Starting phenix.real_space_refine
on Wed Mar  4 01:30:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xqj_33398/03_2026/7xqj_33398.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xqj_33398/03_2026/7xqj_33398.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xqj_33398/03_2026/7xqj_33398.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xqj_33398/03_2026/7xqj_33398.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xqj_33398/03_2026/7xqj_33398.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xqj_33398/03_2026/7xqj_33398.map"
  }
  resolution = 4.0
  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=   0.000 sd=   0.001
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: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    6642      2.51       5
     N    1590      2.21       5
     O    1674      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 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: 9960
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1660
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1660
          Classifications: {'peptide': 204}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 197}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 1.44, per 1000 atoms: 0.14
  Number of scatterers: 9960
  At special positions: 0
  Unit cell: (102.608, 104.304, 101.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1674      8.00
     N    1590      7.00
     C    6642      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  61 " - pdb=" SG  CYS A 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  65 " - pdb=" SG  CYS A 187 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  54 " - pdb=" SG  CYS B 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  54 " - pdb=" SG  CYS C 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  54 " - pdb=" SG  CYS D 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  54 " - pdb=" SG  CYS E 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  54 " - pdb=" SG  CYS F 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  61 " - pdb=" SG  CYS B 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  61 " - pdb=" SG  CYS C 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  61 " - pdb=" SG  CYS D 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  61 " - pdb=" SG  CYS E 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  61 " - pdb=" SG  CYS F 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  65 " - pdb=" SG  CYS B 187 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  65 " - pdb=" SG  CYS C 187 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  65 " - pdb=" SG  CYS D 187 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  65 " - pdb=" SG  CYS E 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  65 " - pdb=" SG  CYS F 187 " distance=2.04

  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: 0.80
  Conformation dependent library (CDL) restraints added in 397.7 milliseconds
  

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2316

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 6 sheets defined
      73.0% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 15
      removed outlier: 4.903A  pdb=" N   LYS A  13 " --> pdb=" O   LYS A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 33
      removed outlier: 3.738A  pdb=" N   ARG A  33 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 40
      removed outlier: 3.544A  pdb=" N   GLY A  38 " --> pdb=" O   ILE A  34 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 45
      removed outlier: 3.943A  pdb=" N   TRP A  45 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 70
      removed outlier: 3.874A  pdb=" N   VAL A  64 " --> pdb=" O   GLY A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 85
      removed outlier: 3.523A  pdb=" N   PHE A  77 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 88
      No H-bonds generated for 'chain 'A' and resid 86 through 88'
    Processing helix  chain 'A' and resid 89 through 107
      removed outlier: 3.714A  pdb=" N   LEU A  93 " --> pdb=" O   THR A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 177
    Processing helix  chain 'A' and resid 202 through 238
      removed outlier: 3.717A  pdb=" N   LYS A 206 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 15
      removed outlier: 4.903A  pdb=" N   LYS B  13 " --> pdb=" O   LYS B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 33
      removed outlier: 3.739A  pdb=" N   ARG B  33 " --> pdb=" O   LEU B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 40
      removed outlier: 3.544A  pdb=" N   GLY B  38 " --> pdb=" O   ILE B  34 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 45
      removed outlier: 3.944A  pdb=" N   TRP B  45 " --> pdb=" O   VAL B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 70
      removed outlier: 3.874A  pdb=" N   VAL B  64 " --> pdb=" O   GLY B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 85
      removed outlier: 3.522A  pdb=" N   PHE B  77 " --> pdb=" O   SER B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 88
      No H-bonds generated for 'chain 'B' and resid 86 through 88'
    Processing helix  chain 'B' and resid 89 through 107
      removed outlier: 3.714A  pdb=" N   LEU B  93 " --> pdb=" O   THR B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 177
    Processing helix  chain 'B' and resid 202 through 238
      removed outlier: 3.717A  pdb=" N   LYS B 206 " --> pdb=" O   ARG B 202 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 15
      removed outlier: 4.903A  pdb=" N   LYS C  13 " --> pdb=" O   LYS C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 19 through 33
      removed outlier: 3.739A  pdb=" N   ARG C  33 " --> pdb=" O   LEU C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 40
      removed outlier: 3.545A  pdb=" N   GLY C  38 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA C  40 " --> pdb=" O   LEU C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 45
      removed outlier: 3.943A  pdb=" N   TRP C  45 " --> pdb=" O   VAL C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 70
      removed outlier: 3.874A  pdb=" N   VAL C  64 " --> pdb=" O   GLY C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 85
      removed outlier: 3.522A  pdb=" N   PHE C  77 " --> pdb=" O   SER C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 88
      No H-bonds generated for 'chain 'C' and resid 86 through 88'
    Processing helix  chain 'C' and resid 89 through 107
      removed outlier: 3.714A  pdb=" N   LEU C  93 " --> pdb=" O   THR C  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 177
    Processing helix  chain 'C' and resid 202 through 238
      removed outlier: 3.717A  pdb=" N   LYS C 206 " --> pdb=" O   ARG C 202 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 15
      removed outlier: 4.903A  pdb=" N   LYS D  13 " --> pdb=" O   LYS D   9 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 33
      removed outlier: 3.738A  pdb=" N   ARG D  33 " --> pdb=" O   LEU D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 33 through 40
      removed outlier: 3.544A  pdb=" N   GLY D  38 " --> pdb=" O   ILE D  34 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA D  40 " --> pdb=" O   LEU D  36 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 45
      removed outlier: 3.944A  pdb=" N   TRP D  45 " --> pdb=" O   VAL D  41 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 60 through 70
      removed outlier: 3.874A  pdb=" N   VAL D  64 " --> pdb=" O   GLY D  60 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 85
      removed outlier: 3.523A  pdb=" N   PHE D  77 " --> pdb=" O   SER D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 86 through 88
      No H-bonds generated for 'chain 'D' and resid 86 through 88'
    Processing helix  chain 'D' and resid 89 through 107
      removed outlier: 3.714A  pdb=" N   LEU D  93 " --> pdb=" O   THR D  89 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 177
    Processing helix  chain 'D' and resid 202 through 238
      removed outlier: 3.718A  pdb=" N   LYS D 206 " --> pdb=" O   ARG D 202 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 7 through 15
      removed outlier: 4.903A  pdb=" N   LYS E  13 " --> pdb=" O   LYS E   9 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 19 through 33
      removed outlier: 3.738A  pdb=" N   ARG E  33 " --> pdb=" O   LEU E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 33 through 40
      removed outlier: 3.544A  pdb=" N   GLY E  38 " --> pdb=" O   ILE E  34 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA E  40 " --> pdb=" O   LEU E  36 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 40 through 45
      removed outlier: 3.943A  pdb=" N   TRP E  45 " --> pdb=" O   VAL E  41 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 60 through 70
      removed outlier: 3.874A  pdb=" N   VAL E  64 " --> pdb=" O   GLY E  60 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 73 through 85
      removed outlier: 3.522A  pdb=" N   PHE E  77 " --> pdb=" O   SER E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 88
      No H-bonds generated for 'chain 'E' and resid 86 through 88'
    Processing helix  chain 'E' and resid 89 through 107
      removed outlier: 3.714A  pdb=" N   LEU E  93 " --> pdb=" O   THR E  89 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 150 through 177
    Processing helix  chain 'E' and resid 202 through 238
      removed outlier: 3.717A  pdb=" N   LYS E 206 " --> pdb=" O   ARG E 202 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 7 through 15
      removed outlier: 4.903A  pdb=" N   LYS F  13 " --> pdb=" O   LYS F   9 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 19 through 33
      removed outlier: 3.739A  pdb=" N   ARG F  33 " --> pdb=" O   LEU F  29 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 33 through 40
      removed outlier: 3.545A  pdb=" N   GLY F  38 " --> pdb=" O   ILE F  34 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA F  40 " --> pdb=" O   LEU F  36 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 40 through 45
      removed outlier: 3.944A  pdb=" N   TRP F  45 " --> pdb=" O   VAL F  41 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 60 through 70
      removed outlier: 3.874A  pdb=" N   VAL F  64 " --> pdb=" O   GLY F  60 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 73 through 85
      removed outlier: 3.522A  pdb=" N   PHE F  77 " --> pdb=" O   SER F  73 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 86 through 88
      No H-bonds generated for 'chain 'F' and resid 86 through 88'
    Processing helix  chain 'F' and resid 89 through 107
      removed outlier: 3.714A  pdb=" N   LEU F  93 " --> pdb=" O   THR F  89 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 150 through 177
    Processing helix  chain 'F' and resid 202 through 238
      removed outlier: 3.717A  pdb=" N   LYS F 206 " --> pdb=" O   ARG F 202 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54
      removed outlier: 3.503A  pdb=" N   ARG A  53 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54
      removed outlier: 3.503A  pdb=" N   ARG B  53 " --> pdb=" O   PHE B 199 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54
      removed outlier: 3.503A  pdb=" N   ARG C  53 " --> pdb=" O   PHE C 199 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54
      removed outlier: 3.503A  pdb=" N   ARG D  53 " --> pdb=" O   PHE D 199 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54
      removed outlier: 3.503A  pdb=" N   ARG E  53 " --> pdb=" O   PHE E 199 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54
      removed outlier: 3.502A  pdb=" N   ARG F  53 " --> pdb=" O   PHE F 199 " (cutoff:3.500A)

    636 hydrogen bonds defined for protein.
    1890 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.64

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2934
        1.34 -     1.46: 2224
        1.46 -     1.57: 4988
        1.57 -     1.69: 0
        1.69 -     1.80: 72
  Bond restraints: 10218
  Sorted by residual:
  bond pdb=" C   VAL C  87 "
       pdb=" N   PRO C  88 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.049 2.34e-02 1.83e+03 4.31e+00
  bond pdb=" C   VAL D  87 "
       pdb=" N   PRO D  88 "
    ideal  model  delta    sigma   weight residual
    1.334  1.382 -0.048 2.34e-02 1.83e+03 4.21e+00
  bond pdb=" C   VAL A  87 "
       pdb=" N   PRO A  88 "
    ideal  model  delta    sigma   weight residual
    1.334  1.382 -0.048 2.34e-02 1.83e+03 4.15e+00
  bond pdb=" C   VAL F  87 "
       pdb=" N   PRO F  88 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 2.34e-02 1.83e+03 4.09e+00
  bond pdb=" C   VAL E  87 "
       pdb=" N   PRO E  88 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 2.34e-02 1.83e+03 4.09e+00
  ... (remaining 10213 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 13172
        1.65 -     3.30: 508
        3.30 -     4.95: 108
        4.95 -     6.61: 24
        6.61 -     8.26: 12
  Bond angle restraints: 13824
  Sorted by residual:
  angle pdb=" N   GLU B  42 "
        pdb=" CA  GLU B  42 "
        pdb=" C   GLU B  42 "
      ideal   model   delta    sigma   weight residual
     112.90  107.89    5.01 1.31e+00 5.83e-01 1.46e+01
  angle pdb=" N   GLU A  42 "
        pdb=" CA  GLU A  42 "
        pdb=" C   GLU A  42 "
      ideal   model   delta    sigma   weight residual
     112.90  107.90    5.00 1.31e+00 5.83e-01 1.46e+01
  angle pdb=" N   GLU D  42 "
        pdb=" CA  GLU D  42 "
        pdb=" C   GLU D  42 "
      ideal   model   delta    sigma   weight residual
     112.90  107.91    4.99 1.31e+00 5.83e-01 1.45e+01
  angle pdb=" N   GLU C  42 "
        pdb=" CA  GLU C  42 "
        pdb=" C   GLU C  42 "
      ideal   model   delta    sigma   weight residual
     112.90  107.93    4.97 1.31e+00 5.83e-01 1.44e+01
  angle pdb=" N   GLU F  42 "
        pdb=" CA  GLU F  42 "
        pdb=" C   GLU F  42 "
      ideal   model   delta    sigma   weight residual
     112.90  107.93    4.97 1.31e+00 5.83e-01 1.44e+01
  ... (remaining 13819 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.83: 5149
       13.83 -    27.65: 479
       27.65 -    41.48: 210
       41.48 -    55.30: 120
       55.30 -    69.13: 54
  Dihedral angle restraints: 6012
    sinusoidal: 2430
      harmonic: 3582
  Sorted by residual:
  dihedral pdb=" CA  PRO B 193 "
           pdb=" C   PRO B 193 "
           pdb=" N   HIS B 194 "
           pdb=" CA  HIS B 194 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.31  -19.69     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  PRO F 193 "
           pdb=" C   PRO F 193 "
           pdb=" N   HIS F 194 "
           pdb=" CA  HIS F 194 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.33  -19.67     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  PRO A 193 "
           pdb=" C   PRO A 193 "
           pdb=" N   HIS A 194 "
           pdb=" CA  HIS A 194 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.35  -19.65     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 6009 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 998
       0.035 -    0.071: 373
       0.071 -    0.106: 157
       0.106 -    0.141: 32
       0.141 -    0.177: 12
  Chirality restraints: 1572
  Sorted by residual:
  chirality pdb=" CA  ALA E   6 "
            pdb=" N   ALA E   6 "
            pdb=" C   ALA E   6 "
            pdb=" CB  ALA E   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.66   -0.18 2.00e-01 2.50e+01 7.82e-01
  chirality pdb=" CA  ALA C   6 "
            pdb=" N   ALA C   6 "
            pdb=" C   ALA C   6 "
            pdb=" CB  ALA C   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.66   -0.18 2.00e-01 2.50e+01 7.80e-01
  chirality pdb=" CA  ALA F   6 "
            pdb=" N   ALA F   6 "
            pdb=" C   ALA F   6 "
            pdb=" CB  ALA F   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.66   -0.17 2.00e-01 2.50e+01 7.60e-01
  ... (remaining 1569 not shown)

  Planarity restraints: 1662
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  87 "    0.035 5.00e-02 4.00e+02   5.19e-02 4.30e+00
        pdb=" N   PRO A  88 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A  88 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  88 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL F  87 "    0.035 5.00e-02 4.00e+02   5.18e-02 4.29e+00
        pdb=" N   PRO F  88 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO F  88 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO F  88 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E  87 "    0.035 5.00e-02 4.00e+02   5.17e-02 4.28e+00
        pdb=" N   PRO E  88 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO E  88 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO E  88 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1659 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 3939
        2.90 -     3.40: 9991
        3.40 -     3.90: 16156
        3.90 -     4.40: 15725
        4.40 -     4.90: 27759
  Nonbonded interactions: 73570
  Sorted by model distance:
  nonbonded pdb=" O   ALA C  40 "
            pdb=" OG  SER C  43 "
     model   vdw
     2.401 3.040
  nonbonded pdb=" O   ALA D  40 "
            pdb=" OG  SER D  43 "
     model   vdw
     2.402 3.040
  nonbonded pdb=" O   ALA A  40 "
            pdb=" OG  SER A  43 "
     model   vdw
     2.402 3.040
  nonbonded pdb=" O   ALA F  40 "
            pdb=" OG  SER F  43 "
     model   vdw
     2.402 3.040
  nonbonded pdb=" O   ALA E  40 "
            pdb=" OG  SER E  43 "
     model   vdw
     2.402 3.040
  ... (remaining 73565 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     9.190
  Find NCS groups from input model:        0.050
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
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      :  0.007   0.049  10236  Z= 0.316
  Angle     :  0.838   8.257  13860  Z= 0.488
  Chirality :  0.045   0.177   1572
  Planarity :  0.007   0.052   1662
  Dihedral  : 15.982  69.127   3642
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 11.48 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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: -2.82 (0.20), residues: 1200
  helix: -1.68 (0.14), residues: 822
  sheet:  2.82 (0.55), residues: 60
  loop : -2.92 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F 148 
 TYR   0.008   0.001   TYR D  92 
 PHE   0.011   0.002   PHE C  97 
 TRP   0.010   0.002   TRP B  25 
 HIS   0.003   0.001   HIS E  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00665 (10218)
  covalent geometry    : angle       0.83804 (13824)
  SS BOND              : bond        0.00378 (   18)
  SS BOND              : angle       0.60095 (   36)
  hydrogen bonds       : bond        0.12044 (  636)
  hydrogen bonds       : angle       4.80179 ( 1890)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 259
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7358 (p90)
REVERT: A   47 ASP cc_start: 0.8821 (p0) cc_final: 0.8565 (p0)
REVERT: A  100 MET cc_start: 0.9574 (ttp) cc_final: 0.8900 (tmm)
REVERT: A  101 ARG cc_start: 0.9461 (ttm170) cc_final: 0.9100 (ttp-110)
REVERT: A  213 MET cc_start: 0.9231 (mmm) cc_final: 0.8886 (mmp)
REVERT: A  224 ASN cc_start: 0.8962 (m110) cc_final: 0.8571 (m110)
REVERT: A  227 GLU cc_start: 0.9450 (tm-30) cc_final: 0.9124 (tm-30)
REVERT: B   17 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.7251 (p90)
REVERT: B  100 MET cc_start: 0.9586 (ttp) cc_final: 0.9011 (ppp)
REVERT: B  101 ARG cc_start: 0.9385 (ttm170) cc_final: 0.9025 (ttp-110)
REVERT: B  104 GLU cc_start: 0.9417 (tp30) cc_final: 0.9077 (mm-30)
REVERT: B  177 TYR cc_start: 0.8513 (m-80) cc_final: 0.8288 (m-80)
REVERT: B  224 ASN cc_start: 0.8974 (m110) cc_final: 0.8559 (m110)
REVERT: B  227 GLU cc_start: 0.9443 (tm-30) cc_final: 0.9010 (tm-30)
REVERT: C   17 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.7324 (p90)
REVERT: C  100 MET cc_start: 0.9549 (ttp) cc_final: 0.9032 (ppp)
REVERT: C  101 ARG cc_start: 0.9407 (ttm170) cc_final: 0.9029 (ttp-110)
REVERT: C  227 GLU cc_start: 0.9469 (tm-30) cc_final: 0.9242 (tm-30)
REVERT: D   17 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7088 (p90)
REVERT: D   47 ASP cc_start: 0.8790 (p0) cc_final: 0.8497 (p0)
REVERT: D   81 GLN cc_start: 0.9439 (tt0) cc_final: 0.9198 (tt0)
REVERT: D  100 MET cc_start: 0.9557 (ttp) cc_final: 0.9051 (tmm)
REVERT: D  101 ARG cc_start: 0.9439 (ttm170) cc_final: 0.9220 (ttp-110)
REVERT: D  104 GLU cc_start: 0.9472 (tp30) cc_final: 0.9244 (mm-30)
REVERT: D  213 MET cc_start: 0.9251 (mmm) cc_final: 0.8936 (mmp)
REVERT: D  224 ASN cc_start: 0.9021 (m110) cc_final: 0.8658 (m110)
REVERT: D  227 GLU cc_start: 0.9438 (tm-30) cc_final: 0.9191 (tm-30)
REVERT: E   17 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7234 (p90)
REVERT: E  100 MET cc_start: 0.9585 (ttp) cc_final: 0.9014 (ppp)
REVERT: E  101 ARG cc_start: 0.9386 (ttm170) cc_final: 0.9019 (ttp-110)
REVERT: E  104 GLU cc_start: 0.9413 (tp30) cc_final: 0.9076 (mm-30)
REVERT: E  177 TYR cc_start: 0.8509 (m-80) cc_final: 0.8277 (m-80)
REVERT: E  224 ASN cc_start: 0.8972 (m110) cc_final: 0.8558 (m110)
REVERT: E  227 GLU cc_start: 0.9438 (tm-30) cc_final: 0.9021 (tm-30)
REVERT: F   17 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.7395 (p90)
REVERT: F  100 MET cc_start: 0.9553 (ttp) cc_final: 0.9041 (ppp)
REVERT: F  101 ARG cc_start: 0.9408 (ttm170) cc_final: 0.9036 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9468 (tm-30) cc_final: 0.9238 (tm-30)
  outliers start: 66
  outliers final: 13
  residues processed: 307
  average time/residue: 0.0861
  time to fit residues: 37.5744
Evaluate side-chains
  204 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  194 HIS
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  194 HIS
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  194 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:   10.0000
   chunk 117 optimal weight:    0.9980
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
A  74 HIS
A 224 ASN
B  74 HIS
B  81 GLN
B 224 ASN
C  74 HIS
D  15 GLN
D 224 ASN
E  74 HIS
E  81 GLN
E 224 ASN
F  74 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.070396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.054070 restraints weight = 41603.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.055843 restraints weight = 20549.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.056990 restraints weight = 13396.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.057742 restraints weight = 10271.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.058106 restraints weight = 8701.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10236  Z= 0.159
  Angle     :  0.751   9.438  13860  Z= 0.383
  Chirality :  0.040   0.146   1572
  Planarity :  0.005   0.034   1662
  Dihedral  :  7.724  54.878   1352
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  7.01 %
    Allowed  : 19.40 %
    Favored  : 73.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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: -0.41 (0.24), residues: 1200
  helix:  0.38 (0.18), residues: 846
  sheet:  2.95 (0.59), residues: 60
  loop : -2.83 (0.34), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  53 
 TYR   0.006   0.001   TYR F 177 
 PHE   0.013   0.001   PHE C  30 
 TRP   0.019   0.001   TRP C  25 
 HIS   0.002   0.001   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (10218)
  covalent geometry    : angle       0.71716 (13824)
  SS BOND              : bond        0.00438 (   18)
  SS BOND              : angle       4.43411 (   36)
  hydrogen bonds       : bond        0.03526 (  636)
  hydrogen bonds       : angle       3.57096 ( 1890)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 187
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.7414 (p90)
REVERT: A   47 ASP cc_start: 0.8661 (p0) cc_final: 0.8432 (p0)
REVERT: A  100 MET cc_start: 0.9417 (ttp) cc_final: 0.9093 (ppp)
REVERT: A  101 ARG cc_start: 0.9388 (ttm170) cc_final: 0.9084 (ttp-110)
REVERT: A  213 MET cc_start: 0.9203 (mmm) cc_final: 0.8874 (mmp)
REVERT: A  224 ASN cc_start: 0.8860 (m-40) cc_final: 0.8484 (m110)
REVERT: A  227 GLU cc_start: 0.9409 (tm-30) cc_final: 0.9050 (tm-30)
REVERT: B   17 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7272 (p90)
REVERT: B  100 MET cc_start: 0.9416 (ttp) cc_final: 0.9126 (ppp)
REVERT: B  101 ARG cc_start: 0.9313 (ttm170) cc_final: 0.9027 (ttp-110)
REVERT: B  224 ASN cc_start: 0.8929 (m-40) cc_final: 0.8494 (m110)
REVERT: B  227 GLU cc_start: 0.9394 (tm-30) cc_final: 0.8977 (tm-30)
REVERT: C   17 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7247 (p90)
REVERT: C  100 MET cc_start: 0.9373 (ttp) cc_final: 0.9062 (ppp)
REVERT: C  101 ARG cc_start: 0.9339 (ttm170) cc_final: 0.9035 (ttp-110)
REVERT: C  227 GLU cc_start: 0.9410 (tm-30) cc_final: 0.9164 (tm-30)
REVERT: D   17 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7087 (p90)
REVERT: D   35 LEU cc_start: 0.9439 (tp) cc_final: 0.9224 (tp)
REVERT: D   47 ASP cc_start: 0.8708 (p0) cc_final: 0.8478 (p0)
REVERT: D  100 MET cc_start: 0.9419 (ttp) cc_final: 0.9200 (ppp)
REVERT: D  213 MET cc_start: 0.9233 (mmm) cc_final: 0.8957 (mmp)
REVERT: D  224 ASN cc_start: 0.8917 (m-40) cc_final: 0.8555 (m110)
REVERT: D  227 GLU cc_start: 0.9397 (tm-30) cc_final: 0.9110 (tm-30)
REVERT: E   17 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.7351 (p90)
REVERT: E  100 MET cc_start: 0.9417 (ttp) cc_final: 0.9126 (ppp)
REVERT: E  101 ARG cc_start: 0.9324 (ttm170) cc_final: 0.9028 (ttp-110)
REVERT: E  224 ASN cc_start: 0.8929 (m-40) cc_final: 0.8490 (m110)
REVERT: E  227 GLU cc_start: 0.9395 (tm-30) cc_final: 0.8978 (tm-30)
REVERT: F   17 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.7242 (p90)
REVERT: F  100 MET cc_start: 0.9366 (ttp) cc_final: 0.9052 (ppp)
REVERT: F  101 ARG cc_start: 0.9351 (ttm170) cc_final: 0.9037 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9407 (tm-30) cc_final: 0.9155 (tm-30)
  outliers start: 77
  outliers final: 28
  residues processed: 248
  average time/residue: 0.0727
  time to fit residues: 27.3965
Evaluate side-chains
  204 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 170
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   30 PHE
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   61 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   30 PHE
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  194 HIS
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   30 PHE
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   61 CYS
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  194 HIS
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   30 PHE
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  194 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 104 optimal weight:    0.7980
   chunk 69 optimal weight:    4.9990
   chunk 106 optimal weight:    5.9990
   chunk 60 optimal weight:    9.9990
   chunk 96 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 43 optimal weight:    9.9990
   chunk 83 optimal weight:   10.0000
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
B  81 GLN
E  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.070092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.053786 restraints weight = 43120.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.055525 restraints weight = 21137.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.056675 restraints weight = 13740.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.057339 restraints weight = 10478.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.057555 restraints weight = 8968.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10236  Z= 0.166
  Angle     :  0.737   8.453  13860  Z= 0.378
  Chirality :  0.041   0.177   1572
  Planarity :  0.004   0.031   1662
  Dihedral  :  7.601  54.757   1352
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 20.04 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.25 (0.25), residues: 1200
  helix:  0.92 (0.18), residues: 852
  sheet:  2.67 (0.58), residues: 60
  loop : -2.71 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 101 
 TYR   0.015   0.001   TYR D  92 
 PHE   0.015   0.001   PHE B  30 
 TRP   0.027   0.001   TRP C  25 
 HIS   0.004   0.001   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (10218)
  covalent geometry    : angle       0.71013 (13824)
  SS BOND              : bond        0.00235 (   18)
  SS BOND              : angle       3.90668 (   36)
  hydrogen bonds       : bond        0.03294 (  636)
  hydrogen bonds       : angle       3.57139 ( 1890)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 185
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.7490 (p90)
REVERT: A   47 ASP cc_start: 0.8723 (p0) cc_final: 0.8518 (p0)
REVERT: A   48 GLU cc_start: 0.9173 (tp30) cc_final: 0.8350 (tm-30)
REVERT: A   49 GLN cc_start: 0.8787 (tt0) cc_final: 0.8516 (tp40)
REVERT: A  100 MET cc_start: 0.9348 (ttp) cc_final: 0.9106 (ppp)
REVERT: A  101 ARG cc_start: 0.9419 (ttm170) cc_final: 0.9073 (ttp-110)
REVERT: A  213 MET cc_start: 0.9176 (mmm) cc_final: 0.8849 (mmp)
REVERT: A  224 ASN cc_start: 0.8846 (m-40) cc_final: 0.8477 (m110)
REVERT: A  227 GLU cc_start: 0.9427 (tm-30) cc_final: 0.9087 (tm-30)
REVERT: B   17 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.7481 (p90)
REVERT: B  100 MET cc_start: 0.9343 (ttp) cc_final: 0.9133 (ppp)
REVERT: B  101 ARG cc_start: 0.9340 (ttm170) cc_final: 0.9021 (ttp-110)
REVERT: B  224 ASN cc_start: 0.8901 (m-40) cc_final: 0.8486 (m110)
REVERT: B  227 GLU cc_start: 0.9413 (tm-30) cc_final: 0.9018 (tm-30)
REVERT: C   17 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.7503 (p90)
REVERT: C   42 GLU cc_start: 0.8980 (tp30) cc_final: 0.8699 (tp30)
REVERT: C   48 GLU cc_start: 0.9135 (tp30) cc_final: 0.8539 (tm-30)
REVERT: C  100 MET cc_start: 0.9323 (ttp) cc_final: 0.9071 (ppp)
REVERT: C  101 ARG cc_start: 0.9379 (ttm170) cc_final: 0.9033 (ttp-110)
REVERT: C  227 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9181 (tm-30)
REVERT: D   17 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7185 (p90)
REVERT: D   47 ASP cc_start: 0.8797 (p0) cc_final: 0.8590 (p0)
REVERT: D   48 GLU cc_start: 0.9153 (tp30) cc_final: 0.8304 (tm-30)
REVERT: D   49 GLN cc_start: 0.8797 (tt0) cc_final: 0.8399 (tp40)
REVERT: D  100 MET cc_start: 0.9399 (ttp) cc_final: 0.9043 (tmm)
REVERT: D  213 MET cc_start: 0.9224 (mmm) cc_final: 0.8938 (mmp)
REVERT: D  224 ASN cc_start: 0.8895 (m-40) cc_final: 0.8522 (m110)
REVERT: D  227 GLU cc_start: 0.9426 (tm-30) cc_final: 0.9150 (tm-30)
REVERT: E   17 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.7489 (p90)
REVERT: E  101 ARG cc_start: 0.9346 (ttm170) cc_final: 0.8914 (ttp-110)
REVERT: E  224 ASN cc_start: 0.8920 (m-40) cc_final: 0.8490 (m110)
REVERT: E  227 GLU cc_start: 0.9414 (tm-30) cc_final: 0.9017 (tm-30)
REVERT: F   17 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7500 (p90)
REVERT: F   42 GLU cc_start: 0.8999 (tp30) cc_final: 0.8709 (tp30)
REVERT: F   48 GLU cc_start: 0.9132 (tp30) cc_final: 0.8552 (tm-30)
REVERT: F  100 MET cc_start: 0.9322 (ttp) cc_final: 0.9069 (ppp)
REVERT: F  101 ARG cc_start: 0.9382 (ttm170) cc_final: 0.9030 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9181 (tm-30)
  outliers start: 64
  outliers final: 39
  residues processed: 229
  average time/residue: 0.0715
  time to fit residues: 24.7497
Evaluate side-chains
  210 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 165
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   30 PHE
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   30 PHE
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  194 HIS
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   30 PHE
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   65 CYS
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  194 HIS
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   30 PHE
Chi-restraints excluded: chain F residue   65 CYS
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  171 LEU
Chi-restraints excluded: chain F residue  194 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 89 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 119 optimal weight:    8.9990
   chunk 93 optimal weight:    9.9990
   chunk 97 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   chunk 88 optimal weight:    7.9990
   chunk 50 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 66 optimal weight:    0.0070
   chunk 101 optimal weight:    4.9990
   overall best weight:    2.2006

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

Flipped N/Q/H residues before XYZ refinement:
B  81 GLN
E  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.070010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.053655 restraints weight = 43175.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.055351 restraints weight = 21241.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.056519 restraints weight = 13836.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.057140 restraints weight = 10627.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.057612 restraints weight = 9121.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10236  Z= 0.151
  Angle     :  0.693   7.781  13860  Z= 0.357
  Chirality :  0.039   0.173   1572
  Planarity :  0.004   0.030   1662
  Dihedral  :  7.514  55.240   1352
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 19.76 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.80 (0.25), residues: 1200
  helix:  1.43 (0.19), residues: 822
  sheet:  1.71 (0.63), residues: 66
  loop : -2.23 (0.32), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  53 
 TYR   0.016   0.001   TYR A  92 
 PHE   0.013   0.001   PHE E  30 
 TRP   0.036   0.001   TRP C  25 
 HIS   0.003   0.001   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (10218)
  covalent geometry    : angle       0.66893 (13824)
  SS BOND              : bond        0.00164 (   18)
  SS BOND              : angle       3.60934 (   36)
  hydrogen bonds       : bond        0.03182 (  636)
  hydrogen bonds       : angle       3.56238 ( 1890)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 173
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.7430 (p90)
REVERT: A   47 ASP cc_start: 0.8767 (p0) cc_final: 0.8558 (p0)
REVERT: A   48 GLU cc_start: 0.9156 (tp30) cc_final: 0.8614 (tm-30)
REVERT: A   49 GLN cc_start: 0.8854 (tt0) cc_final: 0.8652 (tt0)
REVERT: A  100 MET cc_start: 0.9334 (ttp) cc_final: 0.9103 (ppp)
REVERT: A  101 ARG cc_start: 0.9410 (ttm170) cc_final: 0.9072 (ttp-110)
REVERT: A  213 MET cc_start: 0.9153 (mmm) cc_final: 0.8827 (mmp)
REVERT: A  224 ASN cc_start: 0.8849 (m-40) cc_final: 0.8451 (m110)
REVERT: A  227 GLU cc_start: 0.9427 (tm-30) cc_final: 0.9078 (tm-30)
REVERT: B   17 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7521 (p90)
REVERT: B  101 ARG cc_start: 0.9346 (ttm170) cc_final: 0.9031 (ttp-110)
REVERT: B  224 ASN cc_start: 0.8903 (m-40) cc_final: 0.8641 (m110)
REVERT: B  227 GLU cc_start: 0.9402 (tm-30) cc_final: 0.9008 (tm-30)
REVERT: C   17 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.7587 (p90)
REVERT: C   48 GLU cc_start: 0.9086 (tp30) cc_final: 0.8577 (tm-30)
REVERT: C  100 MET cc_start: 0.9345 (ttp) cc_final: 0.9084 (ppp)
REVERT: C  101 ARG cc_start: 0.9375 (ttm170) cc_final: 0.9028 (ttp-110)
REVERT: C  227 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9174 (tm-30)
REVERT: D   17 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.7079 (p90)
REVERT: D   47 ASP cc_start: 0.8789 (p0) cc_final: 0.8582 (p0)
REVERT: D   48 GLU cc_start: 0.9156 (tp30) cc_final: 0.8617 (tm-30)
REVERT: D  100 MET cc_start: 0.9407 (ttp) cc_final: 0.9195 (ppp)
REVERT: D  213 MET cc_start: 0.9231 (mmm) cc_final: 0.8954 (mmp)
REVERT: D  224 ASN cc_start: 0.8919 (m-40) cc_final: 0.8520 (m110)
REVERT: D  227 GLU cc_start: 0.9432 (tm-30) cc_final: 0.9141 (tm-30)
REVERT: E   17 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.7526 (p90)
REVERT: E   48 GLU cc_start: 0.9116 (tp30) cc_final: 0.8572 (tm-30)
REVERT: E  101 ARG cc_start: 0.9348 (ttm170) cc_final: 0.9029 (ttp-110)
REVERT: E  224 ASN cc_start: 0.8903 (m-40) cc_final: 0.8646 (m110)
REVERT: E  227 GLU cc_start: 0.9409 (tm-30) cc_final: 0.9014 (tm-30)
REVERT: F   17 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.7599 (p90)
REVERT: F   48 GLU cc_start: 0.9099 (tp30) cc_final: 0.8580 (tm-30)
REVERT: F  100 MET cc_start: 0.9341 (ttp) cc_final: 0.9078 (ppp)
REVERT: F  101 ARG cc_start: 0.9368 (ttm170) cc_final: 0.9026 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9421 (tm-30) cc_final: 0.9175 (tm-30)
  outliers start: 74
  outliers final: 37
  residues processed: 219
  average time/residue: 0.0716
  time to fit residues: 23.5341
Evaluate side-chains
  204 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 161
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   30 PHE
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   30 PHE
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  224 ASN
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   30 PHE
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   69 SER
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   65 CYS
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  228 LEU
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   30 PHE
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  171 LEU
Chi-restraints excluded: chain F residue  224 ASN
Chi-restraints excluded: chain F residue  228 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 39 optimal weight:    9.9990
   chunk 7 optimal weight:    0.8980
   chunk 50 optimal weight:    8.9990
   chunk 64 optimal weight:    0.1980
   chunk 57 optimal weight:    0.7980
   chunk 83 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
B  81 GLN
E  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.070719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.054810 restraints weight = 43152.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.056546 restraints weight = 21457.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.057754 restraints weight = 13728.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.058349 restraints weight = 10355.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.058799 restraints weight = 8911.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.3188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10236  Z= 0.136
  Angle     :  0.707   9.252  13860  Z= 0.360
  Chirality :  0.040   0.180   1572
  Planarity :  0.004   0.031   1662
  Dihedral  :  6.601  53.089   1336
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 23.04 %
    Favored  : 71.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.93 (0.25), residues: 1200
  helix:  1.51 (0.19), residues: 822
  sheet:  1.84 (0.64), residues: 66
  loop : -2.17 (0.32), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 101 
 TYR   0.016   0.001   TYR B  92 
 PHE   0.015   0.001   PHE E  30 
 TRP   0.030   0.001   TRP B  25 
 HIS   0.003   0.001   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10218)
  covalent geometry    : angle       0.67983 (13824)
  SS BOND              : bond        0.00253 (   18)
  SS BOND              : angle       3.89616 (   36)
  hydrogen bonds       : bond        0.03168 (  636)
  hydrogen bonds       : angle       3.51783 ( 1890)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 179
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.7526 (p90)
REVERT: A   47 ASP cc_start: 0.8730 (p0) cc_final: 0.8525 (p0)
REVERT: A   48 GLU cc_start: 0.9080 (tp30) cc_final: 0.8628 (tm-30)
REVERT: A   72 ILE cc_start: 0.9582 (pt) cc_final: 0.9357 (tt)
REVERT: A  100 MET cc_start: 0.9328 (ttp) cc_final: 0.9116 (ppp)
REVERT: A  101 ARG cc_start: 0.9395 (ttm170) cc_final: 0.9068 (ttp-110)
REVERT: A  205 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8554 (mm-30)
REVERT: A  213 MET cc_start: 0.9141 (mmm) cc_final: 0.8840 (mmp)
REVERT: A  227 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9059 (tm-30)
REVERT: B   17 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.7628 (p90)
REVERT: B   48 GLU cc_start: 0.9045 (tp30) cc_final: 0.8628 (tm-30)
REVERT: B  101 ARG cc_start: 0.9471 (ttm170) cc_final: 0.9020 (ttp-110)
REVERT: B  224 ASN cc_start: 0.9085 (m-40) cc_final: 0.8669 (m110)
REVERT: B  227 GLU cc_start: 0.9398 (tm-30) cc_final: 0.9010 (tm-30)
REVERT: C   17 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.7645 (p90)
REVERT: C   48 GLU cc_start: 0.8994 (tp30) cc_final: 0.8604 (tm-30)
REVERT: C  100 MET cc_start: 0.9354 (ttp) cc_final: 0.9105 (ppp)
REVERT: C  101 ARG cc_start: 0.9358 (ttm170) cc_final: 0.9029 (ttp-110)
REVERT: C  227 GLU cc_start: 0.9414 (tm-30) cc_final: 0.9175 (tm-30)
REVERT: D   17 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7195 (p90)
REVERT: D   47 ASP cc_start: 0.8733 (p0) cc_final: 0.8518 (p0)
REVERT: D   48 GLU cc_start: 0.9058 (tp30) cc_final: 0.8609 (tm-30)
REVERT: D  213 MET cc_start: 0.9217 (mmm) cc_final: 0.8954 (mmp)
REVERT: D  224 ASN cc_start: 0.8890 (m-40) cc_final: 0.8490 (m110)
REVERT: D  227 GLU cc_start: 0.9429 (tm-30) cc_final: 0.9120 (tm-30)
REVERT: E   17 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.7628 (p90)
REVERT: E   48 GLU cc_start: 0.9057 (tp30) cc_final: 0.8630 (tm-30)
REVERT: E  101 ARG cc_start: 0.9474 (ttm170) cc_final: 0.9011 (ttp-110)
REVERT: E  224 ASN cc_start: 0.9094 (m-40) cc_final: 0.8655 (m110)
REVERT: E  227 GLU cc_start: 0.9392 (tm-30) cc_final: 0.9001 (tm-30)
REVERT: F   17 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.7646 (p90)
REVERT: F  100 MET cc_start: 0.9353 (ttp) cc_final: 0.9103 (ppp)
REVERT: F  101 ARG cc_start: 0.9369 (ttm170) cc_final: 0.9026 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9402 (tm-30) cc_final: 0.9163 (tm-30)
  outliers start: 59
  outliers final: 34
  residues processed: 223
  average time/residue: 0.0687
  time to fit residues: 23.1844
Evaluate side-chains
  208 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 168
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   30 PHE
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   30 PHE
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   69 SER
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   30 PHE
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   69 SER
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain D residue  228 LEU
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   65 CYS
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   30 PHE
Chi-restraints excluded: chain F residue   65 CYS
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  171 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 95 optimal weight:   10.0000
   chunk 99 optimal weight:   10.0000
   chunk 75 optimal weight:    4.9990
   chunk 109 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
E  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.069505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.053858 restraints weight = 44244.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.055516 restraints weight = 22347.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.056618 restraints weight = 14635.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.057203 restraints weight = 11159.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.057747 restraints weight = 9626.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.3282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10236  Z= 0.189
  Angle     :  0.732   9.198  13860  Z= 0.379
  Chirality :  0.041   0.189   1572
  Planarity :  0.004   0.034   1662
  Dihedral  :  6.682  53.399   1336
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  6.65 %
    Allowed  : 24.50 %
    Favored  : 68.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  1.01 (0.25), residues: 1200
  helix:  1.55 (0.19), residues: 822
  sheet:  2.05 (0.66), residues: 66
  loop : -2.09 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 101 
 TYR   0.017   0.001   TYR B  92 
 PHE   0.020   0.001   PHE B  30 
 TRP   0.023   0.001   TRP B  25 
 HIS   0.002   0.001   HIS D 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (10218)
  covalent geometry    : angle       0.70337 (13824)
  SS BOND              : bond        0.00225 (   18)
  SS BOND              : angle       4.05340 (   36)
  hydrogen bonds       : bond        0.03409 (  636)
  hydrogen bonds       : angle       3.61145 ( 1890)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 168
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.7440 (p90)
REVERT: A   47 ASP cc_start: 0.8748 (p0) cc_final: 0.8530 (p0)
REVERT: A   48 GLU cc_start: 0.9080 (tp30) cc_final: 0.8641 (tm-30)
REVERT: A  101 ARG cc_start: 0.9361 (ttm170) cc_final: 0.9072 (ttp-110)
REVERT: A  213 MET cc_start: 0.9187 (mmm) cc_final: 0.8903 (mmp)
REVERT: A  227 GLU cc_start: 0.9424 (tm-30) cc_final: 0.9106 (tm-30)
REVERT: B   17 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.7565 (p90)
REVERT: B   48 GLU cc_start: 0.9012 (tp30) cc_final: 0.8668 (tm-30)
REVERT: B  101 ARG cc_start: 0.9458 (ttm170) cc_final: 0.9053 (ttp-110)
REVERT: B  224 ASN cc_start: 0.9111 (m-40) cc_final: 0.8671 (m110)
REVERT: B  227 GLU cc_start: 0.9379 (tm-30) cc_final: 0.8978 (tm-30)
REVERT: C   17 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.7664 (p90)
REVERT: C  100 MET cc_start: 0.9340 (ttp) cc_final: 0.9113 (ppp)
REVERT: C  101 ARG cc_start: 0.9337 (ttm170) cc_final: 0.9028 (ttp-110)
REVERT: C  227 GLU cc_start: 0.9395 (tm-30) cc_final: 0.9152 (tm-30)
REVERT: D   17 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.6992 (p90)
REVERT: D   47 ASP cc_start: 0.8751 (p0) cc_final: 0.8539 (p0)
REVERT: D   48 GLU cc_start: 0.9048 (tp30) cc_final: 0.8613 (tm-30)
REVERT: D  213 MET cc_start: 0.9259 (mmm) cc_final: 0.9006 (mmp)
REVERT: D  224 ASN cc_start: 0.8964 (m-40) cc_final: 0.8560 (m110)
REVERT: D  227 GLU cc_start: 0.9393 (tm-30) cc_final: 0.9106 (tm-30)
REVERT: E   17 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.7557 (p90)
REVERT: E   48 GLU cc_start: 0.9032 (tp30) cc_final: 0.8666 (tm-30)
REVERT: E  101 ARG cc_start: 0.9467 (ttm170) cc_final: 0.9062 (ttp-110)
REVERT: E  224 ASN cc_start: 0.9111 (m-40) cc_final: 0.8669 (m110)
REVERT: E  227 GLU cc_start: 0.9379 (tm-30) cc_final: 0.8983 (tm-30)
REVERT: F   17 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.7674 (p90)
REVERT: F  100 MET cc_start: 0.9338 (ttp) cc_final: 0.9113 (ppp)
REVERT: F  101 ARG cc_start: 0.9336 (ttm170) cc_final: 0.9022 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9401 (tm-30) cc_final: 0.9156 (tm-30)
  outliers start: 73
  outliers final: 41
  residues processed: 222
  average time/residue: 0.0708
  time to fit residues: 23.8358
Evaluate side-chains
  212 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 165
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   30 PHE
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   69 SER
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   30 PHE
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   69 SER
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   30 PHE
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   69 SER
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain D residue  228 LEU
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   65 CYS
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  171 LEU
Chi-restraints excluded: chain E residue  228 LEU
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   30 PHE
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  171 LEU
Chi-restraints excluded: chain F residue  218 LEU
Chi-restraints excluded: chain F residue  228 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 111 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 83 optimal weight:    0.0370
   overall best weight:    1.8064

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

Flipped N/Q/H residues before XYZ refinement:
E  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.070838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.055262 restraints weight = 43270.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.056911 restraints weight = 21437.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.058091 restraints weight = 14007.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.058695 restraints weight = 10522.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.059305 restraints weight = 9003.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.3510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10236  Z= 0.140
  Angle     :  0.734  10.160  13860  Z= 0.374
  Chirality :  0.041   0.180   1572
  Planarity :  0.004   0.035   1662
  Dihedral  :  6.430  51.763   1334
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 26.96 %
    Favored  : 68.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  1.13 (0.25), residues: 1200
  helix:  1.63 (0.19), residues: 822
  sheet:  2.24 (0.68), residues: 66
  loop : -2.06 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 101 
 TYR   0.018   0.001   TYR A  92 
 PHE   0.021   0.001   PHE B  30 
 TRP   0.018   0.001   TRP E  25 
 HIS   0.002   0.001   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (10218)
  covalent geometry    : angle       0.70917 (13824)
  SS BOND              : bond        0.00153 (   18)
  SS BOND              : angle       3.81343 (   36)
  hydrogen bonds       : bond        0.03260 (  636)
  hydrogen bonds       : angle       3.58226 ( 1890)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 174
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.7421 (p90)
REVERT: A   47 ASP cc_start: 0.8730 (p0) cc_final: 0.8490 (p0)
REVERT: A  101 ARG cc_start: 0.9545 (ttm170) cc_final: 0.9111 (ttp80)
REVERT: A  213 MET cc_start: 0.9150 (mmm) cc_final: 0.8859 (mmp)
REVERT: A  227 GLU cc_start: 0.9427 (tm-30) cc_final: 0.9083 (tm-30)
REVERT: B   17 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.7514 (p90)
REVERT: B   48 GLU cc_start: 0.9000 (tp30) cc_final: 0.8638 (tm-30)
REVERT: B  101 ARG cc_start: 0.9462 (ttm170) cc_final: 0.9050 (ttp-110)
REVERT: B  224 ASN cc_start: 0.9082 (m-40) cc_final: 0.8659 (m110)
REVERT: B  227 GLU cc_start: 0.9385 (tm-30) cc_final: 0.8980 (tm-30)
REVERT: C   17 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.7666 (p90)
REVERT: C  100 MET cc_start: 0.9349 (ttp) cc_final: 0.9130 (ppp)
REVERT: C  101 ARG cc_start: 0.9351 (ttm170) cc_final: 0.9023 (ttp-110)
REVERT: C  227 GLU cc_start: 0.9418 (tm-30) cc_final: 0.9173 (tm-30)
REVERT: D   17 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.6984 (p90)
REVERT: D   47 ASP cc_start: 0.8744 (p0) cc_final: 0.8505 (p0)
REVERT: D  213 MET cc_start: 0.9219 (mmm) cc_final: 0.8962 (mmp)
REVERT: D  227 GLU cc_start: 0.9407 (tm-30) cc_final: 0.9104 (tm-30)
REVERT: E   17 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.7504 (p90)
REVERT: E   48 GLU cc_start: 0.9018 (tp30) cc_final: 0.8647 (tm-30)
REVERT: E  101 ARG cc_start: 0.9468 (ttm170) cc_final: 0.9049 (ttp-110)
REVERT: E  224 ASN cc_start: 0.9089 (m-40) cc_final: 0.8661 (m110)
REVERT: E  227 GLU cc_start: 0.9383 (tm-30) cc_final: 0.8984 (tm-30)
REVERT: F   17 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.7681 (p90)
REVERT: F  100 MET cc_start: 0.9353 (ttp) cc_final: 0.9129 (ppp)
REVERT: F  101 ARG cc_start: 0.9354 (ttm170) cc_final: 0.9019 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9426 (tm-30) cc_final: 0.9176 (tm-30)
  outliers start: 50
  outliers final: 30
  residues processed: 208
  average time/residue: 0.0730
  time to fit residues: 22.8434
Evaluate side-chains
  203 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 167
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   30 PHE
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   30 PHE
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   30 PHE
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue   69 SER
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  171 LEU
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   30 PHE
Chi-restraints excluded: chain F residue   65 CYS
Chi-restraints excluded: chain F residue   67 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 57 optimal weight:    0.3980
   chunk 86 optimal weight:    0.7980
   chunk 82 optimal weight:    9.9990
   chunk 108 optimal weight:    0.0060
   chunk 24 optimal weight:    1.9990
   chunk 42 optimal weight:    8.9990
   chunk 39 optimal weight:    7.9990
   chunk 71 optimal weight:   10.0000
   chunk 98 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0770
   chunk 110 optimal weight:    0.9980
   overall best weight:    0.4554

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

Flipped N/Q/H residues before XYZ refinement:
D  74 HIS
D  81 GLN
E  81 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.072531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.056832 restraints weight = 42868.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.058631 restraints weight = 21574.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.059809 restraints weight = 13799.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.060337 restraints weight = 10327.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.060941 restraints weight = 8917.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10236  Z= 0.128
  Angle     :  0.742  10.094  13860  Z= 0.378
  Chirality :  0.041   0.187   1572
  Planarity :  0.004   0.034   1662
  Dihedral  :  6.359  52.164   1334
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 28.32 %
    Favored  : 67.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  1.25 (0.26), residues: 1200
  helix:  1.59 (0.19), residues: 816
  sheet:  2.44 (0.70), residues: 66
  loop : -1.60 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 153 
 TYR   0.017   0.001   TYR A  92 
 PHE   0.029   0.001   PHE E  30 
 TRP   0.031   0.001   TRP D  25 
 HIS   0.004   0.001   HIS D  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (10218)
  covalent geometry    : angle       0.71875 (13824)
  SS BOND              : bond        0.00246 (   18)
  SS BOND              : angle       3.65242 (   36)
  hydrogen bonds       : bond        0.03210 (  636)
  hydrogen bonds       : angle       3.63784 ( 1890)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 182
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.7310 (p90)
REVERT: A   47 ASP cc_start: 0.8710 (p0) cc_final: 0.8444 (p0)
REVERT: A  101 ARG cc_start: 0.9540 (ttm170) cc_final: 0.9087 (ptm-80)
REVERT: A  213 MET cc_start: 0.9138 (mmm) cc_final: 0.8842 (mmp)
REVERT: A  227 GLU cc_start: 0.9441 (tm-30) cc_final: 0.9089 (tm-30)
REVERT: B   17 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7427 (p90)
REVERT: B  101 ARG cc_start: 0.9458 (ttm170) cc_final: 0.9073 (ttp80)
REVERT: B  213 MET cc_start: 0.9143 (mmm) cc_final: 0.8942 (mmp)
REVERT: B  224 ASN cc_start: 0.9063 (m-40) cc_final: 0.8641 (m110)
REVERT: B  227 GLU cc_start: 0.9391 (tm-30) cc_final: 0.8971 (tm-30)
REVERT: C   17 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.7484 (p90)
REVERT: C   42 GLU cc_start: 0.8142 (pp20) cc_final: 0.7688 (pm20)
REVERT: C  100 MET cc_start: 0.9346 (ttp) cc_final: 0.9131 (ppp)
REVERT: C  101 ARG cc_start: 0.9342 (ttm170) cc_final: 0.9082 (ttp-110)
REVERT: C  227 GLU cc_start: 0.9418 (tm-30) cc_final: 0.9174 (tm-30)
REVERT: D   17 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.6931 (p90)
REVERT: D   47 ASP cc_start: 0.8724 (p0) cc_final: 0.8473 (p0)
REVERT: D   81 GLN cc_start: 0.9457 (tt0) cc_final: 0.9239 (tt0)
REVERT: D  213 MET cc_start: 0.9208 (mmm) cc_final: 0.8937 (mmp)
REVERT: D  227 GLU cc_start: 0.9415 (tm-30) cc_final: 0.9113 (tm-30)
REVERT: E   17 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7421 (p90)
REVERT: E  101 ARG cc_start: 0.9459 (ttm170) cc_final: 0.9071 (ttp80)
REVERT: E  213 MET cc_start: 0.9142 (mmm) cc_final: 0.8935 (mmp)
REVERT: E  224 ASN cc_start: 0.9069 (m-40) cc_final: 0.8642 (m110)
REVERT: E  227 GLU cc_start: 0.9384 (tm-30) cc_final: 0.8966 (tm-30)
REVERT: F   17 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.7493 (p90)
REVERT: F   42 GLU cc_start: 0.8125 (pp20) cc_final: 0.7690 (pm20)
REVERT: F  100 MET cc_start: 0.9350 (ttp) cc_final: 0.9131 (ppp)
REVERT: F  101 ARG cc_start: 0.9354 (ttm170) cc_final: 0.9076 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9169 (tm-30)
  outliers start: 42
  outliers final: 28
  residues processed: 214
  average time/residue: 0.0718
  time to fit residues: 23.3621
Evaluate side-chains
  201 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 167
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   30 PHE
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  192 CYS
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   65 CYS
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  171 LEU
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   65 CYS
Chi-restraints excluded: chain F residue   67 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0470
   chunk 66 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 105 optimal weight:    0.7980
   overall best weight:    0.7080

-------------------------------------------------------------------------------
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 = 0.3384 r_free = 0.3384 target = 0.073196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.057461 restraints weight = 42984.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.059249 restraints weight = 21357.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.060439 restraints weight = 13765.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.061070 restraints weight = 10338.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.061676 restraints weight = 8853.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.3990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10236  Z= 0.126
  Angle     :  0.779  12.207  13860  Z= 0.390
  Chirality :  0.040   0.183   1572
  Planarity :  0.004   0.034   1662
  Dihedral  :  6.263  52.183   1334
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 28.05 %
    Favored  : 68.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  1.19 (0.26), residues: 1200
  helix:  1.55 (0.19), residues: 816
  sheet:  2.45 (0.70), residues: 66
  loop : -1.61 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 148 
 TYR   0.016   0.001   TYR A  92 
 PHE   0.027   0.001   PHE E  30 
 TRP   0.063   0.001   TRP D  25 
 HIS   0.002   0.001   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (10218)
  covalent geometry    : angle       0.74318 (13824)
  SS BOND              : bond        0.00125 (   18)
  SS BOND              : angle       4.64916 (   36)
  hydrogen bonds       : bond        0.03187 (  636)
  hydrogen bonds       : angle       3.64241 ( 1890)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 177
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.7183 (p90)
REVERT: A   47 ASP cc_start: 0.8724 (p0) cc_final: 0.8481 (p0)
REVERT: A  101 ARG cc_start: 0.9526 (ttm170) cc_final: 0.9082 (ttp-110)
REVERT: A  213 MET cc_start: 0.9157 (mmm) cc_final: 0.8874 (mmp)
REVERT: A  227 GLU cc_start: 0.9443 (tm-30) cc_final: 0.9094 (tm-30)
REVERT: B   17 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7361 (p90)
REVERT: B  101 ARG cc_start: 0.9454 (ttm170) cc_final: 0.9078 (ttp80)
REVERT: B  224 ASN cc_start: 0.9069 (m-40) cc_final: 0.8640 (m110)
REVERT: B  227 GLU cc_start: 0.9383 (tm-30) cc_final: 0.8965 (tm-30)
REVERT: C   17 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.7364 (p90)
REVERT: C   42 GLU cc_start: 0.8163 (pp20) cc_final: 0.7721 (pm20)
REVERT: C  101 ARG cc_start: 0.9342 (ttm170) cc_final: 0.9083 (ttp-110)
REVERT: C  227 GLU cc_start: 0.9414 (tm-30) cc_final: 0.9165 (tm-30)
REVERT: D   17 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.6942 (p90)
REVERT: D   47 ASP cc_start: 0.8730 (p0) cc_final: 0.8484 (p0)
REVERT: D  213 MET cc_start: 0.9183 (mmm) cc_final: 0.8967 (mmp)
REVERT: D  227 GLU cc_start: 0.9413 (tm-30) cc_final: 0.9099 (tm-30)
REVERT: E   17 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.7260 (p90)
REVERT: E  101 ARG cc_start: 0.9456 (ttm170) cc_final: 0.9075 (ttp80)
REVERT: E  224 ASN cc_start: 0.9069 (m-40) cc_final: 0.8633 (m110)
REVERT: E  227 GLU cc_start: 0.9374 (tm-30) cc_final: 0.8953 (tm-30)
REVERT: F   17 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.7369 (p90)
REVERT: F  100 MET cc_start: 0.9339 (ttp) cc_final: 0.9137 (ppp)
REVERT: F  101 ARG cc_start: 0.9341 (ttm170) cc_final: 0.9077 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9407 (tm-30) cc_final: 0.9159 (tm-30)
  outliers start: 43
  outliers final: 28
  residues processed: 207
  average time/residue: 0.0722
  time to fit residues: 22.2119
Evaluate side-chains
  200 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 166
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  197 ASP
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  192 CYS
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain D residue  197 ASP
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   65 CYS
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  171 LEU
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   67 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 40 optimal weight:    8.9990
   chunk 103 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 27 optimal weight:    0.3980
   chunk 117 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 80 optimal weight:    8.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.6788

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

Flipped N/Q/H residues before XYZ refinement:
E  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.072090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.056285 restraints weight = 41851.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.058033 restraints weight = 20498.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.059234 restraints weight = 13307.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.060015 restraints weight = 10000.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.060428 restraints weight = 8400.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.4052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10236  Z= 0.142
  Angle     :  0.801  11.987  13860  Z= 0.404
  Chirality :  0.041   0.201   1572
  Planarity :  0.004   0.035   1662
  Dihedral  :  6.306  51.877   1334
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 28.51 %
    Favored  : 67.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  1.22 (0.26), residues: 1200
  helix:  1.55 (0.19), residues: 816
  sheet:  2.49 (0.68), residues: 66
  loop : -1.56 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 101 
 TYR   0.017   0.001   TYR A  92 
 PHE   0.028   0.001   PHE E  30 
 TRP   0.052   0.002   TRP B  25 
 HIS   0.002   0.001   HIS C  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (10218)
  covalent geometry    : angle       0.76201 (13824)
  SS BOND              : bond        0.00162 (   18)
  SS BOND              : angle       4.88365 (   36)
  hydrogen bonds       : bond        0.03243 (  636)
  hydrogen bonds       : angle       3.67343 ( 1890)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 173
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.7220 (p90)
REVERT: A   47 ASP cc_start: 0.8770 (p0) cc_final: 0.8515 (p0)
REVERT: A  101 ARG cc_start: 0.9538 (ttm170) cc_final: 0.9110 (ttp80)
REVERT: A  213 MET cc_start: 0.9171 (mmm) cc_final: 0.8904 (mmp)
REVERT: A  227 GLU cc_start: 0.9462 (tm-30) cc_final: 0.9140 (tm-30)
REVERT: B   17 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7354 (p90)
REVERT: B  101 ARG cc_start: 0.9477 (ttm170) cc_final: 0.9085 (ttp80)
REVERT: B  224 ASN cc_start: 0.9115 (m-40) cc_final: 0.8705 (m110)
REVERT: B  227 GLU cc_start: 0.9399 (tm-30) cc_final: 0.8996 (tm-30)
REVERT: C   17 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.7512 (p90)
REVERT: C   42 GLU cc_start: 0.8214 (pp20) cc_final: 0.7875 (pp20)
REVERT: C  227 GLU cc_start: 0.9437 (tm-30) cc_final: 0.9210 (tm-30)
REVERT: D   17 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.6948 (p90)
REVERT: D   47 ASP cc_start: 0.8810 (p0) cc_final: 0.8558 (p0)
REVERT: D  213 MET cc_start: 0.9193 (mmm) cc_final: 0.8964 (mmp)
REVERT: D  227 GLU cc_start: 0.9434 (tm-30) cc_final: 0.9121 (tm-30)
REVERT: E   17 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7335 (p90)
REVERT: E  101 ARG cc_start: 0.9487 (ttm170) cc_final: 0.9083 (ttp80)
REVERT: E  224 ASN cc_start: 0.9104 (m-40) cc_final: 0.8702 (m110)
REVERT: E  227 GLU cc_start: 0.9402 (tm-30) cc_final: 0.9000 (tm-30)
REVERT: F   17 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7421 (p90)
REVERT: F  100 MET cc_start: 0.9345 (ttp) cc_final: 0.9130 (ppp)
REVERT: F  101 ARG cc_start: 0.9362 (ttm170) cc_final: 0.9083 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9438 (tm-30) cc_final: 0.9212 (tm-30)
  outliers start: 41
  outliers final: 26
  residues processed: 201
  average time/residue: 0.0786
  time to fit residues: 23.3035
Evaluate side-chains
  199 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 167
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  197 ASP
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  166 GLU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  192 CYS
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain D residue  197 ASP
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   65 CYS
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   26 LEU
Chi-restraints excluded: chain F residue   67 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 62 optimal weight:    9.9990
   chunk 117 optimal weight:    5.9990
   chunk 105 optimal weight:    0.0170
   chunk 49 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 118 optimal weight:    4.9990
   chunk 68 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    1.1224

-------------------------------------------------------------------------------
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 = 0.3387 r_free = 0.3387 target = 0.073347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.057741 restraints weight = 41536.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.059557 restraints weight = 20764.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.060727 restraints weight = 13356.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.061545 restraints weight = 10061.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.061952 restraints weight = 8365.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10236  Z= 0.134
  Angle     :  0.791  12.413  13860  Z= 0.398
  Chirality :  0.040   0.170   1572
  Planarity :  0.004   0.036   1662
  Dihedral  :  5.953  50.523   1330
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 28.60 %
    Favored  : 68.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.93 (0.25), residues: 1200
  helix:  1.26 (0.18), residues: 852
  sheet:  2.51 (0.68), residues: 66
  loop : -1.82 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 101 
 TYR   0.017   0.001   TYR A  92 
 PHE   0.030   0.001   PHE E  30 
 TRP   0.060   0.001   TRP A  25 
 HIS   0.002   0.001   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (10218)
  covalent geometry    : angle       0.75640 (13824)
  SS BOND              : bond        0.00134 (   18)
  SS BOND              : angle       4.61709 (   36)
  hydrogen bonds       : bond        0.03221 (  636)
  hydrogen bonds       : angle       3.69233 ( 1890)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1314.64 seconds
wall clock time: 23 minutes 38.94 seconds (1418.94 seconds total)