Starting phenix.real_space_refine
on Thu Sep 18 08:27:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9r2p_53536/09_2025/9r2p_53536.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9r2p_53536/09_2025/9r2p_53536.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9r2p_53536/09_2025/9r2p_53536.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9r2p_53536/09_2025/9r2p_53536.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9r2p_53536/09_2025/9r2p_53536.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9r2p_53536/09_2025/9r2p_53536.map"
  }
  resolution = 4.18
  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=  -0.002 sd=   0.044
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: 5
    Type Number    sf(0)   Gaussians
     P     262      5.49       5
     S      14      5.16       5
     C    8803      2.51       5
     N    2948      2.21       5
     O    3433      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  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: 15460
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 646
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "C"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 2667
          Classifications: {'DNA': 131}
          Link IDs: {'rna3p': 130}
    Chain: "J"
      Number of atoms: 2704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 2704
          Classifications: {'DNA': 131}
          Link IDs: {'rna3p': 130}
    Chain: "K"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1017
          Classifications: {'peptide': 200}
          Incomplete info: {'truncation_to_alanine': 165}
          Link IDs: {'PTRANS': 14, 'TRANS': 185}
          Unresolved non-hydrogen bonds: 575
          Unresolved non-hydrogen angles: 731
          Unresolved non-hydrogen dihedrals: 474
          Unresolved non-hydrogen chiralities: 50
          Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11}
          Unresolved non-hydrogen planarities: 343
    Chain: "L"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1017
          Classifications: {'peptide': 200}
          Incomplete info: {'truncation_to_alanine': 165}
          Link IDs: {'PTRANS': 14, 'TRANS': 185}
          Unresolved non-hydrogen bonds: 575
          Unresolved non-hydrogen angles: 731
          Unresolved non-hydrogen dihedrals: 474
          Unresolved non-hydrogen chiralities: 50
          Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11}
          Unresolved non-hydrogen planarities: 343
    Chain: "M"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1017
          Classifications: {'peptide': 200}
          Incomplete info: {'truncation_to_alanine': 165}
          Link IDs: {'PTRANS': 14, 'TRANS': 185}
          Unresolved non-hydrogen bonds: 575
          Unresolved non-hydrogen angles: 731
          Unresolved non-hydrogen dihedrals: 474
          Unresolved non-hydrogen chiralities: 50
          Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11}
          Unresolved non-hydrogen planarities: 343
    Chain: "N"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1017
          Classifications: {'peptide': 200}
          Incomplete info: {'truncation_to_alanine': 165}
          Link IDs: {'PTRANS': 14, 'TRANS': 185}
          Unresolved non-hydrogen bonds: 575
          Unresolved non-hydrogen angles: 731
          Unresolved non-hydrogen dihedrals: 474
          Unresolved non-hydrogen chiralities: 50
          Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11}
          Unresolved non-hydrogen planarities: 343
  Time building chain proxies: 3.97, per 1000 atoms: 0.26
  Number of scatterers: 15460
  At special positions: 0
  Unit cell: (128.037, 195.975, 128.908, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     262     15.00
     O    3433      8.00
     N    2948      7.00
     C    8803      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: 1.61
  Conformation dependent library (CDL) restraints added in 653.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2910

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 18 sheets defined
      41.6% alpha, 15.3% beta
      131 base pairs and 249 stacking pairs defined.
    Time for finding SS restraints: 2.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 58
      removed outlier: 3.612A  pdb=" N   ARG A  50 " --> pdb=" O   THR A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 77
    Processing helix  chain 'A' and resid 86 through 115
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'B' and resid 25 through 30
    Processing helix  chain 'B' and resid 31 through 42
    Processing helix  chain 'B' and resid 50 through 77
    Processing helix  chain 'B' and resid 83 through 93
    Processing helix  chain 'C' and resid 17 through 23
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 46 through 74
      removed outlier: 4.380A  pdb=" N   VAL C  50 " --> pdb=" O   ALA C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 91
      removed outlier: 3.542A  pdb=" N   ASP C  91 " --> pdb=" O   ALA C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 98
    Processing helix  chain 'C' and resid 113 through 117
    Processing helix  chain 'D' and resid 38 through 50
      removed outlier: 3.515A  pdb=" N   GLN D  48 " --> pdb=" O   LYS D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 56 through 85
    Processing helix  chain 'D' and resid 91 through 103
    Processing helix  chain 'D' and resid 104 through 125
    Processing helix  chain 'E' and resid 46 through 58
    Processing helix  chain 'E' and resid 64 through 80
      removed outlier: 3.657A  pdb=" N   PHE E  68 " --> pdb=" O   ARG E  64 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   ASP E  78 " --> pdb=" O   GLU E  74 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   PHE E  79 " --> pdb=" O   ILE E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 115
    Processing helix  chain 'E' and resid 121 through 132
    Processing helix  chain 'F' and resid 26 through 30
    Processing helix  chain 'F' and resid 31 through 42
      removed outlier: 3.543A  pdb=" N   ARG F  41 " --> pdb=" O   ARG F  37 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY F  42 " --> pdb=" O   LEU F  38 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 50 through 78
      removed outlier: 3.649A  pdb=" N   GLU F  54 " --> pdb=" O   LEU F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 94
      removed outlier: 3.952A  pdb=" N   GLN F  94 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 23
    Processing helix  chain 'G' and resid 27 through 36
      removed outlier: 3.624A  pdb=" N   VAL G  31 " --> pdb=" O   PRO G  27 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 74
      removed outlier: 4.563A  pdb=" N   VAL G  50 " --> pdb=" O   ALA G  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 91
    Processing helix  chain 'G' and resid 93 through 98
    Processing helix  chain 'G' and resid 113 through 117
    Processing helix  chain 'H' and resid 38 through 50
    Processing helix  chain 'H' and resid 56 through 85
    Processing helix  chain 'H' and resid 91 through 103
    Processing helix  chain 'H' and resid 104 through 125
      removed outlier: 3.524A  pdb=" N   HIS H 110 " --> pdb=" O   GLU H 106 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 104 through 108
      removed outlier: 3.975A  pdb=" N   TYR K 107 " --> pdb=" O   GLN K 104 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 176 through 182
    Processing helix  chain 'K' and resid 277 through 289
    Processing helix  chain 'L' and resid 165 through 169
    Processing helix  chain 'L' and resid 176 through 182
    Processing helix  chain 'L' and resid 277 through 289
    Processing helix  chain 'M' and resid 165 through 169
    Processing helix  chain 'M' and resid 176 through 182
    Processing helix  chain 'M' and resid 277 through 289
      removed outlier: 3.572A  pdb=" N   LEU M 289 " --> pdb=" O   GLU M 285 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 176 through 182
    Processing helix  chain 'N' and resid 277 through 289
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85
      removed outlier: 7.085A  pdb=" N   ARG A  84 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120
    Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99
    Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44
      removed outlier: 7.225A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103
    Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85
      removed outlier: 6.941A  pdb=" N   ARG E  84 " --> pdb=" O   VAL F  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120
    Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44
      removed outlier: 7.010A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79
    Processing sheet with id=AB2, first strand: chain 'K' and resid 110 through 113
    Processing sheet with id=AB3, first strand: chain 'K' and resid 124 through 127
      removed outlier: 6.213A  pdb=" N   MET K 133 " --> pdb=" O   ARG K 273 " (cutoff:3.500A)
      removed outlier: 7.317A  pdb=" N   CYS K 275 " --> pdb=" O   MET K 133 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   CYS K 135 " --> pdb=" O   CYS K 275 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   LEU K 257 " --> pdb=" O   LEU K 265 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   ARG K 267 " --> pdb=" O   ILE K 255 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ILE K 255 " --> pdb=" O   ARG K 267 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   SER K 269 " --> pdb=" O   THR K 253 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   THR K 253 " --> pdb=" O   SER K 269 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   GLU K 271 " --> pdb=" O   ILE K 251 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   ILE K 251 " --> pdb=" O   GLU K 271 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   ALA K 161 " --> pdb=" O   HIS K 214 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   HIS K 214 " --> pdb=" O   ALA K 161 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 110 through 112
    Processing sheet with id=AB5, first strand: chain 'L' and resid 124 through 127
      removed outlier: 6.238A  pdb=" N   LEU L 257 " --> pdb=" O   LEU L 265 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ARG L 267 " --> pdb=" O   ILE L 255 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ILE L 255 " --> pdb=" O   ARG L 267 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   SER L 269 " --> pdb=" O   THR L 253 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   THR L 253 " --> pdb=" O   SER L 269 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   GLU L 271 " --> pdb=" O   ILE L 251 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   ILE L 251 " --> pdb=" O   GLU L 271 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   ALA L 161 " --> pdb=" O   HIS L 214 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   HIS L 214 " --> pdb=" O   ALA L 161 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'M' and resid 110 through 112
    Processing sheet with id=AB7, first strand: chain 'M' and resid 124 through 127
      removed outlier: 3.772A  pdb=" N   ILE M 251 " --> pdb=" O   VAL M 272 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   ALA M 161 " --> pdb=" O   HIS M 214 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   HIS M 214 " --> pdb=" O   ALA M 161 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'N' and resid 110 through 113
    Processing sheet with id=AB9, first strand: chain 'N' and resid 124 through 127
      removed outlier: 6.403A  pdb=" N   LEU N 257 " --> pdb=" O   LEU N 265 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   ARG N 267 " --> pdb=" O   ILE N 255 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ILE N 255 " --> pdb=" O   ARG N 267 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   SER N 269 " --> pdb=" O   THR N 253 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   THR N 253 " --> pdb=" O   SER N 269 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   GLU N 271 " --> pdb=" O   ILE N 251 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   ILE N 251 " --> pdb=" O   GLU N 271 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   ALA N 161 " --> pdb=" O   HIS N 214 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   HIS N 214 " --> pdb=" O   ALA N 161 " (cutoff:3.500A)

    606 hydrogen bonds defined for protein.
    1707 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      340 hydrogen bonds
      680 hydrogen bond angles
      0 basepair planarities
      131 basepair parallelities
      249 stacking parallelities
  Total time for adding SS restraints: 3.37

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3082
        1.33 -     1.45: 4633
        1.45 -     1.57: 7997
        1.57 -     1.69: 513
        1.69 -     1.81: 24
  Bond restraints: 16249
  Sorted by residual:
  bond pdb=" P    DC I  79 "
       pdb=" O5'  DC I  79 "
    ideal  model  delta    sigma   weight residual
    1.600  1.562  0.038 2.00e-02 2.50e+03 3.66e+00
  bond pdb=" P    DG J  79 "
       pdb=" O5'  DG J  79 "
    ideal  model  delta    sigma   weight residual
    1.600  1.563  0.037 2.00e-02 2.50e+03 3.43e+00
  bond pdb=" C3'  DC I  79 "
       pdb=" O3'  DC I  79 "
    ideal  model  delta    sigma   weight residual
    1.422  1.368  0.054 3.00e-02 1.11e+03 3.19e+00
  bond pdb=" P    DC I  80 "
       pdb=" O5'  DC I  80 "
    ideal  model  delta    sigma   weight residual
    1.600  1.564  0.036 2.00e-02 2.50e+03 3.15e+00
  bond pdb=" C5'  DC I  79 "
       pdb=" C4'  DC I  79 "
    ideal  model  delta    sigma   weight residual
    1.518  1.484  0.034 2.00e-02 2.50e+03 2.95e+00
  ... (remaining 16244 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 21293
        1.61 -     3.22: 1762
        3.22 -     4.84: 167
        4.84 -     6.45: 39
        6.45 -     8.06: 10
  Bond angle restraints: 23271
  Sorted by residual:
  angle pdb=" O3'  DC J  78 "
        pdb=" P    DG J  79 "
        pdb=" O5'  DG J  79 "
      ideal   model   delta    sigma   weight residual
     104.00   96.58    7.42 1.50e+00 4.44e-01 2.45e+01
  angle pdb=" O3'  DC I  79 "
        pdb=" P    DC I  80 "
        pdb=" O5'  DC I  80 "
      ideal   model   delta    sigma   weight residual
     104.00   96.84    7.16 1.50e+00 4.44e-01 2.28e+01
  angle pdb=" O3'  DG I  99 "
        pdb=" P    DG I 100 "
        pdb=" O5'  DG I 100 "
      ideal   model   delta    sigma   weight residual
     104.00   97.16    6.84 1.50e+00 4.44e-01 2.08e+01
  angle pdb=" O3'  DC I  78 "
        pdb=" P    DC I  79 "
        pdb=" O5'  DC I  79 "
      ideal   model   delta    sigma   weight residual
     104.00   97.48    6.52 1.50e+00 4.44e-01 1.89e+01
  angle pdb=" C4'  DC J  78 "
        pdb=" C3'  DC J  78 "
        pdb=" O3'  DC J  78 "
      ideal   model   delta    sigma   weight residual
     110.00  103.56    6.44 1.50e+00 4.44e-01 1.84e+01
  ... (remaining 23266 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.55: 6997
       16.55 -    33.09: 654
       33.09 -    49.64: 930
       49.64 -    66.19: 492
       66.19 -    82.73: 11
  Dihedral angle restraints: 9084
    sinusoidal: 4597
      harmonic: 4487
  Sorted by residual:
  dihedral pdb=" CA  CYS K 275 "
           pdb=" C   CYS K 275 "
           pdb=" N   ALA K 276 "
           pdb=" CA  ALA K 276 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.74   24.26     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  GLU L 224 "
           pdb=" C   GLU L 224 "
           pdb=" N   VAL L 225 "
           pdb=" CA  VAL L 225 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.92  -22.08     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  TYR N 236 "
           pdb=" C   TYR N 236 "
           pdb=" N   MET N 237 "
           pdb=" CA  MET N 237 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.35  -18.65     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 9081 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 2099
       0.068 -    0.137: 510
       0.137 -    0.205: 104
       0.205 -    0.273: 21
       0.273 -    0.341: 4
  Chirality restraints: 2738
  Sorted by residual:
  chirality pdb=" CA  LYS A 116 "
            pdb=" N   LYS A 116 "
            pdb=" C   LYS A 116 "
            pdb=" CB  LYS A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.91e+00
  chirality pdb=" CA  ARG M 248 "
            pdb=" N   ARG M 248 "
            pdb=" C   ARG M 248 "
            pdb=" CB  ARG M 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CA  LYS F  78 "
            pdb=" N   LYS F  78 "
            pdb=" C   LYS F  78 "
            pdb=" CB  LYS F  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.00e+00
  ... (remaining 2735 not shown)

  Planarity restraints: 2159
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J 121 "   -0.042 2.00e-02 2.50e+03   1.70e-02 8.71e+00
        pdb=" N9   DG J 121 "    0.036 2.00e-02 2.50e+03
        pdb=" C8   DG J 121 "    0.008 2.00e-02 2.50e+03
        pdb=" N7   DG J 121 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DG J 121 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG J 121 "   -0.006 2.00e-02 2.50e+03
        pdb=" O6   DG J 121 "   -0.014 2.00e-02 2.50e+03
        pdb=" N1   DG J 121 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DG J 121 "    0.006 2.00e-02 2.50e+03
        pdb=" N2   DG J 121 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DG J 121 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DG J 121 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J  79 "    0.037 2.00e-02 2.50e+03   1.56e-02 7.32e+00
        pdb=" N9   DG J  79 "   -0.037 2.00e-02 2.50e+03
        pdb=" C8   DG J  79 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DG J  79 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5   DG J  79 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DG J  79 "    0.006 2.00e-02 2.50e+03
        pdb=" O6   DG J  79 "    0.008 2.00e-02 2.50e+03
        pdb=" N1   DG J  79 "    0.004 2.00e-02 2.50e+03
        pdb=" C2   DG J  79 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2   DG J  79 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DG J  79 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DG J  79 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J 130 "   -0.037 2.00e-02 2.50e+03   1.55e-02 7.21e+00
        pdb=" N9   DG J 130 "    0.034 2.00e-02 2.50e+03
        pdb=" C8   DG J 130 "    0.006 2.00e-02 2.50e+03
        pdb=" N7   DG J 130 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DG J 130 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG J 130 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6   DG J 130 "   -0.015 2.00e-02 2.50e+03
        pdb=" N1   DG J 130 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DG J 130 "    0.004 2.00e-02 2.50e+03
        pdb=" N2   DG J 130 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DG J 130 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG J 130 "    0.004 2.00e-02 2.50e+03
  ... (remaining 2156 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 7236
        2.99 -     3.47: 14532
        3.47 -     3.94: 27132
        3.94 -     4.42: 30898
        4.42 -     4.90: 41898
  Nonbonded interactions: 121696
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  91 "
            pdb=" OE1 GLU D  94 "
     model   vdw
     2.509 3.040
  nonbonded pdb=" OG1 THR H  91 "
            pdb=" OE1 GLU H  94 "
     model   vdw
     2.522 3.040
  nonbonded pdb=" O3'  DC J  78 "
            pdb=" C5'  DG J  79 "
     model   vdw
     2.533 2.752
  nonbonded pdb=" OG  SER H  33 "
            pdb=" OP1  DG J 104 "
     model   vdw
     2.548 3.040
  nonbonded pdb=" N   SER D  88 "
            pdb=" OP1  DA I  40 "
     model   vdw
     2.564 3.120
  ... (remaining 121691 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 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 23 through 103)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.920
  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:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     18.910
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
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      :  0.006   0.054  16249  Z= 0.273
  Angle     :  0.911   8.061  23271  Z= 0.543
  Chirality :  0.065   0.341   2738
  Planarity :  0.006   0.048   2159
  Dihedral  : 24.600  82.733   6174
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 0.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.88 %
    Favored  : 97.97 %
  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:  0.58 (0.20), residues: 1535
  helix:  0.33 (0.19), residues: 605
  sheet:  0.79 (0.28), residues: 308
  loop :  0.47 (0.24), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  33 
 TYR   0.022   0.003   TYR D  43 
 PHE   0.021   0.003   PHE C  26 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.012   0.002   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00557 (16249)
  covalent geometry    : angle       0.91084 (23271)
  hydrogen bonds       : bond        0.14922 (  946)
  hydrogen bonds       : angle       5.94500 ( 2387)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 326
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ILE cc_start: 0.9511 (mt) cc_final: 0.9282 (mm)
REVERT: A   66 LEU cc_start: 0.9862 (mt) cc_final: 0.9621 (tp)
REVERT: A   68 PHE cc_start: 0.9665 (t80) cc_final: 0.9405 (t80)
REVERT: A   74 GLU cc_start: 0.8792 (tt0) cc_final: 0.8074 (mt-10)
REVERT: A   86 GLN cc_start: 0.9438 (mt0) cc_final: 0.9196 (mt0)
REVERT: A   93 LEU cc_start: 0.9612 (mt) cc_final: 0.9404 (mt)
REVERT: A   97 CYS cc_start: 0.9575 (m) cc_final: 0.9101 (m)
REVERT: A  120 ILE cc_start: 0.9534 (pt) cc_final: 0.9269 (pt)
REVERT: A  125 ILE cc_start: 0.9719 (mt) cc_final: 0.9418 (mp)
REVERT: B   24 ARG cc_start: 0.8762 (mtm110) cc_final: 0.8304 (mpt180)
REVERT: B   38 LEU cc_start: 0.9524 (mt) cc_final: 0.9213 (tt)
REVERT: B   51 ILE cc_start: 0.9724 (mm) cc_final: 0.9271 (mm)
REVERT: B   55 THR cc_start: 0.9793 (m) cc_final: 0.9319 (p)
REVERT: B   63 LEU cc_start: 0.9721 (tp) cc_final: 0.9512 (mm)
REVERT: B   79 ARG cc_start: 0.8603 (mtm-85) cc_final: 0.8174 (mtp180)
REVERT: C   39 ASN cc_start: 0.8725 (m-40) cc_final: 0.8376 (t0)
REVERT: C   52 LEU cc_start: 0.9741 (tp) cc_final: 0.9489 (pp)
REVERT: C   93 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9097 (tt0)
REVERT: D   81 LEU cc_start: 0.9827 (mt) cc_final: 0.9626 (mp)
REVERT: D  100 ARG cc_start: 0.9441 (mtp180) cc_final: 0.9154 (mtp85)
REVERT: D  102 LEU cc_start: 0.8808 (mt) cc_final: 0.8528 (mt)
REVERT: D  107 LEU cc_start: 0.9765 (mt) cc_final: 0.9273 (mt)
REVERT: E   62 LEU cc_start: 0.8856 (mt) cc_final: 0.8577 (mt)
REVERT: E   95 GLU cc_start: 0.9518 (mm-30) cc_final: 0.8845 (mm-30)
REVERT: E  106 GLU cc_start: 0.9533 (mt-10) cc_final: 0.9166 (tm-30)
REVERT: E  110 LEU cc_start: 0.9669 (mt) cc_final: 0.9416 (mm)
REVERT: F   45 LYS cc_start: 0.8823 (tttt) cc_final: 0.8545 (ttmt)
REVERT: F   54 GLU cc_start: 0.9486 (tp30) cc_final: 0.8838 (tt0)
REVERT: F   69 ASP cc_start: 0.9626 (m-30) cc_final: 0.9390 (m-30)
REVERT: F   85 MET cc_start: 0.9261 (mmm) cc_final: 0.8906 (mmm)
REVERT: F   97 THR cc_start: 0.9350 (m) cc_final: 0.8973 (t)
REVERT: G   42 GLU cc_start: 0.9603 (tp30) cc_final: 0.9319 (tp30)
REVERT: G   64 LEU cc_start: 0.9881 (mt) cc_final: 0.9656 (pp)
REVERT: G   73 ASP cc_start: 0.9380 (m-30) cc_final: 0.9170 (m-30)
REVERT: G   85 GLN cc_start: 0.9530 (tp-100) cc_final: 0.9259 (tp-100)
REVERT: G   91 ASP cc_start: 0.9105 (t70) cc_final: 0.8805 (t0)
REVERT: G   93 GLU cc_start: 0.9717 (mp0) cc_final: 0.9395 (mt-10)
REVERT: G   95 ASN cc_start: 0.9540 (t0) cc_final: 0.9229 (m-40)
REVERT: G  102 THR cc_start: 0.9640 (m) cc_final: 0.9405 (p)
REVERT: H   57 SER cc_start: 0.9654 (m) cc_final: 0.9282 (p)
REVERT: H   77 GLU cc_start: 0.9314 (tp30) cc_final: 0.8993 (tp30)
REVERT: H   81 LEU cc_start: 0.9782 (mt) cc_final: 0.9445 (mp)
REVERT: H  122 TYR cc_start: 0.9278 (t80) cc_final: 0.9024 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 327
  average time/residue: 0.1384
  time to fit residues: 66.1538
Evaluate side-chains
  228 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:   40.0000
   chunk 124 optimal weight:   40.0000
   chunk 103 optimal weight:    0.0070
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:   40.0000
   overall best weight:    2.9404

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

Flipped N/Q/H residues before XYZ refinement:
** B  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  40 HIS
E  94 GLN
G  39 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.088227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.054689 restraints weight = 82310.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.055946 restraints weight = 46311.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.056693 restraints weight = 31634.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.057324 restraints weight = 24357.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.057604 restraints weight = 20317.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.2854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.117  16249  Z= 0.245
  Angle     :  0.606   7.903  23271  Z= 0.351
  Chirality :  0.041   0.156   2738
  Planarity :  0.005   0.035   2159
  Dihedral  : 27.098  81.484   4491
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  1.74 %
    Favored  : 97.83 %
  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:  1.48 (0.21), residues: 1535
  helix:  1.63 (0.20), residues: 619
  sheet:  0.95 (0.29), residues: 324
  loop :  0.45 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  46 
 TYR   0.015   0.002   TYR D  43 
 PHE   0.018   0.003   PHE F  62 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.009   0.002   HIS E 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 (16249)
  covalent geometry    : angle       0.60634 (23271)
  hydrogen bonds       : bond        0.06535 (  946)
  hydrogen bonds       : angle       4.15171 ( 2387)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 259
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 PHE cc_start: 0.9753 (t80) cc_final: 0.9335 (t80)
REVERT: A   74 GLU cc_start: 0.8738 (tt0) cc_final: 0.8008 (mt-10)
REVERT: A   86 GLN cc_start: 0.9544 (mt0) cc_final: 0.9118 (mt0)
REVERT: A   94 GLN cc_start: 0.9232 (tt0) cc_final: 0.8580 (tt0)
REVERT: A   97 CYS cc_start: 0.9675 (m) cc_final: 0.9463 (m)
REVERT: A   98 GLU cc_start: 0.9411 (mt-10) cc_final: 0.8773 (mt-10)
REVERT: A  108 THR cc_start: 0.9774 (m) cc_final: 0.9572 (p)
REVERT: A  120 ILE cc_start: 0.9793 (pt) cc_final: 0.9566 (pt)
REVERT: A  121 MET cc_start: 0.8615 (mmp) cc_final: 0.8208 (tpt)
REVERT: B   24 ARG cc_start: 0.8474 (mtm110) cc_final: 0.8185 (mpt180)
REVERT: B   69 ASP cc_start: 0.9624 (m-30) cc_final: 0.9413 (m-30)
REVERT: B   86 ASP cc_start: 0.9249 (m-30) cc_final: 0.8692 (t0)
REVERT: C   39 ASN cc_start: 0.8667 (m-40) cc_final: 0.8329 (t0)
REVERT: D  100 ARG cc_start: 0.9491 (mtp180) cc_final: 0.9052 (mtp180)
REVERT: D  106 GLU cc_start: 0.9555 (tp30) cc_final: 0.9276 (tm-30)
REVERT: D  107 LEU cc_start: 0.9800 (mt) cc_final: 0.9485 (mt)
REVERT: E   56 GLN cc_start: 0.9372 (mt0) cc_final: 0.8916 (pt0)
REVERT: E   91 MET cc_start: 0.9510 (mmp) cc_final: 0.9301 (mmm)
REVERT: E  106 GLU cc_start: 0.9550 (mt-10) cc_final: 0.9255 (tm-30)
REVERT: E  121 MET cc_start: 0.8291 (ttm) cc_final: 0.7751 (ttm)
REVERT: E  125 ILE cc_start: 0.9760 (mt) cc_final: 0.9536 (mt)
REVERT: F   38 LEU cc_start: 0.9831 (mm) cc_final: 0.9611 (mm)
REVERT: F   54 GLU cc_start: 0.9523 (tp30) cc_final: 0.9008 (tt0)
REVERT: F   85 MET cc_start: 0.9311 (mmm) cc_final: 0.8796 (mmm)
REVERT: F   86 ASP cc_start: 0.8779 (m-30) cc_final: 0.8269 (t70)
REVERT: F   97 THR cc_start: 0.9474 (m) cc_final: 0.9273 (t)
REVERT: G   42 GLU cc_start: 0.9340 (tp30) cc_final: 0.9099 (tp30)
REVERT: G   73 ASP cc_start: 0.9146 (m-30) cc_final: 0.8935 (m-30)
REVERT: G   91 ASP cc_start: 0.9225 (t70) cc_final: 0.8915 (t70)
REVERT: G   93 GLU cc_start: 0.9700 (mp0) cc_final: 0.9357 (tt0)
REVERT: G   95 ASN cc_start: 0.9622 (t0) cc_final: 0.9376 (m-40)
REVERT: G   97 LEU cc_start: 0.9521 (mt) cc_final: 0.9269 (mt)
REVERT: G  105 GLN cc_start: 0.9360 (mp10) cc_final: 0.8781 (mp10)
REVERT: H   38 TYR cc_start: 0.9182 (m-80) cc_final: 0.8867 (m-10)
REVERT: H   57 SER cc_start: 0.9495 (m) cc_final: 0.9238 (p)
REVERT: H  122 TYR cc_start: 0.9329 (t80) cc_final: 0.9047 (t80)
  outliers start: 3
  outliers final: 2
  residues processed: 261
  average time/residue: 0.1105
  time to fit residues: 45.3152
Evaluate side-chains
  211 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 209
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 149 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 96 optimal weight:    7.9990
   chunk 105 optimal weight:    0.0270
   chunk 138 optimal weight:    0.0070
   chunk 127 optimal weight:   50.0000
   chunk 94 optimal weight:    5.9990
   chunk 151 optimal weight:   30.0000
   chunk 71 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 150 optimal weight:   30.0000
   overall best weight:    0.9258

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

Flipped N/Q/H residues before XYZ refinement:
A  40 HIS
** B  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  69 GLN
** F  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.115933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.085296 restraints weight = 144777.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.084345 restraints weight = 67932.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.084449 restraints weight = 55460.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.084384 restraints weight = 40635.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.084351 restraints weight = 37853.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  16249  Z= 0.148
  Angle     :  0.558  10.614  23271  Z= 0.317
  Chirality :  0.038   0.186   2738
  Planarity :  0.004   0.047   2159
  Dihedral  : 26.535  74.806   4491
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.17 %
    Favored  : 97.68 %
  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:  1.80 (0.21), residues: 1535
  helix:  2.07 (0.21), residues: 616
  sheet:  0.89 (0.29), residues: 340
  loop :  0.55 (0.25), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG F  93 
 TYR   0.015   0.002   TYR D  84 
 PHE   0.017   0.002   PHE B  62 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.007   0.001   HIS F  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (16249)
  covalent geometry    : angle       0.55823 (23271)
  hydrogen bonds       : bond        0.04049 (  946)
  hydrogen bonds       : angle       3.66551 ( 2387)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 264
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 TYR cc_start: 0.8923 (m-80) cc_final: 0.8714 (m-80)
REVERT: A   68 PHE cc_start: 0.9721 (t80) cc_final: 0.8672 (t80)
REVERT: A   74 GLU cc_start: 0.8571 (tt0) cc_final: 0.7910 (mt-10)
REVERT: A   82 ASP cc_start: 0.9012 (m-30) cc_final: 0.8811 (m-30)
REVERT: A   86 GLN cc_start: 0.9459 (mt0) cc_final: 0.8979 (mt0)
REVERT: A   94 GLN cc_start: 0.9334 (tt0) cc_final: 0.8515 (tp40)
REVERT: A   97 CYS cc_start: 0.9641 (m) cc_final: 0.9339 (p)
REVERT: A  106 GLU cc_start: 0.9515 (tm-30) cc_final: 0.9267 (tm-30)
REVERT: A  108 THR cc_start: 0.9716 (m) cc_final: 0.9501 (p)
REVERT: A  121 MET cc_start: 0.8755 (mmp) cc_final: 0.8314 (mmm)
REVERT: B   64 GLU cc_start: 0.9294 (tm-30) cc_final: 0.8824 (tm-30)
REVERT: B   68 ARG cc_start: 0.9375 (ttp-110) cc_final: 0.8796 (ttp-110)
REVERT: B   69 ASP cc_start: 0.9518 (m-30) cc_final: 0.9271 (m-30)
REVERT: B   92 LYS cc_start: 0.9135 (pttt) cc_final: 0.8843 (pttt)
REVERT: C   26 PHE cc_start: 0.8599 (m-10) cc_final: 0.8089 (m-10)
REVERT: C   39 ASN cc_start: 0.8748 (m-40) cc_final: 0.8450 (t0)
REVERT: C   60 THR cc_start: 0.9690 (p) cc_final: 0.9458 (p)
REVERT: D  100 ARG cc_start: 0.9467 (mtp180) cc_final: 0.9256 (mtp85)
REVERT: D  102 LEU cc_start: 0.9310 (mm) cc_final: 0.9044 (mm)
REVERT: E   56 GLN cc_start: 0.9429 (mt0) cc_final: 0.8962 (pt0)
REVERT: E   85 PHE cc_start: 0.9043 (m-80) cc_final: 0.8667 (m-10)
REVERT: E   95 GLU cc_start: 0.9502 (mm-30) cc_final: 0.8932 (mm-30)
REVERT: E   98 GLU cc_start: 0.9225 (pp20) cc_final: 0.8947 (pp20)
REVERT: E  106 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9261 (tm-30)
REVERT: F   38 LEU cc_start: 0.9789 (mm) cc_final: 0.9548 (mm)
REVERT: F   45 LYS cc_start: 0.8618 (ttmt) cc_final: 0.8319 (tptp)
REVERT: F   54 GLU cc_start: 0.9341 (tp30) cc_final: 0.9040 (tt0)
REVERT: F   59 LEU cc_start: 0.9661 (mm) cc_final: 0.9447 (mm)
REVERT: F   75 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8796 (tm-30)
REVERT: F   85 MET cc_start: 0.9238 (mmm) cc_final: 0.8796 (mmm)
REVERT: F   86 ASP cc_start: 0.8734 (m-30) cc_final: 0.8416 (t70)
REVERT: F   97 THR cc_start: 0.9501 (m) cc_final: 0.9276 (t)
REVERT: G   42 GLU cc_start: 0.9230 (tp30) cc_final: 0.9014 (tp30)
REVERT: G   91 ASP cc_start: 0.9186 (t70) cc_final: 0.8720 (t70)
REVERT: G   93 GLU cc_start: 0.9644 (mp0) cc_final: 0.9284 (tt0)
REVERT: G   97 LEU cc_start: 0.9434 (mt) cc_final: 0.9200 (mt)
REVERT: G  105 GLN cc_start: 0.9290 (mp10) cc_final: 0.8583 (mp10)
REVERT: H   57 SER cc_start: 0.9430 (m) cc_final: 0.9164 (p)
REVERT: H   68 ASN cc_start: 0.9494 (m110) cc_final: 0.8965 (t0)
REVERT: H   95 ILE cc_start: 0.9796 (mt) cc_final: 0.9545 (tt)
REVERT: H  101 LEU cc_start: 0.9508 (tp) cc_final: 0.9094 (tp)
REVERT: H  107 LEU cc_start: 0.9505 (mt) cc_final: 0.9029 (mt)
REVERT: H  122 TYR cc_start: 0.9210 (t80) cc_final: 0.8921 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 264
  average time/residue: 0.1199
  time to fit residues: 48.8460
Evaluate side-chains
  214 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 213
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 100 optimal weight:    1.9990
   chunk 84 optimal weight:   20.0000
   chunk 105 optimal weight:    1.9990
   chunk 101 optimal weight:   50.0000
   chunk 174 optimal weight:   50.0000
   chunk 92 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0470
   chunk 40 optimal weight:    0.8980
   chunk 127 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.9884

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

Flipped N/Q/H residues before XYZ refinement:
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.115323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.079762 restraints weight = 144727.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.081149 restraints weight = 62799.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.082288 restraints weight = 38119.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.082001 restraints weight = 30183.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.082079 restraints weight = 27002.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  16249  Z= 0.147
  Angle     :  0.539   9.598  23271  Z= 0.306
  Chirality :  0.038   0.368   2738
  Planarity :  0.004   0.055   2159
  Dihedral  : 26.204  77.308   4491
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  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:  1.94 (0.21), residues: 1535
  helix:  2.15 (0.21), residues: 618
  sheet:  0.99 (0.29), residues: 340
  loop :  0.64 (0.25), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  41 
 TYR   0.021   0.002   TYR H  84 
 PHE   0.018   0.001   PHE D  71 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.007   0.001   HIS F  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (16249)
  covalent geometry    : angle       0.53902 (23271)
  hydrogen bonds       : bond        0.04069 (  946)
  hydrogen bonds       : angle       3.51992 ( 2387)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 PHE cc_start: 0.9756 (t80) cc_final: 0.8739 (t80)
REVERT: A   71 LEU cc_start: 0.9731 (tp) cc_final: 0.9380 (tp)
REVERT: A   86 GLN cc_start: 0.9441 (mt0) cc_final: 0.9116 (mt0)
REVERT: A   94 GLN cc_start: 0.9306 (tt0) cc_final: 0.8634 (tp40)
REVERT: A  106 GLU cc_start: 0.9437 (tm-30) cc_final: 0.9139 (tm-30)
REVERT: A  108 THR cc_start: 0.9697 (m) cc_final: 0.9466 (p)
REVERT: A  121 MET cc_start: 0.8936 (mmp) cc_final: 0.8472 (mmm)
REVERT: B   44 VAL cc_start: 0.8711 (t) cc_final: 0.8398 (p)
REVERT: B   51 ILE cc_start: 0.9283 (mm) cc_final: 0.9023 (mm)
REVERT: B   69 ASP cc_start: 0.9532 (m-30) cc_final: 0.9266 (m-30)
REVERT: B   74 THR cc_start: 0.9431 (m) cc_final: 0.9196 (m)
REVERT: C   26 PHE cc_start: 0.8626 (m-10) cc_final: 0.8073 (m-10)
REVERT: C   39 ASN cc_start: 0.8766 (m-40) cc_final: 0.8524 (t0)
REVERT: D  102 LEU cc_start: 0.9324 (mm) cc_final: 0.9061 (mm)
REVERT: E   52 ILE cc_start: 0.8737 (mm) cc_final: 0.8314 (mm)
REVERT: E   56 GLN cc_start: 0.9326 (mt0) cc_final: 0.8961 (pt0)
REVERT: E   85 PHE cc_start: 0.8968 (m-80) cc_final: 0.8642 (m-10)
REVERT: E   95 GLU cc_start: 0.9452 (mm-30) cc_final: 0.8829 (mm-30)
REVERT: E   98 GLU cc_start: 0.9189 (pp20) cc_final: 0.8897 (pp20)
REVERT: E  106 GLU cc_start: 0.9450 (mt-10) cc_final: 0.9218 (tm-30)
REVERT: E  121 MET cc_start: 0.8831 (tpt) cc_final: 0.8530 (tpt)
REVERT: E  127 LEU cc_start: 0.9648 (mm) cc_final: 0.9413 (tt)
REVERT: F   38 LEU cc_start: 0.9764 (mm) cc_final: 0.9524 (mm)
REVERT: F   44 VAL cc_start: 0.8513 (t) cc_final: 0.8304 (t)
REVERT: F   54 GLU cc_start: 0.9320 (tp30) cc_final: 0.9076 (tt0)
REVERT: F   59 LEU cc_start: 0.9707 (mm) cc_final: 0.9483 (mm)
REVERT: F   85 MET cc_start: 0.9276 (mmm) cc_final: 0.8875 (mmm)
REVERT: F   86 ASP cc_start: 0.8756 (m-30) cc_final: 0.8449 (t0)
REVERT: F   97 THR cc_start: 0.9516 (m) cc_final: 0.9271 (t)
REVERT: G   26 PHE cc_start: 0.9018 (m-10) cc_final: 0.8278 (m-10)
REVERT: G   42 GLU cc_start: 0.9271 (tp30) cc_final: 0.9012 (tp30)
REVERT: G   91 ASP cc_start: 0.9167 (t70) cc_final: 0.8303 (t70)
REVERT: G   92 GLU cc_start: 0.9766 (mp0) cc_final: 0.9561 (pm20)
REVERT: G   93 GLU cc_start: 0.9574 (mp0) cc_final: 0.9117 (pm20)
REVERT: G   97 LEU cc_start: 0.9453 (mt) cc_final: 0.9164 (mt)
REVERT: G  105 GLN cc_start: 0.9241 (mp10) cc_final: 0.8522 (mp10)
REVERT: H   57 SER cc_start: 0.9438 (m) cc_final: 0.9175 (p)
REVERT: H   66 PHE cc_start: 0.9556 (t80) cc_final: 0.9312 (t80)
REVERT: H   68 ASN cc_start: 0.9475 (m110) cc_final: 0.8921 (t0)
REVERT: H   95 ILE cc_start: 0.9784 (mt) cc_final: 0.9553 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 251
  average time/residue: 0.1136
  time to fit residues: 44.8947
Evaluate side-chains
  212 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 157 optimal weight:   10.0000
   chunk 154 optimal weight:   50.0000
   chunk 156 optimal weight:   20.0000
   chunk 22 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 59 optimal weight:    0.4980
   chunk 129 optimal weight:   50.0000
   chunk 134 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   overall best weight:    2.2784

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

Flipped N/Q/H residues before XYZ refinement:
** C  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.086772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.053026 restraints weight = 83430.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.054223 restraints weight = 47385.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.055031 restraints weight = 32481.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.055493 restraints weight = 25133.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.055900 restraints weight = 21356.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.4371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083  16249  Z= 0.201
  Angle     :  0.558   7.865  23271  Z= 0.323
  Chirality :  0.039   0.221   2738
  Planarity :  0.004   0.041   2159
  Dihedral  : 26.180  80.999   4491
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  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:  2.01 (0.21), residues: 1535
  helix:  2.09 (0.21), residues: 625
  sheet:  1.01 (0.30), residues: 320
  loop :  0.86 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  79 
 TYR   0.022   0.002   TYR D  84 
 PHE   0.021   0.002   PHE B  62 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.007   0.002   HIS F  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (16249)
  covalent geometry    : angle       0.55802 (23271)
  hydrogen bonds       : bond        0.05555 (  946)
  hydrogen bonds       : angle       3.64001 ( 2387)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 PHE cc_start: 0.9756 (t80) cc_final: 0.9155 (t80)
REVERT: A   83 LEU cc_start: 0.9298 (tp) cc_final: 0.8927 (mt)
REVERT: A   95 GLU cc_start: 0.9458 (tp30) cc_final: 0.9076 (tp30)
REVERT: A  106 GLU cc_start: 0.9589 (tm-30) cc_final: 0.9294 (tm-30)
REVERT: A  108 THR cc_start: 0.9740 (m) cc_final: 0.9540 (p)
REVERT: A  121 MET cc_start: 0.8975 (mmp) cc_final: 0.8437 (mmm)
REVERT: B   37 ARG cc_start: 0.9141 (mtm-85) cc_final: 0.8407 (mtt-85)
REVERT: B   64 GLU cc_start: 0.9345 (tm-30) cc_final: 0.8936 (tm-30)
REVERT: B   68 ARG cc_start: 0.9344 (ttp-110) cc_final: 0.8744 (ttp80)
REVERT: B   69 ASP cc_start: 0.9690 (m-30) cc_final: 0.9375 (m-30)
REVERT: B   89 TYR cc_start: 0.8773 (m-10) cc_final: 0.8307 (m-80)
REVERT: C   26 PHE cc_start: 0.8609 (m-10) cc_final: 0.8311 (m-10)
REVERT: C   39 ASN cc_start: 0.8992 (m-40) cc_final: 0.8666 (t0)
REVERT: D  102 LEU cc_start: 0.9355 (mm) cc_final: 0.9135 (mm)
REVERT: D  106 GLU cc_start: 0.9601 (tp30) cc_final: 0.9325 (tm-30)
REVERT: E   52 ILE cc_start: 0.9037 (mm) cc_final: 0.8735 (mm)
REVERT: E   56 GLN cc_start: 0.9490 (mt0) cc_final: 0.9019 (pt0)
REVERT: E   95 GLU cc_start: 0.9505 (mm-30) cc_final: 0.9033 (mm-30)
REVERT: E   98 GLU cc_start: 0.9280 (pp20) cc_final: 0.8885 (pp20)
REVERT: E  106 GLU cc_start: 0.9521 (mt-10) cc_final: 0.9266 (tm-30)
REVERT: E  121 MET cc_start: 0.8911 (tpt) cc_final: 0.8493 (tpt)
REVERT: E  127 LEU cc_start: 0.9631 (mm) cc_final: 0.9338 (tp)
REVERT: F   38 LEU cc_start: 0.9850 (mm) cc_final: 0.9606 (mm)
REVERT: F   54 GLU cc_start: 0.9500 (tp30) cc_final: 0.9162 (tt0)
REVERT: F   85 MET cc_start: 0.9374 (mmm) cc_final: 0.8920 (mmm)
REVERT: F   86 ASP cc_start: 0.8885 (m-30) cc_final: 0.8382 (t0)
REVERT: F   97 THR cc_start: 0.9471 (m) cc_final: 0.9204 (t)
REVERT: G   26 PHE cc_start: 0.9127 (m-10) cc_final: 0.8675 (m-10)
REVERT: G   39 ASN cc_start: 0.9025 (m-40) cc_final: 0.7927 (m-40)
REVERT: G   91 ASP cc_start: 0.9217 (t70) cc_final: 0.8579 (t70)
REVERT: G   93 GLU cc_start: 0.9689 (mp0) cc_final: 0.9219 (pm20)
REVERT: G   94 LEU cc_start: 0.9754 (mt) cc_final: 0.9504 (mt)
REVERT: G   97 LEU cc_start: 0.9409 (mt) cc_final: 0.9180 (mt)
REVERT: G  105 GLN cc_start: 0.9252 (mp10) cc_final: 0.8534 (mp10)
REVERT: H   57 SER cc_start: 0.9430 (m) cc_final: 0.9155 (p)
REVERT: H   68 ASN cc_start: 0.9486 (m110) cc_final: 0.8917 (t0)
REVERT: H   95 ILE cc_start: 0.9766 (mt) cc_final: 0.9486 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.1060
  time to fit residues: 40.3533
Evaluate side-chains
  197 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 100 optimal weight:    8.9990
   chunk 144 optimal weight:    9.9990
   chunk 106 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 129 optimal weight:   50.0000
   chunk 160 optimal weight:    7.9990
   chunk 90 optimal weight:    4.9990
   chunk 170 optimal weight:   30.0000
   chunk 38 optimal weight:    0.0570
   overall best weight:    2.3702

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

Flipped N/Q/H residues before XYZ refinement:
A  94 GLN
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.086501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.052603 restraints weight = 83884.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.053749 restraints weight = 47792.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.054560 restraints weight = 32912.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.055093 restraints weight = 25491.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.055406 restraints weight = 21328.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.4743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  16249  Z= 0.194
  Angle     :  0.557   7.046  23271  Z= 0.322
  Chirality :  0.038   0.167   2738
  Planarity :  0.004   0.035   2159
  Dihedral  : 26.315  82.110   4491
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  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:  1.97 (0.21), residues: 1535
  helix:  2.00 (0.21), residues: 618
  sheet:  1.04 (0.30), residues: 320
  loop :  0.88 (0.25), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG F  93 
 TYR   0.023   0.002   TYR D  84 
 PHE   0.015   0.002   PHE D  71 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.012   0.002   HIS F  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (16249)
  covalent geometry    : angle       0.55731 (23271)
  hydrogen bonds       : bond        0.04940 (  946)
  hydrogen bonds       : angle       3.71523 ( 2387)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ILE cc_start: 0.9337 (mm) cc_final: 0.9072 (mm)
REVERT: A   61 LEU cc_start: 0.8508 (mt) cc_final: 0.8118 (mt)
REVERT: A  104 LEU cc_start: 0.9546 (tt) cc_final: 0.9343 (tt)
REVERT: A  106 GLU cc_start: 0.9579 (tm-30) cc_final: 0.9292 (tm-30)
REVERT: A  108 THR cc_start: 0.9739 (m) cc_final: 0.9529 (p)
REVERT: A  121 MET cc_start: 0.8885 (mmp) cc_final: 0.8327 (mmm)
REVERT: B   64 GLU cc_start: 0.9392 (tm-30) cc_final: 0.8997 (tm-30)
REVERT: B   68 ARG cc_start: 0.9398 (ttp-110) cc_final: 0.8713 (ttp80)
REVERT: B   69 ASP cc_start: 0.9730 (m-30) cc_final: 0.9440 (m-30)
REVERT: C   26 PHE cc_start: 0.8382 (m-10) cc_final: 0.8068 (m-10)
REVERT: C   39 ASN cc_start: 0.9058 (m-40) cc_final: 0.8654 (m-40)
REVERT: C   42 GLU cc_start: 0.9109 (tp30) cc_final: 0.8801 (tp30)
REVERT: D   85 ASN cc_start: 0.8890 (m110) cc_final: 0.8678 (m-40)
REVERT: D  102 LEU cc_start: 0.9349 (mm) cc_final: 0.9098 (mm)
REVERT: E   52 ILE cc_start: 0.9112 (mm) cc_final: 0.8743 (mm)
REVERT: E   95 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9029 (mm-30)
REVERT: E   98 GLU cc_start: 0.9256 (pp20) cc_final: 0.8866 (pp20)
REVERT: E  121 MET cc_start: 0.8934 (tpt) cc_final: 0.8459 (tpt)
REVERT: F   38 LEU cc_start: 0.9856 (mm) cc_final: 0.9622 (mm)
REVERT: F   54 GLU cc_start: 0.9497 (tp30) cc_final: 0.9198 (tt0)
REVERT: F   69 ASP cc_start: 0.9497 (m-30) cc_final: 0.9283 (m-30)
REVERT: F   75 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8925 (tm-30)
REVERT: F   85 MET cc_start: 0.9341 (mmm) cc_final: 0.8784 (mmm)
REVERT: F   86 ASP cc_start: 0.8855 (m-30) cc_final: 0.8352 (t0)
REVERT: F   97 THR cc_start: 0.9493 (m) cc_final: 0.9240 (t)
REVERT: G   26 PHE cc_start: 0.9099 (m-10) cc_final: 0.8764 (m-10)
REVERT: G   39 ASN cc_start: 0.9048 (m-40) cc_final: 0.8488 (t0)
REVERT: G   57 GLU cc_start: 0.9383 (pt0) cc_final: 0.8953 (pp20)
REVERT: G   91 ASP cc_start: 0.9176 (t70) cc_final: 0.8381 (t70)
REVERT: G   93 GLU cc_start: 0.9518 (mp0) cc_final: 0.9156 (pm20)
REVERT: G   94 LEU cc_start: 0.9772 (mt) cc_final: 0.9514 (mm)
REVERT: G   97 LEU cc_start: 0.9411 (mt) cc_final: 0.9150 (mt)
REVERT: G  105 GLN cc_start: 0.9211 (mp10) cc_final: 0.8486 (mp10)
REVERT: H   57 SER cc_start: 0.9416 (m) cc_final: 0.9061 (p)
REVERT: H   68 ASN cc_start: 0.9517 (m110) cc_final: 0.8943 (t0)
REVERT: H   95 ILE cc_start: 0.9762 (mt) cc_final: 0.9484 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.1095
  time to fit residues: 40.7736
Evaluate side-chains
  193 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 111 optimal weight:   40.0000
   chunk 41 optimal weight:    0.5980
   chunk 131 optimal weight:   20.0000
   chunk 86 optimal weight:   20.0000
   chunk 4 optimal weight:    8.9990
   chunk 151 optimal weight:    0.0970
   chunk 76 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 140 optimal weight:   50.0000
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 110 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.086407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.052323 restraints weight = 84788.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.053406 restraints weight = 48868.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.054046 restraints weight = 33989.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.054616 restraints weight = 26885.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.055078 restraints weight = 22541.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.5035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  16249  Z= 0.181
  Angle     :  0.554   7.954  23271  Z= 0.318
  Chirality :  0.038   0.172   2738
  Planarity :  0.004   0.065   2159
  Dihedral  : 26.295  81.448   4491
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  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:  1.98 (0.22), residues: 1535
  helix:  1.99 (0.21), residues: 619
  sheet:  1.05 (0.30), residues: 320
  loop :  0.89 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG G  18 
 TYR   0.018   0.001   TYR D  84 
 PHE   0.014   0.001   PHE D  71 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.010   0.002   HIS F  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (16249)
  covalent geometry    : angle       0.55427 (23271)
  hydrogen bonds       : bond        0.04750 (  946)
  hydrogen bonds       : angle       3.64599 ( 2387)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ILE cc_start: 0.9375 (mm) cc_final: 0.9096 (mm)
REVERT: A   61 LEU cc_start: 0.8436 (mt) cc_final: 0.8175 (mt)
REVERT: A   68 PHE cc_start: 0.9693 (t80) cc_final: 0.9478 (t80)
REVERT: A   83 LEU cc_start: 0.9348 (tp) cc_final: 0.8837 (mt)
REVERT: A   95 GLU cc_start: 0.9505 (mm-30) cc_final: 0.8640 (mm-30)
REVERT: A   98 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8949 (pp20)
REVERT: A  104 LEU cc_start: 0.9523 (tt) cc_final: 0.9314 (tt)
REVERT: A  106 GLU cc_start: 0.9562 (tm-30) cc_final: 0.9294 (tm-30)
REVERT: A  108 THR cc_start: 0.9726 (m) cc_final: 0.9511 (p)
REVERT: A  121 MET cc_start: 0.8936 (mmp) cc_final: 0.8300 (mmm)
REVERT: B   65 ASN cc_start: 0.9440 (m-40) cc_final: 0.9134 (t0)
REVERT: B   68 ARG cc_start: 0.9416 (ttp-110) cc_final: 0.8893 (ttp80)
REVERT: B   69 ASP cc_start: 0.9636 (m-30) cc_final: 0.8990 (m-30)
REVERT: B   74 THR cc_start: 0.9421 (m) cc_final: 0.9209 (p)
REVERT: B   85 MET cc_start: 0.8839 (ppp) cc_final: 0.8570 (ppp)
REVERT: B   86 ASP cc_start: 0.9355 (t0) cc_final: 0.9110 (t0)
REVERT: C   26 PHE cc_start: 0.8431 (m-10) cc_final: 0.8088 (m-10)
REVERT: C   39 ASN cc_start: 0.9030 (m-40) cc_final: 0.8680 (t0)
REVERT: D  100 ARG cc_start: 0.9429 (mtp180) cc_final: 0.8949 (mtp180)
REVERT: D  102 LEU cc_start: 0.9348 (mm) cc_final: 0.9054 (mm)
REVERT: E   52 ILE cc_start: 0.9155 (mm) cc_final: 0.8775 (mm)
REVERT: E   95 GLU cc_start: 0.9433 (mm-30) cc_final: 0.8910 (mm-30)
REVERT: E   98 GLU cc_start: 0.9151 (pp20) cc_final: 0.8885 (pp20)
REVERT: E  106 GLU cc_start: 0.9270 (tm-30) cc_final: 0.8869 (tm-30)
REVERT: E  121 MET cc_start: 0.8964 (tpt) cc_final: 0.8468 (tpt)
REVERT: F   38 LEU cc_start: 0.9818 (mm) cc_final: 0.9616 (pp)
REVERT: F   54 GLU cc_start: 0.9466 (tp30) cc_final: 0.9176 (tt0)
REVERT: F   69 ASP cc_start: 0.9458 (m-30) cc_final: 0.9248 (m-30)
REVERT: F   75 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8851 (tm-30)
REVERT: F   85 MET cc_start: 0.9324 (mmm) cc_final: 0.8711 (mmm)
REVERT: F   86 ASP cc_start: 0.8820 (m-30) cc_final: 0.8366 (t0)
REVERT: F   97 THR cc_start: 0.9511 (m) cc_final: 0.9245 (t)
REVERT: G   26 PHE cc_start: 0.9076 (m-10) cc_final: 0.8796 (m-10)
REVERT: G   42 GLU cc_start: 0.9419 (tp30) cc_final: 0.9176 (tp30)
REVERT: G   57 GLU cc_start: 0.9373 (pt0) cc_final: 0.8977 (pp20)
REVERT: G   91 ASP cc_start: 0.9162 (t70) cc_final: 0.8294 (t0)
REVERT: G   93 GLU cc_start: 0.9520 (mp0) cc_final: 0.9214 (pm20)
REVERT: G   94 LEU cc_start: 0.9757 (mt) cc_final: 0.9492 (mt)
REVERT: G  105 GLN cc_start: 0.8967 (mp10) cc_final: 0.8581 (mp10)
REVERT: H   57 SER cc_start: 0.9414 (m) cc_final: 0.9064 (p)
REVERT: H   68 ASN cc_start: 0.9552 (m110) cc_final: 0.8932 (t0)
REVERT: H   95 ILE cc_start: 0.9748 (mt) cc_final: 0.9494 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.1162
  time to fit residues: 42.4023
Evaluate side-chains
  193 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   chunk 120 optimal weight:   50.0000
   chunk 102 optimal weight:   30.0000
   chunk 104 optimal weight:   30.0000
   chunk 48 optimal weight:    0.9990
   chunk 172 optimal weight:   50.0000
   chunk 155 optimal weight:    9.9990
   chunk 52 optimal weight:    0.0970
   overall best weight:    2.1784

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

Flipped N/Q/H residues before XYZ refinement:
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  96 GLN
** H  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.088604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.054488 restraints weight = 82545.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.055139 restraints weight = 52473.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 16)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.055514 restraints weight = 37478.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.055951 restraints weight = 31597.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.056462 restraints weight = 27596.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.5282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  16249  Z= 0.191
  Angle     :  0.562   6.423  23271  Z= 0.324
  Chirality :  0.038   0.171   2738
  Planarity :  0.005   0.094   2159
  Dihedral  : 26.287  82.464   4491
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  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:  1.92 (0.21), residues: 1535
  helix:  1.92 (0.21), residues: 618
  sheet:  1.00 (0.30), residues: 320
  loop :  0.92 (0.25), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG G  18 
 TYR   0.021   0.002   TYR B  52 
 PHE   0.013   0.001   PHE D  71 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.011   0.002   HIS F  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (16249)
  covalent geometry    : angle       0.56160 (23271)
  hydrogen bonds       : bond        0.05082 (  946)
  hydrogen bonds       : angle       3.65271 ( 2387)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ILE cc_start: 0.9369 (mm) cc_final: 0.9081 (mm)
REVERT: A   65 LYS cc_start: 0.9787 (mptt) cc_final: 0.9416 (mmtp)
REVERT: A   68 PHE cc_start: 0.9726 (t80) cc_final: 0.9522 (t80)
REVERT: A   95 GLU cc_start: 0.9542 (mm-30) cc_final: 0.8868 (mm-30)
REVERT: A   98 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8938 (pp20)
REVERT: A  104 LEU cc_start: 0.9523 (tt) cc_final: 0.9313 (tt)
REVERT: A  106 GLU cc_start: 0.9582 (tm-30) cc_final: 0.9330 (tm-30)
REVERT: A  108 THR cc_start: 0.9716 (m) cc_final: 0.9493 (p)
REVERT: A  121 MET cc_start: 0.8959 (mmp) cc_final: 0.8319 (mmm)
REVERT: B   68 ARG cc_start: 0.9406 (ttp-110) cc_final: 0.9072 (ttp-170)
REVERT: B   69 ASP cc_start: 0.9709 (m-30) cc_final: 0.9028 (m-30)
REVERT: B   89 TYR cc_start: 0.8802 (m-10) cc_final: 0.8400 (m-80)
REVERT: C   26 PHE cc_start: 0.8473 (m-10) cc_final: 0.8148 (m-10)
REVERT: C   39 ASN cc_start: 0.9093 (m-40) cc_final: 0.8689 (t0)
REVERT: C   42 GLU cc_start: 0.9181 (tp30) cc_final: 0.8977 (tp30)
REVERT: D  100 ARG cc_start: 0.9234 (mtp180) cc_final: 0.8867 (mtp-110)
REVERT: D  102 LEU cc_start: 0.9303 (mm) cc_final: 0.8528 (mm)
REVERT: E   95 GLU cc_start: 0.9429 (mm-30) cc_final: 0.8956 (mm-30)
REVERT: E   98 GLU cc_start: 0.9195 (pp20) cc_final: 0.8832 (pp20)
REVERT: E  106 GLU cc_start: 0.9272 (tm-30) cc_final: 0.8901 (tm-30)
REVERT: E  121 MET cc_start: 0.8964 (tpt) cc_final: 0.8491 (tpt)
REVERT: F   38 LEU cc_start: 0.9819 (mm) cc_final: 0.9617 (pp)
REVERT: F   54 GLU cc_start: 0.9534 (tp30) cc_final: 0.9194 (tt0)
REVERT: F   75 GLU cc_start: 0.9249 (tm-30) cc_final: 0.8909 (tm-30)
REVERT: F   85 MET cc_start: 0.9327 (mmm) cc_final: 0.8732 (mmm)
REVERT: F   86 ASP cc_start: 0.8860 (m-30) cc_final: 0.8387 (t0)
REVERT: F   97 THR cc_start: 0.9457 (m) cc_final: 0.9210 (t)
REVERT: G   26 PHE cc_start: 0.9034 (m-10) cc_final: 0.8752 (m-10)
REVERT: G   42 GLU cc_start: 0.9487 (tp30) cc_final: 0.9162 (tp30)
REVERT: G   57 GLU cc_start: 0.9398 (pt0) cc_final: 0.8987 (pp20)
REVERT: G   91 ASP cc_start: 0.9131 (t70) cc_final: 0.8141 (t0)
REVERT: G   93 GLU cc_start: 0.9583 (mp0) cc_final: 0.9266 (pm20)
REVERT: G   94 LEU cc_start: 0.9779 (mt) cc_final: 0.9433 (mp)
REVERT: G  105 GLN cc_start: 0.8956 (mp10) cc_final: 0.8469 (mp10)
REVERT: H   57 SER cc_start: 0.9411 (m) cc_final: 0.9058 (p)
REVERT: H   68 ASN cc_start: 0.9533 (m110) cc_final: 0.8945 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.1074
  time to fit residues: 39.4347
Evaluate side-chains
  188 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 141 optimal weight:   50.0000
   chunk 161 optimal weight:    0.0980
   chunk 105 optimal weight:   10.0000
   chunk 103 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 129 optimal weight:   30.0000
   chunk 69 optimal weight:    0.9990
   chunk 106 optimal weight:    6.9990
   chunk 19 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  96 GLN
** F  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.112294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 88)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.076379 restraints weight = 146283.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.078008 restraints weight = 64508.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.078930 restraints weight = 38378.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.078651 restraints weight = 31037.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.078693 restraints weight = 28367.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.5454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16249  Z= 0.142
  Angle     :  0.552   6.735  23271  Z= 0.312
  Chirality :  0.038   0.198   2738
  Planarity :  0.004   0.061   2159
  Dihedral  : 26.165  78.841   4491
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  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:  2.00 (0.22), residues: 1535
  helix:  2.04 (0.21), residues: 613
  sheet:  1.01 (0.30), residues: 320
  loop :  0.92 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G  18 
 TYR   0.019   0.001   TYR D  84 
 PHE   0.022   0.001   PHE D  71 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.010   0.001   HIS F  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (16249)
  covalent geometry    : angle       0.55216 (23271)
  hydrogen bonds       : bond        0.03656 (  946)
  hydrogen bonds       : angle       3.55716 ( 2387)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ILE cc_start: 0.9315 (mm) cc_final: 0.9016 (mm)
REVERT: A   83 LEU cc_start: 0.9293 (tp) cc_final: 0.8961 (mm)
REVERT: A   95 GLU cc_start: 0.9432 (mm-30) cc_final: 0.8693 (mm-30)
REVERT: A   98 GLU cc_start: 0.9301 (mt-10) cc_final: 0.8938 (pp20)
REVERT: A  104 LEU cc_start: 0.9606 (tt) cc_final: 0.9393 (tt)
REVERT: A  106 GLU cc_start: 0.9396 (tm-30) cc_final: 0.9043 (tm-30)
REVERT: A  108 THR cc_start: 0.9637 (m) cc_final: 0.9402 (p)
REVERT: A  121 MET cc_start: 0.9059 (mmp) cc_final: 0.8349 (mmm)
REVERT: A  126 GLN cc_start: 0.9534 (mt0) cc_final: 0.9269 (pt0)
REVERT: B   65 ASN cc_start: 0.9176 (t0) cc_final: 0.8581 (t0)
REVERT: B   68 ARG cc_start: 0.9467 (ttp-110) cc_final: 0.8916 (ttp80)
REVERT: B   69 ASP cc_start: 0.9536 (m-30) cc_final: 0.8734 (m-30)
REVERT: B   74 THR cc_start: 0.9386 (m) cc_final: 0.9173 (p)
REVERT: B   85 MET cc_start: 0.8830 (ppp) cc_final: 0.8470 (ppp)
REVERT: C   26 PHE cc_start: 0.8414 (m-10) cc_final: 0.8108 (m-10)
REVERT: C   39 ASN cc_start: 0.9012 (m-40) cc_final: 0.8716 (t0)
REVERT: D   84 TYR cc_start: 0.8012 (m-80) cc_final: 0.7698 (m-80)
REVERT: D   96 GLN cc_start: 0.9384 (tm130) cc_final: 0.8968 (tm-30)
REVERT: D  100 ARG cc_start: 0.9120 (mtp180) cc_final: 0.8671 (mtp-110)
REVERT: E   51 GLU cc_start: 0.9224 (mp0) cc_final: 0.8901 (mp0)
REVERT: E   95 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8716 (mm-30)
REVERT: E   98 GLU cc_start: 0.9045 (pp20) cc_final: 0.8752 (pp20)
REVERT: E  106 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8656 (tm-30)
REVERT: E  121 MET cc_start: 0.9130 (tpt) cc_final: 0.8594 (tpt)
REVERT: F   69 ASP cc_start: 0.9300 (m-30) cc_final: 0.8991 (m-30)
REVERT: F   85 MET cc_start: 0.9168 (mmm) cc_final: 0.8647 (mmm)
REVERT: F   86 ASP cc_start: 0.8735 (m-30) cc_final: 0.8363 (t0)
REVERT: F   97 THR cc_start: 0.9558 (m) cc_final: 0.9302 (t)
REVERT: G   26 PHE cc_start: 0.8969 (m-10) cc_final: 0.8669 (m-10)
REVERT: G   42 GLU cc_start: 0.9315 (tp30) cc_final: 0.9053 (tp30)
REVERT: G   91 ASP cc_start: 0.9150 (t70) cc_final: 0.8306 (t70)
REVERT: G   94 LEU cc_start: 0.9678 (mt) cc_final: 0.9210 (mp)
REVERT: G  105 GLN cc_start: 0.8844 (mp10) cc_final: 0.8372 (mp10)
REVERT: H   57 SER cc_start: 0.9435 (m) cc_final: 0.9072 (p)
REVERT: H   64 ASN cc_start: 0.8929 (m-40) cc_final: 0.8569 (m-40)
REVERT: H   68 ASN cc_start: 0.9568 (m110) cc_final: 0.8888 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 233
  average time/residue: 0.1048
  time to fit residues: 38.3770
Evaluate side-chains
  196 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 7 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 177 optimal weight:   20.0000
   chunk 58 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 168 optimal weight:   50.0000
   chunk 156 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 139 optimal weight:    0.6980
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  96 GLN
** F  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.110696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.074546 restraints weight = 148368.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.076240 restraints weight = 66999.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.076864 restraints weight = 41400.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.076890 restraints weight = 32385.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.076890 restraints weight = 29509.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.5680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  16249  Z= 0.168
  Angle     :  0.567   7.238  23271  Z= 0.321
  Chirality :  0.038   0.205   2738
  Planarity :  0.004   0.059   2159
  Dihedral  : 26.083  80.546   4491
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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:  1.97 (0.22), residues: 1535
  helix:  2.01 (0.21), residues: 613
  sheet:  0.96 (0.29), residues: 320
  loop :  0.93 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 130 
 TYR   0.020   0.002   TYR B  52 
 PHE   0.040   0.002   PHE A  68 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.007   0.002   HIS F  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (16249)
  covalent geometry    : angle       0.56730 (23271)
  hydrogen bonds       : bond        0.04655 (  946)
  hydrogen bonds       : angle       3.62709 ( 2387)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 LEU cc_start: 0.9308 (tp) cc_final: 0.8932 (mm)
REVERT: A   95 GLU cc_start: 0.9443 (mm-30) cc_final: 0.8771 (mm-30)
REVERT: A   98 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8994 (pp20)
REVERT: A  104 LEU cc_start: 0.9626 (tt) cc_final: 0.9419 (tt)
REVERT: A  106 GLU cc_start: 0.9395 (tm-30) cc_final: 0.9066 (tm-30)
REVERT: A  108 THR cc_start: 0.9626 (m) cc_final: 0.9384 (p)
REVERT: A  121 MET cc_start: 0.9114 (mmp) cc_final: 0.8393 (mmm)
REVERT: B   41 ARG cc_start: 0.9099 (tpt-90) cc_final: 0.8667 (mmm160)
REVERT: B   64 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8918 (tm-30)
REVERT: B   65 ASN cc_start: 0.9143 (t0) cc_final: 0.8627 (t0)
REVERT: B   68 ARG cc_start: 0.9441 (ttp-110) cc_final: 0.8780 (ttp80)
REVERT: B   69 ASP cc_start: 0.9518 (m-30) cc_final: 0.8957 (m-30)
REVERT: B   74 THR cc_start: 0.9403 (m) cc_final: 0.9181 (p)
REVERT: B   85 MET cc_start: 0.8823 (ppp) cc_final: 0.8544 (ppp)
REVERT: C   26 PHE cc_start: 0.8468 (m-10) cc_final: 0.8166 (m-10)
REVERT: C   39 ASN cc_start: 0.8957 (m-40) cc_final: 0.8473 (m-40)
REVERT: D   96 GLN cc_start: 0.9373 (tm130) cc_final: 0.8951 (tm-30)
REVERT: D  100 ARG cc_start: 0.9110 (mtp180) cc_final: 0.8662 (mtp-110)
REVERT: E   51 GLU cc_start: 0.9212 (mp0) cc_final: 0.8859 (mp0)
REVERT: E   95 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8735 (mm-30)
REVERT: E   98 GLU cc_start: 0.9052 (pp20) cc_final: 0.8698 (pp20)
REVERT: E  106 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8683 (tm-30)
REVERT: E  121 MET cc_start: 0.9164 (tpt) cc_final: 0.8661 (tpp)
REVERT: F   45 LYS cc_start: 0.8506 (ptmm) cc_final: 0.8234 (ptmt)
REVERT: F   69 ASP cc_start: 0.9339 (m-30) cc_final: 0.9070 (m-30)
REVERT: F   85 MET cc_start: 0.9176 (mmm) cc_final: 0.8621 (mmm)
REVERT: F   86 ASP cc_start: 0.8734 (m-30) cc_final: 0.8439 (t0)
REVERT: F   97 THR cc_start: 0.9581 (m) cc_final: 0.9329 (t)
REVERT: G   26 PHE cc_start: 0.8950 (m-10) cc_final: 0.8651 (m-10)
REVERT: G   39 ASN cc_start: 0.8761 (m-40) cc_final: 0.8404 (t0)
REVERT: G   91 ASP cc_start: 0.9046 (t70) cc_final: 0.8810 (t70)
REVERT: G  105 GLN cc_start: 0.8873 (mp10) cc_final: 0.8458 (mp10)
REVERT: H   68 ASN cc_start: 0.9558 (m110) cc_final: 0.8889 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.1050
  time to fit residues: 38.3616
Evaluate side-chains
  188 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   chunk 159 optimal weight:   50.0000
   chunk 177 optimal weight:    0.0980
   chunk 37 optimal weight:    1.9990
   chunk 167 optimal weight:    0.0030
   chunk 56 optimal weight:    0.7980
   chunk 36 optimal weight:    9.9990
   chunk 80 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 101 optimal weight:    0.7980
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  96 GLN
** F  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.112707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.077433 restraints weight = 146644.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.079108 restraints weight = 65597.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.079654 restraints weight = 39929.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 65)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.081503 restraints weight = 31261.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.080810 restraints weight = 24429.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.5784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16249  Z= 0.134
  Angle     :  0.561   8.280  23271  Z= 0.313
  Chirality :  0.038   0.196   2738
  Planarity :  0.004   0.060   2159
  Dihedral  : 26.034  76.579   4491
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  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:  1.96 (0.21), residues: 1535
  helix:  1.95 (0.21), residues: 616
  sheet:  1.02 (0.28), residues: 340
  loop :  0.94 (0.26), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  43 
 TYR   0.018   0.001   TYR D  84 
 PHE   0.008   0.001   PHE C  26 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.008   0.001   HIS F  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (16249)
  covalent geometry    : angle       0.56122 (23271)
  hydrogen bonds       : bond        0.03434 (  946)
  hydrogen bonds       : angle       3.51235 ( 2387)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4702.26 seconds
wall clock time: 80 minutes 47.18 seconds (4847.18 seconds total)