Starting phenix.real_space_refine
on Sun Jul 27 15:05:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xqi_33397/07_2025/7xqi_33397.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xqi_33397/07_2025/7xqi_33397.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xqi_33397/07_2025/7xqi_33397.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xqi_33397/07_2025/7xqi_33397.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xqi_33397/07_2025/7xqi_33397.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xqi_33397/07_2025/7xqi_33397.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
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      48      5.16       5
     C    6396      2.51       5
     N    1518      2.21       5
     O    1620      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9582
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1597
          Classifications: {'peptide': 196}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 4.10, per 1000 atoms: 0.43
  Number of scatterers: 9582
  At special positions: 0
  Unit cell: (102.608, 106, 103.456, 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      48     16.00
     O    1620      8.00
     N    1518      7.00
     C    6396      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=2.03
    Simple disulfide: pdb=" SG  CYS C  54 " - pdb=" SG  CYS C 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  54 " - pdb=" SG  CYS B 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  54 " - pdb=" SG  CYS E 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  54 " - pdb=" SG  CYS D 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  54 " - pdb=" SG  CYS F 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  61 " - pdb=" SG  CYS C 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  61 " - pdb=" SG  CYS B 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  61 " - pdb=" SG  CYS E 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  61 " - pdb=" SG  CYS D 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  61 " - pdb=" SG  CYS F 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  65 " - pdb=" SG  CYS C 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  65 " - pdb=" SG  CYS B 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  65 " - pdb=" SG  CYS E 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  65 " - pdb=" SG  CYS D 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  65 " - pdb=" SG  CYS F 187 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.44
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2232

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 6 sheets defined
      74.6% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 15
    Processing helix  chain 'A' and resid 19 through 31
    Processing helix  chain 'A' and resid 33 through 40
      removed outlier: 3.524A  pdb=" N   GLY A  38 " --> pdb=" O   ILE A  34 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 45
      removed outlier: 3.703A  pdb=" N   ALA A  44 " --> pdb=" O   ALA A  40 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   TRP A  45 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 40 through 45'
    Processing helix  chain 'A' and resid 60 through 70
      removed outlier: 3.802A  pdb=" N   VAL A  64 " --> pdb=" O   GLY A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 85
    Processing helix  chain 'A' and resid 86 through 112
      removed outlier: 3.727A  pdb=" N   GLU A 112 " --> pdb=" O   LYS A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 177
    Processing helix  chain 'A' and resid 204 through 233
      removed outlier: 3.598A  pdb=" N   ILE A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE A 233 " --> pdb=" O   PHE A 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 15
    Processing helix  chain 'B' and resid 19 through 31
    Processing helix  chain 'B' and resid 33 through 40
      removed outlier: 3.524A  pdb=" N   GLY B  38 " --> pdb=" O   ILE B  34 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 45
      removed outlier: 3.703A  pdb=" N   ALA B  44 " --> pdb=" O   ALA B  40 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   TRP B  45 " --> pdb=" O   VAL B  41 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 40 through 45'
    Processing helix  chain 'B' and resid 60 through 70
      removed outlier: 3.803A  pdb=" N   VAL B  64 " --> pdb=" O   GLY B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 85
    Processing helix  chain 'B' and resid 86 through 112
      removed outlier: 3.728A  pdb=" N   GLU B 112 " --> pdb=" O   LYS B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 177
    Processing helix  chain 'B' and resid 204 through 233
      removed outlier: 3.598A  pdb=" N   ILE B 225 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   PHE B 233 " --> pdb=" O   PHE B 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 15
    Processing helix  chain 'C' and resid 19 through 31
    Processing helix  chain 'C' and resid 33 through 40
      removed outlier: 3.524A  pdb=" N   GLY C  38 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA C  40 " --> pdb=" O   LEU C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 45
      removed outlier: 3.703A  pdb=" N   ALA C  44 " --> pdb=" O   ALA C  40 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   TRP C  45 " --> pdb=" O   VAL C  41 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 40 through 45'
    Processing helix  chain 'C' and resid 60 through 70
      removed outlier: 3.802A  pdb=" N   VAL C  64 " --> pdb=" O   GLY C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 85
    Processing helix  chain 'C' and resid 86 through 112
      removed outlier: 3.726A  pdb=" N   GLU C 112 " --> pdb=" O   LYS C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 149 through 177
    Processing helix  chain 'C' and resid 204 through 233
      removed outlier: 3.598A  pdb=" N   ILE C 225 " --> pdb=" O   LEU C 221 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE C 233 " --> pdb=" O   PHE C 229 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 15
    Processing helix  chain 'D' and resid 19 through 31
    Processing helix  chain 'D' and resid 33 through 40
      removed outlier: 3.524A  pdb=" N   GLY D  38 " --> pdb=" O   ILE D  34 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA D  40 " --> pdb=" O   LEU D  36 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 45
      removed outlier: 3.704A  pdb=" N   ALA D  44 " --> pdb=" O   ALA D  40 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   TRP D  45 " --> pdb=" O   VAL D  41 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 40 through 45'
    Processing helix  chain 'D' and resid 60 through 70
      removed outlier: 3.803A  pdb=" N   VAL D  64 " --> pdb=" O   GLY D  60 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 85
    Processing helix  chain 'D' and resid 86 through 112
      removed outlier: 3.727A  pdb=" N   GLU D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 149 through 177
    Processing helix  chain 'D' and resid 204 through 233
      removed outlier: 3.598A  pdb=" N   ILE D 225 " --> pdb=" O   LEU D 221 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE D 233 " --> pdb=" O   PHE D 229 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 7 through 15
    Processing helix  chain 'E' and resid 19 through 31
    Processing helix  chain 'E' and resid 33 through 40
      removed outlier: 3.524A  pdb=" N   GLY E  38 " --> pdb=" O   ILE E  34 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA E  40 " --> pdb=" O   LEU E  36 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 40 through 45
      removed outlier: 3.703A  pdb=" N   ALA E  44 " --> pdb=" O   ALA E  40 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   TRP E  45 " --> pdb=" O   VAL E  41 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 40 through 45'
    Processing helix  chain 'E' and resid 60 through 70
      removed outlier: 3.803A  pdb=" N   VAL E  64 " --> pdb=" O   GLY E  60 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 73 through 85
    Processing helix  chain 'E' and resid 86 through 112
      removed outlier: 3.727A  pdb=" N   GLU E 112 " --> pdb=" O   LYS E 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 149 through 177
    Processing helix  chain 'E' and resid 204 through 233
      removed outlier: 3.597A  pdb=" N   ILE E 225 " --> pdb=" O   LEU E 221 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE E 233 " --> pdb=" O   PHE E 229 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 7 through 15
    Processing helix  chain 'F' and resid 19 through 31
    Processing helix  chain 'F' and resid 33 through 40
      removed outlier: 3.523A  pdb=" N   GLY F  38 " --> pdb=" O   ILE F  34 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA F  40 " --> pdb=" O   LEU F  36 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 40 through 45
      removed outlier: 3.704A  pdb=" N   ALA F  44 " --> pdb=" O   ALA F  40 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   TRP F  45 " --> pdb=" O   VAL F  41 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 40 through 45'
    Processing helix  chain 'F' and resid 60 through 70
      removed outlier: 3.803A  pdb=" N   VAL F  64 " --> pdb=" O   GLY F  60 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 73 through 85
    Processing helix  chain 'F' and resid 86 through 112
      removed outlier: 3.727A  pdb=" N   GLU F 112 " --> pdb=" O   LYS F 108 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 149 through 177
    Processing helix  chain 'F' and resid 204 through 233
      removed outlier: 3.597A  pdb=" N   ILE F 225 " --> pdb=" O   LEU F 221 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE F 233 " --> pdb=" O   PHE F 229 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54
      removed outlier: 3.516A  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: 3.515A  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: 3.515A  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: 3.515A  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: 3.516A  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: 3.515A  pdb=" N   ARG F  53 " --> pdb=" O   PHE F 199 " (cutoff:3.500A)

    643 hydrogen bonds defined for protein.
    1911 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: 2.40

  Time building geometry restraints manager: 2.91 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: 2826
        1.34 -     1.46: 2233
        1.46 -     1.58: 4703
        1.58 -     1.69: 6
        1.69 -     1.81: 60
  Bond restraints: 9828
  Sorted by residual:
  bond pdb=" CA  TYR E  17 "
       pdb=" CB  TYR E  17 "
    ideal  model  delta    sigma   weight residual
    1.531  1.599 -0.069 3.12e-02 1.03e+03 4.85e+00
  bond pdb=" CA  TYR F  17 "
       pdb=" CB  TYR F  17 "
    ideal  model  delta    sigma   weight residual
    1.531  1.599 -0.069 3.12e-02 1.03e+03 4.83e+00
  bond pdb=" CA  TYR B  17 "
       pdb=" CB  TYR B  17 "
    ideal  model  delta    sigma   weight residual
    1.531  1.599 -0.068 3.12e-02 1.03e+03 4.76e+00
  bond pdb=" CA  TYR A  17 "
       pdb=" CB  TYR A  17 "
    ideal  model  delta    sigma   weight residual
    1.531  1.599 -0.068 3.12e-02 1.03e+03 4.75e+00
  bond pdb=" CA  TYR C  17 "
       pdb=" CB  TYR C  17 "
    ideal  model  delta    sigma   weight residual
    1.531  1.598 -0.068 3.12e-02 1.03e+03 4.72e+00
  ... (remaining 9823 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 12951
        1.77 -     3.54: 303
        3.54 -     5.31: 24
        5.31 -     7.08: 18
        7.08 -     8.85: 12
  Bond angle restraints: 13308
  Sorted by residual:
  angle pdb=" C   PRO E 193 "
        pdb=" N   HIS E 194 "
        pdb=" CA  HIS E 194 "
      ideal   model   delta    sigma   weight residual
     121.19  127.65   -6.46 1.59e+00 3.96e-01 1.65e+01
  angle pdb=" C   PRO F 193 "
        pdb=" N   HIS F 194 "
        pdb=" CA  HIS F 194 "
      ideal   model   delta    sigma   weight residual
     121.19  127.65   -6.46 1.59e+00 3.96e-01 1.65e+01
  angle pdb=" C   PRO D 193 "
        pdb=" N   HIS D 194 "
        pdb=" CA  HIS D 194 "
      ideal   model   delta    sigma   weight residual
     121.19  127.63   -6.44 1.59e+00 3.96e-01 1.64e+01
  angle pdb=" C   PRO A 193 "
        pdb=" N   HIS A 194 "
        pdb=" CA  HIS A 194 "
      ideal   model   delta    sigma   weight residual
     121.19  127.63   -6.44 1.59e+00 3.96e-01 1.64e+01
  angle pdb=" C   PRO C 193 "
        pdb=" N   HIS C 194 "
        pdb=" CA  HIS C 194 "
      ideal   model   delta    sigma   weight residual
     121.19  127.63   -6.44 1.59e+00 3.96e-01 1.64e+01
  ... (remaining 13303 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.30: 5088
       14.30 -    28.60: 450
       28.60 -    42.89: 168
       42.89 -    57.19: 42
       57.19 -    71.49: 36
  Dihedral angle restraints: 5784
    sinusoidal: 2334
      harmonic: 3450
  Sorted by residual:
  dihedral pdb=" CA  PRO C 193 "
           pdb=" C   PRO C 193 "
           pdb=" N   HIS C 194 "
           pdb=" CA  HIS C 194 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.08  -19.92     0      5.00e+00 4.00e-02 1.59e+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 -160.10  -19.90     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CA  PRO E 193 "
           pdb=" C   PRO E 193 "
           pdb=" N   HIS E 194 "
           pdb=" CA  HIS E 194 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.11  -19.89     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 5781 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 793
       0.028 -    0.056: 469
       0.056 -    0.084: 182
       0.084 -    0.113: 46
       0.113 -    0.141: 34
  Chirality restraints: 1524
  Sorted by residual:
  chirality pdb=" CA  ARG C 202 "
            pdb=" N   ARG C 202 "
            pdb=" C   ARG C 202 "
            pdb=" CB  ARG C 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.95e-01
  chirality pdb=" CA  ARG F 202 "
            pdb=" N   ARG F 202 "
            pdb=" C   ARG F 202 "
            pdb=" CB  ARG F 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.80e-01
  chirality pdb=" CA  VAL B  14 "
            pdb=" N   VAL B  14 "
            pdb=" C   VAL B  14 "
            pdb=" CB  VAL B  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.30    0.14 2.00e-01 2.50e+01 4.79e-01
  ... (remaining 1521 not shown)

  Planarity restraints: 1608
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 167 "   -0.008 2.00e-02 2.50e+03   1.62e-02 2.63e+00
        pdb=" C   VAL C 167 "    0.028 2.00e-02 2.50e+03
        pdb=" O   VAL C 167 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ALA C 168 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 167 "   -0.008 2.00e-02 2.50e+03   1.61e-02 2.61e+00
        pdb=" C   VAL D 167 "    0.028 2.00e-02 2.50e+03
        pdb=" O   VAL D 167 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ALA D 168 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 167 "    0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   VAL A 167 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   VAL A 167 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ALA A 168 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1605 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2913
        2.82 -     3.34: 8342
        3.34 -     3.86: 15540
        3.86 -     4.38: 14891
        4.38 -     4.90: 27616
  Nonbonded interactions: 69302
  Sorted by model distance:
  nonbonded pdb=" O   ILE C  72 "
            pdb=" OH  TYR C 177 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   ILE B  72 "
            pdb=" OH  TYR B 177 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   ILE E  72 "
            pdb=" OH  TYR E 177 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   ILE A  72 "
            pdb=" OH  TYR A 177 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   ILE F  72 "
            pdb=" OH  TYR F 177 "
     model   vdw
     2.305 3.040
  ... (remaining 69297 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  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:             0.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     22.730
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   9846  Z= 0.252
  Angle     :  0.717   8.849  13344  Z= 0.421
  Chirality :  0.043   0.141   1524
  Planarity :  0.005   0.028   1608
  Dihedral  : 14.155  71.487   3498
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  :  7.39 %
    Favored  : 90.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.21), residues: 1152
  helix: -1.10 (0.15), residues: 828
  sheet: -0.68 (0.55), residues: 102
  loop : -2.78 (0.36), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  25 
 HIS   0.001   0.000   HIS F  95 
 PHE   0.011   0.001   PHE C  52 
 TYR   0.016   0.002   TYR C  17 
 ARG   0.002   0.000   ARG D 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12801 (  643)
  hydrogen bonds       : angle       3.99091 ( 1911)
  SS BOND              : bond        0.00239 (   18)
  SS BOND              : angle       0.98010 (   36)
  covalent geometry    : bond        0.00558 ( 9828)
  covalent geometry    : angle       0.71606 (13308)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 186
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 GLU cc_start: 0.9242 (mm-30) cc_final: 0.9025 (mm-30)
REVERT: B  100 MET cc_start: 0.8049 (tmm) cc_final: 0.7741 (tmm)
REVERT: B  166 GLU cc_start: 0.9288 (mm-30) cc_final: 0.9033 (mm-30)
REVERT: B  231 VAL cc_start: 0.8127 (p) cc_final: 0.7762 (p)
REVERT: C  166 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8978 (mm-30)
REVERT: C  213 MET cc_start: 0.9159 (mmm) cc_final: 0.8923 (mmm)
REVERT: F  166 GLU cc_start: 0.9241 (mm-30) cc_final: 0.9030 (mm-30)
  outliers start: 24
  outliers final: 7
  residues processed: 204
  average time/residue: 0.2498
  time to fit residues: 69.6839
Evaluate side-chains
  104 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   98 TYR
Chi-restraints excluded: chain C residue   98 TYR
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain E residue   98 TYR
Chi-restraints excluded: chain F residue   98 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.4980
   chunk 86 optimal weight:   50.0000
   chunk 47 optimal weight:    6.9990
   chunk 29 optimal weight:   50.0000
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 89 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3727 r_free = 0.3727 target = 0.102049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.073009 restraints weight = 24547.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.075589 restraints weight = 11063.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.077044 restraints weight = 7183.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9846  Z= 0.119
  Angle     :  0.574   5.737  13344  Z= 0.298
  Chirality :  0.038   0.176   1524
  Planarity :  0.003   0.024   1608
  Dihedral  :  5.077  40.432   1280
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 11.84 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.25), residues: 1152
  helix:  1.30 (0.18), residues: 828
  sheet:  3.00 (0.59), residues: 60
  loop : -2.97 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  25 
 HIS   0.001   0.000   HIS C 194 
 PHE   0.006   0.001   PHE E  52 
 TYR   0.010   0.001   TYR A 177 
 ARG   0.002   0.000   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03792 (  643)
  hydrogen bonds       : angle       2.88607 ( 1911)
  SS BOND              : bond        0.00279 (   18)
  SS BOND              : angle       2.38700 (   36)
  covalent geometry    : bond        0.00274 ( 9828)
  covalent geometry    : angle       0.56141 (13308)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 177
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.8272 (tmm) cc_final: 0.7913 (tmm)
REVERT: A  148 ARG cc_start: 0.4047 (mtt-85) cc_final: 0.2938 (tpt170)
REVERT: A  227 GLU cc_start: 0.8724 (tp30) cc_final: 0.8249 (tm-30)
REVERT: B   47 ASP cc_start: 0.8267 (p0) cc_final: 0.8066 (p0)
REVERT: B  148 ARG cc_start: 0.4569 (mtt-85) cc_final: 0.3205 (tpt170)
REVERT: C   47 ASP cc_start: 0.8223 (p0) cc_final: 0.8006 (p0)
REVERT: C  148 ARG cc_start: 0.4603 (mtt-85) cc_final: 0.3519 (tpt170)
REVERT: C  166 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8641 (tp30)
REVERT: C  213 MET cc_start: 0.9133 (mmm) cc_final: 0.8870 (mmm)
REVERT: C  227 GLU cc_start: 0.8760 (tp30) cc_final: 0.8425 (tm-30)
REVERT: D  166 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8681 (tp30)
REVERT: D  227 GLU cc_start: 0.8855 (tp30) cc_final: 0.8368 (tm-30)
REVERT: E   47 ASP cc_start: 0.8389 (p0) cc_final: 0.8163 (p0)
REVERT: E  148 ARG cc_start: 0.4371 (mtt-85) cc_final: 0.3158 (tpt170)
REVERT: E  227 GLU cc_start: 0.8699 (tp30) cc_final: 0.8313 (tm-30)
REVERT: F  148 ARG cc_start: 0.4643 (mtt-85) cc_final: 0.3470 (tpt170)
  outliers start: 30
  outliers final: 20
  residues processed: 203
  average time/residue: 0.1981
  time to fit residues: 56.9189
Evaluate side-chains
  147 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  233 PHE
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   98 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  233 PHE
Chi-restraints excluded: chain C residue   98 TYR
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  233 PHE
Chi-restraints excluded: chain E residue   98 TYR
Chi-restraints excluded: chain E residue  226 ILE
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain E residue  233 PHE
Chi-restraints excluded: chain F residue   98 TYR
Chi-restraints excluded: chain F residue  231 VAL
Chi-restraints excluded: chain F residue  233 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 71 optimal weight:    7.9990
   chunk 66 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 48 optimal weight:   50.0000
   chunk 54 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9980
   chunk 56 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  55 ASN
B  55 ASN
C  55 ASN
D  55 ASN
E  55 ASN
F  55 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.097597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.068673 restraints weight = 25427.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.071090 restraints weight = 11781.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.072488 restraints weight = 7755.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   9846  Z= 0.265
  Angle     :  0.703   9.057  13344  Z= 0.368
  Chirality :  0.043   0.226   1524
  Planarity :  0.004   0.027   1608
  Dihedral  :  5.522  43.456   1280
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 15.25 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.26), residues: 1152
  helix:  1.92 (0.19), residues: 840
  sheet:  2.89 (0.60), residues: 60
  loop : -2.57 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  25 
 HIS   0.001   0.000   HIS A  74 
 PHE   0.011   0.001   PHE E 209 
 TYR   0.014   0.001   TYR A 177 
 ARG   0.003   0.000   ARG C 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05354 (  643)
  hydrogen bonds       : angle       3.23065 ( 1911)
  SS BOND              : bond        0.00716 (   18)
  SS BOND              : angle       2.61469 (   36)
  covalent geometry    : bond        0.00620 ( 9828)
  covalent geometry    : angle       0.69031 (13308)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 138
  time to evaluate  : 1.073 
Fit side-chains
REVERT: A  227 GLU cc_start: 0.8736 (tp30) cc_final: 0.8224 (tm-30)
REVERT: B   31 ILE cc_start: 0.9372 (tp) cc_final: 0.9143 (tt)
REVERT: B  100 MET cc_start: 0.8352 (tmm) cc_final: 0.8106 (tmm)
REVERT: B  101 ARG cc_start: 0.8584 (tpp-160) cc_final: 0.8176 (tpp-160)
REVERT: C  213 MET cc_start: 0.9155 (mmm) cc_final: 0.8932 (mmm)
REVERT: D   31 ILE cc_start: 0.9399 (tp) cc_final: 0.9181 (tt)
REVERT: D   47 ASP cc_start: 0.8313 (p0) cc_final: 0.8112 (p0)
REVERT: D  227 GLU cc_start: 0.8841 (tp30) cc_final: 0.8397 (tm-30)
REVERT: F  100 MET cc_start: 0.8293 (tmm) cc_final: 0.7988 (tmm)
REVERT: F  148 ARG cc_start: 0.4571 (mtt-85) cc_final: 0.3404 (tpt170)
  outliers start: 53
  outliers final: 37
  residues processed: 182
  average time/residue: 0.2419
  time to fit residues: 65.1607
Evaluate side-chains
  159 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 122
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASN
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   55 ASN
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue   98 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue   55 ASN
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain C residue   98 TYR
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   55 ASN
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  226 ILE
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  233 PHE
Chi-restraints excluded: chain E residue   32 PHE
Chi-restraints excluded: chain E residue   55 ASN
Chi-restraints excluded: chain E residue   89 THR
Chi-restraints excluded: chain E residue   98 TYR
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  226 ILE
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain F residue   55 ASN
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain F residue   89 THR
Chi-restraints excluded: chain F residue   98 TYR
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  226 ILE
Chi-restraints excluded: chain F residue  231 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 108 optimal weight:    2.9990
   chunk 86 optimal weight:   50.0000
   chunk 48 optimal weight:   50.0000
   chunk 65 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9980
   chunk 95 optimal weight:    0.0030
   chunk 30 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    2.1996

-------------------------------------------------------------------------------
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 = 0.3685 r_free = 0.3685 target = 0.098947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.070327 restraints weight = 24956.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.072801 restraints weight = 11299.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.074235 restraints weight = 7378.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9846  Z= 0.165
  Angle     :  0.625   9.790  13344  Z= 0.327
  Chirality :  0.039   0.201   1524
  Planarity :  0.003   0.024   1608
  Dihedral  :  5.259  42.069   1280
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 17.14 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.26), residues: 1152
  helix:  2.22 (0.19), residues: 840
  sheet:  2.79 (0.62), residues: 60
  loop : -2.42 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  25 
 HIS   0.001   0.000   HIS E  74 
 PHE   0.018   0.001   PHE A 229 
 TYR   0.008   0.001   TYR A 177 
 ARG   0.004   0.000   ARG D 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04273 (  643)
  hydrogen bonds       : angle       3.04343 ( 1911)
  SS BOND              : bond        0.00744 (   18)
  SS BOND              : angle       2.19447 (   36)
  covalent geometry    : bond        0.00390 ( 9828)
  covalent geometry    : angle       0.61509 (13308)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 159
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.8319 (tmm) cc_final: 0.7970 (tmm)
REVERT: A  148 ARG cc_start: 0.4204 (mtt-85) cc_final: 0.2965 (tpt170)
REVERT: B   31 ILE cc_start: 0.9385 (tp) cc_final: 0.9147 (tt)
REVERT: B  100 MET cc_start: 0.8388 (tmm) cc_final: 0.8038 (tmm)
REVERT: C  148 ARG cc_start: 0.4588 (mtt-85) cc_final: 0.3451 (tpt170)
REVERT: E  148 ARG cc_start: 0.4283 (mtt-85) cc_final: 0.3143 (tpt170)
REVERT: F  148 ARG cc_start: 0.4521 (mtt-85) cc_final: 0.3443 (tpt170)
  outliers start: 42
  outliers final: 35
  residues processed: 189
  average time/residue: 0.1832
  time to fit residues: 50.4848
Evaluate side-chains
  171 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 136
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  233 PHE
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue   98 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  233 PHE
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain C residue   98 TYR
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  226 ILE
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  233 PHE
Chi-restraints excluded: chain E residue   15 GLN
Chi-restraints excluded: chain E residue   32 PHE
Chi-restraints excluded: chain E residue   89 THR
Chi-restraints excluded: chain E residue   98 TYR
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  226 ILE
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain E residue  233 PHE
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain F residue   89 THR
Chi-restraints excluded: chain F residue   98 TYR
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  226 ILE
Chi-restraints excluded: chain F residue  231 VAL
Chi-restraints excluded: chain F residue  233 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 97 optimal weight:    5.9990
   chunk 96 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   chunk 19 optimal weight:   30.0000
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 111 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   chunk 84 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 = 0.3594 r_free = 0.3594 target = 0.097185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.068848 restraints weight = 25265.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.071084 restraints weight = 12453.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.072414 restraints weight = 8394.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   9846  Z= 0.202
  Angle     :  0.646   7.090  13344  Z= 0.340
  Chirality :  0.040   0.140   1524
  Planarity :  0.004   0.027   1608
  Dihedral  :  5.144  42.941   1278
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 19.89 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.26), residues: 1152
  helix:  2.22 (0.19), residues: 834
  sheet:  2.63 (0.62), residues: 60
  loop : -2.29 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  25 
 HIS   0.003   0.000   HIS C  74 
 PHE   0.021   0.001   PHE F 229 
 TYR   0.010   0.001   TYR C 177 
 ARG   0.002   0.000   ARG D 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04634 (  643)
  hydrogen bonds       : angle       3.08605 ( 1911)
  SS BOND              : bond        0.00681 (   18)
  SS BOND              : angle       1.54194 (   36)
  covalent geometry    : bond        0.00470 ( 9828)
  covalent geometry    : angle       0.64168 (13308)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 145
  time to evaluate  : 1.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 PHE cc_start: 0.8838 (m-80) cc_final: 0.8635 (m-10)
REVERT: A  148 ARG cc_start: 0.4223 (mtt-85) cc_final: 0.3063 (tpt170)
REVERT: B   31 ILE cc_start: 0.9384 (tp) cc_final: 0.9149 (tt)
REVERT: B  100 MET cc_start: 0.8394 (tmm) cc_final: 0.8005 (tmm)
REVERT: C  148 ARG cc_start: 0.4516 (mtt-85) cc_final: 0.3523 (tpt170)
REVERT: E  148 ARG cc_start: 0.4421 (mtt-85) cc_final: 0.3227 (tpt170)
REVERT: F   84 PHE cc_start: 0.8817 (m-80) cc_final: 0.8617 (m-10)
REVERT: F  148 ARG cc_start: 0.4522 (mtt-85) cc_final: 0.3507 (tpt170)
  outliers start: 33
  outliers final: 28
  residues processed: 173
  average time/residue: 0.2244
  time to fit residues: 56.4588
Evaluate side-chains
  169 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 141
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue   98 TYR
Chi-restraints excluded: chain B residue  233 PHE
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain C residue   98 TYR
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain E residue   15 GLN
Chi-restraints excluded: chain E residue   32 PHE
Chi-restraints excluded: chain E residue   89 THR
Chi-restraints excluded: chain E residue   98 TYR
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  226 ILE
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain F residue   89 THR
Chi-restraints excluded: chain F residue   98 TYR
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  226 ILE
Chi-restraints excluded: chain F residue  231 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 98 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 101 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 103 optimal weight:   10.0000
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 = 0.3605 r_free = 0.3605 target = 0.097956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.069561 restraints weight = 25317.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.071795 restraints weight = 12367.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.073193 restraints weight = 8307.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9846  Z= 0.171
  Angle     :  0.623   6.436  13344  Z= 0.327
  Chirality :  0.039   0.136   1524
  Planarity :  0.004   0.026   1608
  Dihedral  :  5.061  42.481   1278
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 20.45 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.26), residues: 1152
  helix:  2.32 (0.19), residues: 834
  sheet:  2.55 (0.62), residues: 60
  loop : -2.06 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  25 
 HIS   0.003   0.000   HIS F  74 
 PHE   0.016   0.001   PHE F 229 
 TYR   0.013   0.001   TYR A 177 
 ARG   0.004   0.000   ARG E 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04235 (  643)
  hydrogen bonds       : angle       2.99628 ( 1911)
  SS BOND              : bond        0.00556 (   18)
  SS BOND              : angle       1.37359 (   36)
  covalent geometry    : bond        0.00396 ( 9828)
  covalent geometry    : angle       0.61967 (13308)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 143
  time to evaluate  : 2.321 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 PHE cc_start: 0.8810 (m-80) cc_final: 0.8578 (m-10)
REVERT: A  100 MET cc_start: 0.8384 (tmm) cc_final: 0.8119 (tmm)
REVERT: A  148 ARG cc_start: 0.4210 (mtt-85) cc_final: 0.3099 (tpt170)
REVERT: B   31 ILE cc_start: 0.9377 (tp) cc_final: 0.9153 (tt)
REVERT: B   82 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9115 (tt)
REVERT: B  100 MET cc_start: 0.8429 (tmm) cc_final: 0.8004 (tmm)
REVERT: B  148 ARG cc_start: 0.4481 (mtt-85) cc_final: 0.3193 (tpt170)
REVERT: C   82 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9120 (tt)
REVERT: C  148 ARG cc_start: 0.4504 (mtt-85) cc_final: 0.3490 (tpt170)
REVERT: D  148 ARG cc_start: 0.3795 (mtt-85) cc_final: 0.2896 (tpt170)
REVERT: E   82 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9077 (tt)
REVERT: E  148 ARG cc_start: 0.4424 (mtt-85) cc_final: 0.3239 (tpt170)
REVERT: F  148 ARG cc_start: 0.4521 (mtt-85) cc_final: 0.3518 (tpt170)
  outliers start: 38
  outliers final: 33
  residues processed: 175
  average time/residue: 0.3440
  time to fit residues: 89.2684
Evaluate side-chains
  179 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 143
  time to evaluate  : 2.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  233 PHE
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   82 ILE
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue   98 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  233 PHE
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain C residue   98 TYR
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  233 PHE
Chi-restraints excluded: chain E residue   15 GLN
Chi-restraints excluded: chain E residue   32 PHE
Chi-restraints excluded: chain E residue   82 ILE
Chi-restraints excluded: chain E residue   89 THR
Chi-restraints excluded: chain E residue   98 TYR
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  226 ILE
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain E residue  233 PHE
Chi-restraints excluded: chain F residue   89 THR
Chi-restraints excluded: chain F residue   98 TYR
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  226 ILE
Chi-restraints excluded: chain F residue  231 VAL
Chi-restraints excluded: chain F residue  233 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 95 optimal weight:   30.0000
   chunk 100 optimal weight:    0.0470
   chunk 85 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 15 optimal weight:    0.0980
   chunk 70 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 99 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.6080

-------------------------------------------------------------------------------
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 = 0.3734 r_free = 0.3734 target = 0.101850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.073123 restraints weight = 24635.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.075534 restraints weight = 11061.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.076947 restraints weight = 7234.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.3291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9846  Z= 0.112
  Angle     :  0.585   8.083  13344  Z= 0.306
  Chirality :  0.036   0.124   1524
  Planarity :  0.003   0.028   1608
  Dihedral  :  4.720  39.503   1278
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 22.25 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.33 (0.26), residues: 1152
  helix:  2.47 (0.18), residues: 834
  sheet:  2.42 (0.60), residues: 60
  loop : -2.02 (0.35), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B  25 
 HIS   0.003   0.001   HIS C  74 
 PHE   0.015   0.001   PHE F 229 
 TYR   0.014   0.001   TYR D 177 
 ARG   0.003   0.000   ARG E 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02968 (  643)
  hydrogen bonds       : angle       2.76275 ( 1911)
  SS BOND              : bond        0.00496 (   18)
  SS BOND              : angle       1.25828 (   36)
  covalent geometry    : bond        0.00249 ( 9828)
  covalent geometry    : angle       0.58192 (13308)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 1.181 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.8381 (tmm) cc_final: 0.8128 (tmm)
REVERT: A  148 ARG cc_start: 0.4106 (mtt-85) cc_final: 0.3122 (tpt170)
REVERT: A  197 ASP cc_start: 0.8172 (m-30) cc_final: 0.7565 (p0)
REVERT: B   31 ILE cc_start: 0.9386 (tp) cc_final: 0.9135 (tt)
REVERT: B  100 MET cc_start: 0.8398 (tmm) cc_final: 0.7983 (tmm)
REVERT: B  148 ARG cc_start: 0.4307 (mtt-85) cc_final: 0.3233 (tpt170)
REVERT: C  148 ARG cc_start: 0.4390 (mtt-85) cc_final: 0.3469 (tpt170)
REVERT: D  148 ARG cc_start: 0.4156 (mtt-85) cc_final: 0.3182 (tpt170)
REVERT: E  148 ARG cc_start: 0.4378 (mtt-85) cc_final: 0.3233 (tpt170)
REVERT: F  148 ARG cc_start: 0.4459 (mtt-85) cc_final: 0.3460 (tpt170)
  outliers start: 22
  outliers final: 15
  residues processed: 164
  average time/residue: 0.1952
  time to fit residues: 46.1094
Evaluate side-chains
  154 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  233 PHE
Chi-restraints excluded: chain B residue   98 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  233 PHE
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  233 PHE
Chi-restraints excluded: chain E residue   15 GLN
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain E residue  233 PHE
Chi-restraints excluded: chain F residue  231 VAL
Chi-restraints excluded: chain F residue  233 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 79 optimal weight:    7.9990
   chunk 97 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 59 optimal weight:    7.9990
   chunk 105 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.098260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.069271 restraints weight = 25562.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.071637 restraints weight = 11403.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.073075 restraints weight = 7450.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9846  Z= 0.190
  Angle     :  0.641   8.251  13344  Z= 0.336
  Chirality :  0.039   0.135   1524
  Planarity :  0.004   0.028   1608
  Dihedral  :  4.420  41.665   1270
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 20.83 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.26), residues: 1152
  helix:  2.58 (0.18), residues: 828
  sheet:  2.41 (0.63), residues: 60
  loop : -1.97 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  25 
 HIS   0.001   0.000   HIS B  74 
 PHE   0.014   0.001   PHE F 229 
 TYR   0.014   0.001   TYR D 177 
 ARG   0.003   0.000   ARG C 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04374 (  643)
  hydrogen bonds       : angle       2.92865 ( 1911)
  SS BOND              : bond        0.00627 (   18)
  SS BOND              : angle       1.48291 (   36)
  covalent geometry    : bond        0.00441 ( 9828)
  covalent geometry    : angle       0.63750 (13308)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 134
  time to evaluate  : 1.021 
Fit side-chains
REVERT: A   84 PHE cc_start: 0.8833 (m-80) cc_final: 0.8590 (m-10)
REVERT: A  100 MET cc_start: 0.8400 (tmm) cc_final: 0.8113 (tmm)
REVERT: A  148 ARG cc_start: 0.4078 (mtt-85) cc_final: 0.3083 (tpt170)
REVERT: B   31 ILE cc_start: 0.9385 (tp) cc_final: 0.9160 (tt)
REVERT: B  100 MET cc_start: 0.8383 (tmm) cc_final: 0.7887 (tmm)
REVERT: B  148 ARG cc_start: 0.4319 (mtt-85) cc_final: 0.3145 (tpt170)
REVERT: B  166 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8845 (mm-30)
REVERT: C   82 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9066 (tt)
REVERT: C  148 ARG cc_start: 0.4348 (mtt-85) cc_final: 0.3415 (tpt170)
REVERT: D  148 ARG cc_start: 0.3820 (mtt-85) cc_final: 0.2946 (tpt170)
REVERT: E   82 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.9023 (tt)
REVERT: E  148 ARG cc_start: 0.4562 (mtt-85) cc_final: 0.3260 (tpt170)
REVERT: E  166 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8867 (mm-30)
REVERT: F   84 PHE cc_start: 0.8900 (m-80) cc_final: 0.8671 (m-10)
REVERT: F  148 ARG cc_start: 0.4449 (mtt-85) cc_final: 0.3478 (tpt170)
  outliers start: 35
  outliers final: 30
  residues processed: 166
  average time/residue: 0.1941
  time to fit residues: 46.0662
Evaluate side-chains
  160 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   82 ILE
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue   98 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  233 PHE
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   98 TYR
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  233 PHE
Chi-restraints excluded: chain E residue   15 GLN
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue   82 ILE
Chi-restraints excluded: chain E residue   89 THR
Chi-restraints excluded: chain E residue   98 TYR
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain E residue  233 PHE
Chi-restraints excluded: chain F residue   82 ILE
Chi-restraints excluded: chain F residue   89 THR
Chi-restraints excluded: chain F residue   98 TYR
Chi-restraints excluded: chain F residue  226 ILE
Chi-restraints excluded: chain F residue  231 VAL
Chi-restraints excluded: chain F residue  233 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 77 optimal weight:    9.9990
   chunk 108 optimal weight:    3.9990
   chunk 72 optimal weight:    8.9990
   chunk 6 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 57 optimal weight:   40.0000
   chunk 40 optimal weight:    6.9990
   chunk 29 optimal weight:   50.0000
   overall best weight:    2.7388

-------------------------------------------------------------------------------
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 = 0.3608 r_free = 0.3608 target = 0.097861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.069590 restraints weight = 25456.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.071870 restraints weight = 12194.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.073252 restraints weight = 8087.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.3249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9846  Z= 0.191
  Angle     :  0.661   7.892  13344  Z= 0.344
  Chirality :  0.039   0.133   1524
  Planarity :  0.004   0.028   1608
  Dihedral  :  4.501  42.031   1270
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 21.21 %
    Favored  : 75.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.42 (0.26), residues: 1152
  helix:  2.50 (0.18), residues: 834
  sheet:  2.30 (0.62), residues: 60
  loop : -1.79 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP D  25 
 HIS   0.003   0.000   HIS C  74 
 PHE   0.013   0.001   PHE F 229 
 TYR   0.014   0.001   TYR D 177 
 ARG   0.003   0.000   ARG C 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04429 (  643)
  hydrogen bonds       : angle       2.97607 ( 1911)
  SS BOND              : bond        0.00612 (   18)
  SS BOND              : angle       1.62094 (   36)
  covalent geometry    : bond        0.00444 ( 9828)
  covalent geometry    : angle       0.65609 (13308)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 129
  time to evaluate  : 1.035 
Fit side-chains
REVERT: A   84 PHE cc_start: 0.8858 (m-80) cc_final: 0.8611 (m-10)
REVERT: A  100 MET cc_start: 0.8396 (tmm) cc_final: 0.8080 (tmm)
REVERT: A  148 ARG cc_start: 0.4063 (mtt-85) cc_final: 0.3075 (tpt170)
REVERT: B   31 ILE cc_start: 0.9363 (tp) cc_final: 0.9148 (tt)
REVERT: B  100 MET cc_start: 0.8305 (tmm) cc_final: 0.7819 (tmm)
REVERT: B  148 ARG cc_start: 0.4287 (mtt-85) cc_final: 0.3121 (tpt170)
REVERT: B  166 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8801 (mm-30)
REVERT: C   82 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9081 (tt)
REVERT: C  148 ARG cc_start: 0.4329 (mtt-85) cc_final: 0.3403 (tpt170)
REVERT: D  148 ARG cc_start: 0.3853 (mtt-85) cc_final: 0.2910 (tpt170)
REVERT: E   82 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9040 (tt)
REVERT: E  148 ARG cc_start: 0.4539 (mtt-85) cc_final: 0.3248 (tpt170)
REVERT: E  166 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8811 (mm-30)
REVERT: F  148 ARG cc_start: 0.4427 (mtt-85) cc_final: 0.3469 (tpt170)
REVERT: F  227 GLU cc_start: 0.8839 (tp30) cc_final: 0.8413 (tm-30)
  outliers start: 38
  outliers final: 35
  residues processed: 163
  average time/residue: 0.1896
  time to fit residues: 44.8603
Evaluate side-chains
  157 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 120
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  233 PHE
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   82 ILE
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue   98 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  233 PHE
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain C residue   98 TYR
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   82 ILE
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  233 PHE
Chi-restraints excluded: chain E residue   15 GLN
Chi-restraints excluded: chain E residue   32 PHE
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue   82 ILE
Chi-restraints excluded: chain E residue   98 TYR
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain E residue  233 PHE
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue   82 ILE
Chi-restraints excluded: chain F residue   98 TYR
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  226 ILE
Chi-restraints excluded: chain F residue  231 VAL
Chi-restraints excluded: chain F residue  233 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 41 optimal weight:    7.9990
   chunk 76 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   chunk 95 optimal weight:   20.0000
   chunk 105 optimal weight:    6.9990
   chunk 28 optimal weight:    8.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3624 r_free = 0.3624 target = 0.098792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.070492 restraints weight = 25481.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.072820 restraints weight = 12117.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.074237 restraints weight = 8041.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.3287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9846  Z= 0.154
  Angle     :  0.638   8.144  13344  Z= 0.333
  Chirality :  0.038   0.127   1524
  Planarity :  0.004   0.028   1608
  Dihedral  :  4.398  41.271   1270
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 21.50 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.26), residues: 1152
  helix:  2.53 (0.18), residues: 834
  sheet:  1.26 (0.60), residues: 72
  loop : -1.51 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B  25 
 HIS   0.002   0.000   HIS F  74 
 PHE   0.013   0.001   PHE F 229 
 TYR   0.016   0.001   TYR D 177 
 ARG   0.003   0.000   ARG D 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03965 (  643)
  hydrogen bonds       : angle       2.87481 ( 1911)
  SS BOND              : bond        0.00608 (   18)
  SS BOND              : angle       1.53502 (   36)
  covalent geometry    : bond        0.00358 ( 9828)
  covalent geometry    : angle       0.63414 (13308)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 127
  time to evaluate  : 1.043 
Fit side-chains
REVERT: A   84 PHE cc_start: 0.8820 (m-80) cc_final: 0.8550 (m-10)
REVERT: A  100 MET cc_start: 0.8436 (tmm) cc_final: 0.8112 (tmm)
REVERT: A  148 ARG cc_start: 0.4078 (mtt-85) cc_final: 0.3114 (tpt170)
REVERT: A  166 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8854 (mm-30)
REVERT: B   31 ILE cc_start: 0.9349 (tp) cc_final: 0.9143 (tt)
REVERT: B  100 MET cc_start: 0.8383 (tmm) cc_final: 0.7879 (tmm)
REVERT: B  148 ARG cc_start: 0.4311 (mtt-85) cc_final: 0.3169 (tpt170)
REVERT: B  166 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8757 (mm-30)
REVERT: C   82 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9113 (tt)
REVERT: C  148 ARG cc_start: 0.4462 (mtt-85) cc_final: 0.3479 (tpt170)
REVERT: D  148 ARG cc_start: 0.3844 (mtt-85) cc_final: 0.2992 (tpt170)
REVERT: E  148 ARG cc_start: 0.4504 (mtt-85) cc_final: 0.3295 (tpt170)
REVERT: E  166 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8760 (mm-30)
REVERT: F  101 ARG cc_start: 0.8975 (tpp-160) cc_final: 0.8626 (tpp-160)
REVERT: F  148 ARG cc_start: 0.4442 (mtt-85) cc_final: 0.3501 (tpt170)
REVERT: F  227 GLU cc_start: 0.8802 (tp30) cc_final: 0.8439 (tm-30)
  outliers start: 36
  outliers final: 34
  residues processed: 161
  average time/residue: 0.2052
  time to fit residues: 47.5773
Evaluate side-chains
  166 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 131
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  233 PHE
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   82 ILE
Chi-restraints excluded: chain B residue   98 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  233 PHE
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   82 ILE
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  233 PHE
Chi-restraints excluded: chain E residue   15 GLN
Chi-restraints excluded: chain E residue   32 PHE
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue   89 THR
Chi-restraints excluded: chain E residue   98 TYR
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain E residue  233 PHE
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue   82 ILE
Chi-restraints excluded: chain F residue   89 THR
Chi-restraints excluded: chain F residue   98 TYR
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  231 VAL
Chi-restraints excluded: chain F residue  233 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 8 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 38 optimal weight:   10.0000
   chunk 97 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 74 optimal weight:    0.7980
   chunk 109 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3731 r_free = 0.3731 target = 0.101643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.072867 restraints weight = 24885.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.075309 restraints weight = 11010.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.076781 restraints weight = 7198.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.3541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9846  Z= 0.118
  Angle     :  0.606   8.227  13344  Z= 0.315
  Chirality :  0.036   0.119   1524
  Planarity :  0.004   0.029   1608
  Dihedral  :  4.147  39.032   1270
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 23.01 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.56 (0.26), residues: 1152
  helix:  2.64 (0.18), residues: 834
  sheet:  2.00 (0.61), residues: 60
  loop : -1.80 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B  25 
 HIS   0.001   0.000   HIS C  74 
 PHE   0.013   0.001   PHE F 229 
 TYR   0.018   0.001   TYR D 177 
 ARG   0.003   0.000   ARG D 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03062 (  643)
  hydrogen bonds       : angle       2.70624 ( 1911)
  SS BOND              : bond        0.00569 (   18)
  SS BOND              : angle       1.41789 (   36)
  covalent geometry    : bond        0.00269 ( 9828)
  covalent geometry    : angle       0.60196 (13308)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3096.69 seconds
wall clock time: 57 minutes 17.88 seconds (3437.88 seconds total)