Starting phenix.real_space_refine
on Sat Aug 23 17:55:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fyb_29563/08_2025/8fyb_29563.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fyb_29563/08_2025/8fyb_29563.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fyb_29563/08_2025/8fyb_29563.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fyb_29563/08_2025/8fyb_29563.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fyb_29563/08_2025/8fyb_29563.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fyb_29563/08_2025/8fyb_29563.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 571 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     135      5.49       5
     S      32      5.16       5
     C    8099      2.51       5
     N    2441      2.21       5
     O    2779      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13486
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 737
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 737
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 4, 'TRANS': 87}
    Chain: "B"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2295
          Classifications: {'peptide': 292}
          Link IDs: {'PTRANS': 11, 'TRANS': 280}
    Chain: "C"
      Number of atoms: 2414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 2414
          Classifications: {'peptide': 309}
          Link IDs: {'PTRANS': 13, 'TRANS': 295}
    Chain: "D"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 746
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
    Chain: "E"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2295
          Classifications: {'peptide': 292}
          Link IDs: {'PTRANS': 11, 'TRANS': 280}
    Chain: "F"
      Number of atoms: 2188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2188
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 10, 'TRANS': 270}
    Chain: "G"
      Number of atoms: 1089
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 52, 1067
          Classifications: {'DNA': 52}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 51}
      Conformer: "B"
        Number of residues, atoms: 52, 1067
          Classifications: {'DNA': 52}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 51}
          bond proxies already assigned to first conformer: 1170
    Chain: "H"
      Number of atoms: 632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 632
          Classifications: {'DNA': 31}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 30}
    Chain: "J"
      Number of atoms: 742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 742
          Classifications: {'DNA': 36}
          Link IDs: {'rna3p': 35}
    Chain: "I"
      Number of atoms: 348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 348
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" P  A DG G  29 " occ=0.50
      ... (42 atoms not shown)
      pdb=" C4 B DG G  29 " occ=0.50
  Time building chain proxies: 3.51, per 1000 atoms: 0.26
  Number of scatterers: 13486
  At special positions: 0
  Unit cell: (123.765, 97.005, 163.905, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     P     135     15.00
     O    2779      8.00
     N    2441      7.00
     C    8099      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Conformation dependent library (CDL) restraints added in 531.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2510

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 11 sheets defined
      51.5% alpha, 14.4% beta
      33 base pairs and 109 stacking pairs defined.
    Time for finding SS restraints: 1.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 23
    Processing helix  chain 'A' and resid 36 through 50
    Processing helix  chain 'B' and resid 68 through 77
    Processing helix  chain 'B' and resid 86 through 89
    Processing helix  chain 'B' and resid 97 through 101
    Processing helix  chain 'B' and resid 102 through 114
      removed outlier: 3.838A  pdb=" N   ASN B 114 " --> pdb=" O   GLU B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 130
    Processing helix  chain 'B' and resid 139 through 162
    Processing helix  chain 'B' and resid 180 through 205
      removed outlier: 3.591A  pdb=" N   LEU B 196 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 231
      removed outlier: 4.028A  pdb=" N   LEU B 228 " --> pdb=" O   ASP B 224 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   TYR B 229 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   ALA B 231 " --> pdb=" O   ASP B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 244
    Processing helix  chain 'B' and resid 250 through 263
      removed outlier: 3.535A  pdb=" N   LEU B 254 " --> pdb=" O   ASP B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 280
    Processing helix  chain 'B' and resid 283 through 287
    Processing helix  chain 'B' and resid 298 through 303
    Processing helix  chain 'B' and resid 304 through 306
      No H-bonds generated for 'chain 'B' and resid 304 through 306'
    Processing helix  chain 'C' and resid 17 through 21
      removed outlier: 4.084A  pdb=" N   ARG C  21 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 53
      No H-bonds generated for 'chain 'C' and resid 51 through 53'
    Processing helix  chain 'C' and resid 68 through 77
      removed outlier: 3.643A  pdb=" N   THR C  77 " --> pdb=" O   LEU C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 114
      removed outlier: 3.830A  pdb=" N   LYS C 107 " --> pdb=" O   ARG C 103 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 130
    Processing helix  chain 'C' and resid 139 through 163
    Processing helix  chain 'C' and resid 180 through 204
      removed outlier: 3.799A  pdb=" N   ALA C 192 " --> pdb=" O   ALA C 188 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU C 193 " --> pdb=" O   ALA C 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 219 through 231
      removed outlier: 3.687A  pdb=" N   LEU C 228 " --> pdb=" O   ASP C 224 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   TYR C 229 " --> pdb=" O   VAL C 225 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ALA C 231 " --> pdb=" O   ASP C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 245
    Processing helix  chain 'C' and resid 250 through 267
    Processing helix  chain 'C' and resid 267 through 280
      removed outlier: 3.688A  pdb=" N   LEU C 280 " --> pdb=" O   LEU C 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 12 through 19
    Processing helix  chain 'D' and resid 20 through 22
      No H-bonds generated for 'chain 'D' and resid 20 through 22'
    Processing helix  chain 'D' and resid 36 through 51
    Processing helix  chain 'E' and resid 51 through 55
      removed outlier: 3.790A  pdb=" N   MET E  54 " --> pdb=" O   PRO E  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 68 through 77
    Processing helix  chain 'E' and resid 86 through 89
    Processing helix  chain 'E' and resid 97 through 101
    Processing helix  chain 'E' and resid 102 through 114
      removed outlier: 4.379A  pdb=" N   ASN E 114 " --> pdb=" O   GLU E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 114 through 130
    Processing helix  chain 'E' and resid 139 through 162
    Processing helix  chain 'E' and resid 180 through 205
    Processing helix  chain 'E' and resid 219 through 231
      removed outlier: 4.771A  pdb=" N   LEU E 228 " --> pdb=" O   ASP E 224 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   TYR E 229 " --> pdb=" O   VAL E 225 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   ALA E 231 " --> pdb=" O   ASP E 227 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 233 through 244
    Processing helix  chain 'E' and resid 250 through 266
      removed outlier: 4.022A  pdb=" N   LEU E 254 " --> pdb=" O   ASP E 250 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   GLY E 266 " --> pdb=" O   ALA E 262 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 266 through 280
      removed outlier: 3.854A  pdb=" N   LYS E 270 " --> pdb=" O   GLY E 266 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU E 280 " --> pdb=" O   LEU E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 298 through 303
    Processing helix  chain 'E' and resid 304 through 306
      No H-bonds generated for 'chain 'E' and resid 304 through 306'
    Processing helix  chain 'F' and resid 51 through 53
      No H-bonds generated for 'chain 'F' and resid 51 through 53'
    Processing helix  chain 'F' and resid 67 through 77
      removed outlier: 3.703A  pdb=" N   VAL F  71 " --> pdb=" O   SER F  67 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 102 through 114
      removed outlier: 3.635A  pdb=" N   ASN F 114 " --> pdb=" O   GLU F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 114 through 130
    Processing helix  chain 'F' and resid 139 through 163
    Processing helix  chain 'F' and resid 180 through 205
      removed outlier: 3.681A  pdb=" N   ALA F 192 " --> pdb=" O   ALA F 188 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 219 through 244
      removed outlier: 3.767A  pdb=" N   TYR F 229 " --> pdb=" O   VAL F 225 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   ALA F 231 " --> pdb=" O   ASP F 227 " (cutoff:3.500A)
      removed outlier: 5.452A  pdb=" N   GLU F 232 " --> pdb=" O   LEU F 228 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   VAL F 235 " --> pdb=" O   ALA F 231 " (cutoff:3.500A)
      Proline residue:  F 236  - end of helix
    Processing helix  chain 'F' and resid 250 through 267
    Processing helix  chain 'F' and resid 267 through 280
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27
      removed outlier: 5.939A  pdb=" N   GLU A  25 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   VAL A  32 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   MET A   3 " --> pdb=" O   ALA A  61 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81
      removed outlier: 5.717A  pdb=" N   ILE A  88 " --> pdb=" O   ARG F  49 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   ARG F  49 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   ALA E  30 " --> pdb=" O   ASP E  65 " (cutoff:3.500A)
      removed outlier: 8.395A  pdb=" N   SER E  67 " --> pdb=" O   ALA E  30 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   ILE E  32 " --> pdb=" O   SER E  67 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 94
      removed outlier: 6.608A  pdb=" N   TRP B  83 " --> pdb=" O   TYR B  92 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   SER B  94 " --> pdb=" O   LEU B  81 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   LEU B  81 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   VAL B  57 " --> pdb=" O   ARG B  21 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   THR B  23 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   LEU B  59 " --> pdb=" O   THR B  23 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   ILE B  25 " --> pdb=" O   LEU B  59 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA B  22 " --> pdb=" O   GLU B 291 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 40
      removed outlier: 6.988A  pdb=" N   ALA B  30 " --> pdb=" O   ASP B  65 " (cutoff:3.500A)
      removed outlier: 8.254A  pdb=" N   SER B  67 " --> pdb=" O   ALA B  30 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   ILE B  32 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ARG C  34 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   ARG C  49 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
      removed outlier: 5.518A  pdb=" N   ILE D  88 " --> pdb=" O   ARG C  49 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 48
    Processing sheet with id=AA6, first strand: chain 'B' and resid 214 through 215
    Processing sheet with id=AA7, first strand: chain 'C' and resid 22 through 27
      removed outlier: 6.395A  pdb=" N   THR C  23 " --> pdb=" O   VAL C  57 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   LEU C  59 " --> pdb=" O   THR C  23 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   ILE C  25 " --> pdb=" O   LEU C  59 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ALA C  80 " --> pdb=" O   GLY C  56 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   TYR C  91 " --> pdb=" O   TRP C  83 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   GLY C  85 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   VAL C  89 " --> pdb=" O   GLY C  85 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27
      removed outlier: 5.806A  pdb=" N   GLU D  25 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   VAL D  32 " --> pdb=" O   GLU D  25 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ALA D  27 " --> pdb=" O   VAL D  30 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   MET D   3 " --> pdb=" O   ALA D  61 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA D  61 " --> pdb=" O   MET D   3 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 91 through 94
      removed outlier: 6.049A  pdb=" N   LEU E  58 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   VAL E  84 " --> pdb=" O   LEU E  58 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   LEU E  60 " --> pdb=" O   VAL E  84 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   VAL E  57 " --> pdb=" O   ARG E  21 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   THR E  23 " --> pdb=" O   VAL E  57 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   LEU E  59 " --> pdb=" O   THR E  23 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ILE E  25 " --> pdb=" O   LEU E  59 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   TYR E  26 " --> pdb=" O   LEU E 293 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 47 through 49
      removed outlier: 4.078A  pdb=" N   ASN E 308 " --> pdb=" O   ARG E  49 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 22 through 27
      removed outlier: 6.463A  pdb=" N   THR F  23 " --> pdb=" O   VAL F  57 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   LEU F  59 " --> pdb=" O   THR F  23 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ILE F  25 " --> pdb=" O   LEU F  59 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL F  82 " --> pdb=" O   LEU F  58 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   TYR F  91 " --> pdb=" O   TRP F  83 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   GLY F  85 " --> pdb=" O   VAL F  89 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   VAL F  89 " --> pdb=" O   GLY F  85 " (cutoff:3.500A)

    577 hydrogen bonds defined for protein.
    1656 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      78 hydrogen bonds
      156 hydrogen bond angles
      0 basepair planarities
      33 basepair parallelities
      110 stacking parallelities
  Total time for adding SS restraints: 2.39

  Time building geometry restraints manager: 1.42 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3437
        1.33 -     1.45: 3290
        1.45 -     1.57: 6968
        1.57 -     1.69: 269
        1.69 -     1.82: 62
  Bond restraints: 14026
  Sorted by residual:
  bond pdb=" CA  TRP E 166 "
       pdb=" C   TRP E 166 "
    ideal  model  delta    sigma   weight residual
    1.528  1.506  0.022 1.18e-02 7.18e+03 3.38e+00
  bond pdb=" CA  ARG E 169 "
       pdb=" C   ARG E 169 "
    ideal  model  delta    sigma   weight residual
    1.523  1.502  0.022 1.34e-02 5.57e+03 2.62e+00
  bond pdb=" C3'  DG G   8 "
       pdb=" O3'  DG G   8 "
    ideal  model  delta    sigma   weight residual
    1.422  1.465 -0.043 3.00e-02 1.11e+03 2.01e+00
  bond pdb=" CA  VAL E 170 "
       pdb=" C   VAL E 170 "
    ideal  model  delta    sigma   weight residual
    1.523  1.506  0.017 1.27e-02 6.20e+03 1.77e+00
  bond pdb=" CA  TYR E 171 "
       pdb=" C   TYR E 171 "
    ideal  model  delta    sigma   weight residual
    1.525  1.508  0.016 1.25e-02 6.40e+03 1.69e+00
  ... (remaining 14021 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 19117
        1.82 -     3.64: 414
        3.64 -     5.47: 34
        5.47 -     7.29: 6
        7.29 -     9.11: 2
  Bond angle restraints: 19573
  Sorted by residual:
  angle pdb=" N   LYS E 167 "
        pdb=" CA  LYS E 167 "
        pdb=" C   LYS E 167 "
      ideal   model   delta    sigma   weight residual
     110.53  102.86    7.67 1.29e+00 6.01e-01 3.54e+01
  angle pdb=" N   LYS E 168 "
        pdb=" CA  LYS E 168 "
        pdb=" C   LYS E 168 "
      ideal   model   delta    sigma   weight residual
     110.35  117.00   -6.65 1.36e+00 5.41e-01 2.39e+01
  angle pdb=" N   TRP E 166 "
        pdb=" CA  TRP E 166 "
        pdb=" C   TRP E 166 "
      ideal   model   delta    sigma   weight residual
     107.37  116.48   -9.11 2.07e+00 2.33e-01 1.94e+01
  angle pdb=" CA  PRO E 165 "
        pdb=" C   PRO E 165 "
        pdb=" N   TRP E 166 "
      ideal   model   delta    sigma   weight residual
     114.75  119.47   -4.72 1.45e+00 4.76e-01 1.06e+01
  angle pdb=" CA  PRO E 165 "
        pdb=" C   PRO E 165 "
        pdb=" O   PRO E 165 "
      ideal   model   delta    sigma   weight residual
     122.31  117.91    4.40 1.41e+00 5.03e-01 9.75e+00
  ... (remaining 19568 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.90: 7454
       35.90 -    71.81: 584
       71.81 -   107.71: 17
      107.71 -   143.62: 3
      143.62 -   179.52: 4
  Dihedral angle restraints: 8062
    sinusoidal: 4145
      harmonic: 3917
  Sorted by residual:
  dihedral pdb=" C4'  DA J  30 "
           pdb=" C3'  DA J  30 "
           pdb=" O3'  DA J  30 "
           pdb=" P    DA J  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.52 -179.52     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J  25 "
           pdb=" C3'  DG J  25 "
           pdb=" O3'  DG J  25 "
           pdb=" P    DC J  26 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   41.59  178.41     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DA J  31 "
           pdb=" C3'  DA J  31 "
           pdb=" O3'  DA J  31 "
           pdb=" P    DA J  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.10 -178.10     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 8059 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1624
       0.039 -    0.079: 430
       0.079 -    0.118: 115
       0.118 -    0.157: 24
       0.157 -    0.196: 2
  Chirality restraints: 2195
  Sorted by residual:
  chirality pdb=" CA  LYS E 168 "
            pdb=" N   LYS E 168 "
            pdb=" C   LYS E 168 "
            pdb=" CB  LYS E 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.64e-01
  chirality pdb=" CA  TRP E 166 "
            pdb=" N   TRP E 166 "
            pdb=" C   TRP E 166 "
            pdb=" CB  TRP E 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.65e-01
  chirality pdb=" CA  VAL B 303 "
            pdb=" N   VAL B 303 "
            pdb=" C   VAL B 303 "
            pdb=" CB  VAL B 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.29    0.15 2.00e-01 2.50e+01 5.60e-01
  ... (remaining 2192 not shown)

  Planarity restraints: 2042
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  50 "    0.032 5.00e-02 4.00e+02   4.87e-02 3.80e+00
        pdb=" N   PRO B  51 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B  51 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B  51 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 291 "   -0.028 5.00e-02 4.00e+02   4.31e-02 2.97e+00
        pdb=" N   PRO E 292 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO E 292 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO E 292 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E 160 "    0.008 2.00e-02 2.50e+03   1.69e-02 2.86e+00
        pdb=" C   LYS E 160 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   LYS E 160 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LYS E 161 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2039 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1663
        2.75 -     3.29: 12870
        3.29 -     3.82: 25087
        3.82 -     4.36: 29445
        4.36 -     4.90: 47320
  Nonbonded interactions: 116385
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 223 "
            pdb=" N2   DG G  27 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" NH2 ARG E 124 "
            pdb=" OE1 GLU E 281 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OH  TYR B 126 "
            pdb=" O4   DT H  29 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" NH2 ARG B 256 "
            pdb=" OP1  DT H  23 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" OH  TYR E  92 "
            pdb=" OP2  DC G  24 "
     model   vdw
     2.254 3.040
  ... (remaining 116380 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'D' and resid 1 through 92)
}
ncs_group {
  reference = (chain 'B' and resid 20 through 282)
  selection = (chain 'C' and resid 20 through 282)
  selection = (chain 'E' and resid 20 through 282)
  selection = (chain 'F' and resid 20 through 282)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.750
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14026  Z= 0.194
  Angle     :  0.598   9.109  19573  Z= 0.341
  Chirality :  0.039   0.196   2195
  Planarity :  0.004   0.049   2042
  Dihedral  : 20.880 179.521   5552
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.18 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.23), residues: 1347
  helix:  1.66 (0.20), residues: 635
  sheet: -0.29 (0.37), residues: 214
  loop : -0.85 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 116 
 TYR   0.015   0.002   TYR E 162 
 PHE   0.017   0.002   PHE A  35 
 TRP   0.013   0.001   TRP E 166 
 HIS   0.012   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (14026)
  covalent geometry    : angle       0.59819 (19573)
  hydrogen bonds       : bond        0.14203 (  655)
  hydrogen bonds       : angle       6.27044 ( 1812)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 294
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A    3 MET cc_start: 0.7611 (ttt) cc_final: 0.6837 (ttt)
REVERT: B  175 ASP cc_start: 0.7927 (t0) cc_final: 0.7550 (t70)
REVERT: B  275 ASP cc_start: 0.7542 (m-30) cc_final: 0.7199 (m-30)
REVERT: B  289 GLU cc_start: 0.7826 (tp30) cc_final: 0.7613 (tp30)
REVERT: C  162 TYR cc_start: 0.8341 (m-80) cc_final: 0.7963 (m-80)
REVERT: C  233 ILE cc_start: 0.7577 (mt) cc_final: 0.7260 (mt)
REVERT: C  274 LYS cc_start: 0.8113 (tppt) cc_final: 0.7883 (tptp)
REVERT: E   72 GLU cc_start: 0.7249 (tp30) cc_final: 0.6892 (mm-30)
REVERT: E   76 ASP cc_start: 0.6861 (m-30) cc_final: 0.6636 (m-30)
REVERT: E  154 LYS cc_start: 0.7294 (tppp) cc_final: 0.6566 (tppt)
REVERT: E  172 ASN cc_start: 0.8074 (t0) cc_final: 0.7646 (t0)
REVERT: E  175 ASP cc_start: 0.7559 (t70) cc_final: 0.7091 (m-30)
REVERT: E  193 LEU cc_start: 0.8391 (tp) cc_final: 0.8148 (tp)
REVERT: E  272 MET cc_start: 0.7782 (mtt) cc_final: 0.7550 (mtp)
REVERT: F  101 SER cc_start: 0.8939 (t) cc_final: 0.8702 (p)
REVERT: F  275 ASP cc_start: 0.8134 (m-30) cc_final: 0.7843 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 295
  average time/residue: 0.1247
  time to fit residues: 50.7045
Evaluate side-chains
  186 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    0.4980
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
C  33 ASN
E 183 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.177242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.111146 restraints weight = 15715.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.28
r_work: 0.3235 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  14026  Z= 0.252
  Angle     :  0.638   6.719  19573  Z= 0.355
  Chirality :  0.044   0.171   2195
  Planarity :  0.005   0.048   2042
  Dihedral  : 24.294 177.568   3008
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  9.62 %
    Favored  : 88.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.23), residues: 1347
  helix:  1.61 (0.20), residues: 640
  sheet: -0.49 (0.36), residues: 208
  loop : -0.90 (0.26), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  49 
 TYR   0.018   0.002   TYR B  92 
 PHE   0.011   0.002   PHE E 239 
 TRP   0.011   0.002   TRP C 296 
 HIS   0.011   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00590 (14026)
  covalent geometry    : angle       0.63767 (19573)
  hydrogen bonds       : bond        0.04893 (  655)
  hydrogen bonds       : angle       4.40170 ( 1812)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 197
  time to evaluate  : 0.461 
Fit side-chains
REVERT: A    3 MET cc_start: 0.8275 (ttt) cc_final: 0.7794 (ttt)
REVERT: A   45 ARG cc_start: 0.7765 (mmm-85) cc_final: 0.7474 (mtp85)
REVERT: A   73 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7926 (tp30)
REVERT: B  138 LEU cc_start: 0.8657 (mp) cc_final: 0.8316 (tp)
REVERT: B  175 ASP cc_start: 0.8124 (t0) cc_final: 0.7918 (t0)
REVERT: B  289 GLU cc_start: 0.8279 (tp30) cc_final: 0.7714 (tp30)
REVERT: C  162 TYR cc_start: 0.8290 (m-80) cc_final: 0.8026 (m-80)
REVERT: C  253 GLN cc_start: 0.8256 (tt0) cc_final: 0.8052 (mt0)
REVERT: D   78 SER cc_start: 0.8324 (m) cc_final: 0.7987 (t)
REVERT: E   72 GLU cc_start: 0.7836 (tp30) cc_final: 0.7027 (tm-30)
REVERT: E   76 ASP cc_start: 0.7240 (m-30) cc_final: 0.6655 (m-30)
REVERT: E  172 ASN cc_start: 0.7887 (t0) cc_final: 0.7518 (t0)
REVERT: E  289 GLU cc_start: 0.7708 (tp30) cc_final: 0.7477 (tm-30)
REVERT: F  101 SER cc_start: 0.9231 (t) cc_final: 0.8860 (p)
REVERT: F  275 ASP cc_start: 0.8343 (m-30) cc_final: 0.8035 (m-30)
  outliers start: 17
  outliers final: 11
  residues processed: 206
  average time/residue: 0.1232
  time to fit residues: 35.5099
Evaluate side-chains
  190 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 179
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   35 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 55 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 105 optimal weight:    0.3980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 183 ASN
E 183 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.180093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.117805 restraints weight = 17349.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 2.37
r_work: 0.3259 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3266
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3266
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14026  Z= 0.162
  Angle     :  0.560   6.465  19573  Z= 0.315
  Chirality :  0.040   0.155   2195
  Planarity :  0.004   0.047   2042
  Dihedral  : 24.322 176.776   3008
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.69 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.23), residues: 1347
  helix:  1.84 (0.20), residues: 640
  sheet: -0.52 (0.36), residues: 210
  loop : -0.84 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  49 
 TYR   0.016   0.001   TYR F 229 
 PHE   0.011   0.001   PHE A  89 
 TRP   0.017   0.001   TRP E 166 
 HIS   0.007   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (14026)
  covalent geometry    : angle       0.55962 (19573)
  hydrogen bonds       : bond        0.03995 (  655)
  hydrogen bonds       : angle       4.04871 ( 1812)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 198
  time to evaluate  : 0.420 
Fit side-chains
REVERT: A    3 MET cc_start: 0.7824 (ttt) cc_final: 0.7070 (ttt)
REVERT: A   45 ARG cc_start: 0.7578 (mmm-85) cc_final: 0.7246 (mtp85)
REVERT: A   73 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7594 (tp30)
REVERT: B  281 GLU cc_start: 0.8163 (mp0) cc_final: 0.7466 (mp0)
REVERT: C  125 MET cc_start: 0.7428 (mtt) cc_final: 0.7223 (mtp)
REVERT: C  156 ARG cc_start: 0.7582 (mtm110) cc_final: 0.7320 (ptt90)
REVERT: C  253 GLN cc_start: 0.8018 (tt0) cc_final: 0.7759 (mt0)
REVERT: D   78 SER cc_start: 0.8285 (m) cc_final: 0.7954 (t)
REVERT: E   72 GLU cc_start: 0.7678 (tp30) cc_final: 0.6773 (tm-30)
REVERT: E   76 ASP cc_start: 0.7178 (m-30) cc_final: 0.6504 (m-30)
REVERT: E  155 TYR cc_start: 0.7463 (m-10) cc_final: 0.7175 (m-80)
REVERT: E  172 ASN cc_start: 0.7995 (t0) cc_final: 0.7610 (t0)
REVERT: F  101 SER cc_start: 0.9164 (t) cc_final: 0.8784 (p)
  outliers start: 18
  outliers final: 15
  residues processed: 209
  average time/residue: 0.1099
  time to fit residues: 32.6229
Evaluate side-chains
  189 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 174
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue  163 ASN
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  207 SER
Chi-restraints excluded: chain F residue  277 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 124 optimal weight:    8.9990
   chunk 113 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0980
   chunk 77 optimal weight:    4.9990
   chunk 71 optimal weight:    0.6980
   chunk 126 optimal weight:    0.7980
   chunk 94 optimal weight:    3.9990
   chunk 129 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 127 optimal weight:    4.9990
   chunk 123 optimal weight:    6.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4244 r_free = 0.4244 target = 0.184195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.120295 restraints weight = 20701.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 2.71
r_work: 0.3237 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3244
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3244
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14026  Z= 0.150
  Angle     :  0.548   6.474  19573  Z= 0.309
  Chirality :  0.040   0.192   2195
  Planarity :  0.004   0.050   2042
  Dihedral  : 24.347 176.547   3008
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 12.59 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.23), residues: 1347
  helix:  1.96 (0.20), residues: 641
  sheet: -0.40 (0.37), residues: 198
  loop : -0.92 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 116 
 TYR   0.014   0.001   TYR F 229 
 PHE   0.011   0.001   PHE A  89 
 TRP   0.007   0.001   TRP E 296 
 HIS   0.007   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (14026)
  covalent geometry    : angle       0.54777 (19573)
  hydrogen bonds       : bond        0.03701 (  655)
  hydrogen bonds       : angle       3.86068 ( 1812)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 187
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.8294 (tt0) cc_final: 0.8051 (tt0)
REVERT: A   45 ARG cc_start: 0.7683 (mmm-85) cc_final: 0.7345 (mtp85)
REVERT: A   73 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7713 (tp30)
REVERT: B  281 GLU cc_start: 0.8139 (mp0) cc_final: 0.7408 (mp0)
REVERT: C   49 ARG cc_start: 0.8246 (mtm180) cc_final: 0.8020 (mtp180)
REVERT: C  125 MET cc_start: 0.7188 (mtt) cc_final: 0.6858 (mtp)
REVERT: C  141 GLN cc_start: 0.7800 (tp40) cc_final: 0.7567 (tp40)
REVERT: C  156 ARG cc_start: 0.7514 (mtm110) cc_final: 0.7226 (ptt90)
REVERT: C  253 GLN cc_start: 0.7969 (tt0) cc_final: 0.7445 (mm-40)
REVERT: D   73 GLU cc_start: 0.8035 (tp30) cc_final: 0.7811 (tp30)
REVERT: D   78 SER cc_start: 0.8245 (m) cc_final: 0.7918 (t)
REVERT: E   72 GLU cc_start: 0.7659 (tp30) cc_final: 0.6725 (tm-30)
REVERT: E   76 ASP cc_start: 0.7288 (m-30) cc_final: 0.6735 (m-30)
REVERT: E  155 TYR cc_start: 0.7361 (m-10) cc_final: 0.7088 (m-80)
REVERT: E  172 ASN cc_start: 0.7991 (t0) cc_final: 0.7569 (t0)
REVERT: F  101 SER cc_start: 0.9134 (t) cc_final: 0.8749 (p)
  outliers start: 25
  outliers final: 17
  residues processed: 201
  average time/residue: 0.1440
  time to fit residues: 41.0103
Evaluate side-chains
  193 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 176
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  147 GLU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue  310 SER
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  277 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 134 optimal weight:    2.9990
   chunk 116 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 109 optimal weight:    0.4980
   chunk 85 optimal weight:    4.9990
   chunk 18 optimal weight:    8.9990
   chunk 141 optimal weight:    3.9990
   chunk 78 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    1.4586

-------------------------------------------------------------------------------
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 = 0.4173 r_free = 0.4173 target = 0.176456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.113748 restraints weight = 18246.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 2.44
r_work: 0.3203 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  14026  Z= 0.208
  Angle     :  0.583   6.484  19573  Z= 0.325
  Chirality :  0.041   0.175   2195
  Planarity :  0.004   0.048   2042
  Dihedral  : 24.556 175.989   3008
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 12.95 %
    Favored  : 84.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.23), residues: 1347
  helix:  1.86 (0.20), residues: 639
  sheet: -0.54 (0.37), residues: 200
  loop : -0.96 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  49 
 TYR   0.014   0.002   TYR F 229 
 PHE   0.011   0.001   PHE A  89 
 TRP   0.009   0.001   TRP B  83 
 HIS   0.008   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 (14026)
  covalent geometry    : angle       0.58345 (19573)
  hydrogen bonds       : bond        0.04173 (  655)
  hydrogen bonds       : angle       4.01449 ( 1812)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 181
  time to evaluate  : 0.557 
Fit side-chains
REVERT: A   45 ARG cc_start: 0.7749 (mmm-85) cc_final: 0.7425 (mtp85)
REVERT: B  130 PHE cc_start: 0.7218 (m-80) cc_final: 0.6723 (m-80)
REVERT: C   49 ARG cc_start: 0.8261 (mtm180) cc_final: 0.7935 (mtp85)
REVERT: D   13 GLN cc_start: 0.8248 (mm110) cc_final: 0.8041 (mm-40)
REVERT: D   78 SER cc_start: 0.8313 (m) cc_final: 0.8009 (t)
REVERT: E   72 GLU cc_start: 0.7792 (tp30) cc_final: 0.7578 (tm-30)
REVERT: E  172 ASN cc_start: 0.8032 (t0) cc_final: 0.7634 (t0)
REVERT: E  246 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7380 (tm-30)
REVERT: E  247 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7350 (pm20)
REVERT: F   36 ASP cc_start: 0.7796 (m-30) cc_final: 0.7573 (m-30)
REVERT: F  101 SER cc_start: 0.9118 (t) cc_final: 0.8712 (p)
  outliers start: 28
  outliers final: 19
  residues processed: 195
  average time/residue: 0.1482
  time to fit residues: 40.6626
Evaluate side-chains
  191 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 171
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  147 GLU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue  163 ASN
Chi-restraints excluded: chain E residue  247 GLU
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  207 SER
Chi-restraints excluded: chain F residue  277 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 10 optimal weight:    7.9990
   chunk 139 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 94 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4204 r_free = 0.4204 target = 0.179404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.118324 restraints weight = 18473.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 2.38
r_work: 0.3265 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14026  Z= 0.158
  Angle     :  0.547   6.392  19573  Z= 0.308
  Chirality :  0.040   0.173   2195
  Planarity :  0.004   0.045   2042
  Dihedral  : 24.548 175.306   3008
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.93 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.23), residues: 1347
  helix:  1.98 (0.20), residues: 639
  sheet: -0.52 (0.37), residues: 198
  loop : -0.93 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 116 
 TYR   0.013   0.001   TYR B 309 
 PHE   0.016   0.001   PHE C 239 
 TRP   0.007   0.001   TRP B  83 
 HIS   0.006   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (14026)
  covalent geometry    : angle       0.54739 (19573)
  hydrogen bonds       : bond        0.03677 (  655)
  hydrogen bonds       : angle       3.85484 ( 1812)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 186
  time to evaluate  : 0.572 
Fit side-chains
REVERT: A   45 ARG cc_start: 0.7613 (mmm-85) cc_final: 0.7299 (mtp85)
REVERT: A   73 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7592 (tp30)
REVERT: B  130 PHE cc_start: 0.7089 (m-80) cc_final: 0.6591 (m-80)
REVERT: D   78 SER cc_start: 0.8350 (m) cc_final: 0.7923 (t)
REVERT: E  172 ASN cc_start: 0.8008 (t0) cc_final: 0.7650 (t0)
REVERT: F  101 SER cc_start: 0.9103 (t) cc_final: 0.8664 (p)
  outliers start: 22
  outliers final: 17
  residues processed: 196
  average time/residue: 0.1457
  time to fit residues: 39.8421
Evaluate side-chains
  185 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 168
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  147 GLU
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain E residue   50 ILE
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue  247 GLU
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  277 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 127 optimal weight:    6.9990
   chunk 122 optimal weight:    0.0070
   chunk 143 optimal weight:   10.0000
   chunk 68 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 104 optimal weight:    8.9990
   chunk 69 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.7598

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

Flipped N/Q/H residues before XYZ refinement:
** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  33 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.179710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.117232 restraints weight = 23388.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 2.74
r_work: 0.3220 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3230
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14026  Z= 0.154
  Angle     :  0.542   6.451  19573  Z= 0.305
  Chirality :  0.040   0.169   2195
  Planarity :  0.004   0.047   2042
  Dihedral  : 24.498 175.811   3008
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.38 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.23), residues: 1347
  helix:  2.03 (0.20), residues: 640
  sheet: -0.52 (0.37), residues: 200
  loop : -0.90 (0.25), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 116 
 TYR   0.011   0.001   TYR F 126 
 PHE   0.012   0.001   PHE A  89 
 TRP   0.007   0.001   TRP B  83 
 HIS   0.008   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (14026)
  covalent geometry    : angle       0.54209 (19573)
  hydrogen bonds       : bond        0.03631 (  655)
  hydrogen bonds       : angle       3.76122 ( 1812)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 181
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A    3 MET cc_start: 0.7939 (ttt) cc_final: 0.7526 (ttt)
REVERT: A   45 ARG cc_start: 0.7677 (mmm-85) cc_final: 0.7373 (mtp85)
REVERT: B  130 PHE cc_start: 0.6930 (m-80) cc_final: 0.6435 (m-80)
REVERT: C  156 ARG cc_start: 0.7351 (mtm110) cc_final: 0.7110 (ptt90)
REVERT: D   78 SER cc_start: 0.8274 (m) cc_final: 0.7862 (t)
REVERT: E  172 ASN cc_start: 0.7978 (t0) cc_final: 0.7594 (t0)
REVERT: F   36 ASP cc_start: 0.7812 (m-30) cc_final: 0.7481 (m-30)
REVERT: F  101 SER cc_start: 0.9137 (t) cc_final: 0.8660 (p)
  outliers start: 23
  outliers final: 17
  residues processed: 193
  average time/residue: 0.1348
  time to fit residues: 36.4184
Evaluate side-chains
  188 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 171
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  147 GLU
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue  196 LEU
Chi-restraints excluded: chain E residue  247 GLU
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  277 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 111 optimal weight:    0.9990
   chunk 86 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 142 optimal weight:   10.0000
   chunk 113 optimal weight:    0.0980
   chunk 43 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 118 optimal weight:    4.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN
** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.178854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.116823 restraints weight = 18084.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.41
r_work: 0.3235 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3245
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14026  Z= 0.171
  Angle     :  0.558   6.371  19573  Z= 0.312
  Chirality :  0.040   0.169   2195
  Planarity :  0.004   0.048   2042
  Dihedral  : 24.480 175.942   3008
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.92 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.23), residues: 1347
  helix:  1.97 (0.20), residues: 639
  sheet: -0.55 (0.37), residues: 200
  loop : -0.90 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  49 
 TYR   0.013   0.001   TYR F 126 
 PHE   0.012   0.001   PHE C 239 
 TRP   0.007   0.001   TRP B  83 
 HIS   0.006   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (14026)
  covalent geometry    : angle       0.55825 (19573)
  hydrogen bonds       : bond        0.03761 (  655)
  hydrogen bonds       : angle       3.80304 ( 1812)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 170
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A   45 ARG cc_start: 0.7681 (mmm-85) cc_final: 0.7379 (mtp85)
REVERT: A   73 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7590 (tp30)
REVERT: B  130 PHE cc_start: 0.7037 (m-80) cc_final: 0.6571 (m-80)
REVERT: C  156 ARG cc_start: 0.7442 (mtm110) cc_final: 0.7178 (ptt90)
REVERT: D   51 MET cc_start: 0.8623 (ptt) cc_final: 0.8254 (ptt)
REVERT: D   78 SER cc_start: 0.8305 (m) cc_final: 0.7904 (t)
REVERT: E  172 ASN cc_start: 0.8061 (t0) cc_final: 0.7688 (t0)
REVERT: F   36 ASP cc_start: 0.7789 (m-30) cc_final: 0.7472 (m-30)
REVERT: F  101 SER cc_start: 0.9111 (t) cc_final: 0.8640 (p)
  outliers start: 21
  outliers final: 17
  residues processed: 181
  average time/residue: 0.1277
  time to fit residues: 32.1142
Evaluate side-chains
  182 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 165
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  147 GLU
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue  196 LEU
Chi-restraints excluded: chain E residue  247 GLU
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  277 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 105 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 59 optimal weight:    5.9990
   chunk 112 optimal weight:    2.9990
   chunk 110 optimal weight:    0.6980
   chunk 60 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 128 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** D  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.180141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.118742 restraints weight = 24730.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 2.81
r_work: 0.3218 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3225
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3225
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.3396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14026  Z= 0.152
  Angle     :  0.543   6.563  19573  Z= 0.304
  Chirality :  0.040   0.155   2195
  Planarity :  0.004   0.048   2042
  Dihedral  : 24.444 176.008   3008
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.92 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.23), residues: 1347
  helix:  2.04 (0.20), residues: 640
  sheet: -0.54 (0.37), residues: 200
  loop : -0.85 (0.25), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 116 
 TYR   0.023   0.001   TYR C 171 
 PHE   0.012   0.001   PHE A  89 
 TRP   0.007   0.001   TRP B  83 
 HIS   0.006   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (14026)
  covalent geometry    : angle       0.54255 (19573)
  hydrogen bonds       : bond        0.03592 (  655)
  hydrogen bonds       : angle       3.72947 ( 1812)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 174
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A   45 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7485 (mtp85)
REVERT: B  130 PHE cc_start: 0.6921 (m-80) cc_final: 0.6460 (m-80)
REVERT: C  156 ARG cc_start: 0.7470 (mtm110) cc_final: 0.7200 (ptt90)
REVERT: D   78 SER cc_start: 0.8265 (m) cc_final: 0.7870 (t)
REVERT: E  172 ASN cc_start: 0.8094 (t0) cc_final: 0.7700 (t0)
REVERT: F   36 ASP cc_start: 0.7838 (m-30) cc_final: 0.7516 (m-30)
REVERT: F  101 SER cc_start: 0.9116 (t) cc_final: 0.8635 (p)
  outliers start: 23
  outliers final: 19
  residues processed: 186
  average time/residue: 0.1240
  time to fit residues: 32.6891
Evaluate side-chains
  188 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 169
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  147 GLU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue  163 ASN
Chi-restraints excluded: chain E residue  196 LEU
Chi-restraints excluded: chain E residue  247 GLU
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  277 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 88 optimal weight:    9.9990
   chunk 70 optimal weight:    2.9990
   chunk 67 optimal weight:    7.9990
   chunk 57 optimal weight:    0.7980
   chunk 109 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 122 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9990
   chunk 145 optimal weight:   30.0000
   chunk 123 optimal weight:    7.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN
** D  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.180254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.118169 restraints weight = 22248.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.72
r_work: 0.3227 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3231
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14026  Z= 0.156
  Angle     :  0.555   7.848  19573  Z= 0.308
  Chirality :  0.040   0.193   2195
  Planarity :  0.004   0.048   2042
  Dihedral  : 24.436 176.340   3008
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 16.91 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.23), residues: 1347
  helix:  1.99 (0.20), residues: 640
  sheet: -0.63 (0.36), residues: 202
  loop : -0.82 (0.25), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG C 144 
 TYR   0.024   0.001   TYR F 126 
 PHE   0.012   0.001   PHE A  89 
 TRP   0.007   0.001   TRP B  83 
 HIS   0.006   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (14026)
  covalent geometry    : angle       0.55488 (19573)
  hydrogen bonds       : bond        0.03653 (  655)
  hydrogen bonds       : angle       3.75818 ( 1812)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 170
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A   45 ARG cc_start: 0.7736 (mmm-85) cc_final: 0.7453 (mtp85)
REVERT: A   73 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7635 (tp30)
REVERT: B   76 ASP cc_start: 0.8524 (t0) cc_final: 0.7863 (m-30)
REVERT: B  130 PHE cc_start: 0.6807 (m-80) cc_final: 0.6396 (m-80)
REVERT: B  308 ASN cc_start: 0.8493 (t0) cc_final: 0.8167 (t0)
REVERT: C  156 ARG cc_start: 0.7479 (mtm110) cc_final: 0.7207 (ptt90)
REVERT: D   73 GLU cc_start: 0.7829 (tp30) cc_final: 0.7601 (tp30)
REVERT: D   78 SER cc_start: 0.8256 (m) cc_final: 0.7856 (t)
REVERT: E  172 ASN cc_start: 0.8228 (t0) cc_final: 0.7809 (t0)
REVERT: F   36 ASP cc_start: 0.7825 (m-30) cc_final: 0.7475 (m-30)
REVERT: F  101 SER cc_start: 0.9097 (t) cc_final: 0.8614 (p)
REVERT: F  275 ASP cc_start: 0.8193 (m-30) cc_final: 0.7730 (m-30)
  outliers start: 18
  outliers final: 17
  residues processed: 180
  average time/residue: 0.1189
  time to fit residues: 30.0917
Evaluate side-chains
  183 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  147 GLU
Chi-restraints excluded: chain C residue  244 GLU
Chi-restraints excluded: chain C residue  251 ILE
Chi-restraints excluded: chain C residue  295 LEU
Chi-restraints excluded: chain E residue   98 LEU
Chi-restraints excluded: chain E residue  196 LEU
Chi-restraints excluded: chain E residue  247 GLU
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  277 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0980
   chunk 40 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 50 optimal weight:    0.3980
   chunk 28 optimal weight:    5.9990
   chunk 75 optimal weight:    0.7980
   chunk 139 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0010
   chunk 108 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.3786

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN
** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 127 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.182317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.120441 restraints weight = 22452.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.70
r_work: 0.3263 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3270
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3270
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14026  Z= 0.137
  Angle     :  0.539   8.944  19573  Z= 0.300
  Chirality :  0.039   0.255   2195
  Planarity :  0.004   0.059   2042
  Dihedral  : 24.367 176.487   3008
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.64 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.23), residues: 1347
  helix:  2.01 (0.20), residues: 642
  sheet: -0.48 (0.36), residues: 200
  loop : -0.77 (0.26), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG C 144 
 TYR   0.025   0.001   TYR F 229 
 PHE   0.012   0.001   PHE A  89 
 TRP   0.008   0.001   TRP B  83 
 HIS   0.007   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (14026)
  covalent geometry    : angle       0.53864 (19573)
  hydrogen bonds       : bond        0.03407 (  655)
  hydrogen bonds       : angle       3.71327 ( 1812)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4675.05 seconds
wall clock time: 80 minutes 19.02 seconds (4819.02 seconds total)