Starting phenix.real_space_refine
on Thu Sep 18 02:34:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k29_61993/09_2025/9k29_61993.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k29_61993/09_2025/9k29_61993.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k29_61993/09_2025/9k29_61993.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k29_61993/09_2025/9k29_61993.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k29_61993/09_2025/9k29_61993.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k29_61993/09_2025/9k29_61993.cif"
  }
  resolution = 3.0
  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=   0.002
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     105      5.16       5
     C    8826      2.51       5
     N    2047      2.21       5
     O    2252      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13230
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1618
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 192}
    Chain: "B"
      Number of atoms: 1724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1724
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 206}
    Chain: "C"
      Number of atoms: 1724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1724
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 206}
    Chain: "D"
      Number of atoms: 1724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1724
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 206}
    Chain: "E"
      Number of atoms: 1724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1724
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 206}
    Chain: "F"
      Number of atoms: 2032
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 262, 2018
          Classifications: {'peptide': 262}
          Link IDs: {'PTRANS': 16, 'TRANS': 245}
      Conformer: "B"
        Number of residues, atoms: 262, 2018
          Classifications: {'peptide': 262}
          Link IDs: {'PTRANS': 16, 'TRANS': 245}
          bond proxies already assigned to first conformer: 2051
    Chain: "G"
      Number of atoms: 671
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 671
          Classifications: {'peptide': 89}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
    Chain: "H"
      Number of atoms: 671
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 671
          Classifications: {'peptide': 89}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
    Chain: "I"
      Number of atoms: 671
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 671
          Classifications: {'peptide': 89}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
    Chain: "J"
      Number of atoms: 671
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 671
          Classifications: {'peptide': 89}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATRP F  72 " occ=0.50
      ... (26 atoms not shown)
      pdb=" CH2BTRP F  72 " occ=0.50
  Time building chain proxies: 3.68, per 1000 atoms: 0.28
  Number of scatterers: 13230
  At special positions: 0
  Unit cell: (119.4, 98.505, 102.485, 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     105     16.00
     O    2252      8.00
     N    2047      7.00
     C    8826      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: 1.13
  Conformation dependent library (CDL) restraints added in 724.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3250

  Finding SS restraints...
    Secondary structure from input PDB file:
      79 helices and 2 sheets defined
      84.4% alpha, 2.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 52
      removed outlier: 3.799A  pdb=" N   LEU A  45 " --> pdb=" O   SER A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 62
      removed outlier: 4.084A  pdb=" N   LEU A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 78
      removed outlier: 3.860A  pdb=" N   ILE A  69 " --> pdb=" O   THR A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 101
    Processing helix  chain 'A' and resid 101 through 112
    Processing helix  chain 'A' and resid 113 through 118
      removed outlier: 4.447A  pdb=" N   GLU A 118 " --> pdb=" O   GLN A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 130
      removed outlier: 3.756A  pdb=" N   ASP A 128 " --> pdb=" O   GLN A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 142
      removed outlier: 3.592A  pdb=" N   ARG A 140 " --> pdb=" O   ALA A 136 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLN A 141 " --> pdb=" O   PHE A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 154
      removed outlier: 3.534A  pdb=" N   LEU A 147 " --> pdb=" O   ARG A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 165
    Processing helix  chain 'A' and resid 166 through 207
      Proline residue:  A 172  - end of helix
      Proline residue:  A 192  - end of helix
    Processing helix  chain 'A' and resid 213 through 229
      removed outlier: 4.025A  pdb=" N   ILE A 217 " --> pdb=" O   PRO A 213 " (cutoff:3.500A)
      Proline residue:  A 220  - end of helix
    Processing helix  chain 'A' and resid 230 through 245
      removed outlier: 3.643A  pdb=" N   LEU A 234 " --> pdb=" O   ASP A 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 51
      removed outlier: 3.572A  pdb=" N   LEU B  45 " --> pdb=" O   SER B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 62
      removed outlier: 3.534A  pdb=" N   LEU B  59 " --> pdb=" O   PRO B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 78
      removed outlier: 3.593A  pdb=" N   ILE B  67 " --> pdb=" O   SER B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 112
      Proline residue:  B 103  - end of helix
    Processing helix  chain 'B' and resid 113 through 118
      removed outlier: 4.366A  pdb=" N   GLU B 118 " --> pdb=" O   GLN B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 142
      removed outlier: 3.784A  pdb=" N   ASP B 128 " --> pdb=" O   GLN B 124 " (cutoff:3.500A)
      Proline residue:  B 133  - end of helix
    Processing helix  chain 'B' and resid 143 through 155
    Processing helix  chain 'B' and resid 166 through 208
      Proline residue:  B 172  - end of helix
      removed outlier: 3.691A  pdb=" N   ILE B 191 " --> pdb=" O   PHE B 187 " (cutoff:3.500A)
      Proline residue:  B 192  - end of helix
    Processing helix  chain 'B' and resid 214 through 229
      Proline residue:  B 220  - end of helix
    Processing helix  chain 'B' and resid 230 through 245
      removed outlier: 3.936A  pdb=" N   PHE B 243 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   TYR B 244 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER B 245 " --> pdb=" O   GLN B 241 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 62
      removed outlier: 4.487A  pdb=" N   THR C  52 " --> pdb=" O   ILE C  48 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   PHE C  53 " --> pdb=" O   THR C  49 " (cutoff:3.500A)
      Proline residue:  C  55  - end of helix
    Processing helix  chain 'C' and resid 63 through 78
      removed outlier: 3.713A  pdb=" N   ILE C  67 " --> pdb=" O   SER C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 101
    Processing helix  chain 'C' and resid 101 through 112
    Processing helix  chain 'C' and resid 113 through 118
      removed outlier: 4.230A  pdb=" N   GLU C 118 " --> pdb=" O   GLN C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 142
      removed outlier: 4.040A  pdb=" N   ASP C 128 " --> pdb=" O   GLN C 124 " (cutoff:3.500A)
      Proline residue:  C 133  - end of helix
    Processing helix  chain 'C' and resid 143 through 155
    Processing helix  chain 'C' and resid 161 through 165
    Processing helix  chain 'C' and resid 166 through 208
      Proline residue:  C 172  - end of helix
      removed outlier: 3.732A  pdb=" N   ILE C 191 " --> pdb=" O   PHE C 187 " (cutoff:3.500A)
      Proline residue:  C 192  - end of helix
    Processing helix  chain 'C' and resid 214 through 229
      Proline residue:  C 220  - end of helix
    Processing helix  chain 'C' and resid 230 through 245
      removed outlier: 4.189A  pdb=" N   PHE C 243 " --> pdb=" O   LEU C 239 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   TYR C 244 " --> pdb=" O   ALA C 240 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   SER C 245 " --> pdb=" O   GLN C 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 41 through 52
      removed outlier: 3.559A  pdb=" N   THR D  52 " --> pdb=" O   ILE D  48 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 61
      removed outlier: 3.516A  pdb=" N   MET D  61 " --> pdb=" O   ILE D  57 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 63 through 78
    Processing helix  chain 'D' and resid 85 through 101
    Processing helix  chain 'D' and resid 101 through 112
    Processing helix  chain 'D' and resid 113 through 118
      removed outlier: 4.484A  pdb=" N   GLU D 118 " --> pdb=" O   GLN D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 122 through 141
      removed outlier: 3.883A  pdb=" N   ASP D 128 " --> pdb=" O   GLN D 124 " (cutoff:3.500A)
      Proline residue:  D 133  - end of helix
    Processing helix  chain 'D' and resid 143 through 155
    Processing helix  chain 'D' and resid 166 through 207
      Proline residue:  D 172  - end of helix
      removed outlier: 3.651A  pdb=" N   ILE D 191 " --> pdb=" O   PHE D 187 " (cutoff:3.500A)
      Proline residue:  D 192  - end of helix
    Processing helix  chain 'D' and resid 213 through 229
      removed outlier: 3.788A  pdb=" N   ILE D 217 " --> pdb=" O   PRO D 213 " (cutoff:3.500A)
      Proline residue:  D 220  - end of helix
    Processing helix  chain 'D' and resid 230 through 245
      removed outlier: 3.721A  pdb=" N   LEU D 234 " --> pdb=" O   ASP D 230 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER D 245 " --> pdb=" O   GLN D 241 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 41 through 51
    Processing helix  chain 'E' and resid 53 through 62
      removed outlier: 3.573A  pdb=" N   THR E  62 " --> pdb=" O   LEU E  58 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 78
      removed outlier: 3.872A  pdb=" N   ILE E  69 " --> pdb=" O   THR E  65 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 101
    Processing helix  chain 'E' and resid 101 through 112
    Processing helix  chain 'E' and resid 122 through 140
      removed outlier: 3.638A  pdb=" N   ALA E 126 " --> pdb=" O   SER E 122 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU E 127 " --> pdb=" O   MET E 123 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ASP E 128 " --> pdb=" O   GLN E 124 " (cutoff:3.500A)
      Proline residue:  E 133  - end of helix
    Processing helix  chain 'E' and resid 143 through 155
    Processing helix  chain 'E' and resid 161 through 165
    Processing helix  chain 'E' and resid 166 through 207
      Proline residue:  E 172  - end of helix
      removed outlier: 3.695A  pdb=" N   LYS E 180 " --> pdb=" O   THR E 176 " (cutoff:3.500A)
      Proline residue:  E 192  - end of helix
    Processing helix  chain 'E' and resid 213 through 229
      removed outlier: 4.144A  pdb=" N   ILE E 217 " --> pdb=" O   PRO E 213 " (cutoff:3.500A)
      Proline residue:  E 220  - end of helix
    Processing helix  chain 'E' and resid 230 through 245
      removed outlier: 3.750A  pdb=" N   PHE E 243 " --> pdb=" O   LEU E 239 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   TYR E 244 " --> pdb=" O   ALA E 240 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   SER E 245 " --> pdb=" O   GLN E 241 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 6 through 29
      removed outlier: 3.538A  pdb=" N   LEU F  13 " --> pdb=" O   TRP F   9 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   TRP F  18 " --> pdb=" O   HIS F  14 " (cutoff:3.500A)
      Proline residue:  F  19  - end of helix
      removed outlier: 3.663A  pdb=" N   THR F  29 " --> pdb=" O   ALA F  25 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 39 through 55
      removed outlier: 3.799A  pdb=" N   VAL F  53 " --> pdb=" O   MET F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 67 through 89
    Processing helix  chain 'F' and resid 89 through 107
    Processing helix  chain 'F' and resid 110 through 115
    Processing helix  chain 'F' and resid 123 through 140
    Processing helix  chain 'F' and resid 141 through 157
    Processing helix  chain 'F' and resid 166 through 175
    Processing helix  chain 'F' and resid 177 through 208
      removed outlier: 3.559A  pdb=" N   LEU F 181 " --> pdb=" O   GLY F 177 " (cutoff:3.500A)
      Proline residue:  F 189  - end of helix
      removed outlier: 3.642A  pdb=" N   MET F 207 " --> pdb=" O   LEU F 203 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 216 through 233
    Processing helix  chain 'F' and resid 235 through 258
      removed outlier: 3.561A  pdb=" N   PHE F 239 " --> pdb=" O   LEU F 235 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 259 through 262
      removed outlier: 3.931A  pdb=" N   ASN F 262 " --> pdb=" O   PRO F 259 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 259 through 262'
    Processing helix  chain 'G' and resid 2 through 42
      Proline residue:  G  23  - end of helix
    Processing helix  chain 'G' and resid 46 through 49
      removed outlier: 3.694A  pdb=" N   LEU G  49 " --> pdb=" O   GLU G  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 46 through 49'
    Processing helix  chain 'G' and resid 50 through 88
      Proline residue:  G  67  - end of helix
      Proline residue:  G  85  - end of helix
      removed outlier: 3.582A  pdb=" N   ILE G  88 " --> pdb=" O   LEU G  84 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 2 through 42
      Proline residue:  H  23  - end of helix
    Processing helix  chain 'H' and resid 50 through 88
      Proline residue:  H  67  - end of helix
      Proline residue:  H  85  - end of helix
      removed outlier: 3.893A  pdb=" N   ILE H  88 " --> pdb=" O   LEU H  84 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 2 through 42
      Proline residue:  I  23  - end of helix
    Processing helix  chain 'I' and resid 46 through 49
    Processing helix  chain 'I' and resid 50 through 88
      Proline residue:  I  67  - end of helix
      Proline residue:  I  85  - end of helix
    Processing helix  chain 'J' and resid 2 through 43
      Proline residue:  J  23  - end of helix
      removed outlier: 3.517A  pdb=" N   ALA J  40 " --> pdb=" O   SER J  36 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ALA J  41 " --> pdb=" O   ILE J  37 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 50 through 65
    Processing helix  chain 'J' and resid 65 through 88
      removed outlier: 3.673A  pdb=" N   MET J  69 " --> pdb=" O   ALA J  65 " (cutoff:3.500A)
      Proline residue:  J  85  - end of helix
      removed outlier: 4.097A  pdb=" N   ILE J  88 " --> pdb=" O   LEU J  84 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 30 through 31
    Processing sheet with id=AA2, first strand: chain 'C' and resid 26 through 28
      removed outlier: 3.575A  pdb=" N   SER D  28 " --> pdb=" O   GLN E  36 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   GLN E  36 " --> pdb=" O   SER D  28 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLN E  29 " --> pdb=" O   SER E  37 " (cutoff:3.500A)

    1014 hydrogen bonds defined for protein.
    3001 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: 2.03

  Time building geometry restraints manager: 1.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3975
        1.34 -     1.46: 2181
        1.46 -     1.58: 7165
        1.58 -     1.69: 0
        1.69 -     1.81: 209
  Bond restraints: 13530
  Sorted by residual:
  bond pdb=" N   GLY H  66 "
       pdb=" CA  GLY H  66 "
    ideal  model  delta    sigma   weight residual
    1.443  1.492 -0.049 1.37e-02 5.33e+03 1.28e+01
  bond pdb=" N   GLY B  35 "
       pdb=" CA  GLY B  35 "
    ideal  model  delta    sigma   weight residual
    1.444  1.475 -0.031 1.02e-02 9.61e+03 9.38e+00
  bond pdb=" N   THR J  48 "
       pdb=" CA  THR J  48 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.032 1.12e-02 7.97e+03 7.99e+00
  bond pdb=" N   SER F   6 "
       pdb=" CA  SER F   6 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.19e-02 7.06e+03 7.52e+00
  bond pdb=" N   ILE F   2 "
       pdb=" CA  ILE F   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.035 1.27e-02 6.20e+03 7.49e+00
  ... (remaining 13525 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 17917
        1.91 -     3.82: 432
        3.82 -     5.73: 85
        5.73 -     7.64: 14
        7.64 -     9.55: 3
  Bond angle restraints: 18451
  Sorted by residual:
  angle pdb=" N   SER F   6 "
        pdb=" CA  SER F   6 "
        pdb=" C   SER F   6 "
      ideal   model   delta    sigma   weight residual
     111.07  120.15   -9.08 1.07e+00 8.73e-01 7.20e+01
  angle pdb=" N   ASP D 230 "
        pdb=" CA  ASP D 230 "
        pdb=" C   ASP D 230 "
      ideal   model   delta    sigma   weight residual
     111.28  106.47    4.81 1.35e+00 5.49e-01 1.27e+01
  angle pdb=" CA  GLY B  35 "
        pdb=" C   GLY B  35 "
        pdb=" O   GLY B  35 "
      ideal   model   delta    sigma   weight residual
     121.76  118.10    3.66 1.03e+00 9.43e-01 1.26e+01
  angle pdb=" N   LEU J  49 "
        pdb=" CA  LEU J  49 "
        pdb=" C   LEU J  49 "
      ideal   model   delta    sigma   weight residual
     112.38  116.69   -4.31 1.22e+00 6.72e-01 1.25e+01
  angle pdb=" C   ALA B  32 "
        pdb=" CA  ALA B  32 "
        pdb=" CB  ALA B  32 "
      ideal   model   delta    sigma   weight residual
     115.89  111.53    4.36 1.32e+00 5.74e-01 1.09e+01
  ... (remaining 18446 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 7441
       17.13 -    34.26: 596
       34.26 -    51.39: 80
       51.39 -    68.52: 17
       68.52 -    85.65: 13
  Dihedral angle restraints: 8147
    sinusoidal: 3153
      harmonic: 4994
  Sorted by residual:
  dihedral pdb=" CA  ALA C  83 "
           pdb=" C   ALA C  83 "
           pdb=" N   PRO C  84 "
           pdb=" CA  PRO C  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.66   24.34     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CA  ALA D  83 "
           pdb=" C   ALA D  83 "
           pdb=" N   PRO D  84 "
           pdb=" CA  PRO D  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.24   23.76     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" CA  ALA A  83 "
           pdb=" C   ALA A  83 "
           pdb=" N   PRO A  84 "
           pdb=" CA  PRO A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.95   23.05     0      5.00e+00 4.00e-02 2.13e+01
  ... (remaining 8144 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1995
       0.067 -    0.134: 270
       0.134 -    0.202: 18
       0.202 -    0.269: 5
       0.269 -    0.336: 2
  Chirality restraints: 2290
  Sorted by residual:
  chirality pdb=" CA  SER F   6 "
            pdb=" N   SER F   6 "
            pdb=" C   SER F   6 "
            pdb=" CB  SER F   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.82e+00
  chirality pdb=" CA  MET F 131 "
            pdb=" N   MET F 131 "
            pdb=" C   MET F 131 "
            pdb=" CB  MET F 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CB  THR C  80 "
            pdb=" CA  THR C  80 "
            pdb=" OG1 THR C  80 "
            pdb=" CG2 THR C  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 2287 not shown)

  Planarity restraints: 2261
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY H  66 "   -0.038 5.00e-02 4.00e+02   5.75e-02 5.28e+00
        pdb=" N   PRO H  67 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO H  67 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO H  67 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR I   2 "   -0.034 5.00e-02 4.00e+02   5.18e-02 4.29e+00
        pdb=" N   PRO I   3 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO I   3 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO I   3 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F  30 "    0.031 5.00e-02 4.00e+02   4.73e-02 3.57e+00
        pdb=" N   PRO F  31 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO F  31 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO F  31 "    0.026 5.00e-02 4.00e+02
  ... (remaining 2258 not shown)

  Histogram of nonbonded interaction distances:
        1.82 -     2.43: 35
        2.43 -     3.05: 8895
        3.05 -     3.67: 21323
        3.67 -     4.28: 29533
        4.28 -     4.90: 50447
  Nonbonded interactions: 110233
  Sorted by model distance:
  nonbonded pdb=" O   GLY F 117 "
            pdb=" OG  SER F 118 "
     model   vdw
     1.817 3.040
  nonbonded pdb=" NH2 ARG D 135 "
            pdb=" O   VAL D 165 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" OG1 THR J   2 "
            pdb=" OE1 GLU J   4 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" NE2 GLN B 233 "
            pdb=" OD1 ASP C 146 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" NE2 GLN B 141 "
            pdb=" O   PHE B 243 "
     model   vdw
     2.242 3.120
  ... (remaining 110228 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 38 through 245)
  selection = (chain 'C' and resid 38 through 245)
  selection = (chain 'D' and resid 38 through 245)
  selection = (chain 'E' and resid 38 through 245)
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  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=0.50 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:             0.720
  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:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.520
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  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:6.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13530  Z= 0.202
  Angle     :  0.717   9.546  18451  Z= 0.400
  Chirality :  0.046   0.336   2290
  Planarity :  0.005   0.057   2261
  Dihedral  : 12.676  85.646   4897
  Min Nonbonded Distance : 1.817

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  1.35 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.14 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.21), residues: 1705
  helix:  1.84 (0.14), residues: 1348
  sheet: -0.55 (0.70), residues: 48
  loop : -1.28 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 168 
 TYR   0.010   0.001   TYR I  76 
 PHE   0.023   0.002   PHE F  92 
 TRP   0.011   0.001   TRP I  68 
 HIS   0.001   0.000   HIS F 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (13530)
  covalent geometry    : angle       0.71671 (18451)
  hydrogen bonds       : bond        0.12517 ( 1014)
  hydrogen bonds       : angle       4.89231 ( 3001)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 321
  time to evaluate  : 0.507 
Fit side-chains
REVERT: C  178 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7570 (mm-30)
REVERT: D  230 ASP cc_start: 0.8535 (t0) cc_final: 0.8295 (t0)
REVERT: E   38 TRP cc_start: 0.7920 (m100) cc_final: 0.7715 (m100)
REVERT: F   14 HIS cc_start: 0.7971 (m90) cc_final: 0.7349 (m-70)
REVERT: F   36 ARG cc_start: 0.8392 (mtp85) cc_final: 0.8163 (mtp85)
REVERT: F  134 MET cc_start: 0.8674 (mtm) cc_final: 0.8381 (mtm)
REVERT: H   15 LYS cc_start: 0.7973 (tmtt) cc_final: 0.7713 (tptt)
REVERT: I   12 GLU cc_start: 0.8231 (tp30) cc_final: 0.7712 (tp30)
REVERT: I   59 PHE cc_start: 0.8641 (t80) cc_final: 0.8415 (t80)
  outliers start: 1
  outliers final: 2
  residues processed: 321
  average time/residue: 0.5751
  time to fit residues: 200.2967
Evaluate side-chains
  247 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 245
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain C residue  200 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 141 GLN
B 184 GLN
** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  45 ASN
H  45 ASN
I  83 ASN
J  39 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.077540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.057469 restraints weight = 60530.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.2894 rms_B_bonded: 3.85
r_work: 0.2736 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2742
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2742
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13530  Z= 0.158
  Angle     :  0.693   9.763  18451  Z= 0.328
  Chirality :  0.043   0.233   2290
  Planarity :  0.005   0.056   2261
  Dihedral  :  4.071  22.414   1803
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 11.52 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.21), residues: 1705
  helix:  2.09 (0.14), residues: 1336
  sheet: -0.91 (0.66), residues: 48
  loop : -1.18 (0.39), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 135 
 TYR   0.025   0.001   TYR E 113 
 PHE   0.026   0.002   PHE F  92 
 TRP   0.008   0.001   TRP E  38 
 HIS   0.002   0.001   HIS F 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (13530)
  covalent geometry    : angle       0.69274 (18451)
  hydrogen bonds       : bond        0.03885 ( 1014)
  hydrogen bonds       : angle       3.99286 ( 3001)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 260
  time to evaluate  : 0.396 
Fit side-chains
REVERT: B  107 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8683 (ttpp)
REVERT: D  230 ASP cc_start: 0.8860 (t0) cc_final: 0.8632 (t0)
REVERT: E  167 MET cc_start: 0.8721 (tpp) cc_final: 0.8137 (mpp)
REVERT: E  205 MET cc_start: 0.9425 (tpp) cc_final: 0.9212 (tpt)
REVERT: F   14 HIS cc_start: 0.8591 (m90) cc_final: 0.8039 (m90)
REVERT: G   46 GLU cc_start: 0.8374 (pm20) cc_final: 0.8141 (pm20)
REVERT: H    4 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8203 (mp0)
REVERT: I   12 GLU cc_start: 0.8585 (tp30) cc_final: 0.8068 (tp30)
  outliers start: 35
  outliers final: 15
  residues processed: 275
  average time/residue: 0.5685
  time to fit residues: 170.2301
Evaluate side-chains
  259 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 243
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain C residue  244 TYR
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain E residue  101 MET
Chi-restraints excluded: chain F residue  121 ASN
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   49 LEU
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain I residue   26 LEU
Chi-restraints excluded: chain J residue    7 MET
Chi-restraints excluded: chain J residue   26 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 142 optimal weight:    6.9990
   chunk 119 optimal weight:    0.9990
   chunk 33 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 140 optimal weight:    0.9980
   chunk 110 optimal weight:    0.9990
   chunk 116 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 143 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  39 GLN
I  83 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.077564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.058187 restraints weight = 45859.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 3.38
r_work: 0.2766 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2774
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2774 r_free = 0.2774    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2774 r_free = 0.2774    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2774
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13530  Z= 0.134
  Angle     :  0.648   8.799  18451  Z= 0.307
  Chirality :  0.041   0.152   2290
  Planarity :  0.005   0.055   2261
  Dihedral  :  3.921  23.134   1799
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.21 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.23 (0.21), residues: 1705
  helix:  2.17 (0.14), residues: 1338
  sheet: -0.91 (0.63), residues: 48
  loop : -1.20 (0.39), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 168 
 TYR   0.024   0.001   TYR E 113 
 PHE   0.023   0.001   PHE F  92 
 TRP   0.007   0.001   TRP I  68 
 HIS   0.001   0.000   HIS F 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (13530)
  covalent geometry    : angle       0.64847 (18451)
  hydrogen bonds       : bond        0.03468 ( 1014)
  hydrogen bonds       : angle       3.81470 ( 3001)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 255
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
REVERT: B  168 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8808 (ttt-90)
REVERT: D  120 LYS cc_start: 0.9133 (mppt) cc_final: 0.8601 (mttp)
REVERT: D  230 ASP cc_start: 0.8833 (t0) cc_final: 0.8629 (t0)
REVERT: E  123 MET cc_start: 0.8457 (tpt) cc_final: 0.7458 (tmm)
REVERT: E  205 MET cc_start: 0.9409 (tpp) cc_final: 0.9169 (tpt)
REVERT: E  224 MET cc_start: 0.9085 (mtm) cc_final: 0.8856 (mtt)
REVERT: F   14 HIS cc_start: 0.8726 (m90) cc_final: 0.8174 (m90)
REVERT: F  122 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7228 (ppp)
REVERT: H    4 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8199 (mp0)
REVERT: I   12 GLU cc_start: 0.8569 (tp30) cc_final: 0.8047 (tp30)
REVERT: I   76 TYR cc_start: 0.9072 (t80) cc_final: 0.8841 (t80)
REVERT: J    4 GLU cc_start: 0.8752 (mp0) cc_final: 0.8404 (mp0)
REVERT: J   69 MET cc_start: 0.8859 (mtt) cc_final: 0.8592 (mtt)
  outliers start: 32
  outliers final: 16
  residues processed: 274
  average time/residue: 0.5256
  time to fit residues: 157.6166
Evaluate side-chains
  263 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 245
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  168 ARG
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  244 TYR
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain E residue  101 MET
Chi-restraints excluded: chain E residue  106 ASP
Chi-restraints excluded: chain F residue  122 MET
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain I residue   26 LEU
Chi-restraints excluded: chain J residue    7 MET
Chi-restraints excluded: chain J residue   26 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 90 optimal weight:    1.9990
   chunk 98 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 159 optimal weight:    1.9990
   chunk 114 optimal weight:   10.0000
   chunk 73 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  86 ASN
A 119 GLN
A 141 GLN
B  36 GLN
B  76 ASN
B  86 ASN
H  39 GLN
H  45 ASN
I  83 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.073538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.053730 restraints weight = 58765.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 3.72
r_work: 0.2653 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2666
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  13530  Z= 0.211
  Angle     :  0.705   8.550  18451  Z= 0.334
  Chirality :  0.044   0.151   2290
  Planarity :  0.005   0.055   2261
  Dihedral  :  3.997  25.443   1799
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 14.69 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.19 (0.21), residues: 1705
  helix:  2.10 (0.14), residues: 1350
  sheet: -0.87 (0.63), residues: 48
  loop : -1.11 (0.40), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 168 
 TYR   0.018   0.001   TYR A 109 
 PHE   0.030   0.002   PHE F  92 
 TRP   0.007   0.001   TRP E 232 
 HIS   0.003   0.001   HIS F 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 (13530)
  covalent geometry    : angle       0.70461 (18451)
  hydrogen bonds       : bond        0.03953 ( 1014)
  hydrogen bonds       : angle       3.84548 ( 3001)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 253
  time to evaluate  : 0.537 
Fit side-chains
REVERT: A  144 GLU cc_start: 0.8605 (tp30) cc_final: 0.8401 (tp30)
REVERT: A  178 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8659 (tp30)
REVERT: A  243 PHE cc_start: 0.8436 (t80) cc_final: 0.8215 (t80)
REVERT: B  107 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8650 (ttpp)
REVERT: C  243 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8256 (t80)
REVERT: D  129 LYS cc_start: 0.8977 (mmmt) cc_final: 0.8561 (mmtm)
REVERT: E  123 MET cc_start: 0.8589 (tpt) cc_final: 0.7572 (tmm)
REVERT: E  205 MET cc_start: 0.9444 (tpp) cc_final: 0.9212 (tpt)
REVERT: E  245 SER cc_start: 0.7828 (m) cc_final: 0.7332 (p)
REVERT: F   14 HIS cc_start: 0.8817 (m90) cc_final: 0.8297 (m90)
REVERT: G    7 MET cc_start: 0.8673 (mmp) cc_final: 0.8472 (mmt)
REVERT: G   46 GLU cc_start: 0.8619 (pm20) cc_final: 0.8379 (pm20)
REVERT: H    4 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8309 (mp0)
REVERT: I   12 GLU cc_start: 0.8623 (tp30) cc_final: 0.8099 (tp30)
REVERT: J    4 GLU cc_start: 0.8826 (mp0) cc_final: 0.8406 (mp0)
REVERT: J   46 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7442 (tp30)
REVERT: J   69 MET cc_start: 0.9015 (mtt) cc_final: 0.8734 (mtt)
REVERT: J   86 TYR cc_start: 0.8782 (m-80) cc_final: 0.8502 (m-80)
  outliers start: 46
  outliers final: 21
  residues processed: 277
  average time/residue: 0.5272
  time to fit residues: 159.3840
Evaluate side-chains
  266 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 243
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain B residue   76 ASN
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  243 PHE
Chi-restraints excluded: chain C residue  244 TYR
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain E residue  101 MET
Chi-restraints excluded: chain F residue  185 MET
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   48 THR
Chi-restraints excluded: chain G residue   49 LEU
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain I residue    9 MET
Chi-restraints excluded: chain I residue   26 LEU
Chi-restraints excluded: chain J residue    7 MET
Chi-restraints excluded: chain J residue   26 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 81 optimal weight:    0.8980
   chunk 66 optimal weight:    7.9990
   chunk 111 optimal weight:    3.9990
   chunk 130 optimal weight:    3.9990
   chunk 146 optimal weight:    9.9990
   chunk 26 optimal weight:    0.4980
   chunk 19 optimal weight:    1.9990
   chunk 161 optimal weight:    4.9990
   chunk 149 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   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  36 GLN
B  76 ASN
I  83 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.075050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.055501 restraints weight = 50784.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.2858 rms_B_bonded: 3.51
r_work: 0.2704 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2713
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2713
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13530  Z= 0.144
  Angle     :  0.667   8.223  18451  Z= 0.316
  Chirality :  0.042   0.171   2290
  Planarity :  0.005   0.053   2261
  Dihedral  :  3.968  26.714   1799
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.90 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.21), residues: 1705
  helix:  2.17 (0.14), residues: 1346
  sheet: -0.86 (0.63), residues: 48
  loop : -1.07 (0.40), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  75 
 TYR   0.021   0.001   TYR E 113 
 PHE   0.023   0.002   PHE F  92 
 TRP   0.005   0.001   TRP E  38 
 HIS   0.001   0.000   HIS F 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (13530)
  covalent geometry    : angle       0.66656 (18451)
  hydrogen bonds       : bond        0.03510 ( 1014)
  hydrogen bonds       : angle       3.74966 ( 3001)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 252
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 MET cc_start: 0.8911 (mtt) cc_final: 0.8402 (mtt)
REVERT: A  144 GLU cc_start: 0.8563 (tp30) cc_final: 0.8316 (tp30)
REVERT: B  107 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8637 (ttpp)
REVERT: C   54 LEU cc_start: 0.8994 (mt) cc_final: 0.8786 (mp)
REVERT: C  210 MET cc_start: 0.9214 (ptt) cc_final: 0.9010 (pmm)
REVERT: C  243 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8151 (t80)
REVERT: E  123 MET cc_start: 0.8622 (tpt) cc_final: 0.7613 (tmm)
REVERT: E  205 MET cc_start: 0.9403 (tpp) cc_final: 0.9065 (tpt)
REVERT: E  245 SER cc_start: 0.7654 (m) cc_final: 0.7169 (p)
REVERT: F   14 HIS cc_start: 0.8817 (m90) cc_final: 0.8290 (m90)
REVERT: F  206 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.8062 (ttt90)
REVERT: G   46 GLU cc_start: 0.8679 (pm20) cc_final: 0.8417 (pm20)
REVERT: H    4 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8310 (mp0)
REVERT: I   12 GLU cc_start: 0.8585 (tp30) cc_final: 0.8052 (tp30)
REVERT: J    4 GLU cc_start: 0.8800 (mp0) cc_final: 0.8414 (mp0)
REVERT: J   46 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7416 (tp30)
REVERT: J   69 MET cc_start: 0.8947 (mtt) cc_final: 0.8701 (mtt)
  outliers start: 36
  outliers final: 19
  residues processed: 271
  average time/residue: 0.5231
  time to fit residues: 154.7456
Evaluate side-chains
  263 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 242
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain B residue   76 ASN
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  243 PHE
Chi-restraints excluded: chain C residue  244 TYR
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  101 MET
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   48 THR
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain I residue   26 LEU
Chi-restraints excluded: chain J residue    7 MET
Chi-restraints excluded: chain J residue   26 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 126 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 153 optimal weight:    5.9990
   chunk 143 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   chunk 65 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
B  36 GLN
B  76 ASN
I  83 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.074065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.054294 restraints weight = 58316.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.2832 rms_B_bonded: 3.71
r_work: 0.2671 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2672
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2672
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13530  Z= 0.169
  Angle     :  0.690  16.035  18451  Z= 0.326
  Chirality :  0.042   0.168   2290
  Planarity :  0.005   0.054   2261
  Dihedral  :  3.970  28.712   1799
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.79 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.21), residues: 1705
  helix:  2.17 (0.14), residues: 1347
  sheet: -0.84 (0.63), residues: 48
  loop : -1.10 (0.40), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  75 
 TYR   0.014   0.001   TYR A 109 
 PHE   0.024   0.002   PHE F  92 
 TRP   0.004   0.001   TRP E 232 
 HIS   0.001   0.001   HIS F 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (13530)
  covalent geometry    : angle       0.68979 (18451)
  hydrogen bonds       : bond        0.03580 ( 1014)
  hydrogen bonds       : angle       3.73988 ( 3001)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 243
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 GLU cc_start: 0.8576 (tp30) cc_final: 0.8177 (tp30)
REVERT: A  178 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8696 (tp30)
REVERT: C  210 MET cc_start: 0.9285 (ptt) cc_final: 0.9046 (pmm)
REVERT: C  243 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8285 (t80)
REVERT: E   38 TRP cc_start: 0.8383 (m100) cc_final: 0.8071 (m100)
REVERT: E  123 MET cc_start: 0.8614 (tpt) cc_final: 0.7624 (tmm)
REVERT: E  205 MET cc_start: 0.9428 (tpp) cc_final: 0.9099 (tpt)
REVERT: E  224 MET cc_start: 0.9155 (mtm) cc_final: 0.8933 (mtt)
REVERT: E  245 SER cc_start: 0.7623 (m) cc_final: 0.7117 (p)
REVERT: F   14 HIS cc_start: 0.8826 (m90) cc_final: 0.8328 (m90)
REVERT: F  206 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.8134 (ttt90)
REVERT: G   46 GLU cc_start: 0.8748 (pm20) cc_final: 0.8362 (pm20)
REVERT: H    4 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8350 (mp0)
REVERT: H    7 MET cc_start: 0.8055 (tpt) cc_final: 0.7836 (tpp)
REVERT: H   12 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7597 (tm-30)
REVERT: I   12 GLU cc_start: 0.8603 (tp30) cc_final: 0.8080 (tp30)
REVERT: J    4 GLU cc_start: 0.8815 (mp0) cc_final: 0.8371 (mp0)
REVERT: J   46 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7428 (tp30)
REVERT: J   69 MET cc_start: 0.8989 (mtt) cc_final: 0.8744 (mtt)
  outliers start: 35
  outliers final: 27
  residues processed: 263
  average time/residue: 0.5253
  time to fit residues: 151.0568
Evaluate side-chains
  269 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 241
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   76 ASN
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  243 PHE
Chi-restraints excluded: chain C residue  244 TYR
Chi-restraints excluded: chain D residue  210 MET
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  101 MET
Chi-restraints excluded: chain F residue  207 MET
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   48 THR
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain I residue    9 MET
Chi-restraints excluded: chain I residue   26 LEU
Chi-restraints excluded: chain J residue    7 MET
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain J residue   82 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 85 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 127 optimal weight:    0.9980
   chunk 65 optimal weight:    9.9990
   chunk 111 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 39 optimal weight:    0.4980
   chunk 124 optimal weight:    0.9990
   chunk 157 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B  36 GLN
B  76 ASN
I  83 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.074783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.055265 restraints weight = 50826.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 3.52
r_work: 0.2700 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2711
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2711
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13530  Z= 0.145
  Angle     :  0.664  10.852  18451  Z= 0.314
  Chirality :  0.041   0.204   2290
  Planarity :  0.005   0.053   2261
  Dihedral  :  3.948  29.075   1799
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 18.83 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.21), residues: 1705
  helix:  2.21 (0.14), residues: 1346
  sheet: -0.82 (0.64), residues: 48
  loop : -1.02 (0.40), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  75 
 TYR   0.020   0.001   TYR E 113 
 PHE   0.021   0.002   PHE F  92 
 TRP   0.005   0.001   TRP E 232 
 HIS   0.001   0.001   HIS F 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (13530)
  covalent geometry    : angle       0.66370 (18451)
  hydrogen bonds       : bond        0.03417 ( 1014)
  hydrogen bonds       : angle       3.70621 ( 3001)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 248
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 GLU cc_start: 0.8550 (tp30) cc_final: 0.8183 (tp30)
REVERT: C  210 MET cc_start: 0.9242 (ptt) cc_final: 0.9026 (pmm)
REVERT: C  243 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8293 (t80)
REVERT: E   38 TRP cc_start: 0.8393 (m100) cc_final: 0.8017 (m100)
REVERT: E  123 MET cc_start: 0.8630 (tpt) cc_final: 0.7613 (tmm)
REVERT: E  205 MET cc_start: 0.9415 (tpp) cc_final: 0.9133 (tpt)
REVERT: E  209 MET cc_start: 0.9289 (mtt) cc_final: 0.8896 (mtt)
REVERT: E  245 SER cc_start: 0.7614 (m) cc_final: 0.7129 (p)
REVERT: F   14 HIS cc_start: 0.8813 (m90) cc_final: 0.8313 (m90)
REVERT: F  122 MET cc_start: 0.8016 (mtt) cc_final: 0.7589 (ppp)
REVERT: F  257 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8400 (tm-30)
REVERT: G   46 GLU cc_start: 0.8725 (pm20) cc_final: 0.8351 (pm20)
REVERT: H    4 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8327 (mp0)
REVERT: H    7 MET cc_start: 0.8058 (tpt) cc_final: 0.7824 (tpp)
REVERT: H   12 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7523 (tm-30)
REVERT: I   12 GLU cc_start: 0.8567 (tp30) cc_final: 0.8031 (tp30)
REVERT: J    4 GLU cc_start: 0.8781 (mp0) cc_final: 0.8344 (mp0)
REVERT: J   69 MET cc_start: 0.8973 (mtt) cc_final: 0.8745 (mtt)
  outliers start: 37
  outliers final: 25
  residues processed: 269
  average time/residue: 0.5060
  time to fit residues: 148.8387
Evaluate side-chains
  267 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 241
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  243 PHE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   76 ASN
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  243 PHE
Chi-restraints excluded: chain C residue  244 TYR
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  210 MET
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  101 MET
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   48 THR
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain I residue    9 MET
Chi-restraints excluded: chain I residue   26 LEU
Chi-restraints excluded: chain J residue    7 MET
Chi-restraints excluded: chain J residue   26 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 131 optimal weight:    0.9990
   chunk 120 optimal weight:    4.9990
   chunk 84 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 161 optimal weight:    4.9990
   chunk 153 optimal weight:    4.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
B  76 ASN
H  45 ASN
I  83 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.075992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.056526 restraints weight = 41694.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 3.25
r_work: 0.2729 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2739
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2739
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13530  Z= 0.136
  Angle     :  0.677  10.737  18451  Z= 0.319
  Chirality :  0.042   0.359   2290
  Planarity :  0.005   0.054   2261
  Dihedral  :  3.917  28.130   1799
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 20.07 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.42 (0.21), residues: 1705
  helix:  2.24 (0.14), residues: 1347
  sheet: -0.76 (0.64), residues: 48
  loop : -0.92 (0.41), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 206 
 TYR   0.014   0.001   TYR A 109 
 PHE   0.019   0.001   PHE F  92 
 TRP   0.005   0.001   TRP I  68 
 HIS   0.001   0.000   HIS F 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (13530)
  covalent geometry    : angle       0.67742 (18451)
  hydrogen bonds       : bond        0.03278 ( 1014)
  hydrogen bonds       : angle       3.66579 ( 3001)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 248
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 GLU cc_start: 0.8504 (tp30) cc_final: 0.8156 (tp30)
REVERT: B  107 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8601 (ttpp)
REVERT: B  125 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7898 (tm-30)
REVERT: B  224 MET cc_start: 0.9266 (ttp) cc_final: 0.8999 (ttm)
REVERT: C  243 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8249 (t80)
REVERT: E  123 MET cc_start: 0.8617 (tpt) cc_final: 0.7607 (tmm)
REVERT: E  205 MET cc_start: 0.9409 (tpp) cc_final: 0.9120 (tpt)
REVERT: E  209 MET cc_start: 0.9241 (mtt) cc_final: 0.8818 (mtt)
REVERT: E  245 SER cc_start: 0.7573 (m) cc_final: 0.7092 (p)
REVERT: F   14 HIS cc_start: 0.8810 (m90) cc_final: 0.8270 (m90)
REVERT: F  122 MET cc_start: 0.8000 (mtt) cc_final: 0.7568 (ppp)
REVERT: F  257 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8394 (tm-30)
REVERT: G    8 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8331 (mmm)
REVERT: G   46 GLU cc_start: 0.8674 (pm20) cc_final: 0.8393 (pm20)
REVERT: H    4 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8321 (mp0)
REVERT: H    7 MET cc_start: 0.8081 (tpt) cc_final: 0.7860 (tpp)
REVERT: H   12 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7585 (tm-30)
REVERT: I   12 GLU cc_start: 0.8546 (tp30) cc_final: 0.8010 (tp30)
REVERT: J    4 GLU cc_start: 0.8764 (mp0) cc_final: 0.8334 (mp0)
REVERT: J   69 MET cc_start: 0.8950 (mtt) cc_final: 0.8741 (mtt)
  outliers start: 36
  outliers final: 25
  residues processed: 270
  average time/residue: 0.5158
  time to fit residues: 152.0917
Evaluate side-chains
  268 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 240
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  243 PHE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   76 ASN
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  243 PHE
Chi-restraints excluded: chain C residue  244 TYR
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  101 MET
Chi-restraints excluded: chain F residue  246 GLU
Chi-restraints excluded: chain G residue    8 MET
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   48 THR
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain I residue    9 MET
Chi-restraints excluded: chain I residue   26 LEU
Chi-restraints excluded: chain J residue    7 MET
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain J residue   82 SER
Chi-restraints excluded: chain J residue   83 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 103 optimal weight:    0.1980
   chunk 143 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 94 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 115 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 154 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 114 optimal weight:    6.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
B  76 ASN
H  45 ASN
I  83 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.075211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.055496 restraints weight = 54476.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 3.64
r_work: 0.2702 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2713
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2713
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13530  Z= 0.142
  Angle     :  0.701  13.271  18451  Z= 0.328
  Chirality :  0.042   0.385   2290
  Planarity :  0.005   0.053   2261
  Dihedral  :  3.895  27.449   1799
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 20.48 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.21), residues: 1705
  helix:  2.25 (0.14), residues: 1350
  sheet: -0.71 (0.64), residues: 48
  loop : -0.93 (0.41), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 206 
 TYR   0.012   0.001   TYR E 244 
 PHE   0.022   0.001   PHE F  92 
 TRP   0.005   0.001   TRP I  68 
 HIS   0.001   0.000   HIS F 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (13530)
  covalent geometry    : angle       0.70135 (18451)
  hydrogen bonds       : bond        0.03294 ( 1014)
  hydrogen bonds       : angle       3.65406 ( 3001)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 246
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 GLU cc_start: 0.8505 (tp30) cc_final: 0.8191 (tp30)
REVERT: A  178 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8663 (tp30)
REVERT: C  243 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8270 (t80)
REVERT: D   58 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9289 (tm)
REVERT: E   38 TRP cc_start: 0.8394 (m100) cc_final: 0.8018 (m100)
REVERT: E  205 MET cc_start: 0.9420 (tpp) cc_final: 0.9098 (tpt)
REVERT: E  209 MET cc_start: 0.9265 (mtt) cc_final: 0.8835 (mtt)
REVERT: E  245 SER cc_start: 0.7570 (m) cc_final: 0.7107 (p)
REVERT: F   14 HIS cc_start: 0.8840 (m90) cc_final: 0.8330 (m90)
REVERT: F  122 MET cc_start: 0.8024 (mtt) cc_final: 0.7550 (ppp)
REVERT: F  257 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8414 (tm-30)
REVERT: G    8 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8344 (mmm)
REVERT: G   46 GLU cc_start: 0.8778 (pm20) cc_final: 0.8302 (pm20)
REVERT: H    4 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8339 (mp0)
REVERT: H    7 MET cc_start: 0.8118 (tpt) cc_final: 0.7886 (tpp)
REVERT: H   12 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7610 (tm-30)
REVERT: I   12 GLU cc_start: 0.8578 (tp30) cc_final: 0.8050 (tp30)
REVERT: J    1 MET cc_start: 0.8604 (mmt) cc_final: 0.8374 (mmt)
REVERT: J    4 GLU cc_start: 0.8785 (mp0) cc_final: 0.8349 (mp0)
REVERT: J   69 MET cc_start: 0.8994 (mtt) cc_final: 0.8786 (mtt)
  outliers start: 29
  outliers final: 24
  residues processed: 265
  average time/residue: 0.5556
  time to fit residues: 160.5093
Evaluate side-chains
  263 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 236
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  243 PHE
Chi-restraints excluded: chain B residue   76 ASN
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  243 PHE
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  101 MET
Chi-restraints excluded: chain F residue  246 GLU
Chi-restraints excluded: chain G residue    8 MET
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   48 THR
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain I residue    9 MET
Chi-restraints excluded: chain I residue   26 LEU
Chi-restraints excluded: chain I residue   45 ASN
Chi-restraints excluded: chain J residue    7 MET
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain J residue   82 SER
Chi-restraints excluded: chain J residue   83 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 130 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 101 optimal weight:    0.7980
   chunk 55 optimal weight:    0.1980
   chunk 145 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 165 optimal weight:    2.9990
   chunk 161 optimal weight:    4.9990
   chunk 69 optimal weight:    0.8980
   chunk 86 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
B  76 ASN
C 155 ASN
** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  83 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.074267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.055354 restraints weight = 49235.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 3.36
r_work: 0.2747 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13530  Z= 0.144
  Angle     :  0.706  13.228  18451  Z= 0.333
  Chirality :  0.042   0.376   2290
  Planarity :  0.004   0.053   2261
  Dihedral  :  3.891  26.813   1799
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 20.62 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.46 (0.21), residues: 1705
  helix:  2.27 (0.14), residues: 1349
  sheet: -0.67 (0.64), residues: 48
  loop : -0.95 (0.41), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 152 
 TYR   0.015   0.001   TYR A 109 
 PHE   0.022   0.001   PHE F  92 
 TRP   0.005   0.001   TRP I  68 
 HIS   0.001   0.000   HIS F 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (13530)
  covalent geometry    : angle       0.70600 (18451)
  hydrogen bonds       : bond        0.03287 ( 1014)
  hydrogen bonds       : angle       3.65581 ( 3001)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 239
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 GLU cc_start: 0.8511 (tp30) cc_final: 0.8220 (tp30)
REVERT: A  178 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8593 (tp30)
REVERT: B  205 MET cc_start: 0.9291 (tpp) cc_final: 0.9087 (tpt)
REVERT: C  243 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8252 (t80)
REVERT: D   58 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9327 (tm)
REVERT: E   38 TRP cc_start: 0.8395 (m100) cc_final: 0.8039 (m100)
REVERT: E  205 MET cc_start: 0.9422 (tpp) cc_final: 0.9145 (tpt)
REVERT: E  245 SER cc_start: 0.7503 (m) cc_final: 0.7022 (p)
REVERT: F   14 HIS cc_start: 0.8747 (m90) cc_final: 0.8276 (m90)
REVERT: F  122 MET cc_start: 0.7933 (mtt) cc_final: 0.7497 (ppp)
REVERT: F  257 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8434 (tm-30)
REVERT: G   46 GLU cc_start: 0.8734 (pm20) cc_final: 0.8398 (pm20)
REVERT: H    4 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8360 (mp0)
REVERT: H    7 MET cc_start: 0.8154 (tpt) cc_final: 0.7919 (tpp)
REVERT: H   12 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7679 (tm-30)
REVERT: I   12 GLU cc_start: 0.8548 (tp30) cc_final: 0.8043 (tp30)
REVERT: J    1 MET cc_start: 0.8648 (mmt) cc_final: 0.8422 (mmt)
REVERT: J    4 GLU cc_start: 0.8769 (mp0) cc_final: 0.8347 (mp0)
REVERT: J   69 MET cc_start: 0.8965 (mtt) cc_final: 0.8764 (mtt)
  outliers start: 30
  outliers final: 23
  residues processed: 259
  average time/residue: 0.5057
  time to fit residues: 143.3583
Evaluate side-chains
  262 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 237
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  243 PHE
Chi-restraints excluded: chain B residue   76 ASN
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  243 PHE
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  211 MET
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  101 MET
Chi-restraints excluded: chain F residue  246 GLU
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain I residue    9 MET
Chi-restraints excluded: chain I residue   26 LEU
Chi-restraints excluded: chain J residue    7 MET
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain J residue   82 SER
Chi-restraints excluded: chain J residue   83 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 125 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0040
   chunk 94 optimal weight:    6.9990
   chunk 103 optimal weight:    0.7980
   chunk 90 optimal weight:    0.4980
   chunk 47 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 130 optimal weight:    2.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    1.2596

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

Flipped N/Q/H residues before XYZ refinement:
B  76 ASN
C 184 GLN
** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  83 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.074053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.055292 restraints weight = 46259.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 3.27
r_work: 0.2747 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2723
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2723
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13530  Z= 0.146
  Angle     :  0.712  13.066  18451  Z= 0.335
  Chirality :  0.042   0.374   2290
  Planarity :  0.004   0.053   2261
  Dihedral  :  3.895  26.347   1799
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 20.76 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.21), residues: 1705
  helix:  2.29 (0.14), residues: 1349
  sheet: -0.66 (0.65), residues: 48
  loop : -0.94 (0.41), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 152 
 TYR   0.011   0.001   TYR E 244 
 PHE   0.023   0.001   PHE F  92 
 TRP   0.005   0.001   TRP E 232 
 HIS   0.001   0.000   HIS F 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (13530)
  covalent geometry    : angle       0.71228 (18451)
  hydrogen bonds       : bond        0.03313 ( 1014)
  hydrogen bonds       : angle       3.65550 ( 3001)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4195.90 seconds
wall clock time: 72 minutes 9.76 seconds (4329.76 seconds total)