Starting phenix.real_space_refine
on Sat Oct 11 23:21:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tmk_41392/10_2025/8tmk_41392.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tmk_41392/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tmk_41392/10_2025/8tmk_41392.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tmk_41392/10_2025/8tmk_41392.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tmk_41392/10_2025/8tmk_41392.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tmk_41392/10_2025/8tmk_41392.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 4.79, per 1000 atoms: 0.27
  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: 1.73
  Conformation dependent library (CDL) restraints added in 718.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.75
  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: 3.45

  Time building geometry restraints manager: 2.22 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:             4.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.040
  Process input model:                     18.760
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.690
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (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
 ARG   0.011   0.001   ARG B  75 
 TYR   0.023   0.002   TYR D 344 
 PHE   0.024   0.002   PHE B 315 
 TRP   0.028   0.001   TRP D 350 
 HIS   0.003   0.001   HIS E  68 

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

*********************** 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  : 0.718 
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: 0.1381
  time to fit residues: 83.9915
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  : 0.678 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.9980
   chunk 194 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.7980
   chunk 200 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3898 r_free = 0.3898 target = 0.185252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.144987 restraints weight = 20896.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 3.22
r_work: 0.3011 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3005
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3004
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.0825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  18164  Z= 0.201
  Angle     :  0.632   8.608  24639  Z= 0.329
  Chirality :  0.045   0.211   2791
  Planarity :  0.005   0.067   3081
  Dihedral  :  4.576  30.402   2403
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  9.93 %
    Favored  : 88.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.18), residues: 2148
  helix:  1.95 (0.16), residues: 981
  sheet:  0.64 (0.24), residues: 446
  loop : -1.48 (0.23), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  75 
 TYR   0.023   0.002   TYR D 279 
 PHE   0.018   0.001   PHE B 315 
 TRP   0.023   0.001   TRP D 350 
 HIS   0.005   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (18160)
  covalent geometry    : angle       0.63202 (24631)
  SS BOND              : bond        0.00167 (    4)
  SS BOND              : angle       1.24666 (    8)
  hydrogen bonds       : bond        0.05885 ( 1053)
  hydrogen bonds       : angle       4.83381 ( 3072)

*********************** 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
  403 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 373
  time to evaluate  : 0.734 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8356 (pt0) cc_final: 0.8115 (pt0)
REVERT: L  108 LYS cc_start: 0.4189 (mmtt) cc_final: 0.3258 (mmtt)
REVERT: A  216 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7305 (mtp85)
REVERT: A  267 THR cc_start: 0.8730 (t) cc_final: 0.8400 (t)
REVERT: A  270 ASP cc_start: 0.7485 (m-30) cc_final: 0.7062 (m-30)
REVERT: A  292 LYS cc_start: 0.8057 (mmtt) cc_final: 0.7809 (mmtm)
REVERT: B  160 ILE cc_start: 0.8559 (mt) cc_final: 0.8241 (mm)
REVERT: D  121 GLU cc_start: 0.6993 (pm20) cc_final: 0.6623 (pm20)
REVERT: D  186 GLU cc_start: 0.8445 (tt0) cc_final: 0.8238 (tt0)
REVERT: D  243 ILE cc_start: 0.8807 (mm) cc_final: 0.8516 (mm)
REVERT: E   30 GLU cc_start: 0.6052 (pm20) cc_final: 0.5844 (pm20)
REVERT: E  155 ARG cc_start: 0.6170 (mtp-110) cc_final: 0.5751 (mtp-110)
  outliers start: 30
  outliers final: 23
  residues processed: 389
  average time/residue: 0.1407
  time to fit residues: 83.6348
Evaluate side-chains
  376 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 353
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
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   31 VAL
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 30 optimal weight:    0.8980
   chunk 143 optimal weight:    8.9990
   chunk 72 optimal weight:    0.5980
   chunk 195 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 4 optimal weight:    0.5980
   chunk 126 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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
E 126 GLN
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 = 0.3904 r_free = 0.3904 target = 0.185811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.146338 restraints weight = 21179.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 3.31
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3478
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3478
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.1043

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= 0.168
  Angle     :  0.593   8.610  24639  Z= 0.308
  Chirality :  0.044   0.213   2791
  Planarity :  0.004   0.052   3081
  Dihedral  :  4.434  18.051   2401
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 12.84 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.18), residues: 2148
  helix:  2.11 (0.16), residues: 980
  sheet:  0.67 (0.25), residues: 426
  loop : -1.42 (0.22), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  75 
 TYR   0.018   0.001   TYR H 106 
 PHE   0.016   0.001   PHE B 315 
 TRP   0.020   0.001   TRP D 350 
 HIS   0.004   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (18160)
  covalent geometry    : angle       0.59314 (24631)
  SS BOND              : bond        0.00131 (    4)
  SS BOND              : angle       0.85074 (    8)
  hydrogen bonds       : bond        0.05520 ( 1053)
  hydrogen bonds       : angle       4.65022 ( 3072)

*********************** 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
  424 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 384
  time to evaluate  : 0.668 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7811 (pt0)
REVERT: L  108 LYS cc_start: 0.3373 (mmtt) cc_final: 0.2783 (mmtt)
REVERT: F   49 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8252 (tm-30)
REVERT: A  216 ARG cc_start: 0.7555 (mmm-85) cc_final: 0.7180 (mtp85)
REVERT: A  267 THR cc_start: 0.8811 (t) cc_final: 0.8507 (t)
REVERT: A  270 ASP cc_start: 0.6632 (m-30) cc_final: 0.6278 (m-30)
REVERT: A  275 LEU cc_start: 0.7769 (mt) cc_final: 0.7452 (mt)
REVERT: D  186 GLU cc_start: 0.7835 (tt0) cc_final: 0.7588 (tt0)
REVERT: D  243 ILE cc_start: 0.8668 (mm) cc_final: 0.8344 (mm)
REVERT: E   96 ARG cc_start: 0.7249 (ttp80) cc_final: 0.6279 (ttt180)
REVERT: E  141 GLU cc_start: 0.5520 (tt0) cc_final: 0.5266 (tt0)
REVERT: E  155 ARG cc_start: 0.6185 (mtp-110) cc_final: 0.5902 (mtp180)
REVERT: E  341 MET cc_start: 0.6546 (mtt) cc_final: 0.6268 (mtp)
  outliers start: 40
  outliers final: 35
  residues processed: 403
  average time/residue: 0.1398
  time to fit residues: 86.3272
Evaluate side-chains
  396 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 360
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
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 A residue  125 GLU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  297 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   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  167 ASP
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 59 optimal weight:    0.9980
   chunk 170 optimal weight:    0.5980
   chunk 50 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 187 optimal weight:    0.9990
   chunk 173 optimal weight:    0.5980
   chunk 150 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 164 optimal weight:    3.9990
   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**
A 260 GLN
** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
D 260 GLN
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 = 0.3915 r_free = 0.3915 target = 0.186793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.146863 restraints weight = 21056.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 3.20
r_work: 0.3015 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3002
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3002
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.1190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  18164  Z= 0.186
  Angle     :  0.599   8.867  24639  Z= 0.311
  Chirality :  0.044   0.227   2791
  Planarity :  0.005   0.063   3081
  Dihedral  :  4.450  18.300   2401
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 14.29 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.18), residues: 2148
  helix:  2.09 (0.16), residues: 980
  sheet:  0.63 (0.25), residues: 426
  loop : -1.45 (0.22), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  75 
 TYR   0.020   0.001   TYR H 106 
 PHE   0.019   0.001   PHE F  71 
 TRP   0.019   0.001   TRP D 350 
 HIS   0.004   0.001   HIS B 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (18160)
  covalent geometry    : angle       0.59851 (24631)
  SS BOND              : bond        0.00147 (    4)
  SS BOND              : angle       0.89216 (    8)
  hydrogen bonds       : bond        0.05547 ( 1053)
  hydrogen bonds       : angle       4.61317 ( 3072)

*********************** 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
  431 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 372
  time to evaluate  : 0.700 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8128 (pt0)
REVERT: L  108 LYS cc_start: 0.4240 (mmtt) cc_final: 0.3409 (mmtt)
REVERT: F   49 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8272 (tm-30)
REVERT: A   39 PHE cc_start: 0.7239 (p90) cc_final: 0.6927 (p90)
REVERT: A  126 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7304 (tp40)
REVERT: A  216 ARG cc_start: 0.7909 (mmm-85) cc_final: 0.7349 (mtp85)
REVERT: A  267 THR cc_start: 0.8831 (t) cc_final: 0.8401 (m)
REVERT: A  270 ASP cc_start: 0.7267 (m-30) cc_final: 0.6777 (m-30)
REVERT: B  334 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.6401 (ttt)
REVERT: C   91 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7901 (mm)
REVERT: C  341 MET cc_start: 0.6086 (mmt) cc_final: 0.5773 (mmt)
REVERT: D  186 GLU cc_start: 0.8462 (tt0) cc_final: 0.8257 (tt0)
REVERT: D  198 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6401 (tt0)
REVERT: D  243 ILE cc_start: 0.8805 (mm) cc_final: 0.8497 (mm)
REVERT: D  344 TYR cc_start: 0.5435 (OUTLIER) cc_final: 0.2647 (p90)
REVERT: E  141 GLU cc_start: 0.6043 (tt0) cc_final: 0.5838 (tt0)
REVERT: E  155 ARG cc_start: 0.6198 (mtp-110) cc_final: 0.5806 (mtp-110)
REVERT: E  184 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7717 (mp)
REVERT: E  224 THR cc_start: 0.8523 (t) cc_final: 0.8187 (p)
REVERT: E  341 MET cc_start: 0.6413 (mtt) cc_final: 0.6062 (mtp)
  outliers start: 59
  outliers final: 46
  residues processed: 404
  average time/residue: 0.1358
  time to fit residues: 84.8309
Evaluate side-chains
  408 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 357
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
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 G residue  105 VAL
Chi-restraints excluded: chain F residue    5 VAL
Chi-restraints excluded: chain F residue   54 ILE
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  263 ASP
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  219 VAL
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  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  167 ASP
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  281 SER
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain D residue  307 ILE
Chi-restraints excluded: chain D residue  344 TYR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  183 VAL
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 187 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 186 optimal weight:    2.9990
   chunk 206 optimal weight:    0.9990
   chunk 190 optimal weight:    1.9990
   chunk 201 optimal weight:    3.9990
   chunk 99 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 152 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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
** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
D 260 GLN
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 = 0.3915 r_free = 0.3915 target = 0.186801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.145264 restraints weight = 20923.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 3.07
r_work: 0.3018 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2994
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2994
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  18164  Z= 0.205
  Angle     :  0.610   8.972  24639  Z= 0.316
  Chirality :  0.044   0.241   2791
  Planarity :  0.004   0.051   3081
  Dihedral  :  4.487  18.422   2401
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 15.30 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.18), residues: 2148
  helix:  2.00 (0.16), residues: 980
  sheet:  0.57 (0.25), residues: 435
  loop : -1.48 (0.22), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  67 
 TYR   0.022   0.002   TYR H 106 
 PHE   0.018   0.001   PHE F  71 
 TRP   0.020   0.001   TRP D 350 
 HIS   0.004   0.001   HIS D 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 (18160)
  covalent geometry    : angle       0.60976 (24631)
  SS BOND              : bond        0.00166 (    4)
  SS BOND              : angle       0.91722 (    8)
  hydrogen bonds       : bond        0.05652 ( 1053)
  hydrogen bonds       : angle       4.63030 ( 3072)

*********************** 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
  430 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 354
  time to evaluate  : 0.745 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8112 (pt0)
REVERT: L  108 LYS cc_start: 0.4184 (mmtt) cc_final: 0.3379 (mmtt)
REVERT: F   49 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8244 (tm-30)
REVERT: A   39 PHE cc_start: 0.7324 (p90) cc_final: 0.7036 (p90)
REVERT: A  126 GLN cc_start: 0.7962 (tm130) cc_final: 0.7259 (tp40)
REVERT: A  189 ASP cc_start: 0.8898 (t0) cc_final: 0.8426 (t0)
REVERT: A  216 ARG cc_start: 0.7924 (mmm-85) cc_final: 0.7341 (mtp85)
REVERT: A  270 ASP cc_start: 0.7329 (m-30) cc_final: 0.6862 (m-30)
REVERT: B  334 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6378 (ttp)
REVERT: C  204 GLU cc_start: 0.5252 (OUTLIER) cc_final: 0.4673 (mm-30)
REVERT: D  122 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8491 (pp)
REVERT: D  186 GLU cc_start: 0.8426 (tt0) cc_final: 0.8214 (tt0)
REVERT: D  198 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6376 (tt0)
REVERT: D  243 ILE cc_start: 0.8812 (mm) cc_final: 0.8488 (mm)
REVERT: D  344 TYR cc_start: 0.5421 (OUTLIER) cc_final: 0.2228 (p90)
REVERT: D  345 PHE cc_start: 0.6314 (OUTLIER) cc_final: 0.5990 (m-10)
REVERT: E  100 GLU cc_start: 0.6290 (mt-10) cc_final: 0.5614 (mt-10)
REVERT: E  141 GLU cc_start: 0.6056 (tt0) cc_final: 0.5847 (tt0)
REVERT: E  155 ARG cc_start: 0.6211 (mtp-110) cc_final: 0.5820 (mtp-110)
REVERT: E  184 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7707 (mp)
REVERT: E  291 MET cc_start: 0.8697 (mmm) cc_final: 0.8358 (tpt)
REVERT: E  341 MET cc_start: 0.6273 (mtt) cc_final: 0.5887 (mtp)
  outliers start: 76
  outliers final: 56
  residues processed: 396
  average time/residue: 0.1329
  time to fit residues: 81.7516
Evaluate side-chains
  410 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 347
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   32 VAL
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 G residue  105 VAL
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  263 ASP
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  180 ASP
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  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  167 ASP
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  183 VAL
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 113 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 105 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 166 optimal weight:    0.7980
   chunk 125 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** H  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
D 260 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 = 0.3929 r_free = 0.3929 target = 0.188040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.147202 restraints weight = 20655.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.94
r_work: 0.3053 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3053
-------------------------------------------------------------------------------
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 = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3052
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  18164  Z= 0.175
  Angle     :  0.594   8.745  24639  Z= 0.307
  Chirality :  0.044   0.251   2791
  Planarity :  0.004   0.050   3081
  Dihedral  :  4.430  17.660   2401
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 16.20 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.18), residues: 2148
  helix:  2.07 (0.16), residues: 979
  sheet:  0.58 (0.25), residues: 427
  loop : -1.44 (0.22), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  67 
 TYR   0.019   0.001   TYR H 106 
 PHE   0.016   0.001   PHE C 301 
 TRP   0.019   0.001   TRP D 350 
 HIS   0.003   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (18160)
  covalent geometry    : angle       0.59322 (24631)
  SS BOND              : bond        0.00343 (    4)
  SS BOND              : angle       1.19878 (    8)
  hydrogen bonds       : bond        0.05443 ( 1053)
  hydrogen bonds       : angle       4.56282 ( 3072)

*********************** 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
  433 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 365
  time to evaluate  : 0.532 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8073 (pt0)
REVERT: L  108 LYS cc_start: 0.4107 (mmtt) cc_final: 0.3214 (mmtt)
REVERT: F   49 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8190 (tm-30)
REVERT: F   89 LEU cc_start: 0.7270 (mm) cc_final: 0.7026 (mt)
REVERT: A   39 PHE cc_start: 0.7323 (p90) cc_final: 0.7048 (p90)
REVERT: A  216 ARG cc_start: 0.7890 (mmm-85) cc_final: 0.7311 (mtp85)
REVERT: A  267 THR cc_start: 0.8880 (t) cc_final: 0.8401 (m)
REVERT: A  270 ASP cc_start: 0.7248 (m-30) cc_final: 0.6764 (m-30)
REVERT: A  318 MET cc_start: 0.8141 (tmm) cc_final: 0.7839 (tmm)
REVERT: C  204 GLU cc_start: 0.5191 (OUTLIER) cc_final: 0.4649 (mm-30)
REVERT: D  122 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8370 (pp)
REVERT: D  186 GLU cc_start: 0.8396 (tt0) cc_final: 0.8116 (tt0)
REVERT: D  198 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6316 (tt0)
REVERT: D  243 ILE cc_start: 0.8763 (mm) cc_final: 0.8470 (mm)
REVERT: D  344 TYR cc_start: 0.5425 (OUTLIER) cc_final: 0.2467 (p90)
REVERT: D  345 PHE cc_start: 0.6469 (OUTLIER) cc_final: 0.6125 (m-10)
REVERT: E  100 GLU cc_start: 0.6250 (mt-10) cc_final: 0.5588 (mt-10)
REVERT: E  155 ARG cc_start: 0.6186 (mtp-110) cc_final: 0.5806 (mtp-110)
REVERT: E  184 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7684 (mp)
REVERT: E  341 MET cc_start: 0.6228 (mtt) cc_final: 0.5838 (mtp)
  outliers start: 68
  outliers final: 56
  residues processed: 400
  average time/residue: 0.1288
  time to fit residues: 80.3645
Evaluate side-chains
  417 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 355
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
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  105 VAL
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  263 ASP
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  180 ASP
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  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  157 ASN
Chi-restraints excluded: chain D residue  167 ASP
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  183 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 189 optimal weight:    2.9990
   chunk 181 optimal weight:    0.1980
   chunk 44 optimal weight:    3.9990
   chunk 157 optimal weight:    0.0570
   chunk 55 optimal weight:    5.9990
   chunk 177 optimal weight:    4.9990
   chunk 101 optimal weight:    0.3980
   chunk 196 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9980
   chunk 98 optimal weight:    1.9990
   chunk 167 optimal weight:    0.6980
   overall best weight:    0.4698

-------------------------------------------------------------------------------
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
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 = 0.3904 r_free = 0.3904 target = 0.185770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.146927 restraints weight = 21005.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 3.30
r_work: 0.3016 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3008
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    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 = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3008
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  18164  Z= 0.148
  Angle     :  0.586   8.962  24639  Z= 0.301
  Chirality :  0.043   0.259   2791
  Planarity :  0.004   0.050   3081
  Dihedral  :  4.368  17.076   2401
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 17.15 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.18), residues: 2148
  helix:  2.14 (0.16), residues: 980
  sheet:  0.62 (0.25), residues: 423
  loop : -1.40 (0.22), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 158 
 TYR   0.016   0.001   TYR H 106 
 PHE   0.015   0.001   PHE C 301 
 TRP   0.018   0.001   TRP D 350 
 HIS   0.004   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (18160)
  covalent geometry    : angle       0.58567 (24631)
  SS BOND              : bond        0.00164 (    4)
  SS BOND              : angle       0.96931 (    8)
  hydrogen bonds       : bond        0.05222 ( 1053)
  hydrogen bonds       : angle       4.48947 ( 3072)

*********************** 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
  428 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 359
  time to evaluate  : 0.557 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8171 (pt0)
REVERT: L  108 LYS cc_start: 0.4270 (mmtt) cc_final: 0.3327 (mmtt)
REVERT: F   30 PHE cc_start: 0.8568 (p90) cc_final: 0.8277 (p90)
REVERT: F   49 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8244 (tm-30)
REVERT: A   32 MET cc_start: 0.8226 (mtt) cc_final: 0.7897 (mtt)
REVERT: A  189 ASP cc_start: 0.8800 (t0) cc_final: 0.8455 (t0)
REVERT: A  216 ARG cc_start: 0.7883 (mmm-85) cc_final: 0.7327 (mtp85)
REVERT: A  267 THR cc_start: 0.8891 (t) cc_final: 0.8421 (m)
REVERT: A  270 ASP cc_start: 0.7367 (m-30) cc_final: 0.6895 (m-30)
REVERT: A  318 MET cc_start: 0.8178 (tmm) cc_final: 0.7855 (tmm)
REVERT: B  232 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8479 (mm)
REVERT: C  204 GLU cc_start: 0.5199 (OUTLIER) cc_final: 0.4607 (mm-30)
REVERT: D  122 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8399 (pp)
REVERT: D  198 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6312 (tt0)
REVERT: D  243 ILE cc_start: 0.8747 (mm) cc_final: 0.8486 (mm)
REVERT: D  276 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8175 (mt)
REVERT: D  344 TYR cc_start: 0.5442 (OUTLIER) cc_final: 0.2399 (p90)
REVERT: D  345 PHE cc_start: 0.6465 (OUTLIER) cc_final: 0.6128 (m-10)
REVERT: E  100 GLU cc_start: 0.6310 (mt-10) cc_final: 0.5688 (mt-10)
REVERT: E  155 ARG cc_start: 0.6188 (mtp-110) cc_final: 0.5796 (mtp-110)
REVERT: E  184 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7725 (mp)
REVERT: E  341 MET cc_start: 0.6348 (mtt) cc_final: 0.5956 (mtp)
  outliers start: 69
  outliers final: 55
  residues processed: 395
  average time/residue: 0.1292
  time to fit residues: 79.7030
Evaluate side-chains
  411 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 348
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
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  221 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  180 ASP
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  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  157 ASN
Chi-restraints excluded: chain D residue  167 ASP
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  276 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 D residue  345 PHE
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  183 VAL
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 65 optimal weight:    0.9980
   chunk 144 optimal weight:    0.0470
   chunk 78 optimal weight:    0.0370
   chunk 11 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 178 optimal weight:    0.9980
   chunk 127 optimal weight:    0.7980
   chunk 23 optimal weight:    8.9990
   chunk 92 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 162 optimal weight:    0.9990
   overall best weight:    0.5756

-------------------------------------------------------------------------------
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
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 = 0.185571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.146778 restraints weight = 20978.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 3.33
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3484
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3484 r_free = 0.3484    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3484 r_free = 0.3484    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3484
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.1530

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= 0.158
  Angle     :  0.594   8.885  24639  Z= 0.304
  Chirality :  0.044   0.294   2791
  Planarity :  0.004   0.049   3081
  Dihedral  :  4.345  16.746   2401
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 17.20 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.18), residues: 2148
  helix:  2.11 (0.16), residues: 981
  sheet:  0.64 (0.25), residues: 422
  loop : -1.41 (0.22), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  67 
 TYR   0.018   0.001   TYR H 106 
 PHE   0.026   0.001   PHE A  39 
 TRP   0.017   0.001   TRP D 350 
 HIS   0.003   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (18160)
  covalent geometry    : angle       0.59340 (24631)
  SS BOND              : bond        0.00162 (    4)
  SS BOND              : angle       0.98045 (    8)
  hydrogen bonds       : bond        0.05219 ( 1053)
  hydrogen bonds       : angle       4.47870 ( 3072)

*********************** 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
  432 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 357
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
REVERT: H    9 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7769 (pt0)
REVERT: L  108 LYS cc_start: 0.3469 (mmtt) cc_final: 0.2832 (mmtt)
REVERT: F   30 PHE cc_start: 0.8458 (p90) cc_final: 0.8235 (p90)
REVERT: F   49 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8240 (tm-30)
REVERT: A  216 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.7209 (mtp85)
REVERT: A  267 THR cc_start: 0.8911 (t) cc_final: 0.8555 (t)
REVERT: A  270 ASP cc_start: 0.6704 (m-30) cc_final: 0.6376 (m-30)
REVERT: A  313 MET cc_start: 0.6498 (mmm) cc_final: 0.6089 (mmm)
REVERT: B  232 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8577 (mm)
REVERT: C  266 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6626 (mt-10)
REVERT: D  122 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8404 (pp)
REVERT: D  198 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6421 (tt0)
REVERT: D  243 ILE cc_start: 0.8572 (mm) cc_final: 0.8306 (mm)
REVERT: D  276 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8049 (mt)
REVERT: D  344 TYR cc_start: 0.5679 (OUTLIER) cc_final: 0.2886 (p90)
REVERT: D  345 PHE cc_start: 0.6677 (OUTLIER) cc_final: 0.6387 (m-10)
REVERT: E  100 GLU cc_start: 0.6127 (mt-10) cc_final: 0.5570 (mt-10)
REVERT: E  155 ARG cc_start: 0.6192 (mtp-110) cc_final: 0.5915 (mtp-110)
REVERT: E  184 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7818 (mp)
REVERT: E  341 MET cc_start: 0.6467 (mtt) cc_final: 0.6250 (mtp)
  outliers start: 75
  outliers final: 58
  residues processed: 395
  average time/residue: 0.1275
  time to fit residues: 78.4634
Evaluate side-chains
  413 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 347
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
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  221 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  180 ASP
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 C residue  266 GLU
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  167 ASP
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  276 LEU
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  183 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 200 optimal weight:    0.7980
   chunk 82 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 91 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 127 optimal weight:    0.5980
   chunk 144 optimal weight:    0.0040
   chunk 163 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 206 optimal weight:    0.9990
   overall best weight:    0.5792

-------------------------------------------------------------------------------
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 260 GLN
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 = 0.3937 r_free = 0.3937 target = 0.188954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.148745 restraints weight = 20736.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.97
r_work: 0.3065 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3040
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    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 = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3040
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.1603

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= 0.160
  Angle     :  0.603   9.160  24639  Z= 0.308
  Chirality :  0.044   0.305   2791
  Planarity :  0.004   0.049   3081
  Dihedral  :  4.334  16.574   2401
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 18.05 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.18), residues: 2148
  helix:  2.11 (0.16), residues: 981
  sheet:  0.64 (0.25), residues: 422
  loop : -1.41 (0.22), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  40 
 TYR   0.018   0.001   TYR H 106 
 PHE   0.024   0.001   PHE A  39 
 TRP   0.018   0.001   TRP D 350 
 HIS   0.003   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (18160)
  covalent geometry    : angle       0.60237 (24631)
  SS BOND              : bond        0.00176 (    4)
  SS BOND              : angle       0.94953 (    8)
  hydrogen bonds       : bond        0.05211 ( 1053)
  hydrogen bonds       : angle       4.46515 ( 3072)

*********************** 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
  424 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 354
  time to evaluate  : 0.699 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8030 (pt0)
REVERT: L  108 LYS cc_start: 0.4082 (mmtt) cc_final: 0.3222 (mmtt)
REVERT: F   30 PHE cc_start: 0.8539 (p90) cc_final: 0.8264 (p90)
REVERT: F   49 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8229 (tm-30)
REVERT: A  267 THR cc_start: 0.8888 (t) cc_final: 0.8505 (t)
REVERT: A  270 ASP cc_start: 0.7211 (m-30) cc_final: 0.6760 (m-30)
REVERT: A  313 MET cc_start: 0.6723 (mmm) cc_final: 0.6213 (mmm)
REVERT: B  232 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8497 (mm)
REVERT: C   22 LYS cc_start: 0.7953 (pptt) cc_final: 0.7738 (pptt)
REVERT: C  204 GLU cc_start: 0.5214 (OUTLIER) cc_final: 0.4728 (mp0)
REVERT: C  266 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7831 (mt-10)
REVERT: D  122 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8370 (pp)
REVERT: D  198 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6319 (tt0)
REVERT: D  243 ILE cc_start: 0.8750 (mm) cc_final: 0.8494 (mm)
REVERT: D  276 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8132 (mt)
REVERT: D  344 TYR cc_start: 0.5534 (OUTLIER) cc_final: 0.2587 (p90)
REVERT: D  345 PHE cc_start: 0.6486 (OUTLIER) cc_final: 0.6152 (m-10)
REVERT: E  100 GLU cc_start: 0.6267 (mt-10) cc_final: 0.5638 (mt-10)
REVERT: E  155 ARG cc_start: 0.6175 (mtp-110) cc_final: 0.5786 (mtp-110)
REVERT: E  184 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7686 (mp)
REVERT: E  341 MET cc_start: 0.6299 (mtt) cc_final: 0.5888 (mtp)
  outliers start: 70
  outliers final: 56
  residues processed: 388
  average time/residue: 0.1288
  time to fit residues: 78.0687
Evaluate side-chains
  413 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 348
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   32 VAL
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  221 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  134 ASN
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  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  238 ASP
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 C residue  266 GLU
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  167 ASP
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  276 LEU
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  183 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 23 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 88 optimal weight:    0.2980
   chunk 94 optimal weight:    0.5980
   chunk 144 optimal weight:    0.8980
   chunk 133 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** H  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 257 HIS
** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
D 260 GLN
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 = 0.3899 r_free = 0.3899 target = 0.185217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.146465 restraints weight = 20880.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 3.22
r_work: 0.3012 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3006
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    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 = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3006
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.1630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  18164  Z= 0.174
  Angle     :  0.616   8.737  24639  Z= 0.316
  Chirality :  0.044   0.309   2791
  Planarity :  0.004   0.049   3081
  Dihedral  :  4.387  19.657   2401
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 18.30 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.18), residues: 2148
  helix:  2.05 (0.16), residues: 982
  sheet:  0.63 (0.25), residues: 421
  loop : -1.42 (0.22), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  40 
 TYR   0.019   0.001   TYR H 106 
 PHE   0.024   0.001   PHE A  39 
 TRP   0.018   0.001   TRP D 350 
 HIS   0.003   0.001   HIS B 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (18160)
  covalent geometry    : angle       0.61564 (24631)
  SS BOND              : bond        0.00160 (    4)
  SS BOND              : angle       1.02313 (    8)
  hydrogen bonds       : bond        0.05299 ( 1053)
  hydrogen bonds       : angle       4.49378 ( 3072)

********************** 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
  427 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 357
  time to evaluate  : 0.788 
Fit side-chains
REVERT: H    9 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8082 (pt0)
REVERT: L  108 LYS cc_start: 0.4268 (mmtt) cc_final: 0.3328 (mmtt)
REVERT: F   30 PHE cc_start: 0.8567 (p90) cc_final: 0.8257 (p90)
REVERT: F   49 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8279 (tm-30)
REVERT: A  267 THR cc_start: 0.8912 (t) cc_final: 0.8536 (t)
REVERT: A  270 ASP cc_start: 0.7391 (m-30) cc_final: 0.6930 (m-30)
REVERT: A  318 MET cc_start: 0.8303 (tmm) cc_final: 0.8029 (tmm)
REVERT: B  232 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8515 (mm)
REVERT: C   22 LYS cc_start: 0.8014 (pptt) cc_final: 0.7802 (pptt)
REVERT: C  204 GLU cc_start: 0.5265 (OUTLIER) cc_final: 0.4725 (mp0)
REVERT: C  266 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7930 (mt-10)
REVERT: D  122 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8394 (pp)
REVERT: D  198 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6366 (tt0)
REVERT: D  243 ILE cc_start: 0.8776 (mm) cc_final: 0.8514 (mm)
REVERT: D  276 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8160 (mt)
REVERT: D  291 MET cc_start: 0.8325 (mtt) cc_final: 0.8022 (ttm)
REVERT: D  344 TYR cc_start: 0.5571 (OUTLIER) cc_final: 0.2616 (p90)
REVERT: D  345 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.6153 (m-10)
REVERT: E  100 GLU cc_start: 0.6329 (mt-10) cc_final: 0.5708 (mt-10)
REVERT: E  155 ARG cc_start: 0.6199 (mtp-110) cc_final: 0.5797 (mtp-110)
REVERT: E  184 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7781 (mp)
REVERT: E  291 MET cc_start: 0.7645 (tpt) cc_final: 0.7328 (mmt)
REVERT: E  341 MET cc_start: 0.6371 (mtt) cc_final: 0.5940 (mtp)
  outliers start: 70
  outliers final: 58
  residues processed: 391
  average time/residue: 0.1274
  time to fit residues: 77.6751
Evaluate side-chains
  419 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 352
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   32 VAL
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   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  221 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  134 ASN
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  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  238 ASP
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 C residue  266 GLU
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  157 ASN
Chi-restraints excluded: chain D residue  167 ASP
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  276 LEU
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  183 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 164 optimal weight:    0.9990
   chunk 183 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 136 optimal weight:    0.9980
   chunk 163 optimal weight:    0.9980
   chunk 121 optimal weight:    0.0770
   chunk 173 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 167 optimal weight:    0.9980
   chunk 4 optimal weight:    0.3980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.6738

-------------------------------------------------------------------------------
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 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 140 GLN
D 157 ASN
D 260 GLN
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 = 0.3910 r_free = 0.3910 target = 0.186322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.147579 restraints weight = 20978.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 3.11
r_work: 0.3024 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3035
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    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 = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3035
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.1664

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= 0.174
  Angle     :  0.615   8.606  24639  Z= 0.316
  Chirality :  0.044   0.312   2791
  Planarity :  0.004   0.049   3081
  Dihedral  :  4.390  19.435   2401
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 18.66 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.18), residues: 2148
  helix:  2.04 (0.16), residues: 981
  sheet:  0.62 (0.25), residues: 422
  loop : -1.46 (0.22), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  40 
 TYR   0.019   0.001   TYR H 106 
 PHE   0.023   0.001   PHE A  39 
 TRP   0.020   0.001   TRP D 350 
 HIS   0.003   0.001   HIS B 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (18160)
  covalent geometry    : angle       0.61506 (24631)
  SS BOND              : bond        0.00170 (    4)
  SS BOND              : angle       1.00381 (    8)
  hydrogen bonds       : bond        0.05307 ( 1053)
  hydrogen bonds       : angle       4.49755 ( 3072)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4423.18 seconds
wall clock time: 76 minutes 46.24 seconds (4606.24 seconds total)