Starting phenix.real_space_refine
on Fri Feb  6 09:28:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m68_63661/02_2026/9m68_63661.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m68_63661/02_2026/9m68_63661.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m68_63661/02_2026/9m68_63661.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m68_63661/02_2026/9m68_63661.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m68_63661/02_2026/9m68_63661.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m68_63661/02_2026/9m68_63661.cif"
  }
  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=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C   14575      2.51       5
     N    4070      2.21       5
     O    5070      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 23750
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 3093
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3093
          Classifications: {'peptide': 415}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 409}
    Chain: "F"
      Number of atoms: 1657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1657
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 4, 'TRANS': 218}
    Chain: "B"
      Number of atoms: 3093
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3093
          Classifications: {'peptide': 415}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 409}
    Chain: "C"
      Number of atoms: 1657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1657
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 4, 'TRANS': 218}
    Chain: "D"
      Number of atoms: 3093
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3093
          Classifications: {'peptide': 415}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 409}
    Chain: "E"
      Number of atoms: 1657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1657
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 4, 'TRANS': 218}
    Chain: "G"
      Number of atoms: 3093
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3093
          Classifications: {'peptide': 415}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 409}
    Chain: "H"
      Number of atoms: 1657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1657
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 4, 'TRANS': 218}
    Chain: "I"
      Number of atoms: 3093
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3093
          Classifications: {'peptide': 415}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 409}
    Chain: "J"
      Number of atoms: 1657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1657
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 4, 'TRANS': 218}
  Time building chain proxies: 5.79, per 1000 atoms: 0.24
  Number of scatterers: 23750
  At special positions: 0
  Unit cell: (145.642, 147.909, 126.941, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      35     16.00
     O    5070      8.00
     N    4070      7.00
     C   14575      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.05
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5950

  Finding SS restraints...
    Secondary structure from input PDB file:
      80 helices and 29 sheets defined
      51.8% alpha, 11.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 66
      Proline residue:  A  32  - end of helix
      removed outlier: 3.687A  pdb=" N   LYS A  66 " --> pdb=" O   THR A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 70
    Processing helix  chain 'A' and resid 152 through 163
    Processing helix  chain 'A' and resid 201 through 207
    Processing helix  chain 'A' and resid 269 through 294
    Processing helix  chain 'A' and resid 315 through 330
      removed outlier: 4.009A  pdb=" N   ARG A 319 " --> pdb=" O   ASP A 315 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ALA A 330 " --> pdb=" O   ARG A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 369
    Processing helix  chain 'A' and resid 369 through 378
      removed outlier: 3.613A  pdb=" N   ALA A 373 " --> pdb=" O   ASN A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 400
      removed outlier: 4.116A  pdb=" N   ASP A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 433
    Processing helix  chain 'F' and resid 52 through 98
    Processing helix  chain 'F' and resid 103 through 126
    Processing helix  chain 'F' and resid 134 through 138
      removed outlier: 4.221A  pdb=" N   GLY F 138 " --> pdb=" O   ILE F 135 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 199 through 213
      removed outlier: 3.585A  pdb=" N   MET F 203 " --> pdb=" O   ASN F 199 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU F 204 " --> pdb=" O   LEU F 200 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   THR F 213 " --> pdb=" O   ALA F 209 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 218 through 255
    Processing helix  chain 'F' and resid 255 through 273
    Processing helix  chain 'B' and resid 20 through 66
      Proline residue:  B  32  - end of helix
      removed outlier: 3.649A  pdb=" N   LYS B  66 " --> pdb=" O   THR B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 70
    Processing helix  chain 'B' and resid 152 through 163
    Processing helix  chain 'B' and resid 201 through 207
    Processing helix  chain 'B' and resid 269 through 294
    Processing helix  chain 'B' and resid 315 through 330
      removed outlier: 4.022A  pdb=" N   ARG B 319 " --> pdb=" O   ASP B 315 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ALA B 330 " --> pdb=" O   ARG B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 345
      removed outlier: 4.203A  pdb=" N   ILE B 344 " --> pdb=" O   THR B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 369
    Processing helix  chain 'B' and resid 369 through 378
      removed outlier: 3.594A  pdb=" N   ALA B 373 " --> pdb=" O   ASN B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 400
      removed outlier: 4.110A  pdb=" N   ASP B 400 " --> pdb=" O   SER B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 433
    Processing helix  chain 'C' and resid 52 through 98
    Processing helix  chain 'C' and resid 103 through 126
    Processing helix  chain 'C' and resid 175 through 181
      removed outlier: 3.890A  pdb=" N   ILE C 179 " --> pdb=" O   THR C 175 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE C 180 " --> pdb=" O   GLY C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 213
      removed outlier: 3.594A  pdb=" N   MET C 203 " --> pdb=" O   ASN C 199 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 218 through 253
    Processing helix  chain 'C' and resid 255 through 273
    Processing helix  chain 'D' and resid 20 through 65
      Proline residue:  D  32  - end of helix
    Processing helix  chain 'D' and resid 66 through 70
      removed outlier: 3.819A  pdb=" N   LEU D  69 " --> pdb=" O   LYS D  66 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 152 through 163
      removed outlier: 3.528A  pdb=" N   ALA D 163 " --> pdb=" O   ALA D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 201 through 207
    Processing helix  chain 'D' and resid 269 through 294
    Processing helix  chain 'D' and resid 315 through 330
      removed outlier: 4.253A  pdb=" N   ARG D 319 " --> pdb=" O   ASP D 315 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ALA D 330 " --> pdb=" O   ARG D 326 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 358 through 369
    Processing helix  chain 'D' and resid 369 through 378
    Processing helix  chain 'D' and resid 385 through 400
      removed outlier: 3.842A  pdb=" N   ASP D 400 " --> pdb=" O   SER D 396 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 402 through 433
    Processing helix  chain 'E' and resid 52 through 98
    Processing helix  chain 'E' and resid 103 through 126
    Processing helix  chain 'E' and resid 134 through 138
      removed outlier: 3.706A  pdb=" N   GLY E 138 " --> pdb=" O   ILE E 135 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 199 through 213
      removed outlier: 4.058A  pdb=" N   MET E 203 " --> pdb=" O   ASN E 199 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU E 204 " --> pdb=" O   LEU E 200 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR E 213 " --> pdb=" O   ALA E 209 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 218 through 255
    Processing helix  chain 'E' and resid 255 through 273
    Processing helix  chain 'G' and resid 20 through 65
      Proline residue:  G  32  - end of helix
    Processing helix  chain 'G' and resid 66 through 70
      removed outlier: 3.777A  pdb=" N   LEU G  69 " --> pdb=" O   LYS G  66 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 152 through 163
    Processing helix  chain 'G' and resid 201 through 207
    Processing helix  chain 'G' and resid 269 through 294
    Processing helix  chain 'G' and resid 315 through 330
      removed outlier: 4.294A  pdb=" N   ARG G 319 " --> pdb=" O   ASP G 315 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ALA G 330 " --> pdb=" O   ARG G 326 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 358 through 369
    Processing helix  chain 'G' and resid 369 through 378
      removed outlier: 3.545A  pdb=" N   ALA G 373 " --> pdb=" O   ASN G 369 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 385 through 400
      removed outlier: 4.083A  pdb=" N   ASP G 400 " --> pdb=" O   SER G 396 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 402 through 433
    Processing helix  chain 'H' and resid 52 through 98
    Processing helix  chain 'H' and resid 103 through 126
    Processing helix  chain 'H' and resid 175 through 181
      removed outlier: 3.931A  pdb=" N   ILE H 179 " --> pdb=" O   THR H 175 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   PHE H 180 " --> pdb=" O   GLY H 176 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 200 through 213
      removed outlier: 3.538A  pdb=" N   LEU H 204 " --> pdb=" O   LEU H 200 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 218 through 255
    Processing helix  chain 'H' and resid 255 through 273
    Processing helix  chain 'I' and resid 20 through 66
      Proline residue:  I  32  - end of helix
      removed outlier: 3.631A  pdb=" N   LYS I  66 " --> pdb=" O   THR I  62 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 147 through 151
      removed outlier: 3.688A  pdb=" N   ASP I 150 " --> pdb=" O   ASP I 147 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   THR I 151 " --> pdb=" O   LYS I 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 147 through 151'
    Processing helix  chain 'I' and resid 152 through 163
    Processing helix  chain 'I' and resid 201 through 207
    Processing helix  chain 'I' and resid 269 through 294
    Processing helix  chain 'I' and resid 315 through 330
      removed outlier: 4.233A  pdb=" N   ARG I 319 " --> pdb=" O   ASP I 315 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ALA I 330 " --> pdb=" O   ARG I 326 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 358 through 369
    Processing helix  chain 'I' and resid 369 through 378
      removed outlier: 3.558A  pdb=" N   ALA I 373 " --> pdb=" O   ASN I 369 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 385 through 400
      removed outlier: 4.161A  pdb=" N   ASP I 400 " --> pdb=" O   SER I 396 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 402 through 433
    Processing helix  chain 'J' and resid 52 through 98
    Processing helix  chain 'J' and resid 103 through 126
    Processing helix  chain 'J' and resid 200 through 213
      removed outlier: 3.683A  pdb=" N   LEU J 204 " --> pdb=" O   LEU J 200 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   THR J 213 " --> pdb=" O   ALA J 209 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 218 through 255
    Processing helix  chain 'J' and resid 255 through 273
      removed outlier: 3.561A  pdb=" N   LEU J 273 " --> pdb=" O   LEU J 269 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 77
      removed outlier: 5.991A  pdb=" N   THR A 259 " --> pdb=" O   VAL A  99 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   VAL A  99 " --> pdb=" O   THR A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 86
    Processing sheet with id=AA3, first strand: chain 'A' and resid 168 through 175
      removed outlier: 7.254A  pdb=" N   GLU A 178 " --> pdb=" O   VAL A 174 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   GLN A 106 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   SER A 107 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 146
    Processing sheet with id=AA5, first strand: chain 'A' and resid 209 through 210
    Processing sheet with id=AA6, first strand: chain 'A' and resid 346 through 348
    Processing sheet with id=AA7, first strand: chain 'B' and resid 73 through 77
      removed outlier: 5.949A  pdb=" N   THR B 259 " --> pdb=" O   VAL B  99 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   VAL B  99 " --> pdb=" O   THR B 259 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 86
    Processing sheet with id=AA9, first strand: chain 'B' and resid 168 through 175
      removed outlier: 7.263A  pdb=" N   GLU B 178 " --> pdb=" O   VAL B 174 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   GLN B 106 " --> pdb=" O   ALA B 185 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   SER B 107 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 142 through 146
    Processing sheet with id=AB2, first strand: chain 'B' and resid 346 through 348
    Processing sheet with id=AB3, first strand: chain 'D' and resid 73 through 77
      removed outlier: 5.983A  pdb=" N   THR D 259 " --> pdb=" O   VAL D  99 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   VAL D  99 " --> pdb=" O   THR D 259 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 83 through 86
    Processing sheet with id=AB5, first strand: chain 'D' and resid 168 through 175
      removed outlier: 7.262A  pdb=" N   GLU D 178 " --> pdb=" O   VAL D 174 " (cutoff:3.500A)
      removed outlier: 5.154A  pdb=" N   GLN D 106 " --> pdb=" O   ALA D 185 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   SER D 107 " --> pdb=" O   LEU D 221 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 142 through 146
    Processing sheet with id=AB7, first strand: chain 'D' and resid 346 through 348
    Processing sheet with id=AB8, first strand: chain 'E' and resid 161 through 162
      removed outlier: 4.133A  pdb=" N   GLN E 162 " --> pdb=" O   MET E 170 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   MET E 170 " --> pdb=" O   GLN E 162 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'G' and resid 73 through 77
      removed outlier: 5.962A  pdb=" N   THR G 259 " --> pdb=" O   VAL G  99 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   VAL G  99 " --> pdb=" O   THR G 259 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'G' and resid 83 through 86
    Processing sheet with id=AC2, first strand: chain 'G' and resid 168 through 175
      removed outlier: 7.262A  pdb=" N   GLU G 178 " --> pdb=" O   VAL G 174 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   GLN G 106 " --> pdb=" O   ALA G 185 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   SER G 107 " --> pdb=" O   LEU G 221 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'G' and resid 142 through 146
    Processing sheet with id=AC4, first strand: chain 'G' and resid 209 through 210
    Processing sheet with id=AC5, first strand: chain 'G' and resid 346 through 348
    Processing sheet with id=AC6, first strand: chain 'I' and resid 73 through 77
      removed outlier: 5.947A  pdb=" N   THR I 259 " --> pdb=" O   VAL I  99 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   VAL I  99 " --> pdb=" O   THR I 259 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'I' and resid 83 through 86
    Processing sheet with id=AC8, first strand: chain 'I' and resid 168 through 172
      removed outlier: 5.098A  pdb=" N   GLN I 106 " --> pdb=" O   ALA I 185 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   SER I 107 " --> pdb=" O   LEU I 221 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'I' and resid 142 through 146
    Processing sheet with id=AD1, first strand: chain 'I' and resid 209 through 210
    Processing sheet with id=AD2, first strand: chain 'I' and resid 347 through 348

    1548 hydrogen bonds defined for protein.
    4464 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: 4.49

  Time building geometry restraints manager: 2.69 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 4366
        1.32 -     1.44: 5299
        1.44 -     1.57: 14190
        1.57 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 23925
  Sorted by residual:
  bond pdb=" C   GLU E 249 "
       pdb=" O   GLU E 249 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.043 1.15e-02 7.56e+03 1.42e+01
  bond pdb=" N   VAL B 126 "
       pdb=" CA  VAL B 126 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.32e-02 5.74e+03 9.87e+00
  bond pdb=" N   ILE D 404 "
       pdb=" CA  ILE D 404 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 1.19e-02 7.06e+03 9.85e+00
  bond pdb=" N   VAL B 243 "
       pdb=" CA  VAL B 243 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.19e-02 7.06e+03 8.87e+00
  bond pdb=" N   ASP B 123 "
       pdb=" CA  ASP B 123 "
    ideal  model  delta    sigma   weight residual
    1.455  1.492 -0.037 1.27e-02 6.20e+03 8.61e+00
  ... (remaining 23920 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 31800
        2.20 -     4.39: 543
        4.39 -     6.59: 48
        6.59 -     8.78: 3
        8.78 -    10.98: 1
  Bond angle restraints: 32395
  Sorted by residual:
  angle pdb=" N   ALA D 399 "
        pdb=" CA  ALA D 399 "
        pdb=" C   ALA D 399 "
      ideal   model   delta    sigma   weight residual
     111.14  115.93   -4.79 1.08e+00 8.57e-01 1.97e+01
  angle pdb=" N   GLN D 408 "
        pdb=" CA  GLN D 408 "
        pdb=" C   GLN D 408 "
      ideal   model   delta    sigma   weight residual
     111.28  106.61    4.67 1.09e+00 8.42e-01 1.83e+01
  angle pdb=" N   LEU J 200 "
        pdb=" CA  LEU J 200 "
        pdb=" C   LEU J 200 "
      ideal   model   delta    sigma   weight residual
     112.90  107.52    5.38 1.31e+00 5.83e-01 1.69e+01
  angle pdb=" N   ASN D 406 "
        pdb=" CA  ASN D 406 "
        pdb=" C   ASN D 406 "
      ideal   model   delta    sigma   weight residual
     111.28  107.01    4.27 1.09e+00 8.42e-01 1.53e+01
  angle pdb=" CA  ILE D 403 "
        pdb=" C   ILE D 403 "
        pdb=" O   ILE D 403 "
      ideal   model   delta    sigma   weight residual
     120.95  116.93    4.02 1.04e+00 9.25e-01 1.50e+01
  ... (remaining 32390 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 13610
       17.59 -    35.17: 971
       35.17 -    52.76: 146
       52.76 -    70.35: 15
       70.35 -    87.93: 13
  Dihedral angle restraints: 14755
    sinusoidal: 5565
      harmonic: 9190
  Sorted by residual:
  dihedral pdb=" CA  ALA B 246 "
           pdb=" C   ALA B 246 "
           pdb=" N   PRO B 247 "
           pdb=" CA  PRO B 247 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -39.24   39.24     0      5.00e+00 4.00e-02 6.16e+01
  dihedral pdb=" CA  ALA A 246 "
           pdb=" C   ALA A 246 "
           pdb=" N   PRO A 247 "
           pdb=" CA  PRO A 247 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -33.98   33.98     0      5.00e+00 4.00e-02 4.62e+01
  dihedral pdb=" CA  GLU E 197 "
           pdb=" C   GLU E 197 "
           pdb=" N   LYS E 198 "
           pdb=" CA  LYS E 198 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.25  -22.75     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 14752 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 3696
       0.075 -    0.150: 305
       0.150 -    0.225: 16
       0.225 -    0.299: 1
       0.299 -    0.374: 2
  Chirality restraints: 4020
  Sorted by residual:
  chirality pdb=" CA  ASP A 245 "
            pdb=" N   ASP A 245 "
            pdb=" C   ASP A 245 "
            pdb=" CB  ASP A 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.50e+00
  chirality pdb=" CA  ASP B 245 "
            pdb=" N   ASP B 245 "
            pdb=" C   ASP B 245 "
            pdb=" CB  ASP B 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CA  VAL B 243 "
            pdb=" N   VAL B 243 "
            pdb=" C   VAL B 243 "
            pdb=" CB  VAL B 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 4017 not shown)

  Planarity restraints: 4205
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA E 144 "    0.034 5.00e-02 4.00e+02   5.16e-02 4.27e+00
        pdb=" N   PRO E 145 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO E 145 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO E 145 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN I 135 "   -0.030 5.00e-02 4.00e+02   4.60e-02 3.38e+00
        pdb=" N   PRO I 136 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO I 136 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO I 136 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 135 "    0.030 5.00e-02 4.00e+02   4.51e-02 3.25e+00
        pdb=" N   PRO D 136 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO D 136 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO D 136 "    0.025 5.00e-02 4.00e+02
  ... (remaining 4202 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 1234
        2.73 -     3.27: 25655
        3.27 -     3.81: 39240
        3.81 -     4.36: 46027
        4.36 -     4.90: 78771
  Nonbonded interactions: 190927
  Sorted by model distance:
  nonbonded pdb=" O   GLU E 249 "
            pdb=" OG1 THR E 252 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" O   GLN J 178 "
            pdb=" OG  SER J 182 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   GLU C 249 "
            pdb=" OG1 THR C 252 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   LEU G  30 "
            pdb=" N   THR G  34 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" O   LEU I  30 "
            pdb=" N   THR I  34 "
     model   vdw
     2.229 3.120
  ... (remaining 190922 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'H'
  selection = chain 'J'
}

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=1.00 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:             14.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.820
  Check model and map are aligned:         0.090
  Set scattering table:                    0.090
  Process input model:                     22.380
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
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   0.043  23925  Z= 0.257
  Angle     :  0.655  10.980  32395  Z= 0.413
  Chirality :  0.042   0.374   4020
  Planarity :  0.004   0.052   4205
  Dihedral  : 12.344  87.934   8805
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.65 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.03 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.44 %
    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 are not related in a simple way.
  whole:  1.69 (0.14), residues: 3170
  helix:  2.32 (0.12), residues: 1535
  sheet:  1.67 (0.23), residues: 455
  loop : -0.78 (0.16), residues: 1180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G 129 
 TYR   0.022   0.001   TYR H  62 
 PHE   0.018   0.002   PHE E 180 
 TRP   0.017   0.003   TRP I 279 
 HIS   0.006   0.001   HIS E 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 (23925)
  covalent geometry    : angle       0.65501 (32395)
  hydrogen bonds       : bond        0.09966 ( 1548)
  hydrogen bonds       : angle       4.84390 ( 4464)

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

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

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 274
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 GLU cc_start: 0.6871 (mp0) cc_final: 0.6587 (mp0)
REVERT: F  170 MET cc_start: 0.6267 (pmm) cc_final: 0.5483 (ppp)
REVERT: B  176 GLU cc_start: 0.6831 (mp0) cc_final: 0.6542 (mp0)
REVERT: C  174 HIS cc_start: 0.6445 (m90) cc_final: 0.5792 (m90)
REVERT: C  250 LEU cc_start: 0.8918 (pp) cc_final: 0.8418 (pp)
REVERT: D  375 GLU cc_start: 0.7087 (tp30) cc_final: 0.6642 (tt0)
REVERT: E  198 LYS cc_start: 0.7087 (tppt) cc_final: 0.6880 (tppt)
REVERT: G  356 LYS cc_start: 0.7051 (mmpt) cc_final: 0.5616 (mttp)
REVERT: H   94 ILE cc_start: 0.7420 (tt) cc_final: 0.7155 (mm)
REVERT: H  216 GLU cc_start: 0.2573 (mp0) cc_final: 0.2294 (mt-10)
REVERT: H  231 LYS cc_start: 0.7136 (mmmt) cc_final: 0.6684 (tptt)
REVERT: J  113 ASP cc_start: 0.6932 (m-30) cc_final: 0.6705 (m-30)
REVERT: J  198 LYS cc_start: 0.7395 (tptm) cc_final: 0.7096 (tptp)
  outliers start: 7
  outliers final: 3
  residues processed: 277
  average time/residue: 0.1668
  time to fit residues: 72.2173
Evaluate side-chains
  207 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 204
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   84 THR
Chi-restraints excluded: chain C residue  197 GLU
Chi-restraints excluded: chain C residue  211 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 315
   random chunks:
   chunk 197 optimal weight:    0.9990
   chunk 215 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 132 optimal weight:    3.9990
   chunk 261 optimal weight:    0.0870
   chunk 248 optimal weight:    5.9990
   chunk 207 optimal weight:    0.9990
   chunk 155 optimal weight:   20.0000
   chunk 244 optimal weight:    5.9990
   chunk 183 optimal weight:    9.9990
   chunk 298 optimal weight:    7.9990
   overall best weight:    1.4164

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

Flipped N/Q/H residues before XYZ refinement:
** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  91 GLN
D 408 GLN
** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 242 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 = 0.4715 r_free = 0.4715 target = 0.251203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.194752 restraints weight = 29058.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.4172 rms_B_bonded: 3.37
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6627
moved from start:          0.1071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  23925  Z= 0.169
  Angle     :  0.517   6.775  32395  Z= 0.284
  Chirality :  0.040   0.173   4020
  Planarity :  0.004   0.053   4205
  Dihedral  :  4.468  51.860   3326
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  5.51 %
    Favored  : 93.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.64 (0.14), residues: 3170
  helix:  2.34 (0.12), residues: 1550
  sheet:  1.55 (0.23), residues: 455
  loop : -0.90 (0.16), residues: 1165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG F 234 
 TYR   0.011   0.001   TYR B 283 
 PHE   0.020   0.002   PHE B 329 
 TRP   0.013   0.002   TRP A 279 
 HIS   0.002   0.001   HIS H 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (23925)
  covalent geometry    : angle       0.51662 (32395)
  hydrogen bonds       : bond        0.04381 ( 1548)
  hydrogen bonds       : angle       4.35212 ( 4464)

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

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

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 253
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 GLU cc_start: 0.6943 (mp0) cc_final: 0.6625 (mp0)
REVERT: A  178 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7822 (mt-10)
REVERT: F   75 LEU cc_start: 0.6270 (mt) cc_final: 0.5934 (tp)
REVERT: B  176 GLU cc_start: 0.6984 (mp0) cc_final: 0.6708 (mp0)
REVERT: C  240 LEU cc_start: 0.5524 (OUTLIER) cc_final: 0.4819 (tt)
REVERT: H   94 ILE cc_start: 0.7464 (tt) cc_final: 0.7050 (mm)
  outliers start: 37
  outliers final: 27
  residues processed: 273
  average time/residue: 0.1569
  time to fit residues: 66.6319
Evaluate side-chains
  242 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 214
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain F residue  160 VAL
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain C residue  215 VAL
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  266 THR
Chi-restraints excluded: chain D residue  341 MET
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  231 LYS
Chi-restraints excluded: chain G residue   68 ASP
Chi-restraints excluded: chain G residue  151 THR
Chi-restraints excluded: chain G residue  266 THR
Chi-restraints excluded: chain G residue  388 THR
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain H residue  171 VAL
Chi-restraints excluded: chain H residue  223 GLU
Chi-restraints excluded: chain I residue   68 ASP
Chi-restraints excluded: chain I residue  266 THR
Chi-restraints excluded: chain I residue  388 THR
Chi-restraints excluded: chain J residue  257 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 315
   random chunks:
   chunk 292 optimal weight:    6.9990
   chunk 290 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9990
   chunk 49 optimal weight:    6.9990
   chunk 102 optimal weight:    5.9990
   chunk 187 optimal weight:    7.9990
   chunk 241 optimal weight:   20.0000
   chunk 266 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 109 optimal weight:   20.0000
   chunk 85 optimal weight:    0.7980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 181 ASN
** H 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4714 r_free = 0.4714 target = 0.251089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.195138 restraints weight = 29234.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.4174 rms_B_bonded: 3.23
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6620
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  23925  Z= 0.155
  Angle     :  0.495  11.698  32395  Z= 0.270
  Chirality :  0.039   0.173   4020
  Planarity :  0.003   0.043   4205
  Dihedral  :  4.123  20.674   3320
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  7.84 %
    Favored  : 90.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.66 (0.14), residues: 3170
  helix:  2.39 (0.12), residues: 1565
  sheet:  1.48 (0.23), residues: 455
  loop : -0.94 (0.17), residues: 1150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 107 
 TYR   0.011   0.001   TYR B 283 
 PHE   0.017   0.001   PHE B 329 
 TRP   0.011   0.002   TRP A 279 
 HIS   0.006   0.001   HIS H 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (23925)
  covalent geometry    : angle       0.49518 (32395)
  hydrogen bonds       : bond        0.04117 ( 1548)
  hydrogen bonds       : angle       4.22658 ( 4464)

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

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

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 236
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 GLU cc_start: 0.6949 (mp0) cc_final: 0.6647 (mp0)
REVERT: A  178 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7782 (mt-10)
REVERT: F   75 LEU cc_start: 0.6300 (mt) cc_final: 0.5887 (tp)
REVERT: B  176 GLU cc_start: 0.6970 (mp0) cc_final: 0.6734 (mp0)
REVERT: C  223 GLU cc_start: 0.5449 (mt-10) cc_final: 0.5229 (mt-10)
REVERT: C  240 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.4811 (tt)
REVERT: H   94 ILE cc_start: 0.7423 (tt) cc_final: 0.7010 (mm)
REVERT: J   66 ARG cc_start: 0.6696 (mtt180) cc_final: 0.6463 (mtt180)
  outliers start: 39
  outliers final: 31
  residues processed: 258
  average time/residue: 0.1566
  time to fit residues: 63.7080
Evaluate side-chains
  242 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 210
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain F residue  101 THR
Chi-restraints excluded: chain F residue  164 VAL
Chi-restraints excluded: chain F residue  247 ARG
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  266 THR
Chi-restraints excluded: chain D residue  341 MET
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  231 LYS
Chi-restraints excluded: chain G residue   68 ASP
Chi-restraints excluded: chain G residue  151 THR
Chi-restraints excluded: chain G residue  266 THR
Chi-restraints excluded: chain G residue  388 THR
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain H residue  171 VAL
Chi-restraints excluded: chain H residue  204 LEU
Chi-restraints excluded: chain H residue  223 GLU
Chi-restraints excluded: chain I residue   68 ASP
Chi-restraints excluded: chain I residue  266 THR
Chi-restraints excluded: chain I residue  388 THR
Chi-restraints excluded: chain J residue  164 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 315
   random chunks:
   chunk 225 optimal weight:    0.2980
   chunk 182 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   chunk 168 optimal weight:    5.9990
   chunk 140 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 178 optimal weight:   20.0000
   chunk 57 optimal weight:    0.9980
   chunk 226 optimal weight:    0.7980
   chunk 298 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4716 r_free = 0.4716 target = 0.251370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.196669 restraints weight = 29138.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.4191 rms_B_bonded: 3.23
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6584
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  23925  Z= 0.134
  Angle     :  0.466  11.053  32395  Z= 0.255
  Chirality :  0.038   0.173   4020
  Planarity :  0.003   0.039   4205
  Dihedral  :  3.973  23.957   3320
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  8.95 %
    Favored  : 89.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.74 (0.14), residues: 3170
  helix:  2.50 (0.12), residues: 1565
  sheet:  1.50 (0.23), residues: 455
  loop : -0.97 (0.17), residues: 1150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E 107 
 TYR   0.010   0.001   TYR B 283 
 PHE   0.018   0.001   PHE B 329 
 TRP   0.009   0.002   TRP A 279 
 HIS   0.001   0.000   HIS J 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (23925)
  covalent geometry    : angle       0.46585 (32395)
  hydrogen bonds       : bond        0.03855 ( 1548)
  hydrogen bonds       : angle       4.06791 ( 4464)

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

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

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 240
  time to evaluate  : 1.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   75 LEU cc_start: 0.6216 (mt) cc_final: 0.5726 (tt)
REVERT: H   94 ILE cc_start: 0.7415 (tt) cc_final: 0.7012 (mm)
  outliers start: 42
  outliers final: 34
  residues processed: 262
  average time/residue: 0.1482
  time to fit residues: 62.1623
Evaluate side-chains
  250 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 216
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain F residue  101 THR
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  266 THR
Chi-restraints excluded: chain D residue  341 MET
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  231 LYS
Chi-restraints excluded: chain E residue  253 GLN
Chi-restraints excluded: chain G residue   68 ASP
Chi-restraints excluded: chain G residue  151 THR
Chi-restraints excluded: chain G residue  213 THR
Chi-restraints excluded: chain G residue  266 THR
Chi-restraints excluded: chain G residue  388 THR
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain H residue  171 VAL
Chi-restraints excluded: chain H residue  204 LEU
Chi-restraints excluded: chain H residue  223 GLU
Chi-restraints excluded: chain I residue  266 THR
Chi-restraints excluded: chain I residue  388 THR
Chi-restraints excluded: chain J residue  164 VAL
Chi-restraints excluded: chain J residue  171 VAL
Chi-restraints excluded: chain J residue  257 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 315
   random chunks:
   chunk 244 optimal weight:   20.0000
   chunk 1 optimal weight:    8.9990
   chunk 296 optimal weight:    0.9990
   chunk 179 optimal weight:    7.9990
   chunk 84 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 133 optimal weight:    0.9990
   chunk 271 optimal weight:    4.9990
   chunk 247 optimal weight:    5.9990
   chunk 141 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.251506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.208254 restraints weight = 29153.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.4302 rms_B_bonded: 2.81
r_work: 0.3498 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  23925  Z= 0.125
  Angle     :  0.455  10.569  32395  Z= 0.249
  Chirality :  0.038   0.176   4020
  Planarity :  0.003   0.038   4205
  Dihedral  :  3.884  21.085   3320
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 10.10 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.82 (0.14), residues: 3170
  helix:  2.57 (0.12), residues: 1570
  sheet:  1.52 (0.23), residues: 455
  loop : -0.95 (0.17), residues: 1145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 247 
 TYR   0.008   0.001   TYR D 283 
 PHE   0.013   0.001   PHE C 180 
 TRP   0.008   0.001   TRP G 279 
 HIS   0.004   0.001   HIS H 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (23925)
  covalent geometry    : angle       0.45500 (32395)
  hydrogen bonds       : bond        0.03764 ( 1548)
  hydrogen bonds       : angle       3.99493 ( 4464)

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

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

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 238
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   75 LEU cc_start: 0.7948 (mt) cc_final: 0.7332 (tt)
REVERT: F  198 LYS cc_start: 0.7697 (mtpp) cc_final: 0.7123 (mmmt)
REVERT: H   94 ILE cc_start: 0.7546 (tt) cc_final: 0.7305 (mm)
REVERT: J  260 LEU cc_start: 0.8133 (tp) cc_final: 0.7890 (mt)
  outliers start: 45
  outliers final: 36
  residues processed: 260
  average time/residue: 0.1487
  time to fit residues: 61.6334
Evaluate side-chains
  253 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 217
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain F residue  101 THR
Chi-restraints excluded: chain F residue  160 VAL
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  233 ASN
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  174 VAL
Chi-restraints excluded: chain D residue  266 THR
Chi-restraints excluded: chain D residue  341 MET
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  231 LYS
Chi-restraints excluded: chain E residue  253 GLN
Chi-restraints excluded: chain G residue   68 ASP
Chi-restraints excluded: chain G residue  151 THR
Chi-restraints excluded: chain G residue  266 THR
Chi-restraints excluded: chain G residue  388 THR
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain H residue  171 VAL
Chi-restraints excluded: chain H residue  223 GLU
Chi-restraints excluded: chain I residue   68 ASP
Chi-restraints excluded: chain I residue  266 THR
Chi-restraints excluded: chain I residue  370 THR
Chi-restraints excluded: chain I residue  388 THR
Chi-restraints excluded: chain J residue  164 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 315
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 275 optimal weight:    0.9980
   chunk 102 optimal weight:    7.9990
   chunk 187 optimal weight:    5.9990
   chunk 185 optimal weight:    6.9990
   chunk 290 optimal weight:    1.9990
   chunk 198 optimal weight:    0.1980
   chunk 16 optimal weight:    0.8980
   chunk 278 optimal weight:    1.9990
   chunk 40 optimal weight:   20.0000
   chunk 121 optimal weight:    7.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 174 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4703 r_free = 0.4703 target = 0.250585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.206171 restraints weight = 29291.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.4277 rms_B_bonded: 2.76
r_work: 0.3465 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3306 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  23925  Z= 0.147
  Angle     :  0.484  10.361  32395  Z= 0.261
  Chirality :  0.038   0.169   4020
  Planarity :  0.003   0.038   4205
  Dihedral  :  3.954  18.784   3320
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 10.02 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.77 (0.14), residues: 3170
  helix:  2.57 (0.12), residues: 1565
  sheet:  1.39 (0.23), residues: 455
  loop : -0.99 (0.17), residues: 1150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 234 
 TYR   0.010   0.001   TYR B 283 
 PHE   0.017   0.001   PHE J 180 
 TRP   0.008   0.002   TRP I 279 
 HIS   0.007   0.001   HIS H 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (23925)
  covalent geometry    : angle       0.48356 (32395)
  hydrogen bonds       : bond        0.03823 ( 1548)
  hydrogen bonds       : angle       4.02012 ( 4464)

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

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

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 222
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  341 MET cc_start: 0.7885 (ttm) cc_final: 0.7288 (ttm)
REVERT: F   75 LEU cc_start: 0.7968 (mt) cc_final: 0.7335 (tt)
REVERT: H   94 ILE cc_start: 0.7509 (tt) cc_final: 0.7263 (mm)
REVERT: H  198 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7298 (tptm)
REVERT: H  240 LEU cc_start: 0.5220 (tp) cc_final: 0.4210 (tt)
REVERT: J  260 LEU cc_start: 0.8173 (tp) cc_final: 0.7940 (mt)
  outliers start: 57
  outliers final: 47
  residues processed: 254
  average time/residue: 0.1399
  time to fit residues: 57.6866
Evaluate side-chains
  254 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 206
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain F residue  150 THR
Chi-restraints excluded: chain F residue  160 VAL
Chi-restraints excluded: chain F residue  164 VAL
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  233 ASN
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  174 VAL
Chi-restraints excluded: chain D residue  213 THR
Chi-restraints excluded: chain D residue  266 THR
Chi-restraints excluded: chain D residue  341 MET
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  231 LYS
Chi-restraints excluded: chain E residue  252 THR
Chi-restraints excluded: chain E residue  253 GLN
Chi-restraints excluded: chain G residue   68 ASP
Chi-restraints excluded: chain G residue  151 THR
Chi-restraints excluded: chain G residue  174 VAL
Chi-restraints excluded: chain G residue  213 THR
Chi-restraints excluded: chain G residue  266 THR
Chi-restraints excluded: chain G residue  280 VAL
Chi-restraints excluded: chain G residue  388 THR
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain H residue  171 VAL
Chi-restraints excluded: chain H residue  174 HIS
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain H residue  198 LYS
Chi-restraints excluded: chain H residue  223 GLU
Chi-restraints excluded: chain I residue   68 ASP
Chi-restraints excluded: chain I residue  266 THR
Chi-restraints excluded: chain I residue  370 THR
Chi-restraints excluded: chain I residue  388 THR
Chi-restraints excluded: chain J residue  117 ILE
Chi-restraints excluded: chain J residue  164 VAL
Chi-restraints excluded: chain J residue  171 VAL
Chi-restraints excluded: chain J residue  257 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 315
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   chunk 138 optimal weight:    0.7980
   chunk 130 optimal weight:    0.0170
   chunk 219 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 159 optimal weight:    4.9990
   chunk 134 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 154 optimal weight:   20.0000
   chunk 137 optimal weight:    0.8980
   overall best weight:    1.3422

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

Flipped N/Q/H residues before XYZ refinement:
** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4708 r_free = 0.4708 target = 0.250437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.195281 restraints weight = 28910.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.4175 rms_B_bonded: 3.32
r_work (final): 0.4175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6615
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  23925  Z= 0.156
  Angle     :  0.490   9.625  32395  Z= 0.265
  Chirality :  0.039   0.184   4020
  Planarity :  0.003   0.039   4205
  Dihedral  :  3.973  17.040   3320
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.67 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.72 (0.14), residues: 3170
  helix:  2.56 (0.12), residues: 1565
  sheet:  1.33 (0.23), residues: 455
  loop : -1.03 (0.17), residues: 1150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F 234 
 TYR   0.011   0.001   TYR B 283 
 PHE   0.012   0.001   PHE E 201 
 TRP   0.008   0.002   TRP A 279 
 HIS   0.011   0.001   HIS H 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (23925)
  covalent geometry    : angle       0.49040 (32395)
  hydrogen bonds       : bond        0.03835 ( 1548)
  hydrogen bonds       : angle       4.02503 ( 4464)

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

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

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 213
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   66 ARG cc_start: 0.6783 (mtt180) cc_final: 0.6507 (mtm180)
REVERT: F   75 LEU cc_start: 0.6287 (mt) cc_final: 0.5714 (tt)
REVERT: E  253 GLN cc_start: 0.6801 (OUTLIER) cc_final: 0.6506 (mt0)
REVERT: H   94 ILE cc_start: 0.7330 (tt) cc_final: 0.6942 (mm)
REVERT: H  240 LEU cc_start: 0.4839 (tp) cc_final: 0.3530 (tt)
  outliers start: 53
  outliers final: 46
  residues processed: 247
  average time/residue: 0.1656
  time to fit residues: 65.4144
Evaluate side-chains
  245 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 198
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain F residue  150 THR
Chi-restraints excluded: chain F residue  160 VAL
Chi-restraints excluded: chain F residue  164 VAL
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  233 ASN
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  174 VAL
Chi-restraints excluded: chain D residue  213 THR
Chi-restraints excluded: chain D residue  266 THR
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  341 MET
Chi-restraints excluded: chain E residue  117 ILE
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  231 LYS
Chi-restraints excluded: chain E residue  252 THR
Chi-restraints excluded: chain E residue  253 GLN
Chi-restraints excluded: chain G residue   68 ASP
Chi-restraints excluded: chain G residue  151 THR
Chi-restraints excluded: chain G residue  174 VAL
Chi-restraints excluded: chain G residue  213 THR
Chi-restraints excluded: chain G residue  266 THR
Chi-restraints excluded: chain G residue  280 VAL
Chi-restraints excluded: chain G residue  388 THR
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain H residue  171 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain H residue  223 GLU
Chi-restraints excluded: chain I residue   68 ASP
Chi-restraints excluded: chain I residue  266 THR
Chi-restraints excluded: chain I residue  370 THR
Chi-restraints excluded: chain I residue  388 THR
Chi-restraints excluded: chain J residue  164 VAL
Chi-restraints excluded: chain J residue  171 VAL
Chi-restraints excluded: chain J residue  257 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 315
   random chunks:
   chunk 167 optimal weight:   10.0000
   chunk 207 optimal weight:    0.9980
   chunk 239 optimal weight:    6.9990
   chunk 141 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 162 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4712 r_free = 0.4712 target = 0.251965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.223798 restraints weight = 29042.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.4448 rms_B_bonded: 1.76
r_work: 0.4016 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6992
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  23925  Z= 0.129
  Angle     :  0.473   9.708  32395  Z= 0.255
  Chirality :  0.038   0.175   4020
  Planarity :  0.003   0.039   4205
  Dihedral  :  3.859  17.682   3320
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.24 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.83 (0.15), residues: 3170
  helix:  2.66 (0.12), residues: 1565
  sheet:  1.39 (0.24), residues: 455
  loop : -1.01 (0.17), residues: 1150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG F 234 
 TYR   0.011   0.001   TYR B 283 
 PHE   0.020   0.001   PHE J 180 
 TRP   0.007   0.001   TRP A 279 
 HIS   0.003   0.000   HIS H 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (23925)
  covalent geometry    : angle       0.47252 (32395)
  hydrogen bonds       : bond        0.03658 ( 1548)
  hydrogen bonds       : angle       3.94279 ( 4464)

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

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

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 209
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   66 ARG cc_start: 0.6905 (mtt180) cc_final: 0.6588 (mtm180)
REVERT: F   75 LEU cc_start: 0.6512 (mt) cc_final: 0.5895 (tt)
REVERT: E  203 MET cc_start: 0.8177 (mmm) cc_final: 0.7972 (tpp)
REVERT: E  253 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6795 (mt0)
REVERT: H   94 ILE cc_start: 0.7394 (tt) cc_final: 0.7031 (mm)
REVERT: H  240 LEU cc_start: 0.4940 (tp) cc_final: 0.3500 (tt)
  outliers start: 48
  outliers final: 44
  residues processed: 240
  average time/residue: 0.1543
  time to fit residues: 59.2696
Evaluate side-chains
  244 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 199
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain F residue  160 VAL
Chi-restraints excluded: chain F residue  164 VAL
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  233 ASN
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  174 VAL
Chi-restraints excluded: chain D residue  266 THR
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  341 MET
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  231 LYS
Chi-restraints excluded: chain E residue  252 THR
Chi-restraints excluded: chain E residue  253 GLN
Chi-restraints excluded: chain G residue   68 ASP
Chi-restraints excluded: chain G residue  151 THR
Chi-restraints excluded: chain G residue  174 VAL
Chi-restraints excluded: chain G residue  213 THR
Chi-restraints excluded: chain G residue  266 THR
Chi-restraints excluded: chain G residue  280 VAL
Chi-restraints excluded: chain G residue  388 THR
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain H residue  171 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain H residue  223 GLU
Chi-restraints excluded: chain I residue   68 ASP
Chi-restraints excluded: chain I residue  266 THR
Chi-restraints excluded: chain I residue  370 THR
Chi-restraints excluded: chain I residue  388 THR
Chi-restraints excluded: chain J residue  164 VAL
Chi-restraints excluded: chain J residue  171 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 315
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 51 optimal weight:    8.9990
   chunk 93 optimal weight:    2.9990
   chunk 114 optimal weight:   20.0000
   chunk 170 optimal weight:    8.9990
   chunk 62 optimal weight:   30.0000
   chunk 148 optimal weight:    0.5980
   chunk 273 optimal weight:    0.9980
   chunk 244 optimal weight:    9.9990
   chunk 94 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4703 r_free = 0.4703 target = 0.250890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.226881 restraints weight = 29406.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.4474 rms_B_bonded: 1.47
r_work: 0.4055 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work (final): 0.4055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  23925  Z= 0.186
  Angle     :  0.534   9.255  32395  Z= 0.285
  Chirality :  0.040   0.189   4020
  Planarity :  0.003   0.039   4205
  Dihedral  :  4.106  17.908   3320
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 11.43 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.59 (0.14), residues: 3170
  helix:  2.49 (0.12), residues: 1570
  sheet:  1.17 (0.23), residues: 455
  loop : -1.12 (0.17), residues: 1145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 234 
 TYR   0.010   0.001   TYR D 283 
 PHE   0.010   0.002   PHE A 114 
 TRP   0.008   0.002   TRP G 279 
 HIS   0.004   0.001   HIS H 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (23925)
  covalent geometry    : angle       0.53374 (32395)
  hydrogen bonds       : bond        0.03971 ( 1548)
  hydrogen bonds       : angle       4.08085 ( 4464)

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

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

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 213
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
REVERT: F   66 ARG cc_start: 0.6802 (mtt180) cc_final: 0.6467 (mtm180)
REVERT: C  240 LEU cc_start: 0.5197 (OUTLIER) cc_final: 0.4500 (tt)
REVERT: H   94 ILE cc_start: 0.7292 (tt) cc_final: 0.6907 (mm)
REVERT: H  240 LEU cc_start: 0.4948 (tp) cc_final: 0.3532 (tt)
  outliers start: 51
  outliers final: 46
  residues processed: 247
  average time/residue: 0.1460
  time to fit residues: 58.6863
Evaluate side-chains
  246 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 199
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain F residue  160 VAL
Chi-restraints excluded: chain F residue  164 VAL
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  233 ASN
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  174 VAL
Chi-restraints excluded: chain D residue  213 THR
Chi-restraints excluded: chain D residue  266 THR
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  341 MET
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  231 LYS
Chi-restraints excluded: chain E residue  252 THR
Chi-restraints excluded: chain G residue   68 ASP
Chi-restraints excluded: chain G residue  151 THR
Chi-restraints excluded: chain G residue  174 VAL
Chi-restraints excluded: chain G residue  213 THR
Chi-restraints excluded: chain G residue  266 THR
Chi-restraints excluded: chain G residue  280 VAL
Chi-restraints excluded: chain G residue  388 THR
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue  136 PHE
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain H residue  171 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain H residue  223 GLU
Chi-restraints excluded: chain I residue   68 ASP
Chi-restraints excluded: chain I residue  174 VAL
Chi-restraints excluded: chain I residue  266 THR
Chi-restraints excluded: chain I residue  388 THR
Chi-restraints excluded: chain J residue  117 ILE
Chi-restraints excluded: chain J residue  164 VAL
Chi-restraints excluded: chain J residue  171 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 315
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 92 optimal weight:    9.9990
   chunk 152 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 109 optimal weight:   10.0000
   chunk 285 optimal weight:    4.9990
   chunk 150 optimal weight:    0.9980
   chunk 222 optimal weight:    0.0170
   overall best weight:    0.7220

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

Flipped N/Q/H residues before XYZ refinement:
** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 174 HIS
** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 253 GLN
** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4721 r_free = 0.4721 target = 0.253135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.229123 restraints weight = 29455.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.4499 rms_B_bonded: 1.57
r_work: 0.3919 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3671 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.2854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  23925  Z= 0.116
  Angle     :  0.481   9.461  32395  Z= 0.259
  Chirality :  0.038   0.186   4020
  Planarity :  0.003   0.064   4205
  Dihedral  :  3.871  26.016   3320
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.78 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.77 (0.15), residues: 3170
  helix:  2.62 (0.12), residues: 1575
  sheet:  1.33 (0.24), residues: 455
  loop : -1.06 (0.17), residues: 1140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG F 234 
 TYR   0.009   0.001   TYR D 283 
 PHE   0.019   0.001   PHE J 180 
 TRP   0.007   0.001   TRP I 279 
 HIS   0.004   0.001   HIS H 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (23925)
  covalent geometry    : angle       0.48125 (32395)
  hydrogen bonds       : bond        0.03542 ( 1548)
  hydrogen bonds       : angle       3.92206 ( 4464)

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

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

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6340 Ramachandran restraints generated.
    3170 Oldfield, 0 Emsley, 3170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 201
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  240 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5108 (tt)
REVERT: H   94 ILE cc_start: 0.7492 (tt) cc_final: 0.7148 (mm)
REVERT: H  240 LEU cc_start: 0.5330 (tp) cc_final: 0.3926 (tt)
  outliers start: 46
  outliers final: 43
  residues processed: 233
  average time/residue: 0.1489
  time to fit residues: 55.9565
Evaluate side-chains
  238 residues out of total 2615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 194
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain F residue  160 VAL
Chi-restraints excluded: chain F residue  164 VAL
Chi-restraints excluded: chain B residue   68 ASP
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  233 ASN
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  174 VAL
Chi-restraints excluded: chain D residue  266 THR
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  341 MET
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  231 LYS
Chi-restraints excluded: chain E residue  252 THR
Chi-restraints excluded: chain G residue   68 ASP
Chi-restraints excluded: chain G residue  151 THR
Chi-restraints excluded: chain G residue  174 VAL
Chi-restraints excluded: chain G residue  213 THR
Chi-restraints excluded: chain G residue  266 THR
Chi-restraints excluded: chain G residue  280 VAL
Chi-restraints excluded: chain G residue  388 THR
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain H residue  171 VAL
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain H residue  223 GLU
Chi-restraints excluded: chain I residue   68 ASP
Chi-restraints excluded: chain I residue  174 VAL
Chi-restraints excluded: chain I residue  266 THR
Chi-restraints excluded: chain I residue  388 THR
Chi-restraints excluded: chain J residue  164 VAL
Chi-restraints excluded: chain J residue  171 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 315
   random chunks:
   chunk 167 optimal weight:   20.0000
   chunk 3 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 221 optimal weight:    3.9990
   chunk 45 optimal weight:    9.9990
   chunk 32 optimal weight:    0.6980
   chunk 138 optimal weight:    4.9990
   chunk 299 optimal weight:    6.9990
   chunk 28 optimal weight:   30.0000
   chunk 12 optimal weight:    2.9990
   chunk 134 optimal weight:    0.5980
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 242 ASN
** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.249325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.225175 restraints weight = 29273.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.4468 rms_B_bonded: 1.50
r_work: 0.3884 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3612 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.2984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  23925  Z= 0.231
  Angle     :  0.589   8.920  32395  Z= 0.312
  Chirality :  0.041   0.189   4020
  Planarity :  0.004   0.061   4205
  Dihedral  :  4.275  26.560   3320
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.97 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.41 (0.14), residues: 3170
  helix:  2.35 (0.12), residues: 1570
  sheet:  1.04 (0.23), residues: 455
  loop : -1.21 (0.17), residues: 1145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG F 234 
 TYR   0.011   0.001   TYR D 283 
 PHE   0.011   0.002   PHE C 136 
 TRP   0.008   0.002   TRP A 279 
 HIS   0.005   0.001   HIS H 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 (23925)
  covalent geometry    : angle       0.58860 (32395)
  hydrogen bonds       : bond        0.04145 ( 1548)
  hydrogen bonds       : angle       4.17827 ( 4464)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5700.71 seconds
wall clock time: 98 minutes 47.23 seconds (5927.23 seconds total)