angle restraints: 9914
    sinusoidal: 4122
      harmonic: 5792
  Sorted by residual:
  dihedral pdb=" N   PRO C  59 "
           pdb=" CG  PRO C  59 "
           pdb=" CD  PRO C  59 "
           pdb=" CB  PRO C  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
      30.00   82.53  -52.53     1      1.50e+01 4.44e-03 1.67e+01
  dihedral pdb=" CA  TRP D 325 "
           pdb=" C   TRP D 325 "
           pdb=" N   GLY D 326 "
           pdb=" CA  GLY D 326 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.67   18.33     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  ILE D 300 "
           pdb=" C   ILE D 300 "
           pdb=" N   PHE D 301 "
           pdb=" CA  PHE D 301 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.84  -18.16     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 9911 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1663
       0.033 -    0.067: 574
       0.067 -    0.100: 226
       0.100 -    0.134: 72
       0.134 -    0.167: 9
  Chirality restraints: 2544
  Sorted by residual:
  chirality pdb=" CG  LEU D 185 "
            pdb=" CB  LEU D 185 "
            pdb=" CD1 LEU D 185 "
            pdb=" CD2 LEU D 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 6.98e-01
  chirality pdb=" CB  ILE E 160 "
            pdb=" CA  ILE E 160 "
            pdb=" CG1 ILE E 160 "
            pdb=" CG2 ILE E 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.81   -0.16 2.00e-01 2.50e+01 6.72e-01
  chirality pdb=" CB  ILE E  36 "
            pdb=" CA  ILE E  36 "
            pdb=" CG1 ILE E  36 "
            pdb=" CG2 ILE E  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.32e-01
  ... (remaining 2541 not shown)

  Planarity restraints: 2796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 302 "    0.093 5.00e-02 4.00e+02   1.36e-01 2.98e+01
        pdb=" N   PRO B 303 "   -0.236 5.00e-02 4.00e+02
        pdb=" CA  PRO B 303 "    0.070 5.00e-02 4.00e+02
        pdb=" CD  PRO B 303 "    0.072 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  58 "   -0.048 5.00e-02 4.00e+02   6.73e-02 7.25e+00
        pdb=" N   PRO C  59 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO C  59 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C  59 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 327 "   -0.034 5.00e-02 4.00e+02   5.11e-02 4.18e+00
        pdb=" N   PRO A 328 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 328 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 328 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 2793 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 343
        2.70 -     3.25: 16090
        3.25 -     3.80: 25610
        3.80 -     4.35: 31966
        4.35 -     4.90: 54283
  Nonbonded interactions: 128292
  Sorted by model distance:
  nonbonded pdb=" O   LYS E 111 "
            pdb=" OH  TYR E 181 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" O   GLU B 204 "
            pdb=" OG1 THR B 207 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   THR A 295 "
            pdb=" OG1 THR A 299 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   GLU B 246 "
            pdb=" OG1 THR B 247 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OD1 ASN B  33 "
            pdb=" OG1 THR B  58 "
     model   vdw
     2.235 3.040
  ... (remaining 128287 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 351)
  selection = (chain 'B' and resid 17 through 351)
  selection = chain 'C'
  selection = (chain 'D' and resid 17 through 351)
  selection = (chain 'E' and resid 17 through 351)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.49 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.670
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     37.790
  Find NCS groups from input model:        0.740
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
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      :  0.005   0.448  16494  Z= 0.179
  Angle     :  0.667  31.478  22367  Z= 0.354
  Chirality :  0.042   0.167   2544
  Planarity :  0.005   0.136   2796
  Dihedral  : 14.837  87.808   6164
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.20), residues: 1939
  helix:  2.48 (0.17), residues: 952
  sheet:  0.70 (0.30), residues: 365
  loop : -1.46 (0.24), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 226 
 HIS   0.005   0.001   HIS A  68 
 PHE   0.019   0.001   PHE E  39 
 TYR   0.021   0.001   TYR E 236 
 ARG   0.003   0.000   ARG E 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15120 (  970)
  hydrogen bonds       : angle       6.44416 ( 2850)
  SS BOND              : bond        0.00182 (    2)
  SS BOND              : angle       0.72927 (    4)
  covalent geometry    : bond        0.00494 (16492)
  covalent geometry    : angle       0.66721 (22363)

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

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

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  383 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 383
  time to evaluate  : 1.650 
Fit side-chains
   revert: symmetry clash
REVERT: H   35 TYR cc_start: 0.8257 (m-80) cc_final: 0.7943 (m-80)
REVERT: H  117 ASP cc_start: 0.7584 (m-30) cc_final: 0.7285 (m-30)
REVERT: A  202 ARG cc_start: 0.6592 (ttp80) cc_final: 0.6274 (tmt-80)
REVERT: B   89 ASP cc_start: 0.6818 (m-30) cc_final: 0.6366 (m-30)
REVERT: B  116 ASP cc_start: 0.7474 (t0) cc_final: 0.6957 (t0)
REVERT: B  158 ARG cc_start: 0.7673 (mtp85) cc_final: 0.7430 (mtp85)
REVERT: D  140 GLN cc_start: 0.5855 (mp10) cc_final: 0.5516 (mp10)
REVERT: D  145 ASP cc_start: 0.4853 (p0) cc_final: 0.4600 (p0)
REVERT: E   54 ARG cc_start: 0.6743 (ptt90) cc_final: 0.6447 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 383
  average time/residue: 0.2753
  time to fit residues: 158.8711
Evaluate side-chains
  331 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 331
  time to evaluate  : 1.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 162 optimal weight:    3.9990
   chunk 145 optimal weight:    0.6980
   chunk 80 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 98 optimal weight:    6.9990
   chunk 77 optimal weight:    0.5980
   chunk 150 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0970
   chunk 91 optimal weight:    9.9990
   chunk 112 optimal weight:    9.9990
   chunk 174 optimal weight:    0.9980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
L   7 GLN
** H  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  33 ASN
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 126 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 = 0.4144 r_free = 0.4144 target = 0.207844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.166966 restraints weight = 20333.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 2.76
r_work: 0.3448 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3433
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3433 r_free = 0.3433    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3432
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.0943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  16494  Z= 0.164
  Angle     :  0.585   8.294  22367  Z= 0.309
  Chirality :  0.044   0.153   2544
  Planarity :  0.005   0.085   2796
  Dihedral  :  4.169  21.768   2164
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.18 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.20), residues: 1939
  helix:  2.43 (0.17), residues: 954
  sheet:  0.84 (0.29), residues: 366
  loop : -1.60 (0.24), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H 104 
 HIS   0.004   0.001   HIS A  68 
 PHE   0.028   0.001   PHE E 147 
 TYR   0.031   0.001   TYR B 236 
 ARG   0.003   0.000   ARG L  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05623 (  970)
  hydrogen bonds       : angle       5.01904 ( 2850)
  SS BOND              : bond        0.00362 (    2)
  SS BOND              : angle       0.99088 (    4)
  covalent geometry    : bond        0.00375 (16492)
  covalent geometry    : angle       0.58483 (22363)

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

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

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  375 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 351
  time to evaluate  : 1.916 
Fit side-chains
   revert: symmetry clash
REVERT: L   25 ARG cc_start: 0.7572 (ttm110) cc_final: 0.7220 (ttp-110)
REVERT: H   35 TYR cc_start: 0.8465 (m-80) cc_final: 0.8201 (m-80)
REVERT: H  117 ASP cc_start: 0.7995 (m-30) cc_final: 0.7786 (m-30)
REVERT: A  202 ARG cc_start: 0.6865 (ttp80) cc_final: 0.6486 (tmt-80)
REVERT: A  313 MET cc_start: 0.7141 (mtp) cc_final: 0.6858 (mtp)
REVERT: B   89 ASP cc_start: 0.7686 (m-30) cc_final: 0.7310 (m-30)
REVERT: B  116 ASP cc_start: 0.7484 (t0) cc_final: 0.6632 (t0)
REVERT: B  158 ARG cc_start: 0.8172 (mtp85) cc_final: 0.7895 (mtp85)
REVERT: B  341 MET cc_start: 0.5927 (mmt) cc_final: 0.5526 (mmt)
REVERT: C  116 ASP cc_start: 0.7986 (p0) cc_final: 0.7681 (p0)
REVERT: C  191 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7430 (mm-30)
REVERT: C  216 ARG cc_start: 0.6592 (mmm160) cc_final: 0.5873 (mmm160)
REVERT: D  121 GLU cc_start: 0.6661 (mp0) cc_final: 0.6396 (mp0)
REVERT: D  140 GLN cc_start: 0.6479 (mp10) cc_final: 0.5864 (mp10)
REVERT: D  145 ASP cc_start: 0.4869 (p0) cc_final: 0.4587 (p0)
REVERT: D  228 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8294 (mp)
REVERT: D  233 SER cc_start: 0.7564 (m) cc_final: 0.7003 (m)
REVERT: E   54 ARG cc_start: 0.6915 (ptt90) cc_final: 0.6430 (ptt90)
REVERT: E  133 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7707 (mmmt)
  outliers start: 24
  outliers final: 16
  residues processed: 360
  average time/residue: 0.2584
  time to fit residues: 141.3026
Evaluate side-chains
  358 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 341
  time to evaluate  : 1.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  177 LEU
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  202 ARG
Chi-restraints excluded: chain D residue  228 LEU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  160 ILE
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  242 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 169 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 168 optimal weight:    0.0970
   chunk 90 optimal weight:    5.9990
   chunk 100 optimal weight:    0.0470
   chunk 151 optimal weight:    0.8980
   chunk 175 optimal weight:    0.9980
   chunk 119 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.4476

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

Flipped N/Q/H residues before XYZ refinement:
** H  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 314 ASN
D  33 ASN
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 120 HIS
** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.208556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.168404 restraints weight = 20285.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 2.71
r_work: 0.3461 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3443
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3443
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.1192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  16494  Z= 0.141
  Angle     :  0.543  10.030  22367  Z= 0.286
  Chirality :  0.043   0.144   2544
  Planarity :  0.004   0.069   2796
  Dihedral  :  4.101  20.394   2164
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.15 %
    Favored  : 84.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.20), residues: 1939
  helix:  2.48 (0.17), residues: 956
  sheet:  0.66 (0.29), residues: 351
  loop : -1.55 (0.24), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 104 
 HIS   0.005   0.001   HIS E  68 
 PHE   0.024   0.001   PHE E 147 
 TYR   0.031   0.001   TYR B 236 
 ARG   0.002   0.000   ARG E 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05241 (  970)
  hydrogen bonds       : angle       4.71237 ( 2850)
  SS BOND              : bond        0.00310 (    2)
  SS BOND              : angle       1.07370 (    4)
  covalent geometry    : bond        0.00316 (16492)
  covalent geometry    : angle       0.54333 (22363)

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

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

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  384 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 351
  time to evaluate  : 1.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   25 ARG cc_start: 0.7546 (ttm110) cc_final: 0.7178 (ttp-110)
REVERT: H  117 ASP cc_start: 0.7968 (m-30) cc_final: 0.7744 (m-30)
REVERT: A  202 ARG cc_start: 0.6870 (ttp80) cc_final: 0.6641 (tmt-80)
REVERT: A  313 MET cc_start: 0.7244 (mtp) cc_final: 0.6996 (mtp)
REVERT: B   89 ASP cc_start: 0.7587 (m-30) cc_final: 0.7211 (m-30)
REVERT: B  116 ASP cc_start: 0.7504 (t0) cc_final: 0.6880 (t70)
REVERT: B  158 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7853 (mtp85)
REVERT: B  341 MET cc_start: 0.5940 (mmt) cc_final: 0.5578 (mmt)
REVERT: C  116 ASP cc_start: 0.8028 (p0) cc_final: 0.7765 (p0)
REVERT: C  191 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7317 (mm-30)
REVERT: C  216 ARG cc_start: 0.6606 (mmm160) cc_final: 0.5890 (mmm160)
REVERT: D   40 ARG cc_start: 0.6578 (mtt-85) cc_final: 0.6275 (mpp80)
REVERT: D  140 GLN cc_start: 0.6618 (mp10) cc_final: 0.5411 (mp10)
REVERT: D  145 ASP cc_start: 0.4924 (p0) cc_final: 0.4627 (p0)
REVERT: D  233 SER cc_start: 0.7524 (m) cc_final: 0.6977 (m)
REVERT: E   10 LYS cc_start: 0.6557 (pttp) cc_final: 0.6046 (ptpt)
REVERT: E   54 ARG cc_start: 0.6923 (ptt90) cc_final: 0.6619 (ptt90)
REVERT: E  133 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7738 (mmmt)
  outliers start: 33
  outliers final: 24
  residues processed: 367
  average time/residue: 0.3221
  time to fit residues: 183.0943
Evaluate side-chains
  363 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 339
  time to evaluate  : 1.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   65 ASP
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  133 LYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  177 LEU
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  202 ARG
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  160 ILE
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  284 SER
Chi-restraints excluded: chain E residue  287 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 115 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 189 optimal weight:    2.9990
   chunk 145 optimal weight:    0.6980
   chunk 184 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 117 optimal weight:    0.5980
   chunk 190 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
H  80 ASN
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 120 HIS
** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 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 = 0.4122 r_free = 0.4122 target = 0.205640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.164916 restraints weight = 20169.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 2.77
r_work: 0.3425 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3408
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3408 r_free = 0.3408    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3408 r_free = 0.3408    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3408
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.1392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  16494  Z= 0.185
  Angle     :  0.579  10.014  22367  Z= 0.304
  Chirality :  0.044   0.173   2544
  Planarity :  0.005   0.067   2796
  Dihedral  :  4.210  20.658   2164
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.13 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.20), residues: 1939
  helix:  2.32 (0.16), residues: 958
  sheet:  0.47 (0.29), residues: 357
  loop : -1.59 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 104 
 HIS   0.005   0.001   HIS E  68 
 PHE   0.021   0.001   PHE E 147 
 TYR   0.031   0.002   TYR B 236 
 ARG   0.004   0.000   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05539 (  970)
  hydrogen bonds       : angle       4.66547 ( 2850)
  SS BOND              : bond        0.00344 (    2)
  SS BOND              : angle       1.34953 (    4)
  covalent geometry    : bond        0.00442 (16492)
  covalent geometry    : angle       0.57841 (22363)

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

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

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  399 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 346
  time to evaluate  : 1.847 
Fit side-chains
   revert: symmetry clash
REVERT: L    5 MET cc_start: 0.8351 (mmt) cc_final: 0.8108 (mmt)
REVERT: L   25 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7220 (ttp-110)
REVERT: A  202 ARG cc_start: 0.6884 (ttp80) cc_final: 0.6626 (tmt-80)
REVERT: B   89 ASP cc_start: 0.7579 (m-30) cc_final: 0.7104 (m-30)
REVERT: B  116 ASP cc_start: 0.7547 (t0) cc_final: 0.6921 (t70)
REVERT: C  116 ASP cc_start: 0.8094 (p0) cc_final: 0.7861 (p0)
REVERT: C  191 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7391 (mm-30)
REVERT: C  216 ARG cc_start: 0.6598 (mmm160) cc_final: 0.5918 (mmm160)
REVERT: D  100 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6114 (pm20)
REVERT: D  121 GLU cc_start: 0.6752 (mp0) cc_final: 0.6452 (mp0)
REVERT: D  140 GLN cc_start: 0.6771 (mp10) cc_final: 0.5515 (mp10)
REVERT: D  145 ASP cc_start: 0.5162 (p0) cc_final: 0.4848 (p0)
REVERT: D  233 SER cc_start: 0.7619 (m) cc_final: 0.7093 (m)
REVERT: E   54 ARG cc_start: 0.6935 (ptt90) cc_final: 0.6622 (ptt90)
REVERT: E  133 LYS cc_start: 0.8029 (mmmt) cc_final: 0.7826 (mmmt)
  outliers start: 53
  outliers final: 37
  residues processed: 374
  average time/residue: 0.2573
  time to fit residues: 145.7156
Evaluate side-chains
  375 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 337
  time to evaluate  : 1.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   65 ASP
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  133 LYS
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain D residue  100 GLU
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  177 LEU
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  202 ARG
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  160 ILE
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  247 THR
Chi-restraints excluded: chain E residue  284 SER
Chi-restraints excluded: chain E residue  287 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 21 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 169 optimal weight:    1.9990
   chunk 90 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0870
   chunk 42 optimal weight:    0.5980
   chunk 155 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.6360

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

Flipped N/Q/H residues before XYZ refinement:
H  80 ASN
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 120 HIS
** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 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 = 0.4131 r_free = 0.4131 target = 0.206430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.165059 restraints weight = 20583.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3700 rms_B_bonded: 2.77
r_work: 0.3420 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3400
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3400 r_free = 0.3400    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3400 r_free = 0.3400    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3400
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.1538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  16494  Z= 0.160
  Angle     :  0.561  10.129  22367  Z= 0.294
  Chirality :  0.043   0.162   2544
  Planarity :  0.004   0.063   2796
  Dihedral  :  4.175  20.605   2164
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.84 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.20), residues: 1939
  helix:  2.35 (0.16), residues: 962
  sheet:  0.36 (0.29), residues: 363
  loop : -1.62 (0.24), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 104 
 HIS   0.004   0.001   HIS E  68 
 PHE   0.020   0.001   PHE E 147 
 TYR   0.032   0.001   TYR B 236 
 ARG   0.004   0.000   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05373 (  970)
  hydrogen bonds       : angle       4.55095 ( 2850)
  SS BOND              : bond        0.00316 (    2)
  SS BOND              : angle       1.10422 (    4)
  covalent geometry    : bond        0.00373 (16492)
  covalent geometry    : angle       0.56107 (22363)

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

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

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  395 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 342
  time to evaluate  : 1.916 
Fit side-chains
   revert: symmetry clash
REVERT: L   25 ARG cc_start: 0.7475 (ttm110) cc_final: 0.7173 (ttp-110)
REVERT: A  202 ARG cc_start: 0.6862 (ttp80) cc_final: 0.6571 (tmt-80)
REVERT: A  238 ASP cc_start: 0.7462 (m-30) cc_final: 0.6938 (p0)
REVERT: B   89 ASP cc_start: 0.7615 (m-30) cc_final: 0.7140 (m-30)
REVERT: B  116 ASP cc_start: 0.7498 (t0) cc_final: 0.6845 (t0)
REVERT: B  341 MET cc_start: 0.5974 (mmt) cc_final: 0.5599 (mmt)
REVERT: C  116 ASP cc_start: 0.8129 (p0) cc_final: 0.7558 (p0)
REVERT: C  132 THR cc_start: 0.5466 (OUTLIER) cc_final: 0.4901 (p)
REVERT: C  191 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7422 (mm-30)
REVERT: C  216 ARG cc_start: 0.6500 (mmm160) cc_final: 0.5824 (mmm160)
REVERT: D  125 GLU cc_start: 0.6048 (tm-30) cc_final: 0.5811 (tm-30)
REVERT: D  140 GLN cc_start: 0.6819 (mp10) cc_final: 0.5547 (mp10)
REVERT: D  145 ASP cc_start: 0.5218 (p0) cc_final: 0.4902 (p0)
REVERT: D  180 ASP cc_start: 0.7524 (t70) cc_final: 0.6578 (t0)
REVERT: D  233 SER cc_start: 0.7564 (m) cc_final: 0.7033 (m)
REVERT: E   10 LYS cc_start: 0.6547 (pttp) cc_final: 0.5985 (ptpt)
REVERT: E   54 ARG cc_start: 0.6949 (ptt90) cc_final: 0.6625 (ptt90)
REVERT: E  133 LYS cc_start: 0.8046 (mmmt) cc_final: 0.7824 (mmmt)
  outliers start: 53
  outliers final: 41
  residues processed: 370
  average time/residue: 0.2670
  time to fit residues: 150.0156
Evaluate side-chains
  375 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 333
  time to evaluate  : 1.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   65 ASP
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain H residue  101 ARG
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  177 LEU
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  202 ARG
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   94 HIS
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  160 ILE
Chi-restraints excluded: chain E residue  183 VAL
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  247 THR
Chi-restraints excluded: chain E residue  284 SER
Chi-restraints excluded: chain E residue  287 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 187 optimal weight:    0.6980
   chunk 160 optimal weight:    0.5980
   chunk 98 optimal weight:    0.0870
   chunk 71 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 113 optimal weight:    5.9990
   chunk 62 optimal weight:    0.1980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
H  80 ASN
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 120 HIS
** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 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 = 0.4138 r_free = 0.4138 target = 0.207247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.166778 restraints weight = 20198.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3720 rms_B_bonded: 2.63
r_work: 0.3456 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3439
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  16494  Z= 0.136
  Angle     :  0.534   8.440  22367  Z= 0.281
  Chirality :  0.042   0.144   2544
  Planarity :  0.004   0.059   2796
  Dihedral  :  4.090  20.073   2164
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 18.94 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.20), residues: 1939
  helix:  2.48 (0.16), residues: 959
  sheet:  0.45 (0.29), residues: 359
  loop : -1.63 (0.24), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 104 
 HIS   0.003   0.001   HIS E  68 
 PHE   0.020   0.001   PHE E 147 
 TYR   0.031   0.001   TYR B 236 
 ARG   0.004   0.000   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05102 (  970)
  hydrogen bonds       : angle       4.41781 ( 2850)
  SS BOND              : bond        0.00217 (    2)
  SS BOND              : angle       0.96818 (    4)
  covalent geometry    : bond        0.00304 (16492)
  covalent geometry    : angle       0.53365 (22363)

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

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

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  393 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 340
  time to evaluate  : 1.918 
Fit side-chains
   revert: symmetry clash
REVERT: L   25 ARG cc_start: 0.7389 (ttm110) cc_final: 0.6959 (ttp-110)
REVERT: A  232 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8172 (mm)
REVERT: B   89 ASP cc_start: 0.7493 (m-30) cc_final: 0.7001 (m-30)
REVERT: B  116 ASP cc_start: 0.7520 (t0) cc_final: 0.6871 (t0)
REVERT: B  341 MET cc_start: 0.5884 (mmt) cc_final: 0.5534 (mmt)
REVERT: C  132 THR cc_start: 0.5418 (OUTLIER) cc_final: 0.4909 (p)
REVERT: C  191 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7386 (mm-30)
REVERT: C  216 ARG cc_start: 0.6477 (mmm160) cc_final: 0.5842 (mmm160)
REVERT: C  291 MET cc_start: 0.8201 (tpp) cc_final: 0.7938 (tpp)
REVERT: D  100 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6523 (pm20)
REVERT: D  125 GLU cc_start: 0.6102 (tm-30) cc_final: 0.5778 (tm-30)
REVERT: D  140 GLN cc_start: 0.6526 (mp10) cc_final: 0.5349 (mp10)
REVERT: D  145 ASP cc_start: 0.5212 (p0) cc_final: 0.4898 (p0)
REVERT: D  180 ASP cc_start: 0.7458 (t70) cc_final: 0.6558 (t0)
REVERT: D  228 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8186 (mp)
REVERT: D  233 SER cc_start: 0.7398 (m) cc_final: 0.6867 (m)
REVERT: D  291 MET cc_start: 0.8895 (tpp) cc_final: 0.8609 (tpp)
REVERT: E   10 LYS cc_start: 0.6525 (pttp) cc_final: 0.5993 (ptpt)
REVERT: E   54 ARG cc_start: 0.6928 (ptt90) cc_final: 0.6638 (ptt90)
REVERT: E   69 ARG cc_start: 0.7214 (ttm170) cc_final: 0.6933 (ttp-110)
REVERT: E  133 LYS cc_start: 0.8019 (mmmt) cc_final: 0.7790 (mmmt)
  outliers start: 53
  outliers final: 37
  residues processed: 371
  average time/residue: 0.3306
  time to fit residues: 185.4597
Evaluate side-chains
  371 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 330
  time to evaluate  : 3.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   65 ASP
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain D residue  100 GLU
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  185 LEU
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  228 LEU
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   94 HIS
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  138 MET
Chi-restraints excluded: chain E residue  160 ILE
Chi-restraints excluded: chain E residue  183 VAL
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  247 THR
Chi-restraints excluded: chain E residue  284 SER
Chi-restraints excluded: chain E residue  318 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 160 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 20 optimal weight:    0.4980
   chunk 1 optimal weight:    1.9990
   chunk 164 optimal weight:    1.9990
   chunk 18 optimal weight:    0.2980
   chunk 188 optimal weight:    2.9990
   chunk 151 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
H  80 ASN
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 120 HIS
** E 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 = 0.4131 r_free = 0.4131 target = 0.206464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.166783 restraints weight = 20247.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 2.68
r_work: 0.3440 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3423
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3423
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  16494  Z= 0.155
  Angle     :  0.551   8.220  22367  Z= 0.290
  Chirality :  0.043   0.146   2544
  Planarity :  0.004   0.058   2796
  Dihedral  :  4.127  20.416   2164
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.27 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.20), residues: 1939
  helix:  2.43 (0.16), residues: 959
  sheet:  0.51 (0.29), residues: 356
  loop : -1.66 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 226 
 HIS   0.003   0.001   HIS E  68 
 PHE   0.018   0.001   PHE E 147 
 TYR   0.031   0.001   TYR B 236 
 ARG   0.004   0.000   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05222 (  970)
  hydrogen bonds       : angle       4.42099 ( 2850)
  SS BOND              : bond        0.00261 (    2)
  SS BOND              : angle       1.08497 (    4)
  covalent geometry    : bond        0.00361 (16492)
  covalent geometry    : angle       0.55094 (22363)

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

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

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  387 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 330
  time to evaluate  : 1.739 
Fit side-chains
   revert: symmetry clash
REVERT: L   25 ARG cc_start: 0.7412 (ttm110) cc_final: 0.6984 (ttp-110)
REVERT: A  120 HIS cc_start: 0.6710 (m170) cc_final: 0.6339 (m170)
REVERT: A  202 ARG cc_start: 0.6917 (tmt170) cc_final: 0.6318 (tmt-80)
REVERT: A  232 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8168 (mm)
REVERT: B   89 ASP cc_start: 0.7482 (m-30) cc_final: 0.7055 (m-30)
REVERT: B  116 ASP cc_start: 0.7539 (t0) cc_final: 0.6877 (t0)
REVERT: B  341 MET cc_start: 0.5967 (mmt) cc_final: 0.5606 (mmt)
REVERT: C  132 THR cc_start: 0.5404 (OUTLIER) cc_final: 0.4906 (p)
REVERT: C  191 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7361 (mm-30)
REVERT: C  216 ARG cc_start: 0.6524 (mmm160) cc_final: 0.5924 (mmm160)
REVERT: D  100 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6509 (pm20)
REVERT: D  125 GLU cc_start: 0.6150 (tm-30) cc_final: 0.5860 (tm-30)
REVERT: D  140 GLN cc_start: 0.6557 (mp10) cc_final: 0.5421 (mp10)
REVERT: D  145 ASP cc_start: 0.5120 (p0) cc_final: 0.4838 (p0)
REVERT: D  180 ASP cc_start: 0.7458 (t70) cc_final: 0.6573 (t0)
REVERT: D  228 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8224 (mp)
REVERT: D  233 SER cc_start: 0.7488 (m) cc_final: 0.6997 (m)
REVERT: E   10 LYS cc_start: 0.6301 (pttp) cc_final: 0.5803 (ptpt)
REVERT: E   54 ARG cc_start: 0.6952 (ptt90) cc_final: 0.6645 (ptt90)
  outliers start: 57
  outliers final: 42
  residues processed: 363
  average time/residue: 0.2597
  time to fit residues: 143.4198
Evaluate side-chains
  375 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 329
  time to evaluate  : 1.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   65 ASP
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain H residue  101 ARG
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain D residue  100 GLU
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  177 LEU
Chi-restraints excluded: chain D residue  185 LEU
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  202 ARG
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  228 LEU
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   94 HIS
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  160 ILE
Chi-restraints excluded: chain E residue  183 VAL
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  284 SER
Chi-restraints excluded: chain E residue  318 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 85 optimal weight:    0.0010
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 112 optimal weight:    3.9990
   chunk 141 optimal weight:    0.9990
   chunk 151 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0470
   chunk 53 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 183 optimal weight:    0.6980
   chunk 116 optimal weight:    0.9980
   overall best weight:    0.5084

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

Flipped N/Q/H residues before XYZ refinement:
H  80 ASN
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 120 HIS
** E 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 = 0.4138 r_free = 0.4138 target = 0.207129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.167373 restraints weight = 20047.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 3.00
r_work: 0.3443 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3423
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3423
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  16494  Z= 0.144
  Angle     :  0.546   8.459  22367  Z= 0.287
  Chirality :  0.043   0.151   2544
  Planarity :  0.004   0.059   2796
  Dihedral  :  4.112  20.070   2164
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 19.49 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.20), residues: 1939
  helix:  2.48 (0.17), residues: 959
  sheet:  0.52 (0.29), residues: 357
  loop : -1.65 (0.24), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 226 
 HIS   0.003   0.001   HIS B  68 
 PHE   0.017   0.001   PHE E 147 
 TYR   0.031   0.001   TYR B 236 
 ARG   0.004   0.000   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05127 (  970)
  hydrogen bonds       : angle       4.37140 ( 2850)
  SS BOND              : bond        0.00222 (    2)
  SS BOND              : angle       1.00523 (    4)
  covalent geometry    : bond        0.00332 (16492)
  covalent geometry    : angle       0.54571 (22363)

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

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

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  390 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 331
  time to evaluate  : 1.708 
Fit side-chains
   revert: symmetry clash
REVERT: L   25 ARG cc_start: 0.7467 (ttm110) cc_final: 0.7051 (ttp-110)
REVERT: A  120 HIS cc_start: 0.6718 (m170) cc_final: 0.6357 (m170)
REVERT: A  202 ARG cc_start: 0.6969 (tmt170) cc_final: 0.6444 (tmt-80)
REVERT: A  232 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8190 (mm)
REVERT: B   89 ASP cc_start: 0.7475 (m-30) cc_final: 0.7040 (m-30)
REVERT: B  116 ASP cc_start: 0.7619 (t0) cc_final: 0.6963 (t0)
REVERT: C  132 THR cc_start: 0.5359 (OUTLIER) cc_final: 0.4872 (p)
REVERT: C  191 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7388 (mm-30)
REVERT: C  216 ARG cc_start: 0.6515 (mmm160) cc_final: 0.5923 (mmm160)
REVERT: D  100 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6499 (pm20)
REVERT: D  125 GLU cc_start: 0.6220 (tm-30) cc_final: 0.5856 (tm-30)
REVERT: D  140 GLN cc_start: 0.6566 (mp10) cc_final: 0.5386 (mp10)
REVERT: D  145 ASP cc_start: 0.5110 (p0) cc_final: 0.4813 (p0)
REVERT: D  180 ASP cc_start: 0.7461 (t70) cc_final: 0.6610 (t0)
REVERT: D  228 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8235 (mp)
REVERT: D  233 SER cc_start: 0.7462 (m) cc_final: 0.6984 (m)
REVERT: E   10 LYS cc_start: 0.6254 (pttp) cc_final: 0.5756 (ptpt)
REVERT: E   54 ARG cc_start: 0.6976 (ptt90) cc_final: 0.6668 (ptt90)
REVERT: E   69 ARG cc_start: 0.7221 (ttm170) cc_final: 0.6967 (ttp-170)
  outliers start: 59
  outliers final: 45
  residues processed: 364
  average time/residue: 0.2542
  time to fit residues: 140.7108
Evaluate side-chains
  376 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 327
  time to evaluate  : 1.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   65 ASP
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain H residue  101 ARG
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain D residue  100 GLU
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  177 LEU
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  202 ARG
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  228 LEU
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   94 HIS
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  160 ILE
Chi-restraints excluded: chain E residue  183 VAL
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  284 SER
Chi-restraints excluded: chain E residue  318 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 143 optimal weight:    1.9990
   chunk 139 optimal weight:    0.9990
   chunk 84 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 64 optimal weight:    0.7980
   chunk 95 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
H  80 ASN
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 120 HIS
** E 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 = 0.4129 r_free = 0.4129 target = 0.206244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.166386 restraints weight = 20058.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 2.93
r_work: 0.3420 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3400
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3400 r_free = 0.3400    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3400 r_free = 0.3400    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3400
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  16494  Z= 0.167
  Angle     :  0.570   9.879  22367  Z= 0.299
  Chirality :  0.044   0.172   2544
  Planarity :  0.005   0.062   2796
  Dihedral  :  4.182  20.808   2164
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.60 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.20), residues: 1939
  helix:  2.37 (0.16), residues: 963
  sheet:  0.51 (0.29), residues: 356
  loop : -1.67 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 226 
 HIS   0.003   0.001   HIS B  68 
 PHE   0.018   0.001   PHE E 147 
 TYR   0.032   0.001   TYR B 236 
 ARG   0.004   0.000   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05315 (  970)
  hydrogen bonds       : angle       4.41861 ( 2850)
  SS BOND              : bond        0.00304 (    2)
  SS BOND              : angle       1.13262 (    4)
  covalent geometry    : bond        0.00394 (16492)
  covalent geometry    : angle       0.56999 (22363)

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

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

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  387 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 330
  time to evaluate  : 2.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   25 ARG cc_start: 0.7510 (ttm110) cc_final: 0.7089 (ttp-110)
REVERT: A  120 HIS cc_start: 0.6715 (m170) cc_final: 0.6329 (m170)
REVERT: A  232 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8189 (mm)
REVERT: B   30 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7444 (tt0)
REVERT: B   89 ASP cc_start: 0.7554 (m-30) cc_final: 0.7127 (m-30)
REVERT: B  116 ASP cc_start: 0.7643 (t0) cc_final: 0.6988 (t0)
REVERT: B  245 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7750 (mmmm)
REVERT: B  304 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7950 (mp)
REVERT: C  132 THR cc_start: 0.5395 (OUTLIER) cc_final: 0.4905 (p)
REVERT: C  174 ILE cc_start: 0.3914 (mm) cc_final: 0.3663 (mm)
REVERT: C  191 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7439 (mm-30)
REVERT: C  216 ARG cc_start: 0.6526 (mmm160) cc_final: 0.5943 (mmm160)
REVERT: D  100 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6536 (pm20)
REVERT: D  125 GLU cc_start: 0.6406 (tm-30) cc_final: 0.6109 (tm-30)
REVERT: D  140 GLN cc_start: 0.6618 (mp10) cc_final: 0.5481 (mp10)
REVERT: D  145 ASP cc_start: 0.5153 (p0) cc_final: 0.4842 (p0)
REVERT: D  228 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8236 (mp)
REVERT: D  233 SER cc_start: 0.7406 (m) cc_final: 0.6947 (m)
REVERT: E   10 LYS cc_start: 0.6228 (pttp) cc_final: 0.5711 (ptpt)
REVERT: E  145 ASP cc_start: 0.8649 (p0) cc_final: 0.8373 (p0)
  outliers start: 57
  outliers final: 46
  residues processed: 361
  average time/residue: 0.3273
  time to fit residues: 182.6591
Evaluate side-chains
  381 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 328
  time to evaluate  : 2.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   65 ASP
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain H residue  101 ARG
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   30 GLU
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  245 LYS
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain D residue  100 GLU
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  177 LEU
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  202 ARG
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  228 LEU
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   94 HIS
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  160 ILE
Chi-restraints excluded: chain E residue  183 VAL
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  284 SER
Chi-restraints excluded: chain E residue  318 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 144 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 147 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0670
   chunk 104 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
H  80 ASN
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
E 120 HIS
** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.207192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.167162 restraints weight = 20136.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 2.78
r_work: 0.3449 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3433
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3433 r_free = 0.3433    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3433 r_free = 0.3433    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3433
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  16494  Z= 0.144
  Angle     :  0.558   9.057  22367  Z= 0.292
  Chirality :  0.043   0.158   2544
  Planarity :  0.004   0.062   2796
  Dihedral  :  4.140  20.501   2164
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.10 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.20), residues: 1939
  helix:  2.44 (0.17), residues: 959
  sheet:  0.53 (0.29), residues: 355
  loop : -1.63 (0.24), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 226 
 HIS   0.002   0.001   HIS E  68 
 PHE   0.018   0.001   PHE E  39 
 TYR   0.032   0.001   TYR E 279 
 ARG   0.004   0.000   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05130 (  970)
  hydrogen bonds       : angle       4.36719 ( 2850)
  SS BOND              : bond        0.00222 (    2)
  SS BOND              : angle       0.97224 (    4)
  covalent geometry    : bond        0.00331 (16492)
  covalent geometry    : angle       0.55764 (22363)

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

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

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3878 Ramachandran restraints generated.
    1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  385 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 328
  time to evaluate  : 1.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   25 ARG cc_start: 0.7425 (ttm110) cc_final: 0.7000 (ttp-110)
REVERT: A  120 HIS cc_start: 0.6662 (m170) cc_final: 0.6293 (m170)
REVERT: A  232 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8119 (mm)
REVERT: A  291 MET cc_start: 0.8508 (mmm) cc_final: 0.8063 (mmm)
REVERT: B   89 ASP cc_start: 0.7448 (m-30) cc_final: 0.7000 (m-30)
REVERT: B  116 ASP cc_start: 0.7585 (t0) cc_final: 0.6913 (t0)
REVERT: B  245 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7768 (mmmm)
REVERT: B  304 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7929 (mp)
REVERT: C  132 THR cc_start: 0.5288 (OUTLIER) cc_final: 0.4805 (p)
REVERT: C  191 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7447 (mm-30)
REVERT: C  216 ARG cc_start: 0.6544 (mmm160) cc_final: 0.5938 (mmm160)
REVERT: D  100 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6495 (pm20)
REVERT: D  125 GLU cc_start: 0.6306 (tm-30) cc_final: 0.5978 (tm-30)
REVERT: D  140 GLN cc_start: 0.6572 (mp10) cc_final: 0.5306 (mp10)
REVERT: D  145 ASP cc_start: 0.5085 (p0) cc_final: 0.4778 (p0)
REVERT: D  180 ASP cc_start: 0.7484 (t70) cc_final: 0.6403 (t0)
REVERT: D  185 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8506 (tp)
REVERT: D  228 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8210 (mp)
REVERT: D  233 SER cc_start: 0.7462 (m) cc_final: 0.7027 (m)
REVERT: E   10 LYS cc_start: 0.6257 (pttp) cc_final: 0.5709 (ptpt)
REVERT: E   54 ARG cc_start: 0.6971 (ptt90) cc_final: 0.6591 (ptt90)
REVERT: E  181 TYR cc_start: 0.7329 (m-80) cc_final: 0.7048 (m-80)
  outliers start: 57
  outliers final: 48
  residues processed: 360
  average time/residue: 0.3351
  time to fit residues: 185.0062
Evaluate side-chains
  377 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 322
  time to evaluate  : 3.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   30 VAL
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   65 ASP
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain H residue  101 ARG
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   30 GLU
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  245 LYS
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain D residue   90 ILE
Chi-restraints excluded: chain D residue  100 GLU
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  177 LEU
Chi-restraints excluded: chain D residue  185 LEU
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  202 ARG
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  228 LEU
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  341 MET
Chi-restraints excluded: chain E residue   67 ILE
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   94 HIS
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  160 ILE
Chi-restraints excluded: chain E residue  183 VAL
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  284 SER
Chi-restraints excluded: chain E residue  318 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 123 optimal weight:    1.9990
   chunk 175 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 111 optimal weight:   10.0000
   chunk 108 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 110 optimal weight:    0.6980
   chunk 144 optimal weight:    0.9980
   chunk 185 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
H  80 ASN
** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 120 HIS
** E 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 = 0.4129 r_free = 0.4129 target = 0.206174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.165655 restraints weight = 20204.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 2.99
r_work: 0.3422 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3403
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3403 r_free = 0.3403    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3403 r_free = 0.3403    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3403
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  16494  Z= 0.169
  Angle     :  0.579   8.985  22367  Z= 0.304
  Chirality :  0.044   0.177   2544
  Planarity :  0.005   0.062   2796
  Dihedral  :  4.208  21.023   2164
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 19.71 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.20), residues: 1939
  helix:  2.34 (0.16), residues: 962
  sheet:  0.48 (0.29), residues: 355
  loop : -1.65 (0.24), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 226 
 HIS   0.003   0.001   HIS B  68 
 PHE   0.018   0.001   PHE E 147 
 TYR   0.032   0.001   TYR B 236 
 ARG   0.004   0.000   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05323 (  970)
  hydrogen bonds       : angle       4.41756 ( 2850)
  SS BOND              : bond        0.00313 (    2)
  SS BOND              : angle       1.13247 (    4)
  covalent geometry    : bond        0.00401 (16492)
  covalent geometry    : angle       0.57837 (22363)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9321.70 seconds
wall clock time: 164 minutes 6.69 seconds (9846.69 seconds total)