Starting phenix.real_space_refine (version: dev)
on Tue Apr  5 14:06:09 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/04_2022/7onl_12997.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/04_2022/7onl_12997.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/04_2022/7onl_12997.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/04_2022/7onl_12997.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/04_2022/7onl_12997.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/04_2022/7onl_12997.pdb"
  }
  resolution = 3.9
  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=   0.007
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
    None
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib"
  Total number of atoms: 13923
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1989
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 5, 'TRANS': 255}
    Chain: "B"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1989
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 5, 'TRANS': 255}
    Chain: "C"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1989
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 5, 'TRANS': 255}
    Chain: "D"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1989
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 5, 'TRANS': 255}
    Chain: "E"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1989
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 5, 'TRANS': 255}
    Chain: "F"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1989
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 5, 'TRANS': 255}
    Chain: "G"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1989
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 5, 'TRANS': 255}
  Time building chain proxies: 7.64, per 1000 atoms: 0.55
  Number of scatterers: 13923
  At special positions: 0
  Unit cell: (98.9055, 96.7785, 142.509, 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    2513      8.00
     N    2436      7.00
     C    8932      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: 6.02
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3374

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 9 sheets defined
      55.9% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 59
      removed outlier: 3.502A  pdb=" N   ARG A  59 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 90
    Processing helix  chain 'A' and resid 93 through 128
      removed outlier: 4.729A  pdb=" N   GLY A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   SER A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 172
    Processing helix  chain 'A' and resid 197 through 212
      removed outlier: 3.564A  pdb=" N   GLU A 212 " --> pdb=" O   ILE A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 265
    Processing helix  chain 'B' and resid 22 through 59
      removed outlier: 3.502A  pdb=" N   ARG B  59 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 90
    Processing helix  chain 'B' and resid 93 through 128
      removed outlier: 4.730A  pdb=" N   GLY B 113 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   SER B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 172
    Processing helix  chain 'B' and resid 197 through 212
      removed outlier: 3.564A  pdb=" N   GLU B 212 " --> pdb=" O   ILE B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 265
    Processing helix  chain 'C' and resid 22 through 59
      removed outlier: 3.503A  pdb=" N   ARG C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 90
    Processing helix  chain 'C' and resid 93 through 128
      removed outlier: 4.729A  pdb=" N   GLY C 113 " --> pdb=" O   LEU C 109 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   SER C 114 " --> pdb=" O   ALA C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 172
    Processing helix  chain 'C' and resid 197 through 212
      removed outlier: 3.563A  pdb=" N   GLU C 212 " --> pdb=" O   ILE C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 265
    Processing helix  chain 'D' and resid 22 through 59
      removed outlier: 3.502A  pdb=" N   ARG D  59 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 90
    Processing helix  chain 'D' and resid 93 through 128
      removed outlier: 4.729A  pdb=" N   GLY D 113 " --> pdb=" O   LEU D 109 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   SER D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 172
    Processing helix  chain 'D' and resid 197 through 212
      removed outlier: 3.564A  pdb=" N   GLU D 212 " --> pdb=" O   ILE D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 245 through 265
    Processing helix  chain 'E' and resid 22 through 59
      removed outlier: 3.502A  pdb=" N   ARG E  59 " --> pdb=" O   LEU E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 90
    Processing helix  chain 'E' and resid 93 through 128
      removed outlier: 4.729A  pdb=" N   GLY E 113 " --> pdb=" O   LEU E 109 " (cutoff:3.500A)
      removed outlier: 5.013A  pdb=" N   SER E 114 " --> pdb=" O   ALA E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 167 through 172
    Processing helix  chain 'E' and resid 197 through 212
      removed outlier: 3.563A  pdb=" N   GLU E 212 " --> pdb=" O   ILE E 208 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 245 through 265
    Processing helix  chain 'F' and resid 22 through 59
      removed outlier: 3.502A  pdb=" N   ARG F  59 " --> pdb=" O   LEU F  55 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 62 through 90
    Processing helix  chain 'F' and resid 93 through 128
      removed outlier: 4.729A  pdb=" N   GLY F 113 " --> pdb=" O   LEU F 109 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   SER F 114 " --> pdb=" O   ALA F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 167 through 172
    Processing helix  chain 'F' and resid 197 through 212
      removed outlier: 3.563A  pdb=" N   GLU F 212 " --> pdb=" O   ILE F 208 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 245 through 265
    Processing helix  chain 'G' and resid 22 through 59
      removed outlier: 3.503A  pdb=" N   ARG G  59 " --> pdb=" O   LEU G  55 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 62 through 90
    Processing helix  chain 'G' and resid 93 through 128
      removed outlier: 4.728A  pdb=" N   GLY G 113 " --> pdb=" O   LEU G 109 " (cutoff:3.500A)
      removed outlier: 5.013A  pdb=" N   SER G 114 " --> pdb=" O   ALA G 110 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 167 through 172
    Processing helix  chain 'G' and resid 197 through 212
      removed outlier: 3.563A  pdb=" N   GLU G 212 " --> pdb=" O   ILE G 208 " (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 138
      removed outlier: 3.842A  pdb=" N   VAL A 141 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   THR A 154 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   VAL A 148 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   SER A 152 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL G 141 " --> pdb=" O   LEU G 138 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   THR G 154 " --> pdb=" O   LEU G 146 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   VAL G 148 " --> pdb=" O   SER G 152 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   SER G 152 " --> pdb=" O   VAL G 148 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL F 141 " --> pdb=" O   LEU F 138 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   THR F 154 " --> pdb=" O   LEU F 146 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   VAL F 148 " --> pdb=" O   SER F 152 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   SER F 152 " --> pdb=" O   VAL F 148 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   VAL E 141 " --> pdb=" O   LEU E 138 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   THR E 154 " --> pdb=" O   LEU E 146 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   VAL E 148 " --> pdb=" O   SER E 152 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   SER E 152 " --> pdb=" O   VAL E 148 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL D 141 " --> pdb=" O   LEU D 138 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   THR D 154 " --> pdb=" O   LEU D 146 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   VAL D 148 " --> pdb=" O   SER D 152 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   SER D 152 " --> pdb=" O   VAL D 148 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL C 141 " --> pdb=" O   LEU C 138 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   THR C 154 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   VAL C 148 " --> pdb=" O   SER C 152 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   SER C 152 " --> pdb=" O   VAL C 148 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL B 141 " --> pdb=" O   LEU B 138 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   THR B 154 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   VAL B 148 " --> pdb=" O   SER B 152 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   SER B 152 " --> pdb=" O   VAL B 148 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192
      removed outlier: 7.035A  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 276
      removed outlier: 8.093A  pdb=" N   MET B 273 " --> pdb=" O   GLN A 272 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   ASP A 274 " --> pdb=" O   MET B 273 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   VAL B 275 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   ASN A 276 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 7.459A  pdb=" N   PHE B 277 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
      removed outlier: 8.223A  pdb=" N   MET C 273 " --> pdb=" O   GLN B 272 " (cutoff:3.500A)
      removed outlier: 5.671A  pdb=" N   ASP B 274 " --> pdb=" O   MET C 273 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   VAL C 275 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   ASN B 276 " --> pdb=" O   VAL C 275 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   PHE C 277 " --> pdb=" O   ASN B 276 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   LYS B 278 " --> pdb=" O   PHE C 277 " (cutoff:3.500A)
      removed outlier: 8.266A  pdb=" N   MET D 273 " --> pdb=" O   GLN C 272 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   ASP C 274 " --> pdb=" O   MET D 273 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   VAL D 275 " --> pdb=" O   ASP C 274 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   ASN C 276 " --> pdb=" O   VAL D 275 " (cutoff:3.500A)
      removed outlier: 8.210A  pdb=" N   MET E 273 " --> pdb=" O   GLN D 272 " (cutoff:3.500A)
      removed outlier: 5.689A  pdb=" N   ASP D 274 " --> pdb=" O   MET E 273 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   VAL E 275 " --> pdb=" O   ASP D 274 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   ASN D 276 " --> pdb=" O   VAL E 275 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   PHE E 277 " --> pdb=" O   ASN D 276 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   MET F 273 " --> pdb=" O   GLN E 272 " (cutoff:3.500A)
      removed outlier: 5.688A  pdb=" N   ASP E 274 " --> pdb=" O   MET F 273 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   VAL F 275 " --> pdb=" O   ASP E 274 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   ASN E 276 " --> pdb=" O   VAL F 275 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   PHE F 277 " --> pdb=" O   ASN E 276 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   LYS E 278 " --> pdb=" O   PHE F 277 " (cutoff:3.500A)
      removed outlier: 8.342A  pdb=" N   MET G 273 " --> pdb=" O   GLN F 272 " (cutoff:3.500A)
      removed outlier: 5.805A  pdb=" N   ASP F 274 " --> pdb=" O   MET G 273 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   VAL G 275 " --> pdb=" O   ASP F 274 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   ASN F 276 " --> pdb=" O   VAL G 275 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   PHE G 277 " --> pdb=" O   ASN F 276 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   LYS F 278 " --> pdb=" O   PHE G 277 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL A 275 " --> pdb=" O   ASN G 276 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192
      removed outlier: 7.036A  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: 7.035A  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: 7.035A  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: 7.035A  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: 7.035A  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: 7.035A  pdb=" N   ASN G 234 " --> pdb=" O   ASN G 226 " (cutoff:3.500A)

    1046 hydrogen bonds defined for protein.
    3054 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: 4.40

  Time building geometry restraints manager: 6.48 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: 4655
        1.34 -     1.46: 2538
        1.46 -     1.57: 6821
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 14098
  Sorted by residual:
  bond pdb=" CA  ARG B 128 "
       pdb=" CB  ARG B 128 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.36e+00
  bond pdb=" CA  ARG F 128 "
       pdb=" CB  ARG F 128 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.34e+00
  bond pdb=" CA  ARG E 128 "
       pdb=" CB  ARG E 128 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.29e+00
  bond pdb=" CA  ARG C 128 "
       pdb=" CB  ARG C 128 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.23e+00
  bond pdb=" CA  ARG G 128 "
       pdb=" CB  ARG G 128 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.20e+00
  ... (remaining 14093 not shown)

  Histogram of bond angle deviations from ideal:
      100.33 -   107.06: 230
      107.06 -   113.80: 8265
      113.80 -   120.53: 5314
      120.53 -   127.26: 5245
      127.26 -   134.00: 63
  Bond angle restraints: 19117
  Sorted by residual:
  angle pdb=" C   ARG F 128 "
        pdb=" CA  ARG F 128 "
        pdb=" CB  ARG F 128 "
      ideal   model   delta    sigma   weight residual
     111.00  109.34    1.66 8.70e-01 1.32e+00 3.63e+00
  angle pdb=" C   ARG G 128 "
        pdb=" CA  ARG G 128 "
        pdb=" CB  ARG G 128 "
      ideal   model   delta    sigma   weight residual
     111.00  109.35    1.65 8.70e-01 1.32e+00 3.59e+00
  angle pdb=" C   ARG D 128 "
        pdb=" CA  ARG D 128 "
        pdb=" CB  ARG D 128 "
      ideal   model   delta    sigma   weight residual
     111.00  109.36    1.64 8.70e-01 1.32e+00 3.54e+00
  angle pdb=" C   ARG C 128 "
        pdb=" CA  ARG C 128 "
        pdb=" CB  ARG C 128 "
      ideal   model   delta    sigma   weight residual
     111.00  109.37    1.63 8.70e-01 1.32e+00 3.52e+00
  angle pdb=" C   ARG E 128 "
        pdb=" CA  ARG E 128 "
        pdb=" CB  ARG E 128 "
      ideal   model   delta    sigma   weight residual
     111.00  109.37    1.63 8.70e-01 1.32e+00 3.50e+00
  ... (remaining 19112 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.34: 7296
        8.34 -    16.69: 789
       16.69 -    25.03: 238
       25.03 -    33.38: 119
       33.38 -    41.72: 42
  Dihedral angle restraints: 8484
    sinusoidal: 3248
      harmonic: 5236
  Sorted by residual:
  dihedral pdb=" N   LEU B  72 "
           pdb=" CA  LEU B  72 "
           pdb=" CB  LEU B  72 "
           pdb=" CG  LEU B  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -101.72   41.72     3      1.50e+01 4.44e-03 7.47e+00
  dihedral pdb=" N   LEU G  72 "
           pdb=" CA  LEU G  72 "
           pdb=" CB  LEU G  72 "
           pdb=" CG  LEU G  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -101.70   41.70     3      1.50e+01 4.44e-03 7.47e+00
  dihedral pdb=" N   LEU E  72 "
           pdb=" CA  LEU E  72 "
           pdb=" CB  LEU E  72 "
           pdb=" CG  LEU E  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -101.70   41.70     3      1.50e+01 4.44e-03 7.47e+00
  ... (remaining 8481 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1543
       0.027 -    0.055: 500
       0.055 -    0.082: 140
       0.082 -    0.109: 106
       0.109 -    0.137: 56
  Chirality restraints: 2345
  Sorted by residual:
  chirality pdb=" CA  ILE C 175 "
            pdb=" N   ILE C 175 "
            pdb=" C   ILE C 175 "
            pdb=" CB  ILE C 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.66e-01
  chirality pdb=" CA  ILE A 175 "
            pdb=" N   ILE A 175 "
            pdb=" C   ILE A 175 "
            pdb=" CB  ILE A 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.61e-01
  chirality pdb=" CA  ILE D 165 "
            pdb=" N   ILE D 165 "
            pdb=" C   ILE D 165 "
            pdb=" CB  ILE D 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.60e-01
  ... (remaining 2342 not shown)

  Planarity restraints: 2429
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 111 "    0.005 2.00e-02 2.50e+03   9.22e-03 8.49e-01
        pdb=" C   LEU D 111 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   LEU D 111 "    0.006 2.00e-02 2.50e+03
        pdb=" N   GLN D 112 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU F 111 "    0.005 2.00e-02 2.50e+03   9.14e-03 8.35e-01
        pdb=" C   LEU F 111 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   LEU F 111 "    0.006 2.00e-02 2.50e+03
        pdb=" N   GLN F 112 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 111 "    0.004 2.00e-02 2.50e+03   9.04e-03 8.16e-01
        pdb=" C   LEU A 111 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   LEU A 111 "    0.006 2.00e-02 2.50e+03
        pdb=" N   GLN A 112 "    0.005 2.00e-02 2.50e+03
  ... (remaining 2426 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 626
        2.72 -     3.27: 14169
        3.27 -     3.81: 22931
        3.81 -     4.36: 24538
        4.36 -     4.90: 45458
  Nonbonded interactions: 107722
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 199 "
            pdb=" NH2 ARG C 259 "
     model   vdw
     2.180 2.520
  nonbonded pdb=" OD1 ASN B 174 "
            pdb=" NZ  LYS C 169 "
     model   vdw
     2.206 2.520
  nonbonded pdb=" OD1 ASN A 276 "
            pdb=" NE2 GLN B 272 "
     model   vdw
     2.214 2.520
  nonbonded pdb=" OD1 ASP D 199 "
            pdb=" NH2 ARG E 259 "
     model   vdw
     2.285 2.520
  nonbonded pdb=" O   ALA B  22 "
            pdb=" OG  SER B  26 "
     model   vdw
     2.292 2.440
  ... (remaining 107717 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    8932      2.51       5
     N    2436      2.21       5
     O    2513      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 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:             0.620
  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:          4.820
  Check model and map are aligned:         0.190
  Convert atoms to be neutral:             0.110
  Process input model:                     37.990
  Find NCS groups from input model:        0.920
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
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      :  0.002   0.020  14098  Z= 0.156
  Angle     :  0.379   4.573  19117  Z= 0.224
  Chirality :  0.039   0.137   2345
  Planarity :  0.002   0.010   2429
  Dihedral  :  9.172  41.722   5110
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer Outliers :  0.41 %
  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:  2.97 (0.20), residues: 1813
  helix:  3.44 (0.15), residues: 1001
  sheet:  0.27 (0.27), residues: 308
  loop : -0.03 (0.29), residues: 504

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  403 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 397
  time to evaluate  : 1.851 
Fit side-chains
  outliers start: 6
  outliers final: 0
  residues processed: 403
  average time/residue: 0.2328
  time to fit residues: 138.2048
Evaluate side-chains
  262 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 1.638 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.1653
-------------------------------------------------------------------------------
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:    0.6980
   chunk 137 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9980
   chunk 93 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 142 optimal weight:    7.9990
   chunk 55 optimal weight:    9.9990
   chunk 86 optimal weight:   10.0000
   chunk 106 optimal weight:    8.9990
   chunk 165 optimal weight:    1.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 200 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14098  Z= 0.294
  Angle     :  0.575   6.368  19117  Z= 0.306
  Chirality :  0.041   0.197   2345
  Planarity :  0.004   0.094   2429
  Dihedral  :  3.869  15.942   1988
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer Outliers :  3.93 %
  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:  2.66 (0.20), residues: 1813
  helix:  3.05 (0.16), residues: 1001
  sheet:  0.72 (0.31), residues: 259
  loop : -0.19 (0.26), residues: 553

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 58
    poor density    : 262
  time to evaluate  : 1.536 
Fit side-chains
   revert: symmetry clash
  outliers start: 58
  outliers final: 28
  residues processed: 295
  average time/residue: 0.2200
  time to fit residues: 98.8969
Evaluate side-chains
  265 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 237
  time to evaluate  : 1.633 
Switching outliers to nearest non-outliers
  outliers start: 28
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1268
  time to fit residues: 8.8410
-------------------------------------------------------------------------------
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:    2.9990
   chunk 112 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 165 optimal weight:    3.9990
   chunk 178 optimal weight:    6.9990
   chunk 147 optimal weight:    4.9990
   chunk 164 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 132 optimal weight:    8.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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: 0.8098
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14098  Z= 0.283
  Angle     :  0.542   5.483  19117  Z= 0.291
  Chirality :  0.041   0.145   2345
  Planarity :  0.003   0.070   2429
  Dihedral  :  3.981  15.122   1988
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer Outliers :  2.17 %
  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 (0.19), residues: 1813
  helix:  2.89 (0.16), residues: 1001
  sheet:  1.83 (0.31), residues: 238
  loop : -0.75 (0.25), residues: 574

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 262
  time to evaluate  : 1.458 
Fit side-chains
   revert: symmetry clash
  outliers start: 32
  outliers final: 14
  residues processed: 276
  average time/residue: 0.2106
  time to fit residues: 89.2517
Evaluate side-chains
  246 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 232
  time to evaluate  : 1.735 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 0
  residues processed: 14
  average time/residue: 0.1247
  time to fit residues: 5.5445
-------------------------------------------------------------------------------
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:    2.9990
   chunk 124 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0470
   chunk 18 optimal weight:    0.7980
   chunk 79 optimal weight:   10.0000
   chunk 111 optimal weight:    0.9980
   chunk 166 optimal weight:    1.9990
   chunk 175 optimal weight:    3.9990
   chunk 86 optimal weight:    5.9990
   chunk 157 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
A 272 GLN
A 276 ASN
B 272 GLN
E 203 GLN
G 276 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14098  Z= 0.164
  Angle     :  0.502   5.915  19117  Z= 0.267
  Chirality :  0.040   0.139   2345
  Planarity :  0.003   0.053   2429
  Dihedral  :  3.805  14.146   1988
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer Outliers :  1.90 %
  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: 1813
  helix:  2.96 (0.15), residues: 1001
  sheet:  1.92 (0.30), residues: 238
  loop : -0.75 (0.25), residues: 574

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 267
  time to evaluate  : 1.600 
Fit side-chains
   revert: symmetry clash
  outliers start: 28
  outliers final: 13
  residues processed: 277
  average time/residue: 0.2166
  time to fit residues: 91.4520
Evaluate side-chains
  243 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 230
  time to evaluate  : 1.643 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.1572
  time to fit residues: 5.6679
-------------------------------------------------------------------------------
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:    0.6980
   chunk 99 optimal weight:    6.9990
   chunk 2 optimal weight:    5.9990
   chunk 130 optimal weight:    4.9990
   chunk 72 optimal weight:    5.9990
   chunk 150 optimal weight:    7.9990
   chunk 121 optimal weight:    0.0870
   chunk 0 optimal weight:   20.0000
   chunk 89 optimal weight:    5.9990
   chunk 157 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    2.5362

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

Flipped N/Q/H residues before XYZ refinement:
F 203 GLN
G 276 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.066  14098  Z= 0.301
  Angle     :  0.563   8.794  19117  Z= 0.301
  Chirality :  0.042   0.143   2345
  Planarity :  0.003   0.049   2429
  Dihedral  :  4.027  14.092   1988
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer Outliers :  2.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.36 (0.19), residues: 1813
  helix:  2.77 (0.16), residues: 1008
  sheet:  1.79 (0.30), residues: 238
  loop : -0.88 (0.24), residues: 567

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 246
  time to evaluate  : 1.897 
Fit side-chains
   revert: symmetry clash
  outliers start: 38
  outliers final: 11
  residues processed: 271
  average time/residue: 0.2111
  time to fit residues: 87.8903
Evaluate side-chains
  242 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 231
  time to evaluate  : 1.660 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.1297
  time to fit residues: 4.6167
-------------------------------------------------------------------------------
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:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 176 optimal weight:    3.9990
   chunk 146 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 92 optimal weight:    0.5980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 272 GLN
** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 276 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.095  14098  Z= 0.205
  Angle     :  0.549  10.774  19117  Z= 0.286
  Chirality :  0.041   0.188   2345
  Planarity :  0.003   0.043   2429
  Dihedral  :  3.905  13.555   1988
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer Outliers :  2.10 %
  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:  2.43 (0.19), residues: 1813
  helix:  2.86 (0.15), residues: 1008
  sheet:  1.02 (0.30), residues: 273
  loop : -0.61 (0.26), residues: 532

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 254
  time to evaluate  : 1.658 
Fit side-chains
   revert: symmetry clash
  outliers start: 31
  outliers final: 13
  residues processed: 272
  average time/residue: 0.2137
  time to fit residues: 89.0870
Evaluate side-chains
  255 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 242
  time to evaluate  : 1.542 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.1298
  time to fit residues: 5.1416
-------------------------------------------------------------------------------
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:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 100 optimal weight:    5.9990
   chunk 128 optimal weight:    0.8980
   chunk 99 optimal weight:    4.9990
   chunk 148 optimal weight:    0.0770
   chunk 98 optimal weight:    4.9990
   chunk 175 optimal weight:    3.9990
   chunk 109 optimal weight:   10.0000
   chunk 106 optimal weight:    8.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    2.7944

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

Flipped N/Q/H residues before XYZ refinement:
** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 203 GLN
G 276 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.101  14098  Z= 0.342
  Angle     :  0.616   8.396  19117  Z= 0.323
  Chirality :  0.042   0.184   2345
  Planarity :  0.003   0.044   2429
  Dihedral  :  4.090  13.801   1988
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer Outliers :  1.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.22 (0.19), residues: 1813
  helix:  2.70 (0.15), residues: 1008
  sheet:  1.76 (0.30), residues: 238
  loop : -1.05 (0.24), residues: 567

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 249
  time to evaluate  : 1.642 
Fit side-chains
   revert: symmetry clash
  outliers start: 21
  outliers final: 8
  residues processed: 261
  average time/residue: 0.2129
  time to fit residues: 85.5997
Evaluate side-chains
  249 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 241
  time to evaluate  : 1.568 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1306
  time to fit residues: 4.0729
-------------------------------------------------------------------------------
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:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 104 optimal weight:    8.9990
   chunk 52 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 111 optimal weight:    6.9990
   chunk 119 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 137 optimal weight:    0.2980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 203 GLN
A 272 GLN
** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 276 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.081  14098  Z= 0.217
  Angle     :  0.587   8.847  19117  Z= 0.303
  Chirality :  0.041   0.228   2345
  Planarity :  0.003   0.038   2429
  Dihedral  :  3.958  13.360   1988
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer Outliers :  1.08 %
  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:  2.30 (0.19), residues: 1813
  helix:  2.77 (0.15), residues: 1008
  sheet:  0.97 (0.30), residues: 273
  loop : -0.71 (0.25), residues: 532

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 253
  time to evaluate  : 1.661 
Fit side-chains
   revert: symmetry clash
  outliers start: 16
  outliers final: 11
  residues processed: 259
  average time/residue: 0.2262
  time to fit residues: 89.6224
Evaluate side-chains
  251 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 240
  time to evaluate  : 1.626 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.1691
  time to fit residues: 5.2284
-------------------------------------------------------------------------------
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:    0.8980
   chunk 168 optimal weight:    7.9990
   chunk 153 optimal weight:    0.3980
   chunk 163 optimal weight:    0.3980
   chunk 98 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9990
   chunk 128 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 147 optimal weight:    2.9990
   chunk 154 optimal weight:    0.9990
   chunk 162 optimal weight:    2.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 276 ASN
C 203 GLN
** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 276 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.130  14098  Z= 0.212
  Angle     :  0.600  13.032  19117  Z= 0.310
  Chirality :  0.041   0.165   2345
  Planarity :  0.003   0.062   2429
  Dihedral  :  3.919  15.459   1988
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer Outliers :  0.88 %
  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:  2.30 (0.19), residues: 1813
  helix:  2.78 (0.15), residues: 1008
  sheet:  1.03 (0.29), residues: 273
  loop : -0.74 (0.25), residues: 532

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 248
  time to evaluate  : 1.748 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 6
  residues processed: 256
  average time/residue: 0.2153
  time to fit residues: 84.1043
Evaluate side-chains
  239 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 233
  time to evaluate  : 1.464 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.2711
  time to fit residues: 4.3833
-------------------------------------------------------------------------------
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:    3.9990
   chunk 172 optimal weight:    1.9990
   chunk 105 optimal weight:   10.0000
   chunk 82 optimal weight:    1.9990
   chunk 120 optimal weight:    0.4980
   chunk 181 optimal weight:    1.9990
   chunk 166 optimal weight:    5.9990
   chunk 144 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 111 optimal weight:    3.9990
   chunk 88 optimal weight:    0.6980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 272 GLN
** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 276 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.155  14098  Z= 0.245
  Angle     :  0.633  12.810  19117  Z= 0.328
  Chirality :  0.042   0.209   2345
  Planarity :  0.004   0.093   2429
  Dihedral  :  3.917  14.057   1988
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer Outliers :  0.41 %
  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:  2.28 (0.19), residues: 1813
  helix:  2.73 (0.15), residues: 1008
  sheet:  0.86 (0.29), residues: 259
  loop : -0.57 (0.26), residues: 546

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 249
  time to evaluate  : 1.457 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 253
  average time/residue: 0.2169
  time to fit residues: 84.0400
Evaluate side-chains
  239 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 236
  time to evaluate  : 1.630 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1527
  time to fit residues: 3.0074
-------------------------------------------------------------------------------
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:    1.9990
   chunk 153 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 133 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 144 optimal weight:    1.9990
   chunk 60 optimal weight:   10.0000
   chunk 148 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 276 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.138882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.109757 restraints weight = 23802.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.112226 restraints weight = 14001.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.113712 restraints weight = 9382.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.136  14098  Z= 0.248
  Angle     :  0.627   8.618  19117  Z= 0.323
  Chirality :  0.042   0.250   2345
  Planarity :  0.003   0.068   2429
  Dihedral  :  3.931  15.052   1988
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer Outliers :  1.08 %
  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:  2.22 (0.19), residues: 1813
  helix:  2.69 (0.15), residues: 1008
  sheet:  1.01 (0.28), residues: 273
  loop : -0.75 (0.25), residues: 532

===============================================================================
Job complete
usr+sys time: 2463.77 seconds
wall clock time: 45 minutes 35.95 seconds (2735.95 seconds total)