Starting phenix.real_space_refine
on Wed Sep 25 00:07:06 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5g_27912/09_2024/8e5g_27912.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5g_27912/09_2024/8e5g_27912.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5g_27912/09_2024/8e5g_27912.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5g_27912/09_2024/8e5g_27912.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5g_27912/09_2024/8e5g_27912.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5g_27912/09_2024/8e5g_27912.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe     20      7.16       5
     S      55      5.16       5
     C    5710      2.51       5
     N    1510      2.21       5
     O    1770      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 9065
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1641
          Classifications: {'peptide': 220}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 172
          Unusual residues: {'HEC': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 5.69, per 1000 atoms: 0.63
  Number of scatterers: 9065
  At special positions: 0
  Unit cell: (84.24, 71.28, 250.56, 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)
     Fe     20     26.01
     S      55     16.00
     O    1770      8.00
     N    1510      7.00
     C    5710      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=71, symmetry=0
  Number of additional bonds: simple=71, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.49
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1960

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 10 sheets defined
      20.5% alpha, 16.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 49
      removed outlier: 3.529A  pdb=" N   LYS A  48 " --> pdb=" O   PRO A  45 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   CYS A  49 " --> pdb=" O   CYS A  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 45 through 49'
    Processing helix  chain 'A' and resid 50 through 59
      removed outlier: 3.795A  pdb=" N   ASN A  59 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 86
      removed outlier: 3.524A  pdb=" N   ILE A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 175
    Processing helix  chain 'A' and resid 181 through 186
      removed outlier: 3.998A  pdb=" N   CYS A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 49
      removed outlier: 3.529A  pdb=" N   LYS B  48 " --> pdb=" O   PRO B  45 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   CYS B  49 " --> pdb=" O   CYS B  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 45 through 49'
    Processing helix  chain 'B' and resid 50 through 59
      removed outlier: 3.795A  pdb=" N   ASN B  59 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 86
      removed outlier: 3.524A  pdb=" N   ILE B  77 " --> pdb=" O   THR B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 175
    Processing helix  chain 'B' and resid 181 through 186
      removed outlier: 3.998A  pdb=" N   CYS B 185 " --> pdb=" O   SER B 181 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 49
      removed outlier: 3.529A  pdb=" N   LYS C  48 " --> pdb=" O   PRO C  45 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   CYS C  49 " --> pdb=" O   CYS C  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 49'
    Processing helix  chain 'C' and resid 50 through 59
      removed outlier: 3.796A  pdb=" N   ASN C  59 " --> pdb=" O   ALA C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 86
      removed outlier: 3.523A  pdb=" N   ILE C  77 " --> pdb=" O   THR C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 175
    Processing helix  chain 'C' and resid 181 through 186
      removed outlier: 3.998A  pdb=" N   CYS C 185 " --> pdb=" O   SER C 181 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 49
      removed outlier: 3.529A  pdb=" N   LYS D  48 " --> pdb=" O   PRO D  45 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   CYS D  49 " --> pdb=" O   CYS D  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 45 through 49'
    Processing helix  chain 'D' and resid 50 through 59
      removed outlier: 3.795A  pdb=" N   ASN D  59 " --> pdb=" O   ALA D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 86
      removed outlier: 3.523A  pdb=" N   ILE D  77 " --> pdb=" O   THR D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 175
    Processing helix  chain 'D' and resid 181 through 186
      removed outlier: 3.998A  pdb=" N   CYS D 185 " --> pdb=" O   SER D 181 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 49
      removed outlier: 3.529A  pdb=" N   LYS E  48 " --> pdb=" O   PRO E  45 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   CYS E  49 " --> pdb=" O   CYS E  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 45 through 49'
    Processing helix  chain 'E' and resid 50 through 59
      removed outlier: 3.795A  pdb=" N   ASN E  59 " --> pdb=" O   ALA E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 73 through 86
      removed outlier: 3.523A  pdb=" N   ILE E  77 " --> pdb=" O   THR E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 166 through 175
    Processing helix  chain 'E' and resid 181 through 186
      removed outlier: 3.998A  pdb=" N   CYS E 185 " --> pdb=" O   SER E 181 " (cutoff:3.500A)
    Processing sheet with id=1, first strand: chain 'A' and resid 95 through 96
    Processing sheet with id=2, first strand: chain 'A' and resid 194 through 210
      removed outlier: 4.438A  pdb=" N   LYS A 195 " --> pdb=" O   VAL A 238 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   VAL A 238 " --> pdb=" O   LYS A 195 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   ASN A 197 " --> pdb=" O   THR A 236 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   THR A 236 " --> pdb=" O   ASN A 197 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   THR A 199 " --> pdb=" O   ARG A 234 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   ARG A 234 " --> pdb=" O   THR A 199 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   LYS A 201 " --> pdb=" O   GLY A 232 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   GLY A 232 " --> pdb=" O   LYS A 201 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   SER A 203 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   VAL A 230 " --> pdb=" O   SER A 203 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   GLU A 205 " --> pdb=" O   TRP A 228 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   TRP A 228 " --> pdb=" O   GLU A 205 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASN A 207 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR A 226 " --> pdb=" O   ASN A 207 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER A 247 " --> pdb=" O   PHE A 239 " (cutoff:3.500A)
    Processing sheet with id=3, first strand: chain 'B' and resid 95 through 96
    Processing sheet with id=4, first strand: chain 'B' and resid 194 through 210
      removed outlier: 4.438A  pdb=" N   LYS B 195 " --> pdb=" O   VAL B 238 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   VAL B 238 " --> pdb=" O   LYS B 195 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   ASN B 197 " --> pdb=" O   THR B 236 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   THR B 236 " --> pdb=" O   ASN B 197 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   THR B 199 " --> pdb=" O   ARG B 234 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   ARG B 234 " --> pdb=" O   THR B 199 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   LYS B 201 " --> pdb=" O   GLY B 232 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   GLY B 232 " --> pdb=" O   LYS B 201 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   SER B 203 " --> pdb=" O   VAL B 230 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   VAL B 230 " --> pdb=" O   SER B 203 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   GLU B 205 " --> pdb=" O   TRP B 228 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   TRP B 228 " --> pdb=" O   GLU B 205 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASN B 207 " --> pdb=" O   THR B 226 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   THR B 226 " --> pdb=" O   ASN B 207 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER B 247 " --> pdb=" O   PHE B 239 " (cutoff:3.500A)
    Processing sheet with id=5, first strand: chain 'C' and resid 95 through 96
    Processing sheet with id=6, first strand: chain 'C' and resid 194 through 210
      removed outlier: 4.438A  pdb=" N   LYS C 195 " --> pdb=" O   VAL C 238 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   VAL C 238 " --> pdb=" O   LYS C 195 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   ASN C 197 " --> pdb=" O   THR C 236 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   THR C 236 " --> pdb=" O   ASN C 197 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   THR C 199 " --> pdb=" O   ARG C 234 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   ARG C 234 " --> pdb=" O   THR C 199 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   LYS C 201 " --> pdb=" O   GLY C 232 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   GLY C 232 " --> pdb=" O   LYS C 201 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   SER C 203 " --> pdb=" O   VAL C 230 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   VAL C 230 " --> pdb=" O   SER C 203 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   GLU C 205 " --> pdb=" O   TRP C 228 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   TRP C 228 " --> pdb=" O   GLU C 205 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASN C 207 " --> pdb=" O   THR C 226 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR C 226 " --> pdb=" O   ASN C 207 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER C 247 " --> pdb=" O   PHE C 239 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'D' and resid 95 through 96
    Processing sheet with id=8, first strand: chain 'D' and resid 194 through 210
      removed outlier: 4.438A  pdb=" N   LYS D 195 " --> pdb=" O   VAL D 238 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   VAL D 238 " --> pdb=" O   LYS D 195 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   ASN D 197 " --> pdb=" O   THR D 236 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   THR D 236 " --> pdb=" O   ASN D 197 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   THR D 199 " --> pdb=" O   ARG D 234 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   ARG D 234 " --> pdb=" O   THR D 199 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   LYS D 201 " --> pdb=" O   GLY D 232 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   GLY D 232 " --> pdb=" O   LYS D 201 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   SER D 203 " --> pdb=" O   VAL D 230 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   VAL D 230 " --> pdb=" O   SER D 203 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   GLU D 205 " --> pdb=" O   TRP D 228 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   TRP D 228 " --> pdb=" O   GLU D 205 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ASN D 207 " --> pdb=" O   THR D 226 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR D 226 " --> pdb=" O   ASN D 207 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER D 247 " --> pdb=" O   PHE D 239 " (cutoff:3.500A)
    Processing sheet with id=9, first strand: chain 'E' and resid 95 through 96
    Processing sheet with id=10, first strand: chain 'E' and resid 194 through 210
      removed outlier: 4.437A  pdb=" N   LYS E 195 " --> pdb=" O   VAL E 238 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   VAL E 238 " --> pdb=" O   LYS E 195 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   ASN E 197 " --> pdb=" O   THR E 236 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   THR E 236 " --> pdb=" O   ASN E 197 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   THR E 199 " --> pdb=" O   ARG E 234 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   ARG E 234 " --> pdb=" O   THR E 199 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   LYS E 201 " --> pdb=" O   GLY E 232 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   GLY E 232 " --> pdb=" O   LYS E 201 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   SER E 203 " --> pdb=" O   VAL E 230 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   VAL E 230 " --> pdb=" O   SER E 203 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   GLU E 205 " --> pdb=" O   TRP E 228 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   TRP E 228 " --> pdb=" O   GLU E 205 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASN E 207 " --> pdb=" O   THR E 226 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR E 226 " --> pdb=" O   ASN E 207 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER E 247 " --> pdb=" O   PHE E 239 " (cutoff:3.500A)

    130 hydrogen bonds defined for protein.
    375 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.84

  Time building geometry restraints manager: 3.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.38: 3964
        1.38 -     1.56: 5296
        1.56 -     1.74: 10
        1.74 -     1.91: 65
        1.91 -     2.09: 80
  Bond restraints: 9415
  Sorted by residual:
  bond pdb=" N   GLU B 205 "
       pdb=" CA  GLU B 205 "
    ideal  model  delta    sigma   weight residual
    1.457  1.557 -0.099 1.29e-02 6.01e+03 5.93e+01
  bond pdb=" N   GLU E 205 "
       pdb=" CA  GLU E 205 "
    ideal  model  delta    sigma   weight residual
    1.457  1.557 -0.099 1.29e-02 6.01e+03 5.92e+01
  bond pdb=" N   GLU D 205 "
       pdb=" CA  GLU D 205 "
    ideal  model  delta    sigma   weight residual
    1.457  1.557 -0.099 1.29e-02 6.01e+03 5.92e+01
  bond pdb=" N   GLU A 205 "
       pdb=" CA  GLU A 205 "
    ideal  model  delta    sigma   weight residual
    1.457  1.557 -0.099 1.29e-02 6.01e+03 5.91e+01
  bond pdb=" N   GLU C 205 "
       pdb=" CA  GLU C 205 "
    ideal  model  delta    sigma   weight residual
    1.457  1.556 -0.099 1.29e-02 6.01e+03 5.90e+01
  ... (remaining 9410 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 12756
        2.68 -     5.35: 304
        5.35 -     8.03: 55
        8.03 -    10.71: 25
       10.71 -    13.38: 5
  Bond angle restraints: 13145
  Sorted by residual:
  angle pdb=" N   ASN E 207 "
        pdb=" CA  ASN E 207 "
        pdb=" C   ASN E 207 "
      ideal   model   delta    sigma   weight residual
     109.29  122.67  -13.38 1.41e+00 5.03e-01 9.01e+01
  angle pdb=" N   ASN D 207 "
        pdb=" CA  ASN D 207 "
        pdb=" C   ASN D 207 "
      ideal   model   delta    sigma   weight residual
     109.29  122.67  -13.38 1.41e+00 5.03e-01 9.00e+01
  angle pdb=" N   ASN A 207 "
        pdb=" CA  ASN A 207 "
        pdb=" C   ASN A 207 "
      ideal   model   delta    sigma   weight residual
     109.29  122.64  -13.35 1.41e+00 5.03e-01 8.97e+01
  angle pdb=" N   ASN B 207 "
        pdb=" CA  ASN B 207 "
        pdb=" C   ASN B 207 "
      ideal   model   delta    sigma   weight residual
     109.29  122.63  -13.34 1.41e+00 5.03e-01 8.95e+01
  angle pdb=" N   ASN C 207 "
        pdb=" CA  ASN C 207 "
        pdb=" C   ASN C 207 "
      ideal   model   delta    sigma   weight residual
     109.29  122.62  -13.33 1.41e+00 5.03e-01 8.94e+01
  ... (remaining 13140 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.78: 4280
       16.78 -    33.56: 475
       33.56 -    50.33: 85
       50.33 -    67.11: 45
       67.11 -    83.89: 40
  Dihedral angle restraints: 4925
    sinusoidal: 1820
      harmonic: 3105
  Sorted by residual:
  dihedral pdb=" N   ASN D 207 "
           pdb=" C   ASN D 207 "
           pdb=" CA  ASN D 207 "
           pdb=" CB  ASN D 207 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  151.68  -28.88     0      2.50e+00 1.60e-01 1.33e+02
  dihedral pdb=" N   ASN E 207 "
           pdb=" C   ASN E 207 "
           pdb=" CA  ASN E 207 "
           pdb=" CB  ASN E 207 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  151.65  -28.85     0      2.50e+00 1.60e-01 1.33e+02
  dihedral pdb=" N   ASN A 207 "
           pdb=" C   ASN A 207 "
           pdb=" CA  ASN A 207 "
           pdb=" CB  ASN A 207 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  151.62  -28.82     0      2.50e+00 1.60e-01 1.33e+02
  ... (remaining 4922 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.242: 1255
       0.242 -    0.484: 0
       0.484 -    0.726: 5
       0.726 -    0.968: 0
       0.968 -    1.210: 5
  Chirality restraints: 1265
  Sorted by residual:
  chirality pdb=" CA  ASN D 207 "
            pdb=" N   ASN D 207 "
            pdb=" C   ASN D 207 "
            pdb=" CB  ASN D 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.30    1.21 2.00e-01 2.50e+01 3.66e+01
  chirality pdb=" CA  ASN E 207 "
            pdb=" N   ASN E 207 "
            pdb=" C   ASN E 207 "
            pdb=" CB  ASN E 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.30    1.21 2.00e-01 2.50e+01 3.65e+01
  chirality pdb=" CA  ASN A 207 "
            pdb=" N   ASN A 207 "
            pdb=" C   ASN A 207 "
            pdb=" CB  ASN A 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.30    1.21 2.00e-01 2.50e+01 3.64e+01
  ... (remaining 1262 not shown)

  Planarity restraints: 1655
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C HEC D 301 "   -0.011 2.00e-02 2.50e+03   3.10e-02 2.16e+01
        pdb=" C2C HEC D 301 "    0.084 2.00e-02 2.50e+03
        pdb=" C3C HEC D 301 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4C HEC D 301 "   -0.004 2.00e-02 2.50e+03
        pdb=" CAC HEC D 301 "   -0.019 2.00e-02 2.50e+03
        pdb=" CHC HEC D 301 "   -0.014 2.00e-02 2.50e+03
        pdb=" CHD HEC D 301 "   -0.001 2.00e-02 2.50e+03
        pdb=" CMC HEC D 301 "   -0.029 2.00e-02 2.50e+03
        pdb=" NC  HEC D 301 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C HEC C 301 "   -0.011 2.00e-02 2.50e+03   3.10e-02 2.16e+01
        pdb=" C2C HEC C 301 "    0.084 2.00e-02 2.50e+03
        pdb=" C3C HEC C 301 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4C HEC C 301 "   -0.004 2.00e-02 2.50e+03
        pdb=" CAC HEC C 301 "   -0.019 2.00e-02 2.50e+03
        pdb=" CHC HEC C 301 "   -0.014 2.00e-02 2.50e+03
        pdb=" CHD HEC C 301 "   -0.001 2.00e-02 2.50e+03
        pdb=" CMC HEC C 301 "   -0.029 2.00e-02 2.50e+03
        pdb=" NC  HEC C 301 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C HEC E 301 "   -0.011 2.00e-02 2.50e+03   3.10e-02 2.16e+01
        pdb=" C2C HEC E 301 "    0.084 2.00e-02 2.50e+03
        pdb=" C3C HEC E 301 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4C HEC E 301 "   -0.004 2.00e-02 2.50e+03
        pdb=" CAC HEC E 301 "   -0.019 2.00e-02 2.50e+03
        pdb=" CHC HEC E 301 "   -0.014 2.00e-02 2.50e+03
        pdb=" CHD HEC E 301 "   -0.001 2.00e-02 2.50e+03
        pdb=" CMC HEC E 301 "   -0.029 2.00e-02 2.50e+03
        pdb=" NC  HEC E 301 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1652 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.51: 161
        2.51 -     3.11: 7232
        3.11 -     3.71: 14229
        3.71 -     4.30: 19688
        4.30 -     4.90: 30611
  Nonbonded interactions: 71921
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 197 "
            pdb=" ND2 ASN D 207 "
     model   vdw
     1.918 3.200
  nonbonded pdb=" ND2 ASN B 197 "
            pdb=" ND2 ASN C 207 "
     model   vdw
     1.918 3.200
  nonbonded pdb=" ND2 ASN D 197 "
            pdb=" ND2 ASN E 207 "
     model   vdw
     1.918 3.200
  nonbonded pdb=" ND2 ASN A 207 "
            pdb=" ND2 ASN C 197 "
     model   vdw
     1.918 3.200
  nonbonded pdb=" CD1 ILE D  37 "
            pdb=" O1A HEC E 303 "
     model   vdw
     2.016 3.460
  ... (remaining 71916 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.800
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.099   9415  Z= 0.413
  Angle     :  1.052  13.382  13145  Z= 0.580
  Chirality :  0.097   1.210   1265
  Planarity :  0.005   0.035   1655
  Dihedral  : 17.243  83.885   2965
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 47.42
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  9.63 %
    Favored  : 89.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  1.02 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.25), residues: 1090
  helix:  1.43 (0.42), residues: 145
  sheet: -0.68 (0.50), residues: 100
  loop : -2.43 (0.21), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  34 
 HIS   0.006   0.001   HIS E 189 
 PHE   0.006   0.002   PHE D 239 
 TYR   0.015   0.002   TYR B 223 
 ARG   0.001   0.000   ARG B  86 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
REVERT: B  163 GLU cc_start: 0.7276 (tp30) cc_final: 0.6110 (mm-30)
REVERT: C   59 ASN cc_start: 0.8837 (t0) cc_final: 0.8261 (t0)
REVERT: C   65 LYS cc_start: 0.8241 (ptpt) cc_final: 0.7998 (ptpt)
REVERT: D   65 LYS cc_start: 0.8297 (ptpt) cc_final: 0.8025 (ptpt)
REVERT: E   65 LYS cc_start: 0.8267 (ptpt) cc_final: 0.8059 (ptpt)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.2243
  time to fit residues: 44.0650
Evaluate side-chains
  107 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 83 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 56 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 86 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 64 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A  64 HIS
B  43 ASN
B  60 ASN
C  64 HIS
D  64 HIS
E  64 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.080   9415  Z= 0.377
  Angle     :  0.953  14.756  13145  Z= 0.376
  Chirality :  0.043   0.142   1265
  Planarity :  0.003   0.026   1655
  Dihedral  : 15.532  89.986   1325
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 16.44
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  8.53 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 10.34 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.26), residues: 1090
  helix:  0.44 (0.38), residues: 160
  sheet: -2.10 (0.38), residues: 145
  loop : -2.16 (0.23), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  34 
 HIS   0.008   0.001   HIS A  64 
 PHE   0.014   0.002   PHE D 138 
 TYR   0.019   0.002   TYR A 223 
 ARG   0.003   0.001   ARG A 171 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   33 MET cc_start: 0.6690 (mpp) cc_final: 0.6388 (mpp)
REVERT: C   59 ASN cc_start: 0.8786 (t0) cc_final: 0.7875 (t0)
REVERT: C   60 ASN cc_start: 0.8718 (t0) cc_final: 0.8485 (t0)
REVERT: C   65 LYS cc_start: 0.8096 (ptpt) cc_final: 0.7786 (ptpt)
  outliers start: 16
  outliers final: 13
  residues processed: 131
  average time/residue: 0.2085
  time to fit residues: 38.4345
Evaluate side-chains
  123 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain D residue  200 HIS
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain E residue  179 ILE
Chi-restraints excluded: chain E residue  200 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0470
   chunk 83 optimal weight:    4.9990
   chunk 68 optimal weight:    0.7980
   chunk 27 optimal weight:    0.3980
   chunk 100 optimal weight:    3.9990
   chunk 108 optimal weight:    4.9990
   chunk 89 optimal weight:    0.7980
   chunk 99 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
C  43 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.3049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9415  Z= 0.215
  Angle     :  0.805  12.233  13145  Z= 0.314
  Chirality :  0.040   0.115   1265
  Planarity :  0.002   0.025   1655
  Dihedral  : 15.254  89.606   1325
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  6.79 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.79 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.26), residues: 1090
  helix:  0.41 (0.40), residues: 160
  sheet: -2.36 (0.31), residues: 210
  loop : -2.10 (0.25), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 228 
 HIS   0.003   0.001   HIS A 108 
 PHE   0.011   0.002   PHE E 138 
 TYR   0.012   0.001   TYR A 223 
 ARG   0.001   0.000   ARG C  86 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 11
  residues processed: 130
  average time/residue: 0.1933
  time to fit residues: 35.8803
Evaluate side-chains
  118 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain D residue  200 HIS
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue  200 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    0.3980
   chunk 75 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 47 optimal weight:    7.9990
   chunk 67 optimal weight:    0.0170
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   chunk 95 optimal weight:    6.9990
   chunk 28 optimal weight:    7.9990
   overall best weight:    1.6422

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.3754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.081   9415  Z= 0.370
  Angle     :  0.975  18.179  13145  Z= 0.359
  Chirality :  0.043   0.144   1265
  Planarity :  0.003   0.027   1655
  Dihedral  : 15.682  89.744   1325
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 15.15
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  9.27 %
    Favored  : 90.28 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 15.98 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.66 (0.25), residues: 1090
  helix:  0.08 (0.38), residues: 160
  sheet: -2.42 (0.35), residues: 145
  loop : -2.19 (0.23), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 228 
 HIS   0.004   0.001   HIS E  32 
 PHE   0.015   0.002   PHE C 239 
 TYR   0.015   0.002   TYR C 152 
 ARG   0.002   0.000   ARG B 234 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.8207 (ptpt) cc_final: 0.7935 (ptpt)
REVERT: B   72 ASP cc_start: 0.8800 (p0) cc_final: 0.8397 (p0)
  outliers start: 30
  outliers final: 18
  residues processed: 123
  average time/residue: 0.2027
  time to fit residues: 35.3861
Evaluate side-chains
  111 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  121 PHE
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain D residue   84 CYS
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   84 CYS
Chi-restraints excluded: chain E residue  121 PHE
Chi-restraints excluded: chain E residue  200 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   chunk 43 optimal weight:    8.9990
   chunk 90 optimal weight:    1.9990
   chunk 73 optimal weight:   10.0000
   chunk 0 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 95 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   overall best weight:    1.5184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.4056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081   9415  Z= 0.342
  Angle     :  0.902  16.731  13145  Z= 0.337
  Chirality :  0.041   0.144   1265
  Planarity :  0.003   0.030   1655
  Dihedral  : 15.461  89.052   1325
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  7.16 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 17.59 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.65 (0.25), residues: 1090
  helix:  0.31 (0.39), residues: 160
  sheet: -2.46 (0.35), residues: 145
  loop : -2.23 (0.23), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E  34 
 HIS   0.005   0.001   HIS E  32 
 PHE   0.019   0.002   PHE E  54 
 TYR   0.014   0.002   TYR C 152 
 ARG   0.002   0.000   ARG B 171 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 106
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   65 LYS cc_start: 0.8199 (pttt) cc_final: 0.7939 (ptpt)
REVERT: D  152 TYR cc_start: 0.6756 (m-80) cc_final: 0.6429 (m-10)
REVERT: E   48 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8292 (ttpt)
REVERT: E   76 HIS cc_start: 0.8375 (m170) cc_final: 0.7795 (m-70)
  outliers start: 34
  outliers final: 23
  residues processed: 129
  average time/residue: 0.2032
  time to fit residues: 37.0666
Evaluate side-chains
  121 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  121 PHE
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain B residue  201 LYS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain C residue  121 PHE
Chi-restraints excluded: chain C residue  189 HIS
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain D residue   84 CYS
Chi-restraints excluded: chain D residue  121 PHE
Chi-restraints excluded: chain D residue  200 HIS
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain E residue   84 CYS
Chi-restraints excluded: chain E residue  200 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 95 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 106 optimal weight:    0.7980
   chunk 88 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 102 optimal weight:    5.9990
   overall best weight:    1.9588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.4456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.100   9415  Z= 0.420
  Angle     :  0.981  19.105  13145  Z= 0.369
  Chirality :  0.043   0.159   1265
  Planarity :  0.003   0.032   1655
  Dihedral  : 15.630  89.599   1325
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 10.55 %
    Favored  : 88.99 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 18.05 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.80 (0.25), residues: 1090
  helix:  0.19 (0.38), residues: 160
  sheet: -2.71 (0.35), residues: 145
  loop : -2.30 (0.23), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP E  34 
 HIS   0.004   0.001   HIS E 108 
 PHE   0.023   0.003   PHE E  54 
 TYR   0.020   0.002   TYR B 152 
 ARG   0.002   0.000   ARG B  78 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 104
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 HIS cc_start: 0.8569 (m170) cc_final: 0.8053 (m-70)
REVERT: C   65 LYS cc_start: 0.8071 (pttt) cc_final: 0.7751 (ptpt)
REVERT: E   54 PHE cc_start: 0.8694 (t80) cc_final: 0.8213 (m-80)
REVERT: E   65 LYS cc_start: 0.7742 (mttt) cc_final: 0.7521 (mttt)
REVERT: E   76 HIS cc_start: 0.8540 (m170) cc_final: 0.7975 (m-70)
  outliers start: 42
  outliers final: 27
  residues processed: 137
  average time/residue: 0.1910
  time to fit residues: 37.5741
Evaluate side-chains
  121 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain B residue  201 LYS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain C residue  121 PHE
Chi-restraints excluded: chain C residue  129 TYR
Chi-restraints excluded: chain C residue  189 HIS
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain D residue   84 CYS
Chi-restraints excluded: chain D residue  200 HIS
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain E residue   84 CYS
Chi-restraints excluded: chain E residue  121 PHE
Chi-restraints excluded: chain E residue  130 SER
Chi-restraints excluded: chain E residue  200 HIS
Chi-restraints excluded: chain E residue  248 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   chunk 89 optimal weight:    0.0770
   chunk 59 optimal weight:    0.7980
   chunk 106 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.1542

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.4625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   9415  Z= 0.293
  Angle     :  0.903  19.542  13145  Z= 0.336
  Chirality :  0.042   0.162   1265
  Planarity :  0.003   0.034   1655
  Dihedral  : 15.473  89.794   1325
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  7.80 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 19.89 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.25), residues: 1090
  helix:  0.45 (0.39), residues: 160
  sheet: -2.26 (0.37), residues: 130
  loop : -2.37 (0.23), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  34 
 HIS   0.004   0.001   HIS E 189 
 PHE   0.020   0.002   PHE E 138 
 TYR   0.017   0.002   TYR B 152 
 ARG   0.001   0.000   ARG D 171 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 109
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7985 (mp0)
REVERT: B   65 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8606 (ptpt)
REVERT: B   76 HIS cc_start: 0.8454 (m170) cc_final: 0.7965 (m-70)
REVERT: D   60 ASN cc_start: 0.8178 (t0) cc_final: 0.7720 (t0)
REVERT: E   48 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8204 (mtpp)
REVERT: E   65 LYS cc_start: 0.7675 (mttt) cc_final: 0.7439 (mttt)
REVERT: E   76 HIS cc_start: 0.8447 (m170) cc_final: 0.7840 (m-70)
  outliers start: 36
  outliers final: 23
  residues processed: 138
  average time/residue: 0.1998
  time to fit residues: 39.3738
Evaluate side-chains
  121 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain C residue  121 PHE
Chi-restraints excluded: chain C residue  189 HIS
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain D residue   84 CYS
Chi-restraints excluded: chain D residue  200 HIS
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain E residue   84 CYS
Chi-restraints excluded: chain E residue  121 PHE
Chi-restraints excluded: chain E residue  189 HIS
Chi-restraints excluded: chain E residue  200 HIS
Chi-restraints excluded: chain E residue  248 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0570
   chunk 72 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 83 optimal weight:    7.9990
   chunk 96 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9980
   chunk 92 optimal weight:    7.9990
   overall best weight:    0.6098

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.4879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   9415  Z= 0.230
  Angle     :  0.878  17.968  13145  Z= 0.332
  Chirality :  0.041   0.194   1265
  Planarity :  0.003   0.033   1655
  Dihedral  : 15.260  89.820   1325
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.92 %
    Allowed  :  9.36 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 20.46 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.71 (0.25), residues: 1090
  helix:  0.52 (0.40), residues: 160
  sheet: -2.24 (0.37), residues: 130
  loop : -2.41 (0.22), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 228 
 HIS   0.006   0.001   HIS A 189 
 PHE   0.029   0.002   PHE C 138 
 TYR   0.011   0.001   TYR D 210 
 ARG   0.002   0.000   ARG B  78 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 103
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8518 (ptpt)
REVERT: B   72 ASP cc_start: 0.8790 (p0) cc_final: 0.8467 (p0)
REVERT: B   76 HIS cc_start: 0.8219 (m170) cc_final: 0.7886 (m-70)
REVERT: D   60 ASN cc_start: 0.7981 (t0) cc_final: 0.7563 (t0)
REVERT: D   72 ASP cc_start: 0.8616 (p0) cc_final: 0.8306 (p0)
REVERT: E   48 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8031 (mtpp)
  outliers start: 34
  outliers final: 24
  residues processed: 130
  average time/residue: 0.2102
  time to fit residues: 38.5681
Evaluate side-chains
  116 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain C residue  121 PHE
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain D residue   84 CYS
Chi-restraints excluded: chain D residue  200 HIS
Chi-restraints excluded: chain D residue  221 THR
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain E residue   84 CYS
Chi-restraints excluded: chain E residue  121 PHE
Chi-restraints excluded: chain E residue  189 HIS
Chi-restraints excluded: chain E residue  200 HIS
Chi-restraints excluded: chain E residue  248 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 101 optimal weight:    0.8980
   chunk 59 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 77 optimal weight:    7.9990
   chunk 30 optimal weight:    0.8980
   chunk 89 optimal weight:    0.4980
   chunk 93 optimal weight:    0.0970
   chunk 64 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9980
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.5778

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.5085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9415  Z= 0.232
  Angle     :  0.897  18.397  13145  Z= 0.336
  Chirality :  0.041   0.174   1265
  Planarity :  0.003   0.032   1655
  Dihedral  : 15.099  88.838   1325
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  8.07 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 21.26 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.76 (0.25), residues: 1090
  helix:  0.38 (0.41), residues: 165
  sheet: -2.22 (0.37), residues: 130
  loop : -2.44 (0.22), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 198 
 HIS   0.009   0.001   HIS A 189 
 PHE   0.045   0.002   PHE C  54 
 TYR   0.013   0.001   TYR A 152 
 ARG   0.002   0.000   ARG C  78 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8540 (ptpt)
REVERT: B   72 ASP cc_start: 0.8754 (p0) cc_final: 0.8457 (p0)
REVERT: B  129 TYR cc_start: 0.6729 (m-80) cc_final: 0.6451 (m-80)
REVERT: C   76 HIS cc_start: 0.7966 (m170) cc_final: 0.7566 (m-70)
REVERT: D   33 MET cc_start: 0.7109 (pmm) cc_final: 0.6732 (ptp)
REVERT: D   60 ASN cc_start: 0.8055 (t0) cc_final: 0.7753 (t0)
REVERT: D   72 ASP cc_start: 0.8596 (p0) cc_final: 0.8294 (p0)
  outliers start: 27
  outliers final: 22
  residues processed: 118
  average time/residue: 0.1965
  time to fit residues: 33.0189
Evaluate side-chains
  111 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain C residue  121 PHE
Chi-restraints excluded: chain C residue  189 HIS
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain D residue   84 CYS
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   84 CYS
Chi-restraints excluded: chain E residue  121 PHE
Chi-restraints excluded: chain E residue  189 HIS
Chi-restraints excluded: chain E residue  200 HIS
Chi-restraints excluded: chain E residue  248 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 109 optimal weight:   10.0000
   chunk 100 optimal weight:    0.0170
   chunk 87 optimal weight:    9.9990
   chunk 9 optimal weight:    0.2980
   chunk 67 optimal weight:    0.0030
   chunk 53 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 92 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.6632

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.5259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   9415  Z= 0.242
  Angle     :  0.901  20.104  13145  Z= 0.335
  Chirality :  0.042   0.192   1265
  Planarity :  0.003   0.030   1655
  Dihedral  : 15.008  88.928   1325
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  9.17 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 22.30 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.76 (0.25), residues: 1090
  helix:  0.37 (0.40), residues: 165
  sheet: -2.27 (0.35), residues: 130
  loop : -2.44 (0.22), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 228 
 HIS   0.008   0.001   HIS A 189 
 PHE   0.046   0.002   PHE C  54 
 TYR   0.012   0.001   TYR D 210 
 ARG   0.002   0.000   ARG C  78 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8513 (ptpt)
REVERT: B   72 ASP cc_start: 0.8761 (p0) cc_final: 0.8459 (p0)
REVERT: D   33 MET cc_start: 0.7002 (pmm) cc_final: 0.6770 (ptp)
REVERT: D   60 ASN cc_start: 0.8228 (t0) cc_final: 0.7628 (t0)
REVERT: D   65 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6980 (mttt)
REVERT: D   72 ASP cc_start: 0.8569 (p0) cc_final: 0.8286 (p0)
  outliers start: 27
  outliers final: 23
  residues processed: 113
  average time/residue: 0.1844
  time to fit residues: 30.6824
Evaluate side-chains
  111 residues out of total 875 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain C residue  121 PHE
Chi-restraints excluded: chain C residue  189 HIS
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue   84 CYS
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   84 CYS
Chi-restraints excluded: chain E residue  121 PHE
Chi-restraints excluded: chain E residue  189 HIS
Chi-restraints excluded: chain E residue  200 HIS
Chi-restraints excluded: chain E residue  248 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 12 optimal weight:    0.1980
   chunk 24 optimal weight:    0.7980
   chunk 87 optimal weight:    9.9990
   chunk 36 optimal weight:    8.9990
   chunk 89 optimal weight:    0.0030
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 76 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.5992

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.099722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.081026 restraints weight = 27900.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.083859 restraints weight = 15784.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.085764 restraints weight = 11031.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.5381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9415  Z= 0.234
  Angle     :  0.888  18.764  13145  Z= 0.334
  Chirality :  0.041   0.183   1265
  Planarity :  0.003   0.032   1655
  Dihedral  : 14.966  89.179   1325
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  7.71 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 21.61 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.83 (0.25), residues: 1090
  helix:  0.20 (0.40), residues: 165
  sheet: -2.28 (0.36), residues: 130
  loop : -2.46 (0.22), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  34 
 HIS   0.008   0.001   HIS A 189 
 PHE   0.026   0.002   PHE D 121 
 TYR   0.011   0.001   TYR D 210 
 ARG   0.003   0.000   ARG C  78 

===============================================================================
Job complete
usr+sys time: 1867.45 seconds
wall clock time: 34 minutes 29.89 seconds (2069.89 seconds total)