Starting phenix.real_space_refine (version: dev)
on Tue Apr  5 15:10:42 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwo_20509/04_2022/6pwo_20509.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwo_20509/04_2022/6pwo_20509.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwo_20509/04_2022/6pwo_20509.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwo_20509/04_2022/6pwo_20509.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwo_20509/04_2022/6pwo_20509.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwo_20509/04_2022/6pwo_20509.pdb"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   88": "NH1" <-> "NH2"
    Residue "A GLU  134": "OE1" <-> "OE2"
    Residue "B ARG   88": "NH1" <-> "NH2"
    Residue "B GLU  134": "OE1" <-> "OE2"
    Residue "C ARG   88": "NH1" <-> "NH2"
    Residue "C GLU  134": "OE1" <-> "OE2"
    Residue "D ARG   88": "NH1" <-> "NH2"
    Residue "D GLU  134": "OE1" <-> "OE2"
    Residue "E ARG   88": "NH1" <-> "NH2"
    Residue "E GLU  134": "OE1" <-> "OE2"
    Residue "F ARG   88": "NH1" <-> "NH2"
    Residue "F GLU  134": "OE1" <-> "OE2"
    Residue "G ARG   88": "NH1" <-> "NH2"
    Residue "G GLU  134": "OE1" <-> "OE2"
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib"
  Total number of atoms: 14217
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2031
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 5, 'TRANS': 260}
    Chain: "B"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2031
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 5, 'TRANS': 260}
    Chain: "C"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2031
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 5, 'TRANS': 260}
    Chain: "D"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2031
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 5, 'TRANS': 260}
    Chain: "E"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2031
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 5, 'TRANS': 260}
    Chain: "F"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2031
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 5, 'TRANS': 260}
    Chain: "G"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2031
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 5, 'TRANS': 260}
  Time building chain proxies: 8.23, per 1000 atoms: 0.58
  Number of scatterers: 14217
  At special positions: 0
  Unit cell: (97.888, 100.016, 146.832, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    2555      8.00
     N    2478      7.00
     C    9142      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  - 3.50
        Amino acid           : False - 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: 5.92
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3444

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 9 sheets defined
      56.1% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 20
      removed outlier: 3.698A  pdb=" N   ALA A  19 " --> pdb=" O   SER A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 57
    Processing helix  chain 'A' and resid 65 through 90
    Processing helix  chain 'A' and resid 93 through 128
      removed outlier: 4.438A  pdb=" N   GLY A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   SER A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 173
      removed outlier: 3.855A  pdb=" N   ALA A 172 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY A 173 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 212
      removed outlier: 3.644A  pdb=" N   VAL A 201 " --> pdb=" O   ASP A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 265
    Processing helix  chain 'B' and resid 16 through 20
    Processing helix  chain 'B' and resid 20 through 57
    Processing helix  chain 'B' and resid 65 through 90
    Processing helix  chain 'B' and resid 93 through 128
      removed outlier: 4.438A  pdb=" N   GLY B 113 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   SER B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 173
      removed outlier: 3.855A  pdb=" N   ALA B 172 " --> pdb=" O   GLY B 168 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLY B 173 " --> pdb=" O   LYS B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 212
      removed outlier: 3.644A  pdb=" N   VAL B 201 " --> pdb=" O   ASP B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 265
    Processing helix  chain 'C' and resid 16 through 20
    Processing helix  chain 'C' and resid 20 through 57
    Processing helix  chain 'C' and resid 65 through 90
    Processing helix  chain 'C' and resid 93 through 128
      removed outlier: 4.438A  pdb=" N   GLY C 113 " --> pdb=" O   LEU C 109 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   SER C 114 " --> pdb=" O   ALA C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 173
      removed outlier: 3.855A  pdb=" N   ALA C 172 " --> pdb=" O   GLY C 168 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLY C 173 " --> pdb=" O   LYS C 169 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 212
      removed outlier: 3.644A  pdb=" N   VAL C 201 " --> pdb=" O   ASP C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 265
    Processing helix  chain 'D' and resid 16 through 20
    Processing helix  chain 'D' and resid 20 through 57
    Processing helix  chain 'D' and resid 65 through 90
    Processing helix  chain 'D' and resid 93 through 128
      removed outlier: 4.438A  pdb=" N   GLY D 113 " --> pdb=" O   LEU D 109 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   SER D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 173
      removed outlier: 3.855A  pdb=" N   ALA D 172 " --> pdb=" O   GLY D 168 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY D 173 " --> pdb=" O   LYS D 169 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 212
      removed outlier: 3.645A  pdb=" N   VAL D 201 " --> pdb=" O   ASP D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 245 through 265
    Processing helix  chain 'E' and resid 16 through 20
    Processing helix  chain 'E' and resid 20 through 57
    Processing helix  chain 'E' and resid 65 through 90
    Processing helix  chain 'E' and resid 93 through 128
      removed outlier: 4.438A  pdb=" N   GLY E 113 " --> pdb=" O   LEU E 109 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   SER E 114 " --> pdb=" O   ALA E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 167 through 173
      removed outlier: 3.855A  pdb=" N   ALA E 172 " --> pdb=" O   GLY E 168 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLY E 173 " --> pdb=" O   LYS E 169 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 197 through 212
      removed outlier: 3.644A  pdb=" N   VAL E 201 " --> pdb=" O   ASP E 197 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 245 through 265
    Processing helix  chain 'F' and resid 16 through 20
    Processing helix  chain 'F' and resid 20 through 57
    Processing helix  chain 'F' and resid 65 through 90
    Processing helix  chain 'F' and resid 93 through 128
      removed outlier: 4.438A  pdb=" N   GLY F 113 " --> pdb=" O   LEU F 109 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   SER F 114 " --> pdb=" O   ALA F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 167 through 173
      removed outlier: 3.854A  pdb=" N   ALA F 172 " --> pdb=" O   GLY F 168 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY F 173 " --> pdb=" O   LYS F 169 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 197 through 212
      removed outlier: 3.644A  pdb=" N   VAL F 201 " --> pdb=" O   ASP F 197 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 245 through 265
    Processing helix  chain 'G' and resid 16 through 20
    Processing helix  chain 'G' and resid 20 through 57
    Processing helix  chain 'G' and resid 65 through 90
    Processing helix  chain 'G' and resid 93 through 128
      removed outlier: 4.438A  pdb=" N   GLY G 113 " --> pdb=" O   LEU G 109 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   SER G 114 " --> pdb=" O   ALA G 110 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 167 through 173
      removed outlier: 3.854A  pdb=" N   ALA G 172 " --> pdb=" O   GLY G 168 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLY G 173 " --> pdb=" O   LYS G 169 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 197 through 212
      removed outlier: 3.644A  pdb=" N   VAL G 201 " --> pdb=" O   ASP G 197 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 245 through 265
    Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 137
      removed outlier: 7.360A  pdb=" N   THR A 154 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   VAL A 148 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   SER A 152 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ILE A 162 " --> pdb=" O   ASN B 177 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   THR B 154 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   VAL B 148 " --> pdb=" O   SER B 152 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   SER B 152 " --> pdb=" O   VAL B 148 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ILE B 162 " --> pdb=" O   ASN C 177 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   THR C 154 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   VAL C 148 " --> pdb=" O   SER C 152 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   SER C 152 " --> pdb=" O   VAL C 148 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ILE C 162 " --> pdb=" O   ASN D 177 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   THR D 154 " --> pdb=" O   LEU D 146 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   VAL D 148 " --> pdb=" O   SER D 152 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   SER D 152 " --> pdb=" O   VAL D 148 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ILE D 162 " --> pdb=" O   ASN E 177 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   THR E 154 " --> pdb=" O   LEU E 146 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   VAL E 148 " --> pdb=" O   SER E 152 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   SER E 152 " --> pdb=" O   VAL E 148 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ILE E 162 " --> pdb=" O   ASN F 177 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   THR F 154 " --> pdb=" O   LEU F 146 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   VAL F 148 " --> pdb=" O   SER F 152 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   SER F 152 " --> pdb=" O   VAL F 148 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ILE F 162 " --> pdb=" O   ASN G 177 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   THR G 154 " --> pdb=" O   LEU G 146 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   VAL G 148 " --> pdb=" O   SER G 152 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   SER G 152 " --> pdb=" O   VAL G 148 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ILE G 162 " --> pdb=" O   ASN A 177 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192
      removed outlier: 7.461A  pdb=" N   ASN A 234 " --> pdb=" O   ASN A 226 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 279
      removed outlier: 3.586A  pdb=" N   LYS B 278 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE A 277 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   MET B 273 " --> pdb=" O   ASN C 276 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   LYS C 278 " --> pdb=" O   MET B 273 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   VAL B 275 " --> pdb=" O   LYS C 278 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   MET C 273 " --> pdb=" O   ASN D 276 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   LYS D 278 " --> pdb=" O   MET C 273 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   VAL C 275 " --> pdb=" O   LYS D 278 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   MET D 273 " --> pdb=" O   ASN E 276 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   LYS E 278 " --> pdb=" O   MET D 273 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   VAL D 275 " --> pdb=" O   LYS E 278 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   MET E 273 " --> pdb=" O   ASN F 276 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   LYS F 278 " --> pdb=" O   MET E 273 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   VAL E 275 " --> pdb=" O   LYS F 278 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   MET F 273 " --> pdb=" O   ASN G 276 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   LYS G 278 " --> pdb=" O   MET F 273 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   VAL F 275 " --> pdb=" O   LYS G 278 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LYS A 278 " --> pdb=" O   VAL G 275 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192
      removed outlier: 7.462A  pdb=" N   ASN B 234 " --> pdb=" O   ASN B 226 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192
      removed outlier: 7.461A  pdb=" N   ASN C 234 " --> pdb=" O   ASN C 226 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192
      removed outlier: 7.462A  pdb=" N   ASN D 234 " --> pdb=" O   ASN D 226 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192
      removed outlier: 7.462A  pdb=" N   ASN E 234 " --> pdb=" O   ASN E 226 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192
      removed outlier: 7.462A  pdb=" N   ASN F 234 " --> pdb=" O   ASN F 226 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192
      removed outlier: 7.461A  pdb=" N   ASN G 234 " --> pdb=" O   ASN G 226 " (cutoff:3.500A)

    1022 hydrogen bonds defined for protein.
    3003 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.05

  Time building geometry restraints manager: 6.29 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4725
        1.34 -     1.46: 2750
        1.46 -     1.58: 6847
        1.58 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 14406
  Sorted by residual:
  bond pdb=" N   ARG A  88 "
       pdb=" CA  ARG A  88 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.89e+00
  bond pdb=" N   ARG C  88 "
       pdb=" CA  ARG C  88 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.79e+00
  bond pdb=" N   ARG G  88 "
       pdb=" CA  ARG G  88 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.68e+00
  bond pdb=" N   ARG D  88 "
       pdb=" CA  ARG D  88 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.68e+00
  bond pdb=" N   ARG E  88 "
       pdb=" CA  ARG E  88 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.66e+00
  ... (remaining 14401 not shown)

  Histogram of bond angle deviations from ideal:
       99.50 -   106.40: 189
      106.40 -   113.30: 8340
      113.30 -   120.21: 4771
      120.21 -   127.11: 6167
      127.11 -   134.01: 84
  Bond angle restraints: 19551
  Sorted by residual:
  angle pdb=" C   LEU D 138 "
        pdb=" N   GLY D 139 "
        pdb=" CA  GLY D 139 "
      ideal   model   delta    sigma   weight residual
     121.41  128.76   -7.35 1.96e+00 2.60e-01 1.40e+01
  angle pdb=" C   LEU F 138 "
        pdb=" N   GLY F 139 "
        pdb=" CA  GLY F 139 "
      ideal   model   delta    sigma   weight residual
     121.41  128.75   -7.34 1.96e+00 2.60e-01 1.40e+01
  angle pdb=" C   LEU B 138 "
        pdb=" N   GLY B 139 "
        pdb=" CA  GLY B 139 "
      ideal   model   delta    sigma   weight residual
     121.41  128.75   -7.34 1.96e+00 2.60e-01 1.40e+01
  angle pdb=" C   LEU C 138 "
        pdb=" N   GLY C 139 "
        pdb=" CA  GLY C 139 "
      ideal   model   delta    sigma   weight residual
     121.41  128.74   -7.33 1.96e+00 2.60e-01 1.40e+01
  angle pdb=" C   LEU G 138 "
        pdb=" N   GLY G 139 "
        pdb=" CA  GLY G 139 "
      ideal   model   delta    sigma   weight residual
     121.41  128.73   -7.32 1.96e+00 2.60e-01 1.39e+01
  ... (remaining 19546 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 7806
       17.66 -    35.32: 723
       35.32 -    52.98: 95
       52.98 -    70.64: 7
       70.64 -    88.30: 7
  Dihedral angle restraints: 8638
    sinusoidal: 3297
      harmonic: 5341
  Sorted by residual:
  dihedral pdb=" CA  ASN G 276 "
           pdb=" C   ASN G 276 "
           pdb=" N   PHE G 277 "
           pdb=" CA  PHE G 277 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.07  -25.93     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CA  ASN B 276 "
           pdb=" C   ASN B 276 "
           pdb=" N   PHE B 277 "
           pdb=" CA  PHE B 277 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.08  -25.92     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CA  ASN A 276 "
           pdb=" C   ASN A 276 "
           pdb=" N   PHE A 277 "
           pdb=" CA  PHE A 277 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.09  -25.91     0      5.00e+00 4.00e-02 2.68e+01
  ... (remaining 8635 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1763
       0.042 -    0.084: 452
       0.084 -    0.125: 151
       0.125 -    0.167: 16
       0.167 -    0.209: 19
  Chirality restraints: 2401
  Sorted by residual:
  chirality pdb=" CB  ILE E  61 "
            pdb=" CA  ILE E  61 "
            pdb=" CG1 ILE E  61 "
            pdb=" CG2 ILE E  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CB  ILE C  61 "
            pdb=" CA  ILE C  61 "
            pdb=" CG1 ILE C  61 "
            pdb=" CG2 ILE C  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CB  ILE B  61 "
            pdb=" CA  ILE B  61 "
            pdb=" CG1 ILE B  61 "
            pdb=" CG2 ILE B  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 2398 not shown)

  Planarity restraints: 2471
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY F  90 "    0.008 2.00e-02 2.50e+03   1.67e-02 2.79e+00
        pdb=" C   GLY F  90 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   GLY F  90 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL F  91 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY D  90 "   -0.008 2.00e-02 2.50e+03   1.67e-02 2.79e+00
        pdb=" C   GLY D  90 "    0.029 2.00e-02 2.50e+03
        pdb=" O   GLY D  90 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   VAL D  91 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY G  90 "    0.008 2.00e-02 2.50e+03   1.67e-02 2.78e+00
        pdb=" C   GLY G  90 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   GLY G  90 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL G  91 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2468 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 6203
        2.91 -     3.40: 15330
        3.40 -     3.90: 21746
        3.90 -     4.40: 23887
        4.40 -     4.90: 40510
  Nonbonded interactions: 107676
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E 197 "
            pdb=" N   ILE E 198 "
     model   vdw
     2.407 2.520
  nonbonded pdb=" OD1 ASP F 197 "
            pdb=" N   ILE F 198 "
     model   vdw
     2.407 2.520
  nonbonded pdb=" OD1 ASP B 197 "
            pdb=" N   ILE B 198 "
     model   vdw
     2.407 2.520
  nonbonded pdb=" OD1 ASP C 197 "
            pdb=" N   ILE C 198 "
     model   vdw
     2.407 2.520
  nonbonded pdb=" OD1 ASP D 197 "
            pdb=" N   ILE D 198 "
     model   vdw
     2.407 2.520
  ... (remaining 107671 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    9142      2.51       5
     N    2478      2.21       5
     O    2555      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.610
  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:          4.740
  Check model and map are aligned:         0.200
  Convert atoms to be neutral:             0.120
  Process input model:                     37.250
  Find NCS groups from input model:        0.950
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Set scattering table:                    0.010
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.052  14406  Z= 0.350
  Angle     :  0.607   7.347  19551  Z= 0.363
  Chirality :  0.046   0.209   2401
  Planarity :  0.003   0.017   2471
  Dihedral  : 13.329  88.298   5194
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer Outliers :  0.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.17), residues: 1848
  helix:  0.11 (0.14), residues: 966
  sheet: -0.00 (0.31), residues: 224
  loop : -1.51 (0.20), residues: 658

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 179
  time to evaluate  : 1.599 
Fit side-chains
  outliers start: 7
  outliers final: 1
  residues processed: 186
  average time/residue: 0.2904
  time to fit residues: 76.3173
Evaluate side-chains
  104 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 1.630 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.5654
  time to fit residues: 2.6791
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 153 optimal weight:    2.9990
   chunk 137 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 47 optimal weight:    7.9990
   chunk 93 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 142 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9980
   chunk 165 optimal weight:    2.9990
   overall best weight:    1.5586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.028  14406  Z= 0.195
  Angle     :  0.536   6.737  19551  Z= 0.293
  Chirality :  0.041   0.131   2401
  Planarity :  0.003   0.021   2471
  Dihedral  :  4.349  18.417   2023
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer Outliers :  0.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.19), residues: 1848
  helix:  2.30 (0.15), residues: 980
  sheet:  1.25 (0.31), residues: 238
  loop : -0.74 (0.24), residues: 630

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 138
  time to evaluate  : 1.692 
Fit side-chains
  outliers start: 13
  outliers final: 2
  residues processed: 140
  average time/residue: 0.2434
  time to fit residues: 52.1855
Evaluate side-chains
  113 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 1.695 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1225
  time to fit residues: 2.7278
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 91 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 137 optimal weight:    0.9990
   chunk 112 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 165 optimal weight:    4.9990
   chunk 178 optimal weight:    0.9990
   chunk 147 optimal weight:    5.9990
   chunk 164 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0670
   chunk 132 optimal weight:    6.9990
   overall best weight:    0.8124

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

Flipped N/Q/H residues before XYZ refinement:
C 203 GLN
D 203 GLN
G 203 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.025  14406  Z= 0.151
  Angle     :  0.492   7.414  19551  Z= 0.262
  Chirality :  0.039   0.124   2401
  Planarity :  0.003   0.021   2471
  Dihedral  :  4.146  15.504   2023
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer Outliers :  0.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.19), residues: 1848
  helix:  2.70 (0.16), residues: 980
  sheet:  1.78 (0.32), residues: 238
  loop : -0.69 (0.23), residues: 630

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 122
  time to evaluate  : 1.804 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 123
  average time/residue: 0.2580
  time to fit residues: 47.9092
Evaluate side-chains
  110 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 108
  time to evaluate  : 1.534 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1532
  time to fit residues: 2.7868
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 163 optimal weight:    0.4980
   chunk 124 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 79 optimal weight:    5.9990
   chunk 111 optimal weight:    9.9990
   chunk 166 optimal weight:    0.8980
   chunk 175 optimal weight:    0.6980
   chunk 86 optimal weight:    7.9990
   chunk 157 optimal weight:   10.0000
   chunk 47 optimal weight:    7.9990
   overall best weight:    0.9982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.023  14406  Z= 0.144
  Angle     :  0.475   8.306  19551  Z= 0.250
  Chirality :  0.039   0.124   2401
  Planarity :  0.002   0.021   2471
  Dihedral  :  4.036  15.293   2023
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer Outliers :  1.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.19), residues: 1848
  helix:  2.81 (0.16), residues: 987
  sheet:  2.08 (0.33), residues: 238
  loop : -0.61 (0.23), residues: 623

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 1.798 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 6
  residues processed: 126
  average time/residue: 0.2536
  time to fit residues: 48.3024
Evaluate side-chains
  112 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 1.662 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.1415
  time to fit residues: 3.6957
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 146 optimal weight:    3.9990
   chunk 99 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 130 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 150 optimal weight:    6.9990
   chunk 121 optimal weight:    0.8980
   chunk 0 optimal weight:   50.0000
   chunk 89 optimal weight:    1.9990
   chunk 157 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
D 203 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.3631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.036  14406  Z= 0.334
  Angle     :  0.542   7.655  19551  Z= 0.291
  Chirality :  0.039   0.126   2401
  Planarity :  0.003   0.023   2471
  Dihedral  :  4.408  17.108   2023
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer Outliers :  1.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.50 (0.19), residues: 1848
  helix:  2.77 (0.16), residues: 987
  sheet:  2.42 (0.35), residues: 224
  loop : -0.51 (0.23), residues: 637

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 2.076 
Fit side-chains
   revert: symmetry clash
  outliers start: 16
  outliers final: 9
  residues processed: 118
  average time/residue: 0.3467
  time to fit residues: 62.6965
Evaluate side-chains
  98 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 2.512 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.2659
  time to fit residues: 7.9768
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 158 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 176 optimal weight:    2.9990
   chunk 146 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
G 203 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.3921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.024  14406  Z= 0.194
  Angle     :  0.524   9.601  19551  Z= 0.273
  Chirality :  0.039   0.131   2401
  Planarity :  0.003   0.023   2471
  Dihedral  :  4.214  15.275   2023
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer Outliers :  0.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.19), residues: 1848
  helix:  2.88 (0.16), residues: 987
  sheet:  2.42 (0.35), residues: 224
  loop : -0.56 (0.23), residues: 637

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 1.862 
Fit side-chains
  outliers start: 14
  outliers final: 1
  residues processed: 104
  average time/residue: 0.2722
  time to fit residues: 42.7107
Evaluate side-chains
  88 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 1.701 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1282
  time to fit residues: 2.5942
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 169 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9980
   chunk 128 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 148 optimal weight:    0.4980
   chunk 98 optimal weight:    0.8980
   chunk 175 optimal weight:    0.9980
   chunk 109 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    1.0782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.4148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.030  14406  Z= 0.152
  Angle     :  0.512   9.534  19551  Z= 0.263
  Chirality :  0.039   0.126   2401
  Planarity :  0.002   0.023   2471
  Dihedral  :  4.056  14.883   2023
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer Outliers :  0.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.59 (0.19), residues: 1848
  helix:  2.94 (0.16), residues: 987
  sheet:  2.40 (0.34), residues: 224
  loop : -0.63 (0.22), residues: 637

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 1.681 
Fit side-chains
  outliers start: 13
  outliers final: 4
  residues processed: 100
  average time/residue: 0.2484
  time to fit residues: 38.2276
Evaluate side-chains
  94 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 1.692 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1231
  time to fit residues: 3.1482
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 108 optimal weight:   30.0000
   chunk 70 optimal weight:    0.9990
   chunk 104 optimal weight:   50.0000
   chunk 52 optimal weight:   40.0000
   chunk 34 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 111 optimal weight:    9.9990
   chunk 119 optimal weight:    0.0770
   chunk 86 optimal weight:    8.9990
   chunk 16 optimal weight:    9.9990
   chunk 137 optimal weight:    7.9990
   overall best weight:    3.8146

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.4160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.033  14406  Z= 0.354
  Angle     :  0.573   9.381  19551  Z= 0.301
  Chirality :  0.039   0.139   2401
  Planarity :  0.003   0.023   2471
  Dihedral  :  4.404  16.005   2023
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer Outliers :  0.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.58 (0.20), residues: 1848
  helix:  2.85 (0.16), residues: 987
  sheet:  1.95 (0.34), residues: 259
  loop : -0.41 (0.24), residues: 602

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 1.731 
Fit side-chains
  outliers start: 13
  outliers final: 4
  residues processed: 101
  average time/residue: 0.2576
  time to fit residues: 40.4394
Evaluate side-chains
  92 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 1.848 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1370
  time to fit residues: 3.2667
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 159 optimal weight:    8.9990
   chunk 168 optimal weight:    1.9990
   chunk 153 optimal weight:    0.8980
   chunk 163 optimal weight:    6.9990
   chunk 98 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 128 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 147 optimal weight:    0.8980
   chunk 154 optimal weight:    0.8980
   chunk 162 optimal weight:    7.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
G 203 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.4349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14406  Z= 0.171
  Angle     :  0.533  10.427  19551  Z= 0.272
  Chirality :  0.039   0.131   2401
  Planarity :  0.002   0.023   2471
  Dihedral  :  4.116  15.254   2023
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer Outliers :  0.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.20), residues: 1848
  helix:  2.81 (0.16), residues: 1015
  sheet:  1.92 (0.33), residues: 259
  loop : -0.68 (0.24), residues: 574

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 1.676 
Fit side-chains
  outliers start: 3
  outliers final: 0
  residues processed: 87
  average time/residue: 0.2920
  time to fit residues: 37.8872
Evaluate side-chains
  85 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 1.720 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.2810
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 107 optimal weight:    8.9990
   chunk 172 optimal weight:    5.9990
   chunk 105 optimal weight:    7.9990
   chunk 82 optimal weight:   20.0000
   chunk 120 optimal weight:    0.7980
   chunk 181 optimal weight:    1.9990
   chunk 166 optimal weight:    8.9990
   chunk 144 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 111 optimal weight:    5.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    2.1588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.4366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.030  14406  Z= 0.223
  Angle     :  0.546  10.203  19551  Z= 0.280
  Chirality :  0.039   0.131   2401
  Planarity :  0.003   0.023   2471
  Dihedral  :  4.153  14.948   2023
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer Outliers :  0.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.20), residues: 1848
  helix:  2.80 (0.16), residues: 1015
  sheet:  1.96 (0.34), residues: 259
  loop : -0.69 (0.24), residues: 574

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 1.766 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 88
  average time/residue: 0.2715
  time to fit residues: 36.5090
Evaluate side-chains
  88 residues out of total 1512 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 1.535 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1785
  time to fit residues: 2.6812
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 114 optimal weight:    0.9990
   chunk 153 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 133 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 144 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 148 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 26 optimal weight:   40.0000
   overall best weight:    1.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.067359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.049527 restraints weight = 53232.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 3.51
r_work: 0.2959 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work: 0.2942 rms_B_bonded: 3.26 restraints_weight: 0.1250
r_work: 0.2933 rms_B_bonded: 3.29 restraints_weight: 0.0625
r_work: 0.2924 rms_B_bonded: 3.35 restraints_weight: 0.0312
r_work: 0.2915 rms_B_bonded: 3.42 restraints_weight: 0.0156
r_work: 0.2906 rms_B_bonded: 3.50 restraints_weight: 0.0078
r_work: 0.2896 rms_B_bonded: 3.60 restraints_weight: 0.0039
r_work: 0.2887 rms_B_bonded: 3.71 restraints_weight: 0.0020
r_work: 0.2877 rms_B_bonded: 3.83 restraints_weight: 0.0010
r_work: 0.2867 rms_B_bonded: 3.97 restraints_weight: 0.0005
r_work: 0.2856 rms_B_bonded: 4.12 restraints_weight: 0.0002
r_work: 0.2845 rms_B_bonded: 4.29 restraints_weight: 0.0001
r_work: 0.2834 rms_B_bonded: 4.47 restraints_weight: 0.0001
r_work: 0.2823 rms_B_bonded: 4.66 restraints_weight: 0.0000
r_work: 0.2811 rms_B_bonded: 4.87 restraints_weight: 0.0000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.4494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14406  Z= 0.171
  Angle     :  0.536  10.320  19551  Z= 0.272
  Chirality :  0.038   0.128   2401
  Planarity :  0.002   0.023   2471
  Dihedral  :  4.054  14.987   2023
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer Outliers :  0.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.20), residues: 1848
  helix:  2.84 (0.16), residues: 1015
  sheet:  2.00 (0.33), residues: 259
  loop : -0.72 (0.24), residues: 574

===============================================================================
Job complete
usr+sys time: 2131.19 seconds
wall clock time: 39 minutes 56.63 seconds (2396.63 seconds total)