Starting phenix.real_space_refine
on Mon May 19 18:04:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tmk_41392/05_2025/8tmk_41392.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tmk_41392/05_2025/8tmk_41392.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/8tmk_41392/05_2025/8tmk_41392.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tmk_41392/05_2025/8tmk_41392.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tmk_41392/05_2025/8tmk_41392.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tmk_41392/05_2025/8tmk_41392.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=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1577 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Mg      3      5.21       5
     S      65      5.16       5
     C   11504      2.51       5
     N    2894      2.21       5
     O    3291      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 17757
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "H"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 971
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 2, 'TRANS': 123}
    Chain: "L"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 809
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102}
    Chain: "G"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 794
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
    Chain: "F"
      Number of atoms: 950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 950
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 2, 'TRANS': 120}
    Chain: "A"
      Number of atoms: 2797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2797
          Classifications: {'peptide': 334}
          Link IDs: {'PTRANS': 13, 'TRANS': 320}
    Chain: "B"
      Number of atoms: 2899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 348, 2899
          Classifications: {'peptide': 348}
          Link IDs: {'PTRANS': 15, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 2812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2812
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 13, 'TRANS': 322}
    Chain: "D"
      Number of atoms: 2925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2925
          Classifications: {'peptide': 351}
          Link IDs: {'PTRANS': 15, 'TRANS': 335}
    Chain: "E"
      Number of atoms: 2797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2797
          Classifications: {'peptide': 334}
          Link IDs: {'PTRANS': 13, 'TRANS': 320}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      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: 10.94, per 1000 atoms: 0.62
  Number of scatterers: 17757
  At special positions: 0
  Unit cell: (124.371, 141.379, 143.505, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      65     16.00
     Mg      3     11.99
     O    3291      8.00
     N    2894      7.00
     C   11504      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  24 " - pdb=" SG  CYS G  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  25 " - pdb=" SG  CYS F  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: 4.65
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4134

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 16 sheets defined
      48.6% alpha, 20.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.05
  Creating SS restraints...
    Processing helix  chain 'H' and resid 31 through 34
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.970A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.992A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 84
      removed outlier: 3.885A  pdb=" N   PHE G  84 " --> pdb=" O   PRO G  81 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 31 through 34
    Processing helix  chain 'A' and resid 46 through 55
      removed outlier: 3.579A  pdb=" N   SER A  49 " --> pdb=" O   ASP A  46 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU A  51 " --> pdb=" O   GLU A  48 " (cutoff:3.500A)
      Proline residue:  A  52  - end of helix
      removed outlier: 3.608A  pdb=" N   ASP A  55 " --> pdb=" O   PRO A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 81
      removed outlier: 3.855A  pdb=" N   VAL A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 92
    Processing helix  chain 'A' and resid 147 through 156
    Processing helix  chain 'A' and resid 160 through 164
    Processing helix  chain 'A' and resid 165 through 202
      removed outlier: 3.632A  pdb=" N   LEU A 169 " --> pdb=" O   ARG A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 237
      Proline residue:  A 227  - end of helix
      removed outlier: 3.837A  pdb=" N   GLU A 230 " --> pdb=" O   TRP A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 244
    Processing helix  chain 'A' and resid 247 through 273
      removed outlier: 3.546A  pdb=" N   PHE A 251 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 283
    Processing helix  chain 'A' and resid 286 through 312
      Proline residue:  A 303  - end of helix
    Processing helix  chain 'A' and resid 325 through 349
    Processing helix  chain 'B' and resid 46 through 51
      removed outlier: 3.988A  pdb=" N   VAL B  50 " --> pdb=" O   ASP B  46 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU B  51 " --> pdb=" O   VAL B  47 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 46 through 51'
    Processing helix  chain 'B' and resid 52 through 54
      No H-bonds generated for 'chain 'B' and resid 52 through 54'
    Processing helix  chain 'B' and resid 69 through 80
      removed outlier: 3.554A  pdb=" N   VAL B  73 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 92
    Processing helix  chain 'B' and resid 147 through 156
    Processing helix  chain 'B' and resid 160 through 164
      removed outlier: 3.526A  pdb=" N   LYS B 164 " --> pdb=" O   ILE B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 202
      removed outlier: 3.670A  pdb=" N   LEU B 169 " --> pdb=" O   ARG B 165 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LEU B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   GLU B 201 " --> pdb=" O   GLU B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 237
      Proline residue:  B 227  - end of helix
    Processing helix  chain 'B' and resid 244 through 246
      No H-bonds generated for 'chain 'B' and resid 244 through 246'
    Processing helix  chain 'B' and resid 247 through 312
      removed outlier: 3.756A  pdb=" N   PHE B 251 " --> pdb=" O   THR B 247 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ASP B 277 " --> pdb=" O   SER B 273 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU B 280 " --> pdb=" O   LEU B 276 " (cutoff:3.500A)
      Proline residue:  B 303  - end of helix
    Processing helix  chain 'B' and resid 325 through 346
    Processing helix  chain 'C' and resid 46 through 50
      removed outlier: 3.647A  pdb=" N   SER C  49 " --> pdb=" O   ASP C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 81
      removed outlier: 3.903A  pdb=" N   VAL C  73 " --> pdb=" O   ARG C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 92
    Processing helix  chain 'C' and resid 147 through 157
    Processing helix  chain 'C' and resid 165 through 202
    Processing helix  chain 'C' and resid 204 through 237
      removed outlier: 3.573A  pdb=" N   GLN C 209 " --> pdb=" O   LYS C 205 " (cutoff:3.500A)
      Proline residue:  C 227  - end of helix
      removed outlier: 3.685A  pdb=" N   GLU C 230 " --> pdb=" O   TRP C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 281
      removed outlier: 3.545A  pdb=" N   PHE C 251 " --> pdb=" O   THR C 247 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   TYR C 279 " --> pdb=" O   LEU C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 283 through 300
      removed outlier: 3.638A  pdb=" N   ILE C 300 " --> pdb=" O   ILE C 296 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 312
    Processing helix  chain 'C' and resid 325 through 349
    Processing helix  chain 'D' and resid 46 through 55
      removed outlier: 3.503A  pdb=" N   SER D  49 " --> pdb=" O   ASP D  46 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU D  51 " --> pdb=" O   GLU D  48 " (cutoff:3.500A)
      Proline residue:  D  52  - end of helix
    Processing helix  chain 'D' and resid 69 through 80
      removed outlier: 3.627A  pdb=" N   VAL D  73 " --> pdb=" O   ARG D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 92
    Processing helix  chain 'D' and resid 147 through 157
    Processing helix  chain 'D' and resid 165 through 202
      removed outlier: 3.526A  pdb=" N   LEU D 169 " --> pdb=" O   ARG D 165 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLU D 197 " --> pdb=" O   ASP D 193 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLU D 198 " --> pdb=" O   VAL D 194 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 239
      removed outlier: 3.509A  pdb=" N   VAL D 208 " --> pdb=" O   GLU D 204 " (cutoff:3.500A)
      Proline residue:  D 227  - end of helix
      removed outlier: 3.745A  pdb=" N   VAL D 239 " --> pdb=" O   LEU D 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 240 through 244
      removed outlier: 3.795A  pdb=" N   GLU D 244 " --> pdb=" O   PRO D 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 247 through 311
      Proline residue:  D 303  - end of helix
    Processing helix  chain 'D' and resid 326 through 348
    Processing helix  chain 'E' and resid 47 through 51
      removed outlier: 3.572A  pdb=" N   VAL E  50 " --> pdb=" O   VAL E  47 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 69 through 81
      removed outlier: 3.506A  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 165 through 202
      removed outlier: 3.601A  pdb=" N   LEU E 169 " --> pdb=" O   ARG E 165 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   TYR E 181 " --> pdb=" O   LEU E 177 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   PHE E 182 " --> pdb=" O   VAL E 178 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   VAL E 183 " --> pdb=" O   ASP E 179 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 204 through 237
      removed outlier: 3.711A  pdb=" N   VAL E 208 " --> pdb=" O   GLU E 204 " (cutoff:3.500A)
      Proline residue:  E 227  - end of helix
    Processing helix  chain 'E' and resid 247 through 251
    Processing helix  chain 'E' and resid 252 through 311
      Proline residue:  E 303  - end of helix
    Processing helix  chain 'E' and resid 326 through 347
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA2, first strand: chain 'H' and resid 61 through 63
      removed outlier: 6.620A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   SER H  36 " --> pdb=" O   SER H 102 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   CYS H  99 " --> pdb=" O   TRP H 119 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   TRP H 119 " --> pdb=" O   CYS H  99 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ARG H 101 " --> pdb=" O   ASP H 117 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 61 through 63
      removed outlier: 6.620A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   SER H  36 " --> pdb=" O   SER H 102 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 14
      removed outlier: 6.886A  pdb=" N   LEU L  12 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.490A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 5 through 8
      removed outlier: 3.537A  pdb=" N   VAL G  20 " --> pdb=" O   ILE G  76 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 11 through 13
      removed outlier: 3.605A  pdb=" N   TYR G  88 " --> pdb=" O   TYR G  37 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   TYR G  37 " --> pdb=" O   TYR G  88 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   TRP G  36 " --> pdb=" O   LEU G  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 6 through 10
    Processing sheet with id=AB1, first strand: chain 'F' and resid 60 through 63
      removed outlier: 3.919A  pdb=" N   SER F  60 " --> pdb=" O   SER F  55 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   TRP F  39 " --> pdb=" O   VAL F  51 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   SER F  53 " --> pdb=" O   ILE F  37 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   ILE F  37 " --> pdb=" O   SER F  53 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   SER F  36 " --> pdb=" O   SER F 102 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 60 through 63
      removed outlier: 3.919A  pdb=" N   SER F  60 " --> pdb=" O   SER F  55 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   TRP F  39 " --> pdb=" O   VAL F  51 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   SER F  53 " --> pdb=" O   ILE F  37 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   ILE F  37 " --> pdb=" O   SER F  53 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   SER F  36 " --> pdb=" O   SER F 102 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 39 through 44
      removed outlier: 3.657A  pdb=" N   SER A 128 " --> pdb=" O   PHE A 139 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 39 through 41
    Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 44
      removed outlier: 3.721A  pdb=" N   ILE C  29 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   GLU C 121 " --> pdb=" O   ASP C 116 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASP C 116 " --> pdb=" O   GLU C 121 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLU C 123 " --> pdb=" O   THR C 114 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 39 through 44
    Processing sheet with id=AB7, first strand: chain 'E' and resid 28 through 33
      removed outlier: 6.056A  pdb=" N   THR E  60 " --> pdb=" O   VAL E 136 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   MET E 138 " --> pdb=" O   THR E  60 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ILE E  62 " --> pdb=" O   MET E 138 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   GLU E 123 " --> pdb=" O   THR E 114 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   THR E 114 " --> pdb=" O   GLU E 123 " (cutoff:3.500A)

    1078 hydrogen bonds defined for protein.
    3072 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 6.68

  Time building geometry restraints manager: 5.37 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 5542
        1.34 -     1.46: 3002
        1.46 -     1.57: 9498
        1.57 -     1.69: 1
        1.69 -     1.81: 117
  Bond restraints: 18160
  Sorted by residual:
  bond pdb=" CG  PRO B 227 "
       pdb=" CD  PRO B 227 "
    ideal  model  delta    sigma   weight residual
    1.503  1.381  0.122 3.40e-02 8.65e+02 1.29e+01
  bond pdb=" CB  PRO B 227 "
       pdb=" CG  PRO B 227 "
    ideal  model  delta    sigma   weight residual
    1.492  1.605 -0.113 5.00e-02 4.00e+02 5.13e+00
  bond pdb=" N   PRO B 227 "
       pdb=" CD  PRO B 227 "
    ideal  model  delta    sigma   weight residual
    1.473  1.497 -0.024 1.40e-02 5.10e+03 2.94e+00
  bond pdb=" CG  LEU B 184 "
       pdb=" CD1 LEU B 184 "
    ideal  model  delta    sigma   weight residual
    1.521  1.466  0.055 3.30e-02 9.18e+02 2.78e+00
  bond pdb=" N   PRO B 227 "
       pdb=" CA  PRO B 227 "
    ideal  model  delta    sigma   weight residual
    1.471  1.451  0.020 1.32e-02 5.74e+03 2.22e+00
  ... (remaining 18155 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 24337
        2.51 -     5.02: 258
        5.02 -     7.53: 30
        7.53 -    10.04: 5
       10.04 -    12.55: 1
  Bond angle restraints: 24631
  Sorted by residual:
  angle pdb=" CA  PRO B 227 "
        pdb=" N   PRO B 227 "
        pdb=" CD  PRO B 227 "
      ideal   model   delta    sigma   weight residual
     112.00   99.45   12.55 1.40e+00 5.10e-01 8.03e+01
  angle pdb=" N   PRO B 227 "
        pdb=" CD  PRO B 227 "
        pdb=" CG  PRO B 227 "
      ideal   model   delta    sigma   weight residual
     103.20   93.18   10.02 1.50e+00 4.44e-01 4.46e+01
  angle pdb=" C   LEU C 235 "
        pdb=" N   TYR C 236 "
        pdb=" CA  TYR C 236 "
      ideal   model   delta    sigma   weight residual
     122.53  113.80    8.73 1.92e+00 2.71e-01 2.07e+01
  angle pdb=" C   VAL D 343 "
        pdb=" N   TYR D 344 "
        pdb=" CA  TYR D 344 "
      ideal   model   delta    sigma   weight residual
     121.58  114.53    7.05 1.95e+00 2.63e-01 1.31e+01
  angle pdb=" C   ASP B 179 "
        pdb=" N   ASP B 180 "
        pdb=" CA  ASP B 180 "
      ideal   model   delta    sigma   weight residual
     121.14  115.15    5.99 1.75e+00 3.27e-01 1.17e+01
  ... (remaining 24626 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 9694
       17.96 -    35.92: 967
       35.92 -    53.89: 170
       53.89 -    71.85: 25
       71.85 -    89.81: 24
  Dihedral angle restraints: 10880
    sinusoidal: 4470
      harmonic: 6410
  Sorted by residual:
  dihedral pdb=" CB  CYS L  24 "
           pdb=" SG  CYS L  24 "
           pdb=" SG  CYS L  89 "
           pdb=" CB  CYS L  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.29  -68.29     1      1.00e+01 1.00e-02 6.05e+01
  dihedral pdb=" CA  LYS C 349 "
           pdb=" C   LYS C 349 "
           pdb=" N   TRP C 350 "
           pdb=" CA  TRP C 350 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.22   22.78     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CB  CYS G  24 "
           pdb=" SG  CYS G  24 "
           pdb=" SG  CYS G  89 "
           pdb=" CB  CYS G  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  127.98  -34.98     1      1.00e+01 1.00e-02 1.73e+01
  ... (remaining 10877 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1765
       0.036 -    0.072: 710
       0.072 -    0.108: 250
       0.108 -    0.143: 55
       0.143 -    0.179: 11
  Chirality restraints: 2791
  Sorted by residual:
  chirality pdb=" CB  ILE G   3 "
            pdb=" CA  ILE G   3 "
            pdb=" CG1 ILE G   3 "
            pdb=" CG2 ILE G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.03e-01
  chirality pdb=" CA  ILE C  64 "
            pdb=" N   ILE C  64 "
            pdb=" C   ILE C  64 "
            pdb=" CB  ILE C  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.14e-01
  chirality pdb=" CB  VAL E 239 "
            pdb=" CA  VAL E 239 "
            pdb=" CG1 VAL E 239 "
            pdb=" CG2 VAL E 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.05e-01
  ... (remaining 2788 not shown)

  Planarity restraints: 3081
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 226 "    0.097 5.00e-02 4.00e+02   1.37e-01 3.00e+01
        pdb=" N   PRO B 227 "   -0.236 5.00e-02 4.00e+02
        pdb=" CA  PRO B 227 "    0.067 5.00e-02 4.00e+02
        pdb=" CD  PRO B 227 "    0.072 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  96 "    0.040 5.00e-02 4.00e+02   6.10e-02 5.95e+00
        pdb=" N   PRO E  97 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO E  97 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO E  97 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN F  16 "   -0.034 5.00e-02 4.00e+02   5.20e-02 4.33e+00
        pdb=" N   PRO F  17 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO F  17 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO F  17 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 3078 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 330
        2.68 -     3.24: 17522
        3.24 -     3.79: 28227
        3.79 -     4.35: 36826
        4.35 -     4.90: 61538
  Nonbonded interactions: 144443
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 314 "
            pdb="MG    MG B 401 "
     model   vdw
     2.128 2.170
  nonbonded pdb=" OD1 ASN B 288 "
            pdb=" OG1 THR C 287 "
     model   vdw
     2.129 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" O   LEU C 280 "
     model   vdw
     2.134 3.040
  nonbonded pdb=" OD1 ASN D 288 "
            pdb=" OG1 THR E 287 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" O   ARG E  54 "
            pdb=" NZ  LYS E 133 "
     model   vdw
     2.188 3.120
  ... (remaining 144438 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 17 through 350)
  selection = (chain 'C' and resid 17 through 350)
  selection = (chain 'D' and resid 17 through 350)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'F'
  selection = (chain 'H' and resid 4 through 126)
}
ncs_group {
  reference = chain 'G'
  selection = (chain 'L' and resid 2 through 107)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.49 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.120
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.780
  Check model and map are aligned:         0.140
  Set scattering table:                    0.190
  Process input model:                     42.340
  Find NCS groups from input model:        0.830
  Set up NCS constraints:                  0.090
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
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   0.122  18164  Z= 0.193
  Angle     :  0.660  12.548  24639  Z= 0.350
  Chirality :  0.045   0.179   2791
  Planarity :  0.005   0.137   3081
  Dihedral  : 14.866  89.810   6734
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.93 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.35 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.18), residues: 2148
  helix:  1.78 (0.16), residues: 974
  sheet:  0.71 (0.25), residues: 427
  loop : -1.54 (0.22), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP D 350 
 HIS   0.003   0.001   HIS E  68 
 PHE   0.024   0.002   PHE B 315 
 TYR   0.023   0.002   TYR D 344 
 ARG   0.011   0.001   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11047 ( 1053)
  hydrogen bonds       : angle       5.84488 ( 3072)
  SS BOND              : bond        0.00234 (    4)
  SS BOND              : angle       1.22949 (    8)
  covalent geometry    : bond        0.00456 (18160)
  covalent geometry    : angle       0.65996 (24631)

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  396 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 395
  time to evaluate  : 1.851 
Fit side-chains
REVERT: L   46 LYS cc_start: 0.8352 (ttmm) cc_final: 0.8090 (ttmm)
REVERT: L  108 LYS cc_start: 0.3329 (mmtt) cc_final: 0.2671 (mmtt)
REVERT: A  270 ASP cc_start: 0.6625 (m-30) cc_final: 0.6326 (m-30)
REVERT: B  160 ILE cc_start: 0.8421 (mt) cc_final: 0.8217 (mt)
REVERT: C  193 ASP cc_start: 0.8231 (t70) cc_final: 0.8020 (t70)
REVERT: C  230 GLU cc_start: 0.6788 (tt0) cc_final: 0.6532 (tt0)
REVERT: D  186 GLU cc_start: 0.7810 (tt0) cc_final: 0.7460 (tt0)
REVERT: D  243 ILE cc_start: 0.8659 (mm) cc_final: 0.8239 (mm)
REVERT: E  267 THR cc_start: 0.8194 (p) cc_final: 0.7977 (t)
  outliers start: 1
  outliers final: 1
  residues processed: 396
  average time/residue: 0.2742
  time to fit residues: 165.6697
Evaluate side-chains
  364 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 363
  time to evaluate  : 2.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  157 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 179 optimal weight:    8.9990
   chunk 160 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 108 optimal weight:   10.0000
   chunk 85 optimal weight:    0.6980
   chunk 166 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 101 optimal weight:    0.8980
   chunk 123 optimal weight:    0.9990
   chunk 192 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** H  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 157 ASN
** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 213 GLN
** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.185614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.145626 restraints weight = 20979.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 3.16
r_work: 0.3018 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3014 r_free = 0.3014    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3014
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.0792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  18164  Z= 0.194
  Angle     :  0.628   8.797  24639  Z= 0.326
  Chirality :  0.045   0.220   2791
  Planarity :  0.005   0.065   3081
  Dihedral  :  4.552  30.334   2403
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  9.63 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.18), residues: 2148
  helix:  1.98 (0.16), residues: 981
  sheet:  0.65 (0.24), residues: 446
  loop : -1.47 (0.23), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP D 350 
 HIS   0.005   0.001   HIS A  83 
 PHE   0.017   0.001   PHE B 315 
 TYR   0.023   0.002   TYR D 279 
 ARG   0.006   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05845 ( 1053)
  hydrogen bonds       : angle       4.82591 ( 3072)
  SS BOND              : bond        0.00163 (    4)
  SS BOND              : angle       1.19759 (    8)
  covalent geometry    : bond        0.00452 (18160)
  covalent geometry    : angle       0.62782 (24631)

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  399 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 371
  time to evaluate  : 1.909 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8355 (pt0) cc_final: 0.8120 (pt0)
REVERT: L  108 LYS cc_start: 0.4196 (mmtt) cc_final: 0.3272 (mmtt)
REVERT: A  216 ARG cc_start: 0.7866 (mmm-85) cc_final: 0.7306 (mtp85)
REVERT: A  270 ASP cc_start: 0.7463 (m-30) cc_final: 0.7008 (m-30)
REVERT: A  292 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7807 (mmtm)
REVERT: D  121 GLU cc_start: 0.6994 (pm20) cc_final: 0.6630 (pm20)
REVERT: D  186 GLU cc_start: 0.8451 (tt0) cc_final: 0.8248 (tt0)
REVERT: D  243 ILE cc_start: 0.8812 (mm) cc_final: 0.8481 (mm)
REVERT: E   30 GLU cc_start: 0.6106 (pm20) cc_final: 0.5868 (pm20)
REVERT: E   96 ARG cc_start: 0.7340 (ttp80) cc_final: 0.6835 (ttp80)
REVERT: E  155 ARG cc_start: 0.6187 (mtp-110) cc_final: 0.5769 (mtp-110)
  outliers start: 28
  outliers final: 22
  residues processed: 385
  average time/residue: 0.2816
  time to fit residues: 164.9727
Evaluate side-chains
  380 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 358
  time to evaluate  : 1.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue   34 VAL
Chi-restraints excluded: chain G residue   48 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  279 TYR
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain E residue  183 VAL
Chi-restraints excluded: chain E residue  310 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 197 optimal weight:    0.9990
   chunk 133 optimal weight:    2.9990
   chunk 157 optimal weight:    0.6980
   chunk 94 optimal weight:    0.4980
   chunk 43 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 199 optimal weight:    1.9990
   chunk 167 optimal weight:    0.6980
   chunk 177 optimal weight:    4.9990
   chunk 149 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** H  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 126 GLN
E 213 GLN
** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.188480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.148277 restraints weight = 20713.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 3.06
r_work: 0.3055 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3052
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3052
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  18164  Z= 0.176
  Angle     :  0.597   8.670  24639  Z= 0.310
  Chirality :  0.044   0.207   2791
  Planarity :  0.004   0.051   3081
  Dihedral  :  4.443  18.163   2401
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 12.59 %
    Favored  : 85.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.18), residues: 2148
  helix:  2.10 (0.16), residues: 980
  sheet:  0.68 (0.25), residues: 426
  loop : -1.43 (0.22), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D 350 
 HIS   0.004   0.001   HIS B 257 
 PHE   0.017   0.001   PHE B 315 
 TYR   0.019   0.001   TYR H 106 
 ARG   0.010   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05546 ( 1053)
  hydrogen bonds       : angle       4.64910 ( 3072)
  SS BOND              : bond        0.00126 (    4)
  SS BOND              : angle       0.90970 (    8)
  covalent geometry    : bond        0.00409 (18160)
  covalent geometry    : angle       0.59719 (24631)

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  428 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 384
  time to evaluate  : 2.059 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8067 (pt0)
REVERT: L  108 LYS cc_start: 0.3997 (mmtt) cc_final: 0.3151 (mmtt)
REVERT: F   49 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8267 (tm-30)
REVERT: A  216 ARG cc_start: 0.7897 (mmm-85) cc_final: 0.7330 (mtp85)
REVERT: A  267 THR cc_start: 0.8800 (t) cc_final: 0.8470 (t)
REVERT: A  270 ASP cc_start: 0.7191 (m-30) cc_final: 0.6724 (m-30)
REVERT: A  275 LEU cc_start: 0.8139 (mt) cc_final: 0.7769 (mt)
REVERT: D  186 GLU cc_start: 0.8415 (tt0) cc_final: 0.8158 (tt0)
REVERT: D  243 ILE cc_start: 0.8798 (mm) cc_final: 0.8498 (mm)
REVERT: D  260 GLN cc_start: 0.7944 (mt0) cc_final: 0.7593 (tt0)
REVERT: E   30 GLU cc_start: 0.6168 (pm20) cc_final: 0.5848 (pm20)
REVERT: E   96 ARG cc_start: 0.6969 (ttp80) cc_final: 0.6333 (ttt180)
REVERT: E  141 GLU cc_start: 0.5921 (tt0) cc_final: 0.5716 (tt0)
REVERT: E  155 ARG cc_start: 0.6169 (mtp-110) cc_final: 0.5777 (mtp180)
REVERT: E  198 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6609 (mt-10)
REVERT: E  341 MET cc_start: 0.6357 (mtt) cc_final: 0.5940 (mtp)
  outliers start: 44
  outliers final: 36
  residues processed: 404
  average time/residue: 0.2754
  time to fit residues: 169.6085
Evaluate side-chains
  398 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 361
  time to evaluate  : 1.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue   34 VAL
Chi-restraints excluded: chain G residue   48 LEU
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue  157 ASN
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  265 VAL
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  183 VAL
Chi-restraints excluded: chain E residue  289 GLU
Chi-restraints excluded: chain E residue  299 THR
Chi-restraints excluded: chain E residue  310 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 120 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0370
   chunk 189 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0030
   chunk 27 optimal weight:    0.0040
   chunk 110 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 78 optimal weight:    0.3980
   chunk 150 optimal weight:    0.8980
   overall best weight:    0.2680

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

Flipped N/Q/H residues before XYZ refinement:
** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 213 GLN
** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 213 GLN
** E 288 ASN ** 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 = 0.3923 r_free = 0.3923 target = 0.187781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.146892 restraints weight = 20877.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 2.81
r_work: 0.3107 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3083
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3083
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  18164  Z= 0.128
  Angle     :  0.557   8.847  24639  Z= 0.289
  Chirality :  0.042   0.227   2791
  Planarity :  0.004   0.071   3081
  Dihedral  :  4.282  17.524   2401
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.64 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.19), residues: 2148
  helix:  2.30 (0.16), residues: 981
  sheet:  0.73 (0.25), residues: 434
  loop : -1.38 (0.23), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 350 
 HIS   0.004   0.001   HIS H  38 
 PHE   0.016   0.001   PHE F  71 
 TYR   0.013   0.001   TYR H 106 
 ARG   0.006   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05048 ( 1053)
  hydrogen bonds       : angle       4.46646 ( 3072)
  SS BOND              : bond        0.00171 (    4)
  SS BOND              : angle       0.49648 (    8)
  covalent geometry    : bond        0.00271 (18160)
  covalent geometry    : angle       0.55729 (24631)

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  428 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 384
  time to evaluate  : 1.850 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8097 (pt0)
REVERT: L  108 LYS cc_start: 0.3946 (mmtt) cc_final: 0.3287 (mmtt)
REVERT: F   30 PHE cc_start: 0.8467 (p90) cc_final: 0.8196 (p90)
REVERT: F   49 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8261 (tm-30)
REVERT: A  126 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7259 (tp40)
REVERT: A  216 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7294 (mtp85)
REVERT: A  267 THR cc_start: 0.8827 (t) cc_final: 0.8387 (m)
REVERT: A  270 ASP cc_start: 0.7085 (m-30) cc_final: 0.6771 (m-30)
REVERT: A  275 LEU cc_start: 0.8162 (mt) cc_final: 0.7851 (mt)
REVERT: A  286 LYS cc_start: 0.7784 (mtmm) cc_final: 0.7551 (ptpp)
REVERT: B  334 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.6233 (ttt)
REVERT: C   91 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7774 (mm)
REVERT: C  291 MET cc_start: 0.7904 (tpp) cc_final: 0.7701 (tpp)
REVERT: D  155 ARG cc_start: 0.8623 (mtt180) cc_final: 0.8379 (mtt180)
REVERT: D  198 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6330 (tt0)
REVERT: D  243 ILE cc_start: 0.8713 (mm) cc_final: 0.8480 (mm)
REVERT: D  260 GLN cc_start: 0.7926 (mt0) cc_final: 0.7630 (tt0)
REVERT: D  344 TYR cc_start: 0.5528 (OUTLIER) cc_final: 0.2737 (p90)
REVERT: E   30 GLU cc_start: 0.6220 (pm20) cc_final: 0.5905 (pm20)
REVERT: E  141 GLU cc_start: 0.5981 (tt0) cc_final: 0.5759 (tt0)
REVERT: E  155 ARG cc_start: 0.6160 (mtp-110) cc_final: 0.5784 (mtp-110)
REVERT: E  184 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7657 (mp)
REVERT: E  341 MET cc_start: 0.6321 (mtt) cc_final: 0.5985 (mtp)
  outliers start: 44
  outliers final: 34
  residues processed: 407
  average time/residue: 0.2726
  time to fit residues: 170.1485
Evaluate side-chains
  407 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 368
  time to evaluate  : 1.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   61 THR
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue   34 VAL
Chi-restraints excluded: chain G residue   48 LEU
Chi-restraints excluded: chain F residue    5 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain D residue  344 TYR
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  289 GLU
Chi-restraints excluded: chain E residue  299 THR
Chi-restraints excluded: chain E residue  310 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 86 optimal weight:    0.5980
   chunk 99 optimal weight:    0.6980
   chunk 170 optimal weight:    0.7980
   chunk 137 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 205 optimal weight:    0.5980
   chunk 128 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** H  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 126 GLN
A 260 GLN
** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 213 GLN
** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.187065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.146260 restraints weight = 21026.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 3.44
r_work: 0.3049 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3028
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3028 r_free = 0.3028    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3027
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  18164  Z= 0.169
  Angle     :  0.587   8.613  24639  Z= 0.302
  Chirality :  0.044   0.240   2791
  Planarity :  0.004   0.069   3081
  Dihedral  :  4.313  16.804   2401
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 15.35 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.18), residues: 2148
  helix:  2.20 (0.16), residues: 980
  sheet:  0.67 (0.25), residues: 428
  loop : -1.39 (0.23), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 350 
 HIS   0.004   0.001   HIS B 257 
 PHE   0.023   0.001   PHE A  39 
 TYR   0.019   0.001   TYR H 106 
 ARG   0.010   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05265 ( 1053)
  hydrogen bonds       : angle       4.48140 ( 3072)
  SS BOND              : bond        0.00125 (    4)
  SS BOND              : angle       0.79546 (    8)
  covalent geometry    : bond        0.00393 (18160)
  covalent geometry    : angle       0.58655 (24631)

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  433 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 366
  time to evaluate  : 2.046 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8073 (pt0)
REVERT: L  108 LYS cc_start: 0.4094 (mmtt) cc_final: 0.3319 (mmtt)
REVERT: F   30 PHE cc_start: 0.8508 (p90) cc_final: 0.8214 (p90)
REVERT: F   49 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8241 (tm-30)
REVERT: A  126 GLN cc_start: 0.7885 (tm130) cc_final: 0.6996 (tp40)
REVERT: A  216 ARG cc_start: 0.7884 (mmm-85) cc_final: 0.7307 (mtp85)
REVERT: A  267 THR cc_start: 0.8886 (t) cc_final: 0.8365 (m)
REVERT: A  270 ASP cc_start: 0.7438 (m-30) cc_final: 0.6952 (m-30)
REVERT: B  334 MET cc_start: 0.6531 (OUTLIER) cc_final: 0.6290 (ttp)
REVERT: C  204 GLU cc_start: 0.5197 (OUTLIER) cc_final: 0.4610 (mm-30)
REVERT: D  122 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8455 (pp)
REVERT: D  198 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6402 (tt0)
REVERT: D  243 ILE cc_start: 0.8766 (mm) cc_final: 0.8483 (mm)
REVERT: D  344 TYR cc_start: 0.5435 (OUTLIER) cc_final: 0.2207 (p90)
REVERT: D  345 PHE cc_start: 0.6304 (OUTLIER) cc_final: 0.5978 (m-10)
REVERT: E   30 GLU cc_start: 0.6217 (pm20) cc_final: 0.5868 (pm20)
REVERT: E  100 GLU cc_start: 0.6235 (mt-10) cc_final: 0.5584 (mt-10)
REVERT: E  155 ARG cc_start: 0.6176 (mtp-110) cc_final: 0.5793 (mtp-110)
REVERT: E  184 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7653 (mp)
REVERT: E  224 THR cc_start: 0.8549 (t) cc_final: 0.8233 (p)
REVERT: E  291 MET cc_start: 0.8524 (mmm) cc_final: 0.8181 (tpt)
REVERT: E  341 MET cc_start: 0.6273 (mtt) cc_final: 0.5905 (mtp)
  outliers start: 67
  outliers final: 45
  residues processed: 406
  average time/residue: 0.2664
  time to fit residues: 167.4622
Evaluate side-chains
  400 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 348
  time to evaluate  : 2.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   61 THR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue   34 VAL
Chi-restraints excluded: chain G residue   48 LEU
Chi-restraints excluded: chain F residue    5 VAL
Chi-restraints excluded: chain F residue   54 ILE
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  204 GLU
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  265 VAL
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain D residue  344 TYR
Chi-restraints excluded: chain D residue  345 PHE
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  289 GLU
Chi-restraints excluded: chain E residue  299 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 23 optimal weight:    0.0010
   chunk 75 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 167 optimal weight:    0.7980
   chunk 161 optimal weight:    0.5980
   chunk 175 optimal weight:    0.9980
   chunk 151 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.6586

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

Flipped N/Q/H residues before XYZ refinement:
** H  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 213 GLN
** E 288 ASN ** 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 = 0.3907 r_free = 0.3907 target = 0.186110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.145336 restraints weight = 20939.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 3.22
r_work: 0.3046 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3023
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3023 r_free = 0.3023    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3023 r_free = 0.3023    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3023
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  18164  Z= 0.167
  Angle     :  0.587   8.642  24639  Z= 0.302
  Chirality :  0.044   0.255   2791
  Planarity :  0.004   0.048   3081
  Dihedral  :  4.313  16.954   2401
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.50 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.18), residues: 2148
  helix:  2.18 (0.16), residues: 980
  sheet:  0.67 (0.25), residues: 428
  loop : -1.40 (0.23), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 350 
 HIS   0.004   0.001   HIS B 257 
 PHE   0.019   0.001   PHE A  39 
 TYR   0.019   0.001   TYR H 106 
 ARG   0.007   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05243 ( 1053)
  hydrogen bonds       : angle       4.46020 ( 3072)
  SS BOND              : bond        0.00131 (    4)
  SS BOND              : angle       0.68449 (    8)
  covalent geometry    : bond        0.00388 (18160)
  covalent geometry    : angle       0.58694 (24631)

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  422 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 359
  time to evaluate  : 2.072 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8053 (pt0)
REVERT: L  108 LYS cc_start: 0.4095 (mmtt) cc_final: 0.3307 (mmtt)
REVERT: F   30 PHE cc_start: 0.8510 (p90) cc_final: 0.8215 (p90)
REVERT: F   49 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8241 (tm-30)
REVERT: F   89 LEU cc_start: 0.7255 (mm) cc_final: 0.7047 (mt)
REVERT: A  126 GLN cc_start: 0.7875 (tm130) cc_final: 0.7510 (tm-30)
REVERT: A  216 ARG cc_start: 0.7895 (mmm-85) cc_final: 0.7315 (mtp85)
REVERT: A  267 THR cc_start: 0.8881 (t) cc_final: 0.8495 (t)
REVERT: A  270 ASP cc_start: 0.7435 (m-30) cc_final: 0.6961 (m-30)
REVERT: B  232 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8480 (mm)
REVERT: B  334 MET cc_start: 0.6558 (OUTLIER) cc_final: 0.6294 (ttp)
REVERT: C  204 GLU cc_start: 0.5196 (OUTLIER) cc_final: 0.4635 (mm-30)
REVERT: D  122 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8363 (pp)
REVERT: D  198 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6349 (tt0)
REVERT: D  243 ILE cc_start: 0.8763 (mm) cc_final: 0.8496 (mm)
REVERT: D  344 TYR cc_start: 0.5390 (OUTLIER) cc_final: 0.2398 (p90)
REVERT: D  345 PHE cc_start: 0.6414 (OUTLIER) cc_final: 0.6062 (m-10)
REVERT: E   30 GLU cc_start: 0.6253 (pm20) cc_final: 0.5906 (pm20)
REVERT: E  100 GLU cc_start: 0.6257 (mt-10) cc_final: 0.5608 (mt-10)
REVERT: E  155 ARG cc_start: 0.6197 (mtp-110) cc_final: 0.5811 (mtp-110)
REVERT: E  184 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7684 (mp)
REVERT: E  318 MET cc_start: 0.5915 (tmt) cc_final: 0.5711 (tmt)
REVERT: E  341 MET cc_start: 0.6260 (mtt) cc_final: 0.5870 (mtp)
  outliers start: 63
  outliers final: 48
  residues processed: 393
  average time/residue: 0.2752
  time to fit residues: 167.6532
Evaluate side-chains
  405 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 349
  time to evaluate  : 1.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   61 THR
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue   34 VAL
Chi-restraints excluded: chain G residue   48 LEU
Chi-restraints excluded: chain F residue    5 VAL
Chi-restraints excluded: chain F residue   54 ILE
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  204 GLU
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  157 ASN
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  233 SER
Chi-restraints excluded: chain D residue  265 VAL
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain D residue  344 TYR
Chi-restraints excluded: chain D residue  345 PHE
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  289 GLU
Chi-restraints excluded: chain E residue  299 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 52 optimal weight:    0.1980
   chunk 126 optimal weight:    0.9990
   chunk 160 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 58 optimal weight:    0.6980
   chunk 54 optimal weight:    6.9990
   chunk 154 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0570
   chunk 166 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
** H  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 213 GLN
** E 288 ASN ** 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 = 0.3914 r_free = 0.3914 target = 0.186780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.147260 restraints weight = 20934.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 3.08
r_work: 0.3050 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3047
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  18164  Z= 0.152
  Angle     :  0.582   8.537  24639  Z= 0.298
  Chirality :  0.043   0.268   2791
  Planarity :  0.004   0.048   3081
  Dihedral  :  4.292  16.522   2401
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.75 %
    Favored  : 79.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.18), residues: 2148
  helix:  2.19 (0.16), residues: 980
  sheet:  0.67 (0.25), residues: 428
  loop : -1.38 (0.23), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 350 
 HIS   0.003   0.001   HIS H  38 
 PHE   0.016   0.001   PHE A  39 
 TYR   0.017   0.001   TYR H 106 
 ARG   0.005   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05139 ( 1053)
  hydrogen bonds       : angle       4.42029 ( 3072)
  SS BOND              : bond        0.00195 (    4)
  SS BOND              : angle       1.19447 (    8)
  covalent geometry    : bond        0.00348 (18160)
  covalent geometry    : angle       0.58142 (24631)

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  424 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 359
  time to evaluate  : 1.836 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8058 (pt0)
REVERT: L  108 LYS cc_start: 0.4196 (mmtt) cc_final: 0.3399 (mmtt)
REVERT: F   30 PHE cc_start: 0.8525 (p90) cc_final: 0.8231 (p90)
REVERT: F   49 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8258 (tm-30)
REVERT: A   32 MET cc_start: 0.8223 (mtt) cc_final: 0.7915 (mtt)
REVERT: A  189 ASP cc_start: 0.8797 (t0) cc_final: 0.8424 (t0)
REVERT: A  216 ARG cc_start: 0.7869 (mmm-85) cc_final: 0.7292 (mtp85)
REVERT: A  267 THR cc_start: 0.8896 (t) cc_final: 0.8529 (t)
REVERT: A  270 ASP cc_start: 0.7457 (m-30) cc_final: 0.7014 (m-30)
REVERT: A  318 MET cc_start: 0.8201 (tmm) cc_final: 0.7916 (tmm)
REVERT: B  232 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8481 (mm)
REVERT: B  334 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.6302 (ttp)
REVERT: C  204 GLU cc_start: 0.5207 (OUTLIER) cc_final: 0.4729 (mp0)
REVERT: D  122 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8377 (pp)
REVERT: D  155 ARG cc_start: 0.8663 (mtt180) cc_final: 0.8378 (mtt180)
REVERT: D  198 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6343 (tt0)
REVERT: D  243 ILE cc_start: 0.8745 (mm) cc_final: 0.8479 (mm)
REVERT: D  344 TYR cc_start: 0.5462 (OUTLIER) cc_final: 0.2429 (p90)
REVERT: D  345 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.6160 (m-10)
REVERT: E   30 GLU cc_start: 0.6308 (pm20) cc_final: 0.5973 (pm20)
REVERT: E  155 ARG cc_start: 0.6195 (mtp-110) cc_final: 0.5801 (mtp-110)
REVERT: E  184 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7721 (mp)
REVERT: E  341 MET cc_start: 0.6363 (mtt) cc_final: 0.6002 (mtp)
  outliers start: 65
  outliers final: 52
  residues processed: 393
  average time/residue: 0.2823
  time to fit residues: 171.5139
Evaluate side-chains
  409 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 349
  time to evaluate  : 2.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   61 THR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue   34 VAL
Chi-restraints excluded: chain G residue   48 LEU
Chi-restraints excluded: chain G residue   91 GLN
Chi-restraints excluded: chain F residue    5 VAL
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  334 MET
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  204 GLU
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  157 ASN
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  233 SER
Chi-restraints excluded: chain D residue  265 VAL
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain D residue  313 MET
Chi-restraints excluded: chain D residue  344 TYR
Chi-restraints excluded: chain D residue  345 PHE
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  289 GLU
Chi-restraints excluded: chain E residue  299 THR
Chi-restraints excluded: chain E residue  310 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0770
   chunk 201 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 200 optimal weight:    1.9990
   chunk 114 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0470
   chunk 17 optimal weight:    0.9990
   chunk 94 optimal weight:    0.4980
   chunk 131 optimal weight:    1.9990
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 213 GLN
** E 288 ASN ** 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 = 0.3922 r_free = 0.3922 target = 0.187546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.148756 restraints weight = 20870.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 3.08
r_work: 0.3039 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3039
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3039
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  18164  Z= 0.144
  Angle     :  0.583   8.754  24639  Z= 0.298
  Chirality :  0.043   0.290   2791
  Planarity :  0.004   0.059   3081
  Dihedral  :  4.271  16.198   2401
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 17.35 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.18), residues: 2148
  helix:  2.20 (0.16), residues: 982
  sheet:  0.72 (0.25), residues: 422
  loop : -1.37 (0.22), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 350 
 HIS   0.003   0.001   HIS H  38 
 PHE   0.023   0.001   PHE F  71 
 TYR   0.016   0.001   TYR H 106 
 ARG   0.014   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05035 ( 1053)
  hydrogen bonds       : angle       4.37753 ( 3072)
  SS BOND              : bond        0.00167 (    4)
  SS BOND              : angle       0.98485 (    8)
  covalent geometry    : bond        0.00326 (18160)
  covalent geometry    : angle       0.58310 (24631)

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  419 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 356
  time to evaluate  : 1.882 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8129 (pt0)
REVERT: L  108 LYS cc_start: 0.4206 (mmtt) cc_final: 0.3422 (mmtt)
REVERT: F   30 PHE cc_start: 0.8538 (p90) cc_final: 0.8246 (p90)
REVERT: F   49 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8332 (tm-30)
REVERT: A   40 ARG cc_start: 0.6746 (ttt-90) cc_final: 0.6545 (tmt170)
REVERT: A  216 ARG cc_start: 0.7877 (mmm-85) cc_final: 0.7320 (mtp85)
REVERT: A  267 THR cc_start: 0.8900 (t) cc_final: 0.8544 (t)
REVERT: A  270 ASP cc_start: 0.7432 (m-30) cc_final: 0.6977 (m-30)
REVERT: A  318 MET cc_start: 0.8136 (tmm) cc_final: 0.7834 (tmm)
REVERT: B  232 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8481 (mm)
REVERT: C  204 GLU cc_start: 0.5202 (OUTLIER) cc_final: 0.4708 (mp0)
REVERT: D  122 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8372 (pp)
REVERT: D  198 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6328 (tt0)
REVERT: D  243 ILE cc_start: 0.8739 (mm) cc_final: 0.8500 (mm)
REVERT: D  344 TYR cc_start: 0.5604 (OUTLIER) cc_final: 0.2580 (p90)
REVERT: D  345 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.6178 (m-10)
REVERT: E   30 GLU cc_start: 0.6324 (pm20) cc_final: 0.6067 (pm20)
REVERT: E  100 GLU cc_start: 0.6315 (mt-10) cc_final: 0.5699 (mt-10)
REVERT: E  155 ARG cc_start: 0.6193 (mtp-110) cc_final: 0.5801 (mtp-110)
REVERT: E  341 MET cc_start: 0.6392 (mtt) cc_final: 0.5956 (mtp)
  outliers start: 63
  outliers final: 49
  residues processed: 390
  average time/residue: 0.2700
  time to fit residues: 161.4934
Evaluate side-chains
  403 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 348
  time to evaluate  : 1.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   61 THR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue   34 VAL
Chi-restraints excluded: chain G residue   48 LEU
Chi-restraints excluded: chain G residue   91 GLN
Chi-restraints excluded: chain F residue    5 VAL
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  204 GLU
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  233 SER
Chi-restraints excluded: chain D residue  265 VAL
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain D residue  313 MET
Chi-restraints excluded: chain D residue  344 TYR
Chi-restraints excluded: chain D residue  345 PHE
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  289 GLU
Chi-restraints excluded: chain E residue  299 THR
Chi-restraints excluded: chain E residue  310 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 66 optimal weight:    0.0040
   chunk 206 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 129 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 126 optimal weight:    1.9990
   chunk 183 optimal weight:    0.9990
   chunk 155 optimal weight:    0.9990
   chunk 109 optimal weight:   10.0000
   chunk 164 optimal weight:    0.0470
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.4890

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

Flipped N/Q/H residues before XYZ refinement:
** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 213 GLN
** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.188869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.150720 restraints weight = 20905.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 3.10
r_work: 0.3044 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.1593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  18164  Z= 0.147
  Angle     :  0.588   8.657  24639  Z= 0.300
  Chirality :  0.043   0.307   2791
  Planarity :  0.004   0.050   3081
  Dihedral  :  4.246  15.911   2401
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 17.75 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.18), residues: 2148
  helix:  2.19 (0.16), residues: 982
  sheet:  0.73 (0.25), residues: 422
  loop : -1.35 (0.23), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 350 
 HIS   0.003   0.001   HIS H  38 
 PHE   0.018   0.001   PHE F  71 
 TYR   0.016   0.001   TYR H 106 
 ARG   0.011   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05032 ( 1053)
  hydrogen bonds       : angle       4.37339 ( 3072)
  SS BOND              : bond        0.00173 (    4)
  SS BOND              : angle       0.95247 (    8)
  covalent geometry    : bond        0.00336 (18160)
  covalent geometry    : angle       0.58783 (24631)

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  420 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 360
  time to evaluate  : 1.942 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8055 (pt0)
REVERT: L  108 LYS cc_start: 0.4183 (mmtt) cc_final: 0.3406 (mmtt)
REVERT: F   30 PHE cc_start: 0.8529 (p90) cc_final: 0.8244 (p90)
REVERT: A  216 ARG cc_start: 0.7877 (mmm-85) cc_final: 0.7318 (mtp85)
REVERT: A  267 THR cc_start: 0.8901 (t) cc_final: 0.8545 (t)
REVERT: A  270 ASP cc_start: 0.7440 (m-30) cc_final: 0.7005 (m-30)
REVERT: A  291 MET cc_start: 0.7158 (mmp) cc_final: 0.6890 (mmp)
REVERT: A  318 MET cc_start: 0.8125 (tmm) cc_final: 0.7801 (tmm)
REVERT: B  232 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8484 (mm)
REVERT: C  204 GLU cc_start: 0.5205 (OUTLIER) cc_final: 0.4704 (mp0)
REVERT: D  122 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8379 (pp)
REVERT: D  198 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6334 (tt0)
REVERT: D  243 ILE cc_start: 0.8740 (mm) cc_final: 0.8506 (mm)
REVERT: D  344 TYR cc_start: 0.5496 (OUTLIER) cc_final: 0.2532 (p90)
REVERT: D  345 PHE cc_start: 0.6467 (OUTLIER) cc_final: 0.6139 (m-10)
REVERT: E   30 GLU cc_start: 0.6310 (pm20) cc_final: 0.6038 (pm20)
REVERT: E  100 GLU cc_start: 0.6270 (mt-10) cc_final: 0.5645 (mt-10)
REVERT: E  155 ARG cc_start: 0.6179 (mtp-110) cc_final: 0.5804 (mtp-110)
REVERT: E  341 MET cc_start: 0.6327 (mtt) cc_final: 0.5934 (mtp)
  outliers start: 60
  outliers final: 51
  residues processed: 392
  average time/residue: 0.2712
  time to fit residues: 165.1435
Evaluate side-chains
  405 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 348
  time to evaluate  : 1.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   61 THR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue   34 VAL
Chi-restraints excluded: chain G residue   48 LEU
Chi-restraints excluded: chain G residue   91 GLN
Chi-restraints excluded: chain F residue    5 VAL
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  204 GLU
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  233 SER
Chi-restraints excluded: chain D residue  265 VAL
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain D residue  313 MET
Chi-restraints excluded: chain D residue  344 TYR
Chi-restraints excluded: chain D residue  345 PHE
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  289 GLU
Chi-restraints excluded: chain E residue  299 THR
Chi-restraints excluded: chain E residue  310 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 201 optimal weight:    0.0970
   chunk 133 optimal weight:    0.0980
   chunk 171 optimal weight:    0.9980
   chunk 211 optimal weight:    5.9990
   chunk 138 optimal weight:    0.7980
   chunk 113 optimal weight:    1.9990
   chunk 154 optimal weight:    0.5980
   chunk 172 optimal weight:    1.9990
   chunk 69 optimal weight:    0.4980
   chunk 27 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
E 213 GLN
** E 288 ASN ** 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 = 0.3917 r_free = 0.3917 target = 0.187144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.148591 restraints weight = 20892.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 3.11
r_work: 0.3050 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3046
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  18164  Z= 0.139
  Angle     :  0.588  11.683  24639  Z= 0.299
  Chirality :  0.043   0.318   2791
  Planarity :  0.004   0.047   3081
  Dihedral  :  4.216  15.742   2401
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 18.41 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.19), residues: 2148
  helix:  2.20 (0.16), residues: 981
  sheet:  0.75 (0.25), residues: 422
  loop : -1.34 (0.23), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D 350 
 HIS   0.003   0.001   HIS H  38 
 PHE   0.017   0.001   PHE F  71 
 TYR   0.015   0.001   TYR H 106 
 ARG   0.011   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04891 ( 1053)
  hydrogen bonds       : angle       4.32912 ( 3072)
  SS BOND              : bond        0.00167 (    4)
  SS BOND              : angle       0.85842 (    8)
  covalent geometry    : bond        0.00312 (18160)
  covalent geometry    : angle       0.58817 (24631)

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  406 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 351
  time to evaluate  : 1.835 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8065 (pt0)
REVERT: L  108 LYS cc_start: 0.4122 (mmtt) cc_final: 0.3384 (mmtt)
REVERT: F   30 PHE cc_start: 0.8530 (p90) cc_final: 0.8271 (p90)
REVERT: A  216 ARG cc_start: 0.7872 (mmm-85) cc_final: 0.7306 (mtp85)
REVERT: A  267 THR cc_start: 0.8888 (t) cc_final: 0.8513 (t)
REVERT: A  270 ASP cc_start: 0.7324 (m-30) cc_final: 0.6848 (m-30)
REVERT: A  275 LEU cc_start: 0.8204 (mt) cc_final: 0.7852 (mt)
REVERT: A  294 LEU cc_start: 0.8778 (tp) cc_final: 0.8501 (tp)
REVERT: A  318 MET cc_start: 0.8167 (tmm) cc_final: 0.7844 (tmm)
REVERT: B  232 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8487 (mm)
REVERT: C   91 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8146 (mm)
REVERT: C  204 GLU cc_start: 0.5193 (OUTLIER) cc_final: 0.4700 (mp0)
REVERT: C  291 MET cc_start: 0.7907 (tpp) cc_final: 0.7695 (tpp)
REVERT: D  122 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8365 (pp)
REVERT: D  198 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6332 (tt0)
REVERT: D  243 ILE cc_start: 0.8722 (mm) cc_final: 0.8515 (mm)
REVERT: D  344 TYR cc_start: 0.5497 (OUTLIER) cc_final: 0.2546 (p90)
REVERT: D  345 PHE cc_start: 0.6418 (OUTLIER) cc_final: 0.6117 (m-10)
REVERT: E   30 GLU cc_start: 0.6376 (pm20) cc_final: 0.6080 (pm20)
REVERT: E  100 GLU cc_start: 0.6283 (mt-10) cc_final: 0.5659 (mt-10)
REVERT: E  155 ARG cc_start: 0.6176 (mtp-110) cc_final: 0.5800 (mtp-110)
REVERT: E  341 MET cc_start: 0.6342 (mtt) cc_final: 0.5919 (mtp)
  outliers start: 55
  outliers final: 48
  residues processed: 379
  average time/residue: 0.2667
  time to fit residues: 159.3310
Evaluate side-chains
  400 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 345
  time to evaluate  : 2.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   61 THR
Chi-restraints excluded: chain H residue   96 VAL
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain G residue   34 VAL
Chi-restraints excluded: chain G residue   48 LEU
Chi-restraints excluded: chain G residue   91 GLN
Chi-restraints excluded: chain F residue    5 VAL
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  204 GLU
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  157 ASN
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  233 SER
Chi-restraints excluded: chain D residue  265 VAL
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain D residue  313 MET
Chi-restraints excluded: chain D residue  344 TYR
Chi-restraints excluded: chain D residue  345 PHE
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  289 GLU
Chi-restraints excluded: chain E residue  310 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 188 optimal weight:    0.7980
   chunk 113 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   chunk 122 optimal weight:    3.9990
   chunk 127 optimal weight:    0.9980
   chunk 202 optimal weight:    1.9990
   chunk 186 optimal weight:    2.9990
   chunk 142 optimal weight:    3.9990
   chunk 152 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** H  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 257 HIS
** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
E 213 GLN
** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.186349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.148044 restraints weight = 20824.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 3.10
r_work: 0.3007 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3001
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3001
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  18164  Z= 0.198
  Angle     :  0.628  10.023  24639  Z= 0.321
  Chirality :  0.045   0.296   2791
  Planarity :  0.004   0.047   3081
  Dihedral  :  4.352  19.107   2401
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 18.25 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.18), residues: 2148
  helix:  2.02 (0.16), residues: 981
  sheet:  0.65 (0.25), residues: 426
  loop : -1.42 (0.22), residues: 741

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP D 350 
 HIS   0.004   0.001   HIS B 257 
 PHE   0.019   0.001   PHE C 301 
 TYR   0.022   0.002   TYR H 106 
 ARG   0.017   0.001   ARG D 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05319 ( 1053)
  hydrogen bonds       : angle       4.46523 ( 3072)
  SS BOND              : bond        0.00157 (    4)
  SS BOND              : angle       1.23102 (    8)
  covalent geometry    : bond        0.00471 (18160)
  covalent geometry    : angle       0.62778 (24631)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9126.27 seconds
wall clock time: 158 minutes 47.70 seconds (9527.70 seconds total)