Starting phenix.real_space_refine
on Thu Mar  5 06:52:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6l3v_0827/03_2026/6l3v_0827_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6l3v_0827/03_2026/6l3v_0827.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6l3v_0827/03_2026/6l3v_0827_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6l3v_0827/03_2026/6l3v_0827_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6l3v_0827/03_2026/6l3v_0827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6l3v_0827/03_2026/6l3v_0827.map"
  }
  resolution = 2.63
  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=   0.276
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
     S      66      5.16       5
     C    6516      2.51       5
     N    1620      2.21       5
     O    1686      1.98       5
     H    9528      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 19416
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 3167
          Classifications: {'peptide': 201}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 69
          Unusual residues: {'LMN': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 3.11, per 1000 atoms: 0.16
  Number of scatterers: 19416
  At special positions: 0
  Unit cell: (114.779, 121.683, 94.067, 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      66     16.00
     O    1686      8.00
     N    1620      7.00
     C    6516      6.00
     H    9528      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A 169 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  53 " - pdb=" SG  CYS B 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  53 " - pdb=" SG  CYS C 180 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  53 " - pdb=" SG  CYS D 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  53 " - pdb=" SG  CYS E 180 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  53 " - pdb=" SG  CYS F 180 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  60 " - pdb=" SG  CYS B 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  60 " - pdb=" SG  CYS C 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  60 " - pdb=" SG  CYS D 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  60 " - pdb=" SG  CYS E 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  60 " - pdb=" SG  CYS F 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  64 " - pdb=" SG  CYS B 169 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  64 " - pdb=" SG  CYS C 169 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  64 " - pdb=" SG  CYS D 169 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  64 " - pdb=" SG  CYS E 169 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  64 " - pdb=" SG  CYS F 169 " distance=2.03

  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: 1.67
  Conformation dependent library (CDL) restraints added in 538.6 milliseconds
  

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 6 sheets defined
      77.7% alpha, 4.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 14
      removed outlier: 3.806A  pdb=" N   LEU A   6 " --> pdb=" O   CYS A   2 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   ALA A  11 " --> pdb=" O   ARG A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 18 through 23
    Processing helix  chain 'A' and resid 23 through 45
      removed outlier: 3.519A  pdb=" N   VAL A  27 " --> pdb=" O   LEU A  23 " (cutoff:3.500A)
      Proline residue:  A  41  - end of helix
    Processing helix  chain 'A' and resid 59 through 69
    Processing helix  chain 'A' and resid 72 through 101
      Proline residue:  A  87  - end of helix
    Processing helix  chain 'A' and resid 102 through 107
    Processing helix  chain 'A' and resid 129 through 159
      removed outlier: 3.543A  pdb=" N   LEU A 133 " --> pdb=" O   GLY A 129 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU A 134 " --> pdb=" O   SER A 130 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   TRP A 135 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ALA A 136 " --> pdb=" O   ARG A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 212
      removed outlier: 3.640A  pdb=" N   LYS A 188 " --> pdb=" O   ARG A 184 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU A 210 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 221
      removed outlier: 3.708A  pdb=" N   THR A 221 " --> pdb=" O   ARG A 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 14
      removed outlier: 4.207A  pdb=" N   ALA B  11 " --> pdb=" O   ARG B   7 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 23
    Processing helix  chain 'B' and resid 23 through 45
      removed outlier: 3.519A  pdb=" N   VAL B  27 " --> pdb=" O   LEU B  23 " (cutoff:3.500A)
      Proline residue:  B  41  - end of helix
    Processing helix  chain 'B' and resid 59 through 69
    Processing helix  chain 'B' and resid 72 through 101
      Proline residue:  B  87  - end of helix
    Processing helix  chain 'B' and resid 102 through 107
    Processing helix  chain 'B' and resid 129 through 159
      removed outlier: 3.544A  pdb=" N   LEU B 133 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU B 134 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   TRP B 135 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ALA B 136 " --> pdb=" O   ARG B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 212
      removed outlier: 3.639A  pdb=" N   LYS B 188 " --> pdb=" O   ARG B 184 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU B 210 " --> pdb=" O   THR B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 221
      removed outlier: 3.707A  pdb=" N   THR B 221 " --> pdb=" O   ARG B 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 14
      removed outlier: 4.207A  pdb=" N   ALA C  11 " --> pdb=" O   ARG C   7 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 23
    Processing helix  chain 'C' and resid 23 through 45
      removed outlier: 3.519A  pdb=" N   VAL C  27 " --> pdb=" O   LEU C  23 " (cutoff:3.500A)
      Proline residue:  C  41  - end of helix
    Processing helix  chain 'C' and resid 59 through 69
    Processing helix  chain 'C' and resid 72 through 101
      Proline residue:  C  87  - end of helix
    Processing helix  chain 'C' and resid 102 through 107
    Processing helix  chain 'C' and resid 129 through 159
      removed outlier: 3.545A  pdb=" N   LEU C 133 " --> pdb=" O   GLY C 129 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LEU C 134 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   TRP C 135 " --> pdb=" O   LEU C 131 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ALA C 136 " --> pdb=" O   ARG C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 184 through 212
      removed outlier: 3.640A  pdb=" N   LYS C 188 " --> pdb=" O   ARG C 184 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU C 210 " --> pdb=" O   THR C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 214 through 221
      removed outlier: 3.708A  pdb=" N   THR C 221 " --> pdb=" O   ARG C 217 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 14
      removed outlier: 4.207A  pdb=" N   ALA D  11 " --> pdb=" O   ARG D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 23
    Processing helix  chain 'D' and resid 23 through 45
      removed outlier: 3.520A  pdb=" N   VAL D  27 " --> pdb=" O   LEU D  23 " (cutoff:3.500A)
      Proline residue:  D  41  - end of helix
    Processing helix  chain 'D' and resid 59 through 69
    Processing helix  chain 'D' and resid 72 through 101
      Proline residue:  D  87  - end of helix
    Processing helix  chain 'D' and resid 102 through 107
    Processing helix  chain 'D' and resid 129 through 159
      removed outlier: 3.544A  pdb=" N   LEU D 133 " --> pdb=" O   GLY D 129 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU D 134 " --> pdb=" O   SER D 130 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   TRP D 135 " --> pdb=" O   LEU D 131 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ALA D 136 " --> pdb=" O   ARG D 132 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 184 through 212
      removed outlier: 3.639A  pdb=" N   LYS D 188 " --> pdb=" O   ARG D 184 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU D 210 " --> pdb=" O   THR D 206 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 214 through 221
      removed outlier: 3.707A  pdb=" N   THR D 221 " --> pdb=" O   ARG D 217 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 14
      removed outlier: 4.207A  pdb=" N   ALA E  11 " --> pdb=" O   ARG E   7 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 23
    Processing helix  chain 'E' and resid 23 through 45
      removed outlier: 3.519A  pdb=" N   VAL E  27 " --> pdb=" O   LEU E  23 " (cutoff:3.500A)
      Proline residue:  E  41  - end of helix
    Processing helix  chain 'E' and resid 59 through 69
    Processing helix  chain 'E' and resid 72 through 101
      Proline residue:  E  87  - end of helix
    Processing helix  chain 'E' and resid 102 through 107
    Processing helix  chain 'E' and resid 129 through 159
      removed outlier: 3.543A  pdb=" N   LEU E 133 " --> pdb=" O   GLY E 129 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU E 134 " --> pdb=" O   SER E 130 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   TRP E 135 " --> pdb=" O   LEU E 131 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ALA E 136 " --> pdb=" O   ARG E 132 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 184 through 212
      removed outlier: 3.639A  pdb=" N   LYS E 188 " --> pdb=" O   ARG E 184 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU E 210 " --> pdb=" O   THR E 206 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 214 through 221
      removed outlier: 3.708A  pdb=" N   THR E 221 " --> pdb=" O   ARG E 217 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 3 through 14
      removed outlier: 4.207A  pdb=" N   ALA F  11 " --> pdb=" O   ARG F   7 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 18 through 23
    Processing helix  chain 'F' and resid 23 through 45
      removed outlier: 3.519A  pdb=" N   VAL F  27 " --> pdb=" O   LEU F  23 " (cutoff:3.500A)
      Proline residue:  F  41  - end of helix
    Processing helix  chain 'F' and resid 59 through 69
    Processing helix  chain 'F' and resid 72 through 101
      Proline residue:  F  87  - end of helix
    Processing helix  chain 'F' and resid 102 through 107
    Processing helix  chain 'F' and resid 129 through 159
      removed outlier: 3.544A  pdb=" N   LEU F 133 " --> pdb=" O   GLY F 129 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LEU F 134 " --> pdb=" O   SER F 130 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   TRP F 135 " --> pdb=" O   LEU F 131 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ALA F 136 " --> pdb=" O   ARG F 132 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 184 through 212
      removed outlier: 3.639A  pdb=" N   LYS F 188 " --> pdb=" O   ARG F 184 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU F 210 " --> pdb=" O   THR F 206 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 214 through 221
      removed outlier: 3.707A  pdb=" N   THR F 221 " --> pdb=" O   ARG F 217 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 53
      removed outlier: 3.530A  pdb=" N   ILE A 178 " --> pdb=" O   CYS A 169 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   CYS A 169 " --> pdb=" O   ILE A 178 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 53
      removed outlier: 3.530A  pdb=" N   ILE B 178 " --> pdb=" O   CYS B 169 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   CYS B 169 " --> pdb=" O   ILE B 178 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 53
      removed outlier: 3.530A  pdb=" N   ILE C 178 " --> pdb=" O   CYS C 169 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   CYS C 169 " --> pdb=" O   ILE C 178 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 53
      removed outlier: 3.530A  pdb=" N   ILE D 178 " --> pdb=" O   CYS D 169 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   CYS D 169 " --> pdb=" O   ILE D 178 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 51 through 53
      removed outlier: 3.530A  pdb=" N   ILE E 178 " --> pdb=" O   CYS E 169 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   CYS E 169 " --> pdb=" O   ILE E 178 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 51 through 53
      removed outlier: 3.530A  pdb=" N   ILE F 178 " --> pdb=" O   CYS F 169 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   CYS F 169 " --> pdb=" O   ILE F 178 " (cutoff:3.500A)

    654 hydrogen bonds defined for protein.
    1962 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: 3.45

  Time building geometry restraints manager: 2.26 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 9516
        1.03 -     1.23: 22
        1.23 -     1.42: 4350
        1.42 -     1.62: 5738
        1.62 -     1.82: 84
  Bond restraints: 19710
  Sorted by residual:
  bond pdb=" CBS LMN F 301 "
       pdb=" CCM LMN F 301 "
    ideal  model  delta    sigma   weight residual
    1.529  1.617 -0.088 2.00e-02 2.50e+03 1.93e+01
  bond pdb=" CBS LMN B 301 "
       pdb=" CCM LMN B 301 "
    ideal  model  delta    sigma   weight residual
    1.529  1.617 -0.088 2.00e-02 2.50e+03 1.93e+01
  bond pdb=" CBS LMN A 301 "
       pdb=" CCM LMN A 301 "
    ideal  model  delta    sigma   weight residual
    1.529  1.617 -0.088 2.00e-02 2.50e+03 1.92e+01
  bond pdb=" CBS LMN C 301 "
       pdb=" CCM LMN C 301 "
    ideal  model  delta    sigma   weight residual
    1.529  1.617 -0.088 2.00e-02 2.50e+03 1.92e+01
  bond pdb=" CBS LMN E 301 "
       pdb=" CCM LMN E 301 "
    ideal  model  delta    sigma   weight residual
    1.529  1.617 -0.088 2.00e-02 2.50e+03 1.92e+01
  ... (remaining 19705 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 33458
        1.47 -     2.94: 1495
        2.94 -     4.41: 302
        4.41 -     5.88: 73
        5.88 -     7.35: 42
  Bond angle restraints: 35370
  Sorted by residual:
  angle pdb=" CA  ARG A 220 "
        pdb=" CB  ARG A 220 "
        pdb=" CG  ARG A 220 "
      ideal   model   delta    sigma   weight residual
     114.10  120.12   -6.02 2.00e+00 2.50e-01 9.05e+00
  angle pdb=" CA  ARG C 220 "
        pdb=" CB  ARG C 220 "
        pdb=" CG  ARG C 220 "
      ideal   model   delta    sigma   weight residual
     114.10  120.05   -5.95 2.00e+00 2.50e-01 8.86e+00
  angle pdb=" CA  ARG B 220 "
        pdb=" CB  ARG B 220 "
        pdb=" CG  ARG B 220 "
      ideal   model   delta    sigma   weight residual
     114.10  120.05   -5.95 2.00e+00 2.50e-01 8.86e+00
  angle pdb=" CA  ARG D 220 "
        pdb=" CB  ARG D 220 "
        pdb=" CG  ARG D 220 "
      ideal   model   delta    sigma   weight residual
     114.10  120.05   -5.95 2.00e+00 2.50e-01 8.85e+00
  angle pdb=" CA  ARG F 220 "
        pdb=" CB  ARG F 220 "
        pdb=" CG  ARG F 220 "
      ideal   model   delta    sigma   weight residual
     114.10  120.05   -5.95 2.00e+00 2.50e-01 8.84e+00
  ... (remaining 35365 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.14: 8850
       24.14 -    48.27: 612
       48.27 -    72.41: 252
       72.41 -    96.55: 60
       96.55 -   120.68: 78
  Dihedral angle restraints: 9852
    sinusoidal: 5562
      harmonic: 4290
  Sorted by residual:
  dihedral pdb=" OAU LMN A 301 "
           pdb=" CCR LMN A 301 "
           pdb=" CCV LMN A 301 "
           pdb=" OBY LMN A 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     182.69   62.01  120.68     1      3.00e+01 1.11e-03 1.61e+01
  dihedral pdb=" OAU LMN E 301 "
           pdb=" CCR LMN E 301 "
           pdb=" CCV LMN E 301 "
           pdb=" OBY LMN E 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     182.69   62.04  120.65     1      3.00e+01 1.11e-03 1.61e+01
  dihedral pdb=" OAU LMN C 301 "
           pdb=" CCR LMN C 301 "
           pdb=" CCV LMN C 301 "
           pdb=" OBY LMN C 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     182.69   62.05  120.64     1      3.00e+01 1.11e-03 1.61e+01
  ... (remaining 9849 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1272
       0.044 -    0.087: 198
       0.087 -    0.131: 75
       0.131 -    0.174: 9
       0.174 -    0.218: 18
  Chirality restraints: 1572
  Sorted by residual:
  chirality pdb=" CCQ LMN C 301 "
            pdb=" CCF LMN C 301 "
            pdb=" CCH LMN C 301 "
            pdb=" OCB LMN C 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.61   -2.39   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CCQ LMN A 301 "
            pdb=" CCF LMN A 301 "
            pdb=" CCH LMN A 301 "
            pdb=" OCB LMN A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.61   -2.39   -0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CCQ LMN D 301 "
            pdb=" CCF LMN D 301 "
            pdb=" CCH LMN D 301 "
            pdb=" OCB LMN D 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.61   -2.39   -0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 1569 not shown)

  Planarity restraints: 2778
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F  18 "    0.028 5.00e-02 4.00e+02   4.20e-02 2.82e+00
        pdb=" N   PRO F  19 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO F  19 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO F  19 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  18 "    0.028 5.00e-02 4.00e+02   4.20e-02 2.82e+00
        pdb=" N   PRO C  19 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO C  19 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C  19 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  18 "    0.028 5.00e-02 4.00e+02   4.20e-02 2.82e+00
        pdb=" N   PRO B  19 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B  19 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  19 "    0.023 5.00e-02 4.00e+02
  ... (remaining 2775 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 3139
        2.30 -     2.88: 40176
        2.88 -     3.45: 43494
        3.45 -     4.03: 61000
        4.03 -     4.60: 94149
  Nonbonded interactions: 241958
  Sorted by model distance:
  nonbonded pdb=" O   CYS B 202 "
            pdb=" HG1 THR B 206 "
     model   vdw
     1.725 2.450
  nonbonded pdb=" O   CYS D 202 "
            pdb=" HG1 THR D 206 "
     model   vdw
     1.726 2.450
  nonbonded pdb=" O   CYS E 202 "
            pdb=" HG1 THR E 206 "
     model   vdw
     1.726 2.450
  nonbonded pdb=" O   CYS F 202 "
            pdb=" HG1 THR F 206 "
     model   vdw
     1.727 2.450
  nonbonded pdb=" O   CYS C 202 "
            pdb=" HG1 THR C 206 "
     model   vdw
     1.728 2.450
  ... (remaining 241953 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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 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:             2.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.080
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     17.060
  Find NCS groups from input model:        0.080
  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:5.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
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      :  0.009   0.088  10200  Z= 0.416
  Angle     :  0.925   7.353  13854  Z= 0.403
  Chirality :  0.043   0.218   1572
  Planarity :  0.006   0.042   1644
  Dihedral  : 24.543 120.682   4164
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 1.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  :  3.03 %
    Favored  : 91.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole: -5.00 (0.16), residues: 1182
  helix: -3.18 (0.11), residues: 858
  sheet: -1.56 (0.56), residues: 60
  loop : -3.20 (0.29), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 132 
 TYR   0.006   0.001   TYR F 137 
 PHE   0.010   0.001   PHE C  31 
 TRP   0.010   0.001   TRP A 103 
 HIS   0.006   0.001   HIS E  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00898 (10182)
  covalent geometry    : angle       0.92455 (13818)
  SS BOND              : bond        0.00263 (   18)
  SS BOND              : angle       1.05989 (   36)
  hydrogen bonds       : bond        0.35198 (  654)
  hydrogen bonds       : angle       9.14155 ( 1962)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 149
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A    8 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7252 (ttp-170)
REVERT: A   47 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7829 (mt-10)
REVERT: A  132 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6180 (tpm170)
REVERT: A  135 TRP cc_start: 0.7789 (m-10) cc_final: 0.7270 (m100)
REVERT: A  220 ARG cc_start: 0.4292 (OUTLIER) cc_final: 0.3600 (mtt-85)
REVERT: B    4 ARG cc_start: 0.6383 (ttt-90) cc_final: 0.6115 (ttp-110)
REVERT: B    8 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7395 (ttp80)
REVERT: B  132 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6333 (tpm170)
REVERT: B  135 TRP cc_start: 0.7696 (m-10) cc_final: 0.7190 (m100)
REVERT: B  220 ARG cc_start: 0.3899 (OUTLIER) cc_final: 0.3371 (mtt90)
REVERT: C    4 ARG cc_start: 0.6414 (ttt-90) cc_final: 0.6206 (ttp-110)
REVERT: C    8 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7285 (ttp-170)
REVERT: C   12 GLU cc_start: 0.7878 (tp30) cc_final: 0.7642 (tp30)
REVERT: C  132 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6130 (tpm170)
REVERT: C  135 TRP cc_start: 0.7808 (m-10) cc_final: 0.7275 (m100)
REVERT: C  220 ARG cc_start: 0.4204 (OUTLIER) cc_final: 0.3534 (mtt-85)
REVERT: D    8 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7315 (ttp-170)
REVERT: D  132 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6073 (tpm170)
REVERT: D  135 TRP cc_start: 0.7764 (m-10) cc_final: 0.7272 (m100)
REVERT: D  220 ARG cc_start: 0.4344 (OUTLIER) cc_final: 0.3549 (mtt-85)
REVERT: E    8 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7372 (ttp80)
REVERT: E   47 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7823 (mt-10)
REVERT: E  132 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6230 (tpt170)
REVERT: E  135 TRP cc_start: 0.7691 (m-10) cc_final: 0.7218 (m100)
REVERT: E  187 GLU cc_start: 0.8344 (tt0) cc_final: 0.8108 (tt0)
REVERT: E  220 ARG cc_start: 0.3850 (OUTLIER) cc_final: 0.3345 (mtt-85)
REVERT: F    4 ARG cc_start: 0.6311 (ttt-90) cc_final: 0.6006 (ttp-110)
REVERT: F    8 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7368 (ttp80)
REVERT: F   47 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7928 (mt-10)
REVERT: F  132 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6463 (tpm170)
REVERT: F  135 TRP cc_start: 0.7650 (m-10) cc_final: 0.7131 (m100)
REVERT: F  220 ARG cc_start: 0.4060 (OUTLIER) cc_final: 0.3549 (mtt90)
  outliers start: 54
  outliers final: 4
  residues processed: 184
  average time/residue: 2.0945
  time to fit residues: 400.7901
Evaluate side-chains
  142 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 CYS
Chi-restraints excluded: chain A residue    8 ARG
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain B residue    8 ARG
Chi-restraints excluded: chain B residue  132 ARG
Chi-restraints excluded: chain B residue  220 ARG
Chi-restraints excluded: chain C residue    2 CYS
Chi-restraints excluded: chain C residue    8 ARG
Chi-restraints excluded: chain C residue  132 ARG
Chi-restraints excluded: chain C residue  220 ARG
Chi-restraints excluded: chain D residue    2 CYS
Chi-restraints excluded: chain D residue    8 ARG
Chi-restraints excluded: chain D residue  132 ARG
Chi-restraints excluded: chain D residue  220 ARG
Chi-restraints excluded: chain E residue    8 ARG
Chi-restraints excluded: chain E residue  132 ARG
Chi-restraints excluded: chain E residue  220 ARG
Chi-restraints excluded: chain F residue    2 CYS
Chi-restraints excluded: chain F residue    8 ARG
Chi-restraints excluded: chain F residue  132 ARG
Chi-restraints excluded: chain F residue  220 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0570
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0470
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.152482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.112969 restraints weight = 29294.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 1.82
r_work: 0.3252 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024  10200  Z= 0.189
  Angle     :  0.825   9.272  13854  Z= 0.390
  Chirality :  0.042   0.212   1572
  Planarity :  0.006   0.039   1644
  Dihedral  : 20.327  95.124   2146
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 1.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  :  7.88 %
    Favored  : 89.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole: -0.30 (0.23), residues: 1182
  helix:  0.70 (0.16), residues: 888
  sheet: -1.31 (0.58), residues: 60
  loop : -3.29 (0.30), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 220 
 TYR   0.008   0.001   TYR A 137 
 PHE   0.009   0.002   PHE F  94 
 TRP   0.003   0.001   TRP C 103 
 HIS   0.002   0.001   HIS D  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (10182)
  covalent geometry    : angle       0.82552 (13818)
  SS BOND              : bond        0.00177 (   18)
  SS BOND              : angle       0.57415 (   36)
  hydrogen bonds       : bond        0.09357 (  654)
  hydrogen bonds       : angle       4.88406 ( 1962)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A    8 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6756 (ttp80)
REVERT: A   12 GLU cc_start: 0.8059 (tp30) cc_final: 0.7853 (tp30)
REVERT: A  132 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.5731 (tpt170)
REVERT: A  220 ARG cc_start: 0.4503 (OUTLIER) cc_final: 0.3681 (mtt-85)
REVERT: B    8 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6731 (ttp80)
REVERT: B   12 GLU cc_start: 0.7981 (tp30) cc_final: 0.7779 (tp30)
REVERT: B   47 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7855 (mt-10)
REVERT: B  132 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.5895 (tpm170)
REVERT: B  220 ARG cc_start: 0.4232 (OUTLIER) cc_final: 0.3485 (mtt-85)
REVERT: C    8 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6599 (ttp-170)
REVERT: C  132 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.5647 (tpm170)
REVERT: C  220 ARG cc_start: 0.4033 (OUTLIER) cc_final: 0.3368 (mtt-85)
REVERT: D    8 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6620 (ttp-170)
REVERT: D   12 GLU cc_start: 0.8053 (tp30) cc_final: 0.7847 (tp30)
REVERT: D  132 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.5730 (tpm170)
REVERT: D  220 ARG cc_start: 0.4511 (OUTLIER) cc_final: 0.3674 (mtt-85)
REVERT: E    8 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6664 (ttp80)
REVERT: E   47 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7809 (mt-10)
REVERT: E  132 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.5842 (tpm170)
REVERT: E  220 ARG cc_start: 0.4166 (OUTLIER) cc_final: 0.3437 (mtt-85)
REVERT: F    8 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6560 (ttp-170)
REVERT: F   12 GLU cc_start: 0.7844 (tp30) cc_final: 0.7585 (tp30)
REVERT: F   16 ARG cc_start: 0.7187 (ptp90) cc_final: 0.6876 (ptp90)
REVERT: F   47 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7763 (mt-10)
REVERT: F  132 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6016 (tpm170)
REVERT: F  220 ARG cc_start: 0.4006 (OUTLIER) cc_final: 0.3437 (mtt-85)
  outliers start: 30
  outliers final: 12
  residues processed: 150
  average time/residue: 1.9530
  time to fit residues: 306.1150
Evaluate side-chains
  151 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 121
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 CYS
Chi-restraints excluded: chain A residue    8 ARG
Chi-restraints excluded: chain A residue   69 HIS
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain B residue    2 CYS
Chi-restraints excluded: chain B residue    8 ARG
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  132 ARG
Chi-restraints excluded: chain B residue  220 ARG
Chi-restraints excluded: chain C residue    2 CYS
Chi-restraints excluded: chain C residue    8 ARG
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  132 ARG
Chi-restraints excluded: chain C residue  220 ARG
Chi-restraints excluded: chain D residue    2 CYS
Chi-restraints excluded: chain D residue    8 ARG
Chi-restraints excluded: chain D residue   69 HIS
Chi-restraints excluded: chain D residue  132 ARG
Chi-restraints excluded: chain D residue  220 ARG
Chi-restraints excluded: chain E residue    2 CYS
Chi-restraints excluded: chain E residue    8 ARG
Chi-restraints excluded: chain E residue   69 HIS
Chi-restraints excluded: chain E residue  132 ARG
Chi-restraints excluded: chain E residue  220 ARG
Chi-restraints excluded: chain F residue    2 CYS
Chi-restraints excluded: chain F residue    8 ARG
Chi-restraints excluded: chain F residue   69 HIS
Chi-restraints excluded: chain F residue  132 ARG
Chi-restraints excluded: chain F residue  220 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 116 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 108 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3715 r_free = 0.3715 target = 0.146562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.106032 restraints weight = 29488.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.83
r_work: 0.3147 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10200  Z= 0.179
  Angle     :  0.717   8.037  13854  Z= 0.333
  Chirality :  0.045   0.351   1572
  Planarity :  0.006   0.032   1644
  Dihedral  : 16.984  91.426   2146
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 0.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 10.00 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole:  0.76 (0.24), residues: 1182
  helix:  1.68 (0.17), residues: 864
  sheet: -0.91 (0.58), residues: 60
  loop : -3.39 (0.27), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  22 
 TYR   0.009   0.002   TYR F 159 
 PHE   0.009   0.002   PHE F  94 
 TRP   0.004   0.001   TRP B 219 
 HIS   0.002   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (10182)
  covalent geometry    : angle       0.71688 (13818)
  SS BOND              : bond        0.00363 (   18)
  SS BOND              : angle       0.89862 (   36)
  hydrogen bonds       : bond        0.09477 (  654)
  hydrogen bonds       : angle       4.58167 ( 1962)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6737 (ttp-170)
REVERT: A  132 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.5776 (tpm170)
REVERT: A  220 ARG cc_start: 0.4487 (OUTLIER) cc_final: 0.4049 (ttm110)
REVERT: B    8 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6615 (ttp-170)
REVERT: B  132 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.5864 (tpt170)
REVERT: B  220 ARG cc_start: 0.4311 (OUTLIER) cc_final: 0.3425 (mtt-85)
REVERT: C    8 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6644 (ttp-170)
REVERT: C  132 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.5668 (tpm170)
REVERT: C  220 ARG cc_start: 0.4161 (OUTLIER) cc_final: 0.3459 (mtt-85)
REVERT: D    8 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6741 (ttp-170)
REVERT: D  132 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.5863 (tpm170)
REVERT: D  220 ARG cc_start: 0.4680 (OUTLIER) cc_final: 0.4197 (ttm110)
REVERT: E    8 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6523 (ttp-170)
REVERT: E  132 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.5857 (tpm170)
REVERT: E  220 ARG cc_start: 0.4290 (OUTLIER) cc_final: 0.3451 (mtt-85)
REVERT: F    4 ARG cc_start: 0.5481 (ttt-90) cc_final: 0.5265 (ttp80)
REVERT: F    8 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6591 (ttp-170)
REVERT: F   12 GLU cc_start: 0.7952 (tp30) cc_final: 0.7699 (tp30)
REVERT: F   16 ARG cc_start: 0.7307 (ptp90) cc_final: 0.6949 (ptp90)
REVERT: F   47 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7863 (mt-10)
REVERT: F  132 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.5985 (tpm170)
REVERT: F  220 ARG cc_start: 0.4171 (OUTLIER) cc_final: 0.3578 (mtt-85)
  outliers start: 33
  outliers final: 8
  residues processed: 139
  average time/residue: 2.0196
  time to fit residues: 292.8199
Evaluate side-chains
  140 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ARG
Chi-restraints excluded: chain A residue   69 HIS
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain B residue    2 CYS
Chi-restraints excluded: chain B residue    8 ARG
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  132 ARG
Chi-restraints excluded: chain B residue  220 ARG
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue    8 ARG
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  132 ARG
Chi-restraints excluded: chain C residue  220 ARG
Chi-restraints excluded: chain D residue    8 ARG
Chi-restraints excluded: chain D residue   69 HIS
Chi-restraints excluded: chain D residue  132 ARG
Chi-restraints excluded: chain D residue  220 ARG
Chi-restraints excluded: chain E residue    8 ARG
Chi-restraints excluded: chain E residue   69 HIS
Chi-restraints excluded: chain E residue  132 ARG
Chi-restraints excluded: chain E residue  220 ARG
Chi-restraints excluded: chain F residue    8 ARG
Chi-restraints excluded: chain F residue   69 HIS
Chi-restraints excluded: chain F residue  132 ARG
Chi-restraints excluded: chain F residue  220 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 86 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0570
   chunk 117 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.7704

-------------------------------------------------------------------------------
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 = 0.3728 r_free = 0.3728 target = 0.148167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.107832 restraints weight = 29576.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 1.82
r_work: 0.3133 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020  10200  Z= 0.138
  Angle     :  0.631   5.091  13854  Z= 0.297
  Chirality :  0.039   0.264   1572
  Planarity :  0.005   0.033   1644
  Dihedral  : 15.022 100.437   2142
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 1.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  :  9.70 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole:  1.45 (0.25), residues: 1182
  helix:  2.17 (0.17), residues: 870
  sheet: -0.03 (0.64), residues: 60
  loop : -3.41 (0.27), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  16 
 TYR   0.009   0.002   TYR F 156 
 PHE   0.009   0.001   PHE C  51 
 TRP   0.004   0.001   TRP D 103 
 HIS   0.001   0.000   HIS C 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (10182)
  covalent geometry    : angle       0.63059 (13818)
  SS BOND              : bond        0.00217 (   18)
  SS BOND              : angle       0.66896 (   36)
  hydrogen bonds       : bond        0.06999 (  654)
  hydrogen bonds       : angle       4.28225 ( 1962)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 123
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6583 (ttp-170)
REVERT: A  101 TRP cc_start: 0.6897 (m-10) cc_final: 0.6504 (m100)
REVERT: A  132 ARG cc_start: 0.7194 (ttt-90) cc_final: 0.5718 (tpm170)
REVERT: A  220 ARG cc_start: 0.4642 (OUTLIER) cc_final: 0.4190 (ttm110)
REVERT: B    8 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6379 (ttp-170)
REVERT: B  101 TRP cc_start: 0.6801 (m-10) cc_final: 0.6365 (m100)
REVERT: B  132 ARG cc_start: 0.7239 (ttt-90) cc_final: 0.5671 (tpt170)
REVERT: B  220 ARG cc_start: 0.4205 (OUTLIER) cc_final: 0.3422 (mtt-85)
REVERT: C    8 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6450 (ttp-170)
REVERT: C  101 TRP cc_start: 0.6739 (m-10) cc_final: 0.6327 (m100)
REVERT: C  132 ARG cc_start: 0.7132 (ttt-90) cc_final: 0.5667 (tpm170)
REVERT: C  220 ARG cc_start: 0.4536 (OUTLIER) cc_final: 0.3615 (mtt-85)
REVERT: D    8 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6392 (ttp-170)
REVERT: D  101 TRP cc_start: 0.6914 (m-10) cc_final: 0.6552 (m-10)
REVERT: D  132 ARG cc_start: 0.7235 (ttt-90) cc_final: 0.5725 (tpm170)
REVERT: D  220 ARG cc_start: 0.4609 (OUTLIER) cc_final: 0.3673 (mtt-85)
REVERT: E    8 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6329 (ttp-170)
REVERT: E  101 TRP cc_start: 0.6760 (m-10) cc_final: 0.6498 (m-10)
REVERT: E  132 ARG cc_start: 0.7200 (ttt-90) cc_final: 0.5632 (tpt170)
REVERT: E  220 ARG cc_start: 0.4320 (OUTLIER) cc_final: 0.3413 (mtt-85)
REVERT: F    8 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6466 (ttp-170)
REVERT: F   12 GLU cc_start: 0.8014 (tp30) cc_final: 0.7776 (tp30)
REVERT: F   16 ARG cc_start: 0.7314 (ptp90) cc_final: 0.7082 (ptp90)
REVERT: F   47 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7815 (mt-10)
REVERT: F  101 TRP cc_start: 0.6486 (m-10) cc_final: 0.6259 (m-10)
REVERT: F  132 ARG cc_start: 0.7265 (ttt-90) cc_final: 0.5856 (tpm170)
REVERT: F  220 ARG cc_start: 0.4542 (OUTLIER) cc_final: 0.3753 (mtt-85)
  outliers start: 32
  outliers final: 9
  residues processed: 145
  average time/residue: 1.8955
  time to fit residues: 287.1405
Evaluate side-chains
  131 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ARG
Chi-restraints excluded: chain A residue   69 HIS
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain B residue    2 CYS
Chi-restraints excluded: chain B residue    8 ARG
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  220 ARG
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue    8 ARG
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  220 ARG
Chi-restraints excluded: chain D residue    8 ARG
Chi-restraints excluded: chain D residue   69 HIS
Chi-restraints excluded: chain D residue  220 ARG
Chi-restraints excluded: chain E residue    2 CYS
Chi-restraints excluded: chain E residue    8 ARG
Chi-restraints excluded: chain E residue   69 HIS
Chi-restraints excluded: chain E residue  220 ARG
Chi-restraints excluded: chain F residue    8 ARG
Chi-restraints excluded: chain F residue   69 HIS
Chi-restraints excluded: chain F residue  220 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 78 optimal weight:    5.9990
   chunk 107 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 = 0.3693 r_free = 0.3693 target = 0.144784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.104432 restraints weight = 29474.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 1.83
r_work: 0.3125 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.3050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10200  Z= 0.176
  Angle     :  0.647   5.533  13854  Z= 0.308
  Chirality :  0.039   0.232   1572
  Planarity :  0.006   0.034   1644
  Dihedral  : 15.110  97.158   2118
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 1.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 11.72 %
    Favored  : 85.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole:  1.60 (0.24), residues: 1182
  helix:  2.25 (0.17), residues: 876
  sheet:  0.07 (0.62), residues: 60
  loop : -3.36 (0.28), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  16 
 TYR   0.012   0.002   TYR B 156 
 PHE   0.009   0.002   PHE A  51 
 TRP   0.003   0.001   TRP F 219 
 HIS   0.001   0.000   HIS D  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (10182)
  covalent geometry    : angle       0.64586 (13818)
  SS BOND              : bond        0.00363 (   18)
  SS BOND              : angle       0.93816 (   36)
  hydrogen bonds       : bond        0.08266 (  654)
  hydrogen bonds       : angle       4.30646 ( 1962)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6675 (ttp-170)
REVERT: A  101 TRP cc_start: 0.7027 (m-10) cc_final: 0.6586 (m100)
REVERT: A  132 ARG cc_start: 0.7387 (ttt-90) cc_final: 0.5890 (tpm170)
REVERT: A  220 ARG cc_start: 0.4624 (OUTLIER) cc_final: 0.3775 (mtt-85)
REVERT: B    8 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6473 (ttp-170)
REVERT: B  101 TRP cc_start: 0.6965 (m-10) cc_final: 0.6481 (m100)
REVERT: B  132 ARG cc_start: 0.7404 (ttt-90) cc_final: 0.5888 (tpt170)
REVERT: B  220 ARG cc_start: 0.4315 (OUTLIER) cc_final: 0.3467 (mtt-85)
REVERT: C    8 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6548 (ttp-170)
REVERT: C  101 TRP cc_start: 0.6932 (m-10) cc_final: 0.6485 (m100)
REVERT: C  132 ARG cc_start: 0.7286 (ttt-90) cc_final: 0.5838 (tpm170)
REVERT: C  220 ARG cc_start: 0.4520 (OUTLIER) cc_final: 0.3601 (mtt-85)
REVERT: D    8 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6610 (ttp-170)
REVERT: D  101 TRP cc_start: 0.7025 (m-10) cc_final: 0.6680 (m-10)
REVERT: D  132 ARG cc_start: 0.7474 (ttt-90) cc_final: 0.5941 (tpm170)
REVERT: D  220 ARG cc_start: 0.4643 (OUTLIER) cc_final: 0.3701 (mtt-85)
REVERT: E    8 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6380 (ttp-170)
REVERT: E  101 TRP cc_start: 0.6980 (m-10) cc_final: 0.6707 (m-10)
REVERT: E  132 ARG cc_start: 0.7340 (ttt-90) cc_final: 0.5799 (tpt170)
REVERT: E  220 ARG cc_start: 0.4299 (OUTLIER) cc_final: 0.3439 (mtt-85)
REVERT: F    8 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6571 (ttp-170)
REVERT: F   16 ARG cc_start: 0.7423 (ptp90) cc_final: 0.7220 (mtm110)
REVERT: F   47 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7879 (mt-10)
REVERT: F  132 ARG cc_start: 0.7317 (ttt-90) cc_final: 0.5929 (tpm170)
REVERT: F  220 ARG cc_start: 0.4567 (OUTLIER) cc_final: 0.3724 (mtt-85)
  outliers start: 23
  outliers final: 10
  residues processed: 136
  average time/residue: 2.0149
  time to fit residues: 285.5759
Evaluate side-chains
  139 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ARG
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   69 HIS
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain B residue    2 CYS
Chi-restraints excluded: chain B residue    8 ARG
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  220 ARG
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue    8 ARG
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  162 GLN
Chi-restraints excluded: chain C residue  220 ARG
Chi-restraints excluded: chain D residue    8 ARG
Chi-restraints excluded: chain D residue   69 HIS
Chi-restraints excluded: chain D residue  220 ARG
Chi-restraints excluded: chain E residue    8 ARG
Chi-restraints excluded: chain E residue   69 HIS
Chi-restraints excluded: chain E residue  220 ARG
Chi-restraints excluded: chain F residue    8 ARG
Chi-restraints excluded: chain F residue   69 HIS
Chi-restraints excluded: chain F residue  220 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 70 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 50 optimal weight:    9.9990
   chunk 63 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    2.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.144880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.104659 restraints weight = 29656.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 1.82
r_work: 0.3129 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10200  Z= 0.152
  Angle     :  0.608   5.695  13854  Z= 0.292
  Chirality :  0.037   0.179   1572
  Planarity :  0.005   0.035   1644
  Dihedral  : 14.889  97.919   2118
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 1.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 11.92 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole:  1.82 (0.25), residues: 1182
  helix:  2.38 (0.17), residues: 876
  sheet:  0.59 (0.68), residues: 60
  loop : -3.26 (0.28), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  16 
 TYR   0.011   0.002   TYR B 156 
 PHE   0.009   0.001   PHE C  51 
 TRP   0.004   0.001   TRP D 103 
 HIS   0.001   0.000   HIS C  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (10182)
  covalent geometry    : angle       0.60784 (13818)
  SS BOND              : bond        0.00302 (   18)
  SS BOND              : angle       0.82325 (   36)
  hydrogen bonds       : bond        0.07590 (  654)
  hydrogen bonds       : angle       4.25542 ( 1962)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6699 (ttp-170)
REVERT: A   16 ARG cc_start: 0.7632 (ptp90) cc_final: 0.7410 (mtm110)
REVERT: A  101 TRP cc_start: 0.6992 (m-10) cc_final: 0.6580 (m100)
REVERT: A  132 ARG cc_start: 0.7445 (ttt-90) cc_final: 0.5965 (tpm170)
REVERT: A  220 ARG cc_start: 0.4575 (OUTLIER) cc_final: 0.4137 (ttm110)
REVERT: B    6 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6851 (mp)
REVERT: B    8 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6454 (ttp-170)
REVERT: B  132 ARG cc_start: 0.7423 (ttt-90) cc_final: 0.5918 (tpt170)
REVERT: B  220 ARG cc_start: 0.4298 (OUTLIER) cc_final: 0.3458 (mtt-85)
REVERT: C    8 ARG cc_start: 0.7153 (ttt-90) cc_final: 0.6561 (ttp-170)
REVERT: C  101 TRP cc_start: 0.6910 (m-10) cc_final: 0.6646 (m-10)
REVERT: C  132 ARG cc_start: 0.7379 (ttt-90) cc_final: 0.5877 (tpm170)
REVERT: C  220 ARG cc_start: 0.4448 (OUTLIER) cc_final: 0.3523 (mtt-85)
REVERT: D    8 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6621 (ttp-170)
REVERT: D   16 ARG cc_start: 0.7707 (ptp90) cc_final: 0.7412 (mtm110)
REVERT: D  101 TRP cc_start: 0.6962 (m-10) cc_final: 0.6579 (m-10)
REVERT: D  132 ARG cc_start: 0.7487 (ttt-90) cc_final: 0.6002 (tpm170)
REVERT: D  220 ARG cc_start: 0.4448 (OUTLIER) cc_final: 0.4041 (ttm110)
REVERT: E    8 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6393 (ttp-170)
REVERT: E  101 TRP cc_start: 0.6927 (m-10) cc_final: 0.6699 (m-10)
REVERT: E  132 ARG cc_start: 0.7415 (ttt-90) cc_final: 0.5922 (tpt170)
REVERT: E  220 ARG cc_start: 0.4224 (OUTLIER) cc_final: 0.3445 (mtt-85)
REVERT: F    8 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6597 (ttp-170)
REVERT: F   16 ARG cc_start: 0.7428 (ptp90) cc_final: 0.7228 (mtm110)
REVERT: F   47 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7881 (mt-10)
REVERT: F  101 TRP cc_start: 0.6748 (m-10) cc_final: 0.6517 (m-10)
REVERT: F  132 ARG cc_start: 0.7365 (ttt-90) cc_final: 0.5890 (tpm170)
REVERT: F  220 ARG cc_start: 0.4473 (OUTLIER) cc_final: 0.4189 (ttm110)
  outliers start: 25
  outliers final: 9
  residues processed: 133
  average time/residue: 1.9924
  time to fit residues: 276.7324
Evaluate side-chains
  136 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ARG
Chi-restraints excluded: chain A residue   69 HIS
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain B residue    2 CYS
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue    8 ARG
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  220 ARG
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  220 ARG
Chi-restraints excluded: chain D residue    8 ARG
Chi-restraints excluded: chain D residue   69 HIS
Chi-restraints excluded: chain D residue  220 ARG
Chi-restraints excluded: chain E residue    2 CYS
Chi-restraints excluded: chain E residue    8 ARG
Chi-restraints excluded: chain E residue   69 HIS
Chi-restraints excluded: chain E residue  220 ARG
Chi-restraints excluded: chain F residue    8 ARG
Chi-restraints excluded: chain F residue   69 HIS
Chi-restraints excluded: chain F residue  220 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 110 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   chunk 106 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.142605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.102382 restraints weight = 29604.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 1.83
r_work: 0.3096 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10200  Z= 0.198
  Angle     :  0.660   5.974  13854  Z= 0.317
  Chirality :  0.039   0.168   1572
  Planarity :  0.006   0.033   1644
  Dihedral  : 15.040  94.033   2114
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 12.73 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole:  1.80 (0.25), residues: 1182
  helix:  2.32 (0.17), residues: 876
  sheet:  0.69 (0.65), residues: 60
  loop : -3.13 (0.30), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  22 
 TYR   0.014   0.002   TYR E 156 
 PHE   0.010   0.002   PHE C  51 
 TRP   0.004   0.001   TRP A  77 
 HIS   0.001   0.000   HIS D  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (10182)
  covalent geometry    : angle       0.65814 (13818)
  SS BOND              : bond        0.00437 (   18)
  SS BOND              : angle       1.10966 (   36)
  hydrogen bonds       : bond        0.08721 (  654)
  hydrogen bonds       : angle       4.30202 ( 1962)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A    8 ARG cc_start: 0.7357 (ttt-90) cc_final: 0.6718 (ttp-170)
REVERT: A   16 ARG cc_start: 0.7688 (ptp90) cc_final: 0.7481 (mtm110)
REVERT: A  101 TRP cc_start: 0.7077 (m-10) cc_final: 0.6666 (m-10)
REVERT: A  132 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6065 (tpm170)
REVERT: A  220 ARG cc_start: 0.4383 (OUTLIER) cc_final: 0.4017 (ttm110)
REVERT: B    6 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6875 (mp)
REVERT: B    8 ARG cc_start: 0.7094 (ttt-90) cc_final: 0.6454 (ttp-170)
REVERT: B  101 TRP cc_start: 0.7129 (m-10) cc_final: 0.6683 (m100)
REVERT: B  132 ARG cc_start: 0.7560 (ttt-90) cc_final: 0.6002 (tpt170)
REVERT: B  135 TRP cc_start: 0.7538 (m-10) cc_final: 0.6906 (m100)
REVERT: B  220 ARG cc_start: 0.4348 (OUTLIER) cc_final: 0.3529 (mtt-85)
REVERT: C    6 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6768 (mp)
REVERT: C    8 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6572 (ttp-170)
REVERT: C  101 TRP cc_start: 0.6995 (m-10) cc_final: 0.6720 (m-10)
REVERT: C  132 ARG cc_start: 0.7456 (ttt-90) cc_final: 0.5967 (tpm170)
REVERT: C  135 TRP cc_start: 0.7581 (m-10) cc_final: 0.6904 (m100)
REVERT: C  220 ARG cc_start: 0.4468 (OUTLIER) cc_final: 0.3581 (mtt-85)
REVERT: D    8 ARG cc_start: 0.7329 (ttt-90) cc_final: 0.6732 (ttp-170)
REVERT: D   16 ARG cc_start: 0.7729 (ptp90) cc_final: 0.7403 (mtm110)
REVERT: D  101 TRP cc_start: 0.7023 (m-10) cc_final: 0.6612 (m-10)
REVERT: D  132 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6076 (tpm170)
REVERT: D  220 ARG cc_start: 0.4559 (OUTLIER) cc_final: 0.3571 (mtt-85)
REVERT: E    6 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7170 (mt)
REVERT: E    8 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6551 (ttp-170)
REVERT: E  101 TRP cc_start: 0.7072 (m-10) cc_final: 0.6848 (m-10)
REVERT: E  132 ARG cc_start: 0.7557 (ttt-90) cc_final: 0.6037 (tpt170)
REVERT: E  135 TRP cc_start: 0.7523 (m-10) cc_final: 0.6907 (m100)
REVERT: E  220 ARG cc_start: 0.4225 (OUTLIER) cc_final: 0.3496 (mtt-85)
REVERT: F    8 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6613 (ttp-170)
REVERT: F   47 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7832 (mt-10)
REVERT: F  132 ARG cc_start: 0.7428 (ttt-90) cc_final: 0.5953 (tpm170)
REVERT: F  135 TRP cc_start: 0.7571 (m-10) cc_final: 0.6889 (m100)
REVERT: F  220 ARG cc_start: 0.4494 (OUTLIER) cc_final: 0.3662 (mtt-85)
  outliers start: 25
  outliers final: 8
  residues processed: 139
  average time/residue: 2.0129
  time to fit residues: 291.6093
Evaluate side-chains
  143 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 HIS
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain B residue    2 CYS
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  220 ARG
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue    8 ARG
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  162 GLN
Chi-restraints excluded: chain C residue  220 ARG
Chi-restraints excluded: chain D residue   69 HIS
Chi-restraints excluded: chain D residue  132 ARG
Chi-restraints excluded: chain D residue  220 ARG
Chi-restraints excluded: chain E residue    6 LEU
Chi-restraints excluded: chain E residue    8 ARG
Chi-restraints excluded: chain E residue   69 HIS
Chi-restraints excluded: chain E residue  220 ARG
Chi-restraints excluded: chain F residue    8 ARG
Chi-restraints excluded: chain F residue   69 HIS
Chi-restraints excluded: chain F residue  220 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 86 optimal weight:    4.9990
   chunk 109 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 104 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.3686 r_free = 0.3686 target = 0.143771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.103636 restraints weight = 29687.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.83
r_work: 0.3107 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10200  Z= 0.152
  Angle     :  0.610   5.678  13854  Z= 0.294
  Chirality :  0.036   0.148   1572
  Planarity :  0.005   0.067   1644
  Dihedral  : 14.722  94.450   2102
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 13.74 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole:  1.97 (0.25), residues: 1182
  helix:  2.42 (0.17), residues: 876
  sheet:  0.97 (0.69), residues: 60
  loop : -3.01 (0.30), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG F  16 
 TYR   0.012   0.002   TYR B 156 
 PHE   0.008   0.001   PHE C  51 
 TRP   0.003   0.001   TRP A 103 
 HIS   0.001   0.000   HIS C  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (10182)
  covalent geometry    : angle       0.60941 (13818)
  SS BOND              : bond        0.00305 (   18)
  SS BOND              : angle       0.84172 (   36)
  hydrogen bonds       : bond        0.07781 (  654)
  hydrogen bonds       : angle       4.25225 ( 1962)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.535 
Fit side-chains
REVERT: A    8 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6686 (ttp-170)
REVERT: A  101 TRP cc_start: 0.6986 (m-10) cc_final: 0.6606 (m-10)
REVERT: A  132 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6016 (tpm170)
REVERT: A  220 ARG cc_start: 0.4417 (OUTLIER) cc_final: 0.3510 (mtt-85)
REVERT: B    6 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6826 (mp)
REVERT: B    8 ARG cc_start: 0.7006 (ttt-90) cc_final: 0.6385 (ttp-170)
REVERT: B  101 TRP cc_start: 0.6970 (m-10) cc_final: 0.6552 (m100)
REVERT: B  132 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.5911 (tpt170)
REVERT: B  135 TRP cc_start: 0.7398 (m-10) cc_final: 0.6756 (m100)
REVERT: B  220 ARG cc_start: 0.4309 (OUTLIER) cc_final: 0.3569 (mtt-85)
REVERT: C    6 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6700 (mp)
REVERT: C    8 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6536 (ttp-170)
REVERT: C  101 TRP cc_start: 0.6839 (m-10) cc_final: 0.6564 (m-10)
REVERT: C  132 ARG cc_start: 0.7383 (ttt-90) cc_final: 0.5882 (tpm170)
REVERT: C  220 ARG cc_start: 0.4506 (OUTLIER) cc_final: 0.3634 (mtt-85)
REVERT: D    8 ARG cc_start: 0.7293 (ttt-90) cc_final: 0.6686 (ttp-170)
REVERT: D   16 ARG cc_start: 0.7657 (ptp90) cc_final: 0.7311 (mtm-85)
REVERT: D  132 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6033 (tpm170)
REVERT: D  220 ARG cc_start: 0.4614 (OUTLIER) cc_final: 0.3604 (mtt-85)
REVERT: E    8 ARG cc_start: 0.7060 (ttt-90) cc_final: 0.6455 (ttp-170)
REVERT: E  101 TRP cc_start: 0.6983 (m-10) cc_final: 0.6722 (m-10)
REVERT: E  132 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.5997 (tpt170)
REVERT: E  135 TRP cc_start: 0.7378 (m-10) cc_final: 0.6757 (m100)
REVERT: E  220 ARG cc_start: 0.4235 (OUTLIER) cc_final: 0.3572 (mtt-85)
REVERT: F    8 ARG cc_start: 0.7169 (ttt-90) cc_final: 0.6556 (ttp-170)
REVERT: F   12 GLU cc_start: 0.7960 (tp30) cc_final: 0.7676 (tp30)
REVERT: F   16 ARG cc_start: 0.7264 (mtm110) cc_final: 0.6908 (pmm150)
REVERT: F   47 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7776 (mt-10)
REVERT: F  132 ARG cc_start: 0.7402 (ttt-90) cc_final: 0.5906 (tpm170)
REVERT: F  220 ARG cc_start: 0.4458 (OUTLIER) cc_final: 0.3641 (mtt-85)
  outliers start: 23
  outliers final: 9
  residues processed: 132
  average time/residue: 2.0853
  time to fit residues: 286.8382
Evaluate side-chains
  140 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ARG
Chi-restraints excluded: chain A residue   69 HIS
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain B residue    2 CYS
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  132 ARG
Chi-restraints excluded: chain B residue  220 ARG
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue    8 ARG
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  162 GLN
Chi-restraints excluded: chain C residue  220 ARG
Chi-restraints excluded: chain D residue   69 HIS
Chi-restraints excluded: chain D residue  132 ARG
Chi-restraints excluded: chain D residue  220 ARG
Chi-restraints excluded: chain E residue    2 CYS
Chi-restraints excluded: chain E residue   69 HIS
Chi-restraints excluded: chain E residue  132 ARG
Chi-restraints excluded: chain E residue  220 ARG
Chi-restraints excluded: chain F residue   69 HIS
Chi-restraints excluded: chain F residue  220 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 94 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.144272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.104236 restraints weight = 29500.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 1.82
r_work: 0.3129 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.3492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10200  Z= 0.144
  Angle     :  0.591   5.470  13854  Z= 0.285
  Chirality :  0.035   0.139   1572
  Planarity :  0.006   0.083   1644
  Dihedral  : 14.326  94.534   2094
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.08 %
    Favored  : 99.92 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 13.74 %
    Favored  : 83.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole:  2.16 (0.25), residues: 1182
  helix:  2.53 (0.17), residues: 876
  sheet:  1.13 (0.71), residues: 60
  loop : -2.88 (0.31), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A  16 
 TYR   0.012   0.002   TYR E 156 
 PHE   0.009   0.001   PHE C  51 
 TRP   0.003   0.001   TRP A 101 
 HIS   0.001   0.000   HIS C  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (10182)
  covalent geometry    : angle       0.59072 (13818)
  SS BOND              : bond        0.00294 (   18)
  SS BOND              : angle       0.79660 (   36)
  hydrogen bonds       : bond        0.07347 (  654)
  hydrogen bonds       : angle       4.16124 ( 1962)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.553 
Fit side-chains
REVERT: A    8 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6702 (ttp-170)
REVERT: A   16 ARG cc_start: 0.7393 (mtm110) cc_final: 0.6873 (ptp-110)
REVERT: A  101 TRP cc_start: 0.6928 (m-10) cc_final: 0.6554 (m-10)
REVERT: A  132 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.5993 (tpm170)
REVERT: A  220 ARG cc_start: 0.4594 (OUTLIER) cc_final: 0.3600 (mtt-85)
REVERT: B    8 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6432 (ttp-170)
REVERT: B  101 TRP cc_start: 0.6934 (m-10) cc_final: 0.6515 (m100)
REVERT: B  132 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.5961 (tpt170)
REVERT: B  220 ARG cc_start: 0.4232 (OUTLIER) cc_final: 0.3560 (mtt-85)
REVERT: C    4 ARG cc_start: 0.5841 (ttt-90) cc_final: 0.5438 (ttp-110)
REVERT: C    6 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6766 (mp)
REVERT: C    8 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6582 (ttp-170)
REVERT: C  101 TRP cc_start: 0.6872 (m-10) cc_final: 0.6551 (m-10)
REVERT: C  132 ARG cc_start: 0.7380 (ttt-90) cc_final: 0.5925 (tpm170)
REVERT: C  220 ARG cc_start: 0.4563 (OUTLIER) cc_final: 0.3666 (mtt-85)
REVERT: D    8 ARG cc_start: 0.7252 (ttt-90) cc_final: 0.6638 (ttp-170)
REVERT: D   16 ARG cc_start: 0.7637 (ptp90) cc_final: 0.7339 (mtm-85)
REVERT: D  132 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6089 (tpm170)
REVERT: D  220 ARG cc_start: 0.4602 (OUTLIER) cc_final: 0.3600 (mtt-85)
REVERT: E    8 ARG cc_start: 0.7085 (ttt-90) cc_final: 0.6482 (ttp-170)
REVERT: E  101 TRP cc_start: 0.6924 (m-10) cc_final: 0.6652 (m-10)
REVERT: E  132 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.5991 (tpt170)
REVERT: E  220 ARG cc_start: 0.4204 (OUTLIER) cc_final: 0.3512 (mtt-85)
REVERT: F    8 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6580 (ttp-170)
REVERT: F   12 GLU cc_start: 0.8026 (tp30) cc_final: 0.7769 (tp30)
REVERT: F   16 ARG cc_start: 0.7396 (mtm110) cc_final: 0.7011 (pmm150)
REVERT: F   47 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7764 (mt-10)
REVERT: F  132 ARG cc_start: 0.7432 (ttt-90) cc_final: 0.5950 (tpm170)
REVERT: F  220 ARG cc_start: 0.4480 (OUTLIER) cc_final: 0.4188 (ttm110)
  outliers start: 25
  outliers final: 9
  residues processed: 132
  average time/residue: 2.1534
  time to fit residues: 295.6504
Evaluate side-chains
  137 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ARG
Chi-restraints excluded: chain A residue   69 HIS
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain B residue    2 CYS
Chi-restraints excluded: chain B residue    8 ARG
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  132 ARG
Chi-restraints excluded: chain B residue  220 ARG
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue    8 ARG
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  162 GLN
Chi-restraints excluded: chain C residue  220 ARG
Chi-restraints excluded: chain D residue   69 HIS
Chi-restraints excluded: chain D residue  132 ARG
Chi-restraints excluded: chain D residue  220 ARG
Chi-restraints excluded: chain E residue    2 CYS
Chi-restraints excluded: chain E residue   69 HIS
Chi-restraints excluded: chain E residue  132 ARG
Chi-restraints excluded: chain E residue  220 ARG
Chi-restraints excluded: chain F residue    8 ARG
Chi-restraints excluded: chain F residue   69 HIS
Chi-restraints excluded: chain F residue  220 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   chunk 86 optimal weight:    5.9990
   chunk 117 optimal weight:    0.1980
   chunk 41 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   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 = 0.3744 r_free = 0.3744 target = 0.148723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.109273 restraints weight = 29496.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.82
r_work: 0.3108 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.3699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10200  Z= 0.113
  Angle     :  0.534   5.177  13854  Z= 0.260
  Chirality :  0.033   0.101   1572
  Planarity :  0.005   0.052   1644
  Dihedral  : 13.889  96.833   2094
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.24 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole:  2.50 (0.25), residues: 1182
  helix:  2.80 (0.18), residues: 876
  sheet:  1.27 (0.73), residues: 60
  loop : -2.88 (0.31), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG F  16 
 TYR   0.008   0.001   TYR B 156 
 PHE   0.005   0.001   PHE F  51 
 TRP   0.004   0.000   TRP F 101 
 HIS   0.001   0.000   HIS C  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (10182)
  covalent geometry    : angle       0.53421 (13818)
  SS BOND              : bond        0.00134 (   18)
  SS BOND              : angle       0.50488 (   36)
  hydrogen bonds       : bond        0.05589 (  654)
  hydrogen bonds       : angle       3.97486 ( 1962)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 ARG cc_start: 0.7023 (ttt-90) cc_final: 0.6450 (ttp-170)
REVERT: A   16 ARG cc_start: 0.7422 (mtm110) cc_final: 0.6779 (ptp-110)
REVERT: A  101 TRP cc_start: 0.6678 (m-10) cc_final: 0.6398 (m-10)
REVERT: A  132 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.5716 (tpm170)
REVERT: A  220 ARG cc_start: 0.4581 (OUTLIER) cc_final: 0.3584 (mtt-85)
REVERT: B    8 ARG cc_start: 0.6870 (ttt-90) cc_final: 0.6365 (ttp-170)
REVERT: B  101 TRP cc_start: 0.6758 (m-10) cc_final: 0.6370 (m100)
REVERT: B  132 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.5777 (tpt170)
REVERT: B  220 ARG cc_start: 0.4316 (OUTLIER) cc_final: 0.3574 (mtt-85)
REVERT: C    4 ARG cc_start: 0.5615 (ttt-90) cc_final: 0.5279 (ttp-110)
REVERT: C    8 ARG cc_start: 0.6971 (ttt-90) cc_final: 0.6382 (ttp-170)
REVERT: C  132 ARG cc_start: 0.7247 (ttt-90) cc_final: 0.5717 (tpm170)
REVERT: C  220 ARG cc_start: 0.4455 (OUTLIER) cc_final: 0.3602 (mtt-85)
REVERT: D    8 ARG cc_start: 0.7012 (ttt-90) cc_final: 0.6457 (ttp-170)
REVERT: D   16 ARG cc_start: 0.7503 (ptp90) cc_final: 0.7235 (mtm-85)
REVERT: D  132 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.5775 (tpm170)
REVERT: D  220 ARG cc_start: 0.4571 (OUTLIER) cc_final: 0.3669 (mtt-85)
REVERT: E    8 ARG cc_start: 0.6898 (ttt-90) cc_final: 0.6364 (ttp-170)
REVERT: E  132 ARG cc_start: 0.7345 (ttt-90) cc_final: 0.5788 (tpt170)
REVERT: E  220 ARG cc_start: 0.4176 (OUTLIER) cc_final: 0.3558 (mtt-85)
REVERT: F    8 ARG cc_start: 0.6964 (ttt-90) cc_final: 0.6386 (ttp-170)
REVERT: F   16 ARG cc_start: 0.7266 (mtm110) cc_final: 0.6888 (pmm150)
REVERT: F   47 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7772 (mt-10)
REVERT: F  132 ARG cc_start: 0.7267 (ttt-90) cc_final: 0.5760 (tpm170)
REVERT: F  220 ARG cc_start: 0.4380 (OUTLIER) cc_final: 0.3610 (mtt-85)
  outliers start: 18
  outliers final: 9
  residues processed: 126
  average time/residue: 2.1831
  time to fit residues: 286.4990
Evaluate side-chains
  130 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 HIS
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain B residue    2 CYS
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  132 ARG
Chi-restraints excluded: chain B residue  220 ARG
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  220 ARG
Chi-restraints excluded: chain D residue   69 HIS
Chi-restraints excluded: chain D residue  132 ARG
Chi-restraints excluded: chain D residue  220 ARG
Chi-restraints excluded: chain E residue    2 CYS
Chi-restraints excluded: chain E residue   69 HIS
Chi-restraints excluded: chain E residue  220 ARG
Chi-restraints excluded: chain F residue   69 HIS
Chi-restraints excluded: chain F residue  220 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 111 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   chunk 50 optimal weight:   10.0000
   chunk 1 optimal weight:    0.5980
   chunk 51 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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 = 0.3724 r_free = 0.3724 target = 0.146838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.107177 restraints weight = 29649.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 1.82
r_work: 0.3150 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.3703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  10200  Z= 0.124
  Angle     :  0.548   5.238  13854  Z= 0.264
  Chirality :  0.033   0.123   1572
  Planarity :  0.005   0.058   1644
  Dihedral  : 13.698  96.394   2094
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.08 %
    Favored  : 99.92 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.04 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole:  2.55 (0.25), residues: 1182
  helix:  2.83 (0.17), residues: 876
  sheet:  1.37 (0.73), residues: 60
  loop : -2.81 (0.31), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A  16 
 TYR   0.011   0.002   TYR E 156 
 PHE   0.007   0.001   PHE C  51 
 TRP   0.003   0.001   TRP E 101 
 HIS   0.001   0.000   HIS C  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (10182)
  covalent geometry    : angle       0.54726 (13818)
  SS BOND              : bond        0.00237 (   18)
  SS BOND              : angle       0.67281 (   36)
  hydrogen bonds       : bond        0.06252 (  654)
  hydrogen bonds       : angle       3.95502 ( 1962)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7423.54 seconds
wall clock time: 125 minutes 40.14 seconds (7540.14 seconds total)