Starting phenix.real_space_refine
on Fri Mar 14 02:20:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xqi_33397/03_2025/7xqi_33397.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xqi_33397/03_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_33397/03_2025/7xqi_33397.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xqi_33397/03_2025/7xqi_33397.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xqi_33397/03_2025/7xqi_33397.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xqi_33397/03_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.63, per 1000 atoms: 0.38
  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: 2.23
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.85
  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: 2.41

  Time building geometry restraints manager: 2.67 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: 0.16
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:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.430
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.010
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.120
-------------------------------------------------------------------------------
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   9828  Z= 0.352
  Angle     :  0.716   8.849  13308  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 

*********************** 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  : 1.153 
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: 0.2551
  time to fit residues: 70.7796
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  : 1.381 
-------------------------------------------------------------------------------
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   9828  Z= 0.173
  Angle     :  0.561   5.737  13308  Z= 0.292
  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 

*********************** 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  : 1.075 
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: 0.2059
  time to fit residues: 59.1654
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  : 1.215 
-------------------------------------------------------------------------------
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:    0.5980
   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:    3.9186

-------------------------------------------------------------------------------
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 = 0.3665 r_free = 0.3665 target = 0.098107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.069196 restraints weight = 25360.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.071614 restraints weight = 11701.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.073042 restraints weight = 7687.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   9828  Z= 0.386
  Angle     :  0.677   8.777  13308  Z= 0.356
  Chirality :  0.042   0.219   1524
  Planarity :  0.004   0.026   1608
  Dihedral  :  5.434  42.891   1280
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 15.25 %
    Favored  : 79.83 %
  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:  1.53 (0.26), residues: 1152
  helix:  1.89 (0.19), residues: 834
  sheet:  2.95 (0.61), residues: 60
  loop : -2.60 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  25 
 HIS   0.002   0.000   HIS A  74 
 PHE   0.011   0.001   PHE C 229 
 TYR   0.014   0.001   TYR A 177 
 ARG   0.004   0.000   ARG B 101 

*********************** 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
  189 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 137
  time to evaluate  : 1.134 
Fit side-chains
REVERT: B   31 ILE cc_start: 0.9390 (tp) cc_final: 0.9158 (tt)
REVERT: B  100 MET cc_start: 0.8372 (tmm) cc_final: 0.8094 (tmm)
REVERT: B  101 ARG cc_start: 0.8584 (tpp-160) cc_final: 0.8192 (tpp-160)
REVERT: C  166 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8928 (mm-30)
REVERT: C  213 MET cc_start: 0.9137 (mmm) cc_final: 0.8896 (mmm)
REVERT: D   31 ILE cc_start: 0.9395 (tp) cc_final: 0.9176 (tt)
REVERT: D  227 GLU cc_start: 0.8849 (tp30) cc_final: 0.8400 (tm-30)
REVERT: F  148 ARG cc_start: 0.4503 (mtt-85) cc_final: 0.3415 (tpt170)
  outliers start: 52
  outliers final: 38
  residues processed: 179
  average time/residue: 0.2029
  time to fit residues: 52.8279
Evaluate side-chains
  160 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 122
  time to evaluate  : 1.261 
-------------------------------------------------------------------------------
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 B residue  233 PHE
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:    0.9990
   chunk 108 optimal weight:    3.9990
   chunk 86 optimal weight:   50.0000
   chunk 48 optimal weight:   50.0000
   chunk 65 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 95 optimal weight:    0.0270
   chunk 30 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    0.9844

-------------------------------------------------------------------------------
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 = 0.3726 r_free = 0.3726 target = 0.101366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.073004 restraints weight = 24450.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.075522 restraints weight = 10839.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.076937 restraints weight = 7042.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9828  Z= 0.179
  Angle     :  0.572   8.822  13308  Z= 0.300
  Chirality :  0.038   0.174   1524
  Planarity :  0.003   0.024   1608
  Dihedral  :  4.976  40.009   1280
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.66 %
    Favored  : 78.79 %
  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:  2.04 (0.26), residues: 1152
  helix:  2.29 (0.19), residues: 834
  sheet:  2.71 (0.61), residues: 60
  loop : -2.36 (0.35), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  25 
 HIS   0.001   0.000   HIS F 194 
 PHE   0.019   0.001   PHE A 229 
 TYR   0.009   0.001   TYR A 177 
 ARG   0.004   0.000   ARG D 101 

*********************** 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
  192 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 165
  time to evaluate  : 1.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.8299 (tmm) cc_final: 0.7960 (tmm)
REVERT: A  148 ARG cc_start: 0.4201 (mtt-85) cc_final: 0.3064 (tpt170)
REVERT: B   31 ILE cc_start: 0.9394 (tp) cc_final: 0.9100 (tt)
REVERT: B  100 MET cc_start: 0.8411 (tmm) cc_final: 0.8056 (tmm)
REVERT: B  148 ARG cc_start: 0.4707 (mtt-85) cc_final: 0.3351 (tpt170)
REVERT: C  148 ARG cc_start: 0.4540 (mtt-85) cc_final: 0.3503 (tpt170)
REVERT: C  166 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8565 (tp30)
REVERT: C  213 MET cc_start: 0.9126 (mmm) cc_final: 0.8907 (mmm)
REVERT: D  148 ARG cc_start: 0.4114 (mtt-85) cc_final: 0.2980 (tpt170)
REVERT: D  197 ASP cc_start: 0.8182 (m-30) cc_final: 0.7796 (p0)
REVERT: D  227 GLU cc_start: 0.8767 (tp30) cc_final: 0.8324 (tm-30)
REVERT: E   47 ASP cc_start: 0.8251 (p0) cc_final: 0.8044 (p0)
REVERT: E  148 ARG cc_start: 0.4525 (mtt-85) cc_final: 0.3209 (tpt170)
REVERT: F  148 ARG cc_start: 0.4593 (mtt-85) cc_final: 0.3517 (tpt170)
REVERT: F  166 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8605 (tp30)
  outliers start: 27
  outliers final: 18
  residues processed: 185
  average time/residue: 0.2145
  time to fit residues: 56.9937
Evaluate side-chains
  154 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 136
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
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  233 PHE
Chi-restraints excluded: chain C residue   85 VAL
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  231 VAL
Chi-restraints excluded: chain D residue  233 PHE
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   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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 66 optimal weight:   20.0000
   chunk 97 optimal weight:    2.9990
   chunk 96 optimal weight:    0.6980
   chunk 75 optimal weight:    7.9990
   chunk 19 optimal weight:    0.1980
   chunk 36 optimal weight:    0.8980
   chunk 28 optimal weight:   20.0000
   chunk 111 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 84 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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 = 0.3697 r_free = 0.3697 target = 0.099934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.070019 restraints weight = 25682.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.072432 restraints weight = 11981.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.073354 restraints weight = 8069.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.2930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9828  Z= 0.196
  Angle     :  0.582   7.788  13308  Z= 0.306
  Chirality :  0.037   0.126   1524
  Planarity :  0.003   0.026   1608
  Dihedral  :  4.526  40.151   1274
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 21.12 %
    Favored  : 77.08 %
  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:  2.26 (0.26), residues: 1152
  helix:  2.46 (0.19), residues: 834
  sheet:  1.53 (0.60), residues: 72
  loop : -2.11 (0.36), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  25 
 HIS   0.001   0.000   HIS C 194 
 PHE   0.022   0.001   PHE F 229 
 TYR   0.011   0.001   TYR A 177 
 ARG   0.002   0.000   ARG D 101 

*********************** 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
  153 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 1.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 ARG cc_start: 0.4155 (mtt-85) cc_final: 0.3044 (tpt170)
REVERT: B   31 ILE cc_start: 0.9361 (tp) cc_final: 0.9093 (tt)
REVERT: B  100 MET cc_start: 0.8307 (tmm) cc_final: 0.7932 (tmm)
REVERT: B  148 ARG cc_start: 0.4484 (mtt-85) cc_final: 0.3261 (tpt170)
REVERT: C  148 ARG cc_start: 0.4533 (mtt-85) cc_final: 0.3456 (tpt170)
REVERT: C  166 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8808 (mm-30)
REVERT: D  148 ARG cc_start: 0.3814 (mtt-85) cc_final: 0.3010 (tpt170)
REVERT: D  197 ASP cc_start: 0.8063 (m-30) cc_final: 0.7589 (p0)
REVERT: E  148 ARG cc_start: 0.4430 (mtt-85) cc_final: 0.3182 (tpt170)
REVERT: F  148 ARG cc_start: 0.4488 (mtt-85) cc_final: 0.3392 (tpt170)
REVERT: F  166 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8635 (tp30)
  outliers start: 19
  outliers final: 17
  residues processed: 153
  average time/residue: 0.2046
  time to fit residues: 44.5675
Evaluate side-chains
  151 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 1.213 
-------------------------------------------------------------------------------
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  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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0270
   chunk 7 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 10 optimal weight:   10.0000
   chunk 101 optimal weight:    0.6980
   chunk 76 optimal weight:   30.0000
   chunk 103 optimal weight:    5.9990
   overall best weight:    0.8642

-------------------------------------------------------------------------------
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 = 0.3735 r_free = 0.3735 target = 0.101924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.071958 restraints weight = 25704.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.074393 restraints weight = 11855.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.075737 restraints weight = 7937.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9828  Z= 0.155
  Angle     :  0.561   7.989  13308  Z= 0.293
  Chirality :  0.036   0.115   1524
  Planarity :  0.003   0.028   1608
  Dihedral  :  4.345  38.840   1274
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 21.02 %
    Favored  : 77.18 %
  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:  2.35 (0.26), residues: 1152
  helix:  2.59 (0.19), residues: 828
  sheet:  1.33 (0.60), residues: 72
  loop : -2.18 (0.35), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B  25 
 HIS   0.003   0.000   HIS C  74 
 PHE   0.017   0.001   PHE F 229 
 TYR   0.013   0.001   TYR A 177 
 ARG   0.005   0.000   ARG E 101 

*********************** 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
  155 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.8299 (tmm) cc_final: 0.8060 (tmm)
REVERT: A  148 ARG cc_start: 0.4043 (mtt-85) cc_final: 0.3092 (tpt170)
REVERT: B   31 ILE cc_start: 0.9370 (tp) cc_final: 0.9107 (tt)
REVERT: B  100 MET cc_start: 0.8295 (tmm) cc_final: 0.7892 (tmm)
REVERT: B  148 ARG cc_start: 0.4615 (mtt-85) cc_final: 0.3360 (tpt170)
REVERT: C  148 ARG cc_start: 0.4469 (mtt-85) cc_final: 0.3474 (tpt170)
REVERT: C  166 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8519 (tp30)
REVERT: D  148 ARG cc_start: 0.3979 (mtt-85) cc_final: 0.3019 (tpt170)
REVERT: D  197 ASP cc_start: 0.7977 (m-30) cc_final: 0.7599 (p0)
REVERT: D  227 GLU cc_start: 0.8850 (tp30) cc_final: 0.8355 (tm-30)
REVERT: E  148 ARG cc_start: 0.4347 (mtt-85) cc_final: 0.3216 (tpt170)
REVERT: F  148 ARG cc_start: 0.4459 (mtt-85) cc_final: 0.3432 (tpt170)
REVERT: F  166 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8584 (tp30)
  outliers start: 19
  outliers final: 16
  residues processed: 154
  average time/residue: 0.2003
  time to fit residues: 43.9645
Evaluate side-chains
  146 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  233 PHE
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  219 VAL
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain E residue  233 PHE
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 95 optimal weight:    6.9990
   chunk 100 optimal weight:    0.7980
   chunk 85 optimal weight:    8.9990
   chunk 11 optimal weight:    9.9990
   chunk 15 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 99 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.7184

-------------------------------------------------------------------------------
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 = 0.3707 r_free = 0.3707 target = 0.100193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.071399 restraints weight = 25055.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.073844 restraints weight = 11130.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.075265 restraints weight = 7265.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.3144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9828  Z= 0.200
  Angle     :  0.582   8.198  13308  Z= 0.303
  Chirality :  0.037   0.141   1524
  Planarity :  0.004   0.028   1608
  Dihedral  :  3.863  16.524   1266
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 21.12 %
    Favored  : 76.89 %
  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:  2.45 (0.26), residues: 1152
  helix:  2.57 (0.19), residues: 834
  sheet:  1.19 (0.60), residues: 72
  loop : -1.77 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B  25 
 HIS   0.000   0.000   HIS F 194 
 PHE   0.016   0.001   PHE F 229 
 TYR   0.013   0.001   TYR D 177 
 ARG   0.003   0.000   ARG E 101 

*********************** 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
  154 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 1.189 
Fit side-chains
REVERT: A   84 PHE cc_start: 0.8817 (m-80) cc_final: 0.8598 (m-10)
REVERT: A  100 MET cc_start: 0.8390 (tmm) cc_final: 0.8108 (tmm)
REVERT: A  148 ARG cc_start: 0.4032 (mtt-85) cc_final: 0.3115 (tpt170)
REVERT: B   31 ILE cc_start: 0.9357 (tp) cc_final: 0.9092 (tt)
REVERT: B  100 MET cc_start: 0.8390 (tmm) cc_final: 0.7926 (tmm)
REVERT: B  148 ARG cc_start: 0.4395 (mtt-85) cc_final: 0.3244 (tpt170)
REVERT: C  148 ARG cc_start: 0.4423 (mtt-85) cc_final: 0.3500 (tpt170)
REVERT: D  148 ARG cc_start: 0.3832 (mtt-85) cc_final: 0.2982 (tpt170)
REVERT: D  197 ASP cc_start: 0.8032 (m-30) cc_final: 0.7474 (p0)
REVERT: E  148 ARG cc_start: 0.4463 (mtt-85) cc_final: 0.3257 (tpt170)
REVERT: E  166 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8824 (mm-30)
REVERT: F  148 ARG cc_start: 0.4438 (mtt-85) cc_final: 0.3577 (tpt170)
REVERT: F  166 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8596 (tp30)
  outliers start: 21
  outliers final: 18
  residues processed: 153
  average time/residue: 0.2042
  time to fit residues: 44.7827
Evaluate side-chains
  147 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   98 TYR
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   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  219 VAL
Chi-restraints excluded: chain E residue  231 VAL
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 38 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 79 optimal weight:    8.9990
   chunk 97 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 59 optimal weight:    9.9990
   chunk 105 optimal weight:    8.9990
   chunk 29 optimal weight:   50.0000
   overall best weight:    3.7988

-------------------------------------------------------------------------------
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 = 0.3579 r_free = 0.3579 target = 0.096389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.067899 restraints weight = 26036.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.070137 restraints weight = 12552.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.071520 restraints weight = 8403.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   9828  Z= 0.358
  Angle     :  0.683   8.319  13308  Z= 0.356
  Chirality :  0.041   0.140   1524
  Planarity :  0.004   0.028   1608
  Dihedral  :  4.289  20.271   1266
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 20.55 %
    Favored  : 76.80 %
  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:  2.29 (0.26), residues: 1152
  helix:  2.41 (0.19), residues: 834
  sheet:  1.02 (0.63), residues: 72
  loop : -1.62 (0.39), residues: 246

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

*********************** 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
  146 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 1.307 
Fit side-chains
REVERT: A  100 MET cc_start: 0.8433 (tmm) cc_final: 0.8124 (tmm)
REVERT: A  148 ARG cc_start: 0.3902 (mtt-85) cc_final: 0.3037 (tpt170)
REVERT: B   31 ILE cc_start: 0.9352 (tp) cc_final: 0.9124 (tt)
REVERT: B  100 MET cc_start: 0.8357 (tmm) cc_final: 0.7848 (tmm)
REVERT: B  148 ARG cc_start: 0.4417 (mtt-85) cc_final: 0.3187 (tpt170)
REVERT: C  148 ARG cc_start: 0.4400 (mtt-85) cc_final: 0.3472 (tpt170)
REVERT: D  100 MET cc_start: 0.8307 (tmm) cc_final: 0.7859 (tmm)
REVERT: E  148 ARG cc_start: 0.4547 (mtt-85) cc_final: 0.3263 (tpt170)
REVERT: E  166 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8860 (mm-30)
REVERT: F  101 ARG cc_start: 0.8977 (tpp-160) cc_final: 0.8616 (tpp-160)
REVERT: F  148 ARG cc_start: 0.4447 (mtt-85) cc_final: 0.3517 (tpt170)
  outliers start: 28
  outliers final: 23
  residues processed: 144
  average time/residue: 0.2347
  time to fit residues: 49.5583
Evaluate side-chains
  139 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 1.231 
-------------------------------------------------------------------------------
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 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  231 VAL
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  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  231 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   chunk 108 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 57 optimal weight:    0.5980
   chunk 40 optimal weight:    7.9990
   chunk 29 optimal weight:    8.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3725 r_free = 0.3725 target = 0.101257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.071105 restraints weight = 26053.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.073600 restraints weight = 11753.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.075047 restraints weight = 7795.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.3307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9828  Z= 0.176
  Angle     :  0.598   9.543  13308  Z= 0.312
  Chirality :  0.037   0.120   1524
  Planarity :  0.004   0.028   1608
  Dihedral  :  3.950  15.862   1266
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 22.44 %
    Favored  : 76.23 %
  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:  2.35 (0.26), residues: 1152
  helix:  2.49 (0.18), residues: 834
  sheet:  1.84 (0.65), residues: 60
  loop : -1.85 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP D  25 
 HIS   0.001   0.000   HIS B  74 
 PHE   0.013   0.001   PHE F 229 
 TYR   0.017   0.001   TYR D 177 
 ARG   0.003   0.000   ARG E 101 

*********************** 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
  147 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 1.110 
Fit side-chains
REVERT: A  100 MET cc_start: 0.8308 (tmm) cc_final: 0.8040 (tmm)
REVERT: A  148 ARG cc_start: 0.4036 (mtt-85) cc_final: 0.3112 (tpt170)
REVERT: B   31 ILE cc_start: 0.9338 (tp) cc_final: 0.9114 (tt)
REVERT: B  100 MET cc_start: 0.8219 (tmm) cc_final: 0.7771 (tmm)
REVERT: B  148 ARG cc_start: 0.4558 (mtt-85) cc_final: 0.3250 (tpt170)
REVERT: C  148 ARG cc_start: 0.4423 (mtt-85) cc_final: 0.3500 (tpt170)
REVERT: D  100 MET cc_start: 0.8062 (tmm) cc_final: 0.7661 (tmm)
REVERT: D  148 ARG cc_start: 0.4036 (mtt-85) cc_final: 0.3041 (tpt170)
REVERT: D  197 ASP cc_start: 0.8291 (m-30) cc_final: 0.7729 (p0)
REVERT: E  148 ARG cc_start: 0.4424 (mtt-85) cc_final: 0.3215 (tpt170)
REVERT: F  101 ARG cc_start: 0.8926 (tpp-160) cc_final: 0.8615 (tpp-160)
REVERT: F  148 ARG cc_start: 0.4523 (mtt-85) cc_final: 0.3591 (tpt170)
REVERT: F  166 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8697 (tp30)
REVERT: F  227 GLU cc_start: 0.8852 (tp30) cc_final: 0.8634 (tp30)
  outliers start: 14
  outliers final: 14
  residues processed: 147
  average time/residue: 0.1944
  time to fit residues: 41.0192
Evaluate side-chains
  144 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   41 VAL
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   98 TYR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain E residue   41 VAL
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  219 VAL
Chi-restraints excluded: chain F residue  231 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9990
   chunk 15 optimal weight:    9.9990
   chunk 95 optimal weight:   20.0000
   chunk 105 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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 = 0.3709 r_free = 0.3709 target = 0.100132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.071285 restraints weight = 25228.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.073734 restraints weight = 11242.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.075174 restraints weight = 7330.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9828  Z= 0.206
  Angle     :  0.605   7.464  13308  Z= 0.317
  Chirality :  0.037   0.125   1524
  Planarity :  0.004   0.030   1608
  Dihedral  :  3.939  15.549   1266
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 22.06 %
    Favored  : 76.42 %
  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:  2.43 (0.26), residues: 1152
  helix:  2.56 (0.19), residues: 834
  sheet:  1.82 (0.67), residues: 60
  loop : -1.87 (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 D  74 
 PHE   0.014   0.001   PHE F 229 
 TYR   0.016   0.001   TYR D 177 
 ARG   0.003   0.000   ARG E 101 

********************** 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
  144 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 1.202 
Fit side-chains
REVERT: A  100 MET cc_start: 0.8389 (tmm) cc_final: 0.8083 (tmm)
REVERT: A  148 ARG cc_start: 0.4048 (mtt-85) cc_final: 0.3112 (tpt170)
REVERT: B   31 ILE cc_start: 0.9341 (tp) cc_final: 0.9139 (tt)
REVERT: B  100 MET cc_start: 0.8286 (tmm) cc_final: 0.7729 (tmm)
REVERT: B  148 ARG cc_start: 0.4365 (mtt-85) cc_final: 0.3336 (tpt170)
REVERT: B  166 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8830 (mm-30)
REVERT: C  148 ARG cc_start: 0.4538 (mtt-85) cc_final: 0.3576 (tpt170)
REVERT: D  100 MET cc_start: 0.8181 (tmm) cc_final: 0.7756 (tmm)
REVERT: D  148 ARG cc_start: 0.3967 (mtt-85) cc_final: 0.3094 (tpt170)
REVERT: D  197 ASP cc_start: 0.8297 (m-30) cc_final: 0.7729 (p0)
REVERT: E  148 ARG cc_start: 0.4504 (mtt-85) cc_final: 0.3265 (tpt170)
REVERT: F  101 ARG cc_start: 0.8931 (tpp-160) cc_final: 0.8606 (tpp-160)
REVERT: F  148 ARG cc_start: 0.4401 (mtt-85) cc_final: 0.3552 (tpt170)
REVERT: F  227 GLU cc_start: 0.8875 (tp30) cc_final: 0.8650 (tp30)
  outliers start: 16
  outliers final: 16
  residues processed: 143
  average time/residue: 0.2002
  time to fit residues: 41.2859
Evaluate side-chains
  142 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   41 VAL
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   98 TYR
Chi-restraints excluded: chain D residue  231 VAL
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  219 VAL
Chi-restraints excluded: chain F residue  231 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:   10.0000
   chunk 97 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   chunk 109 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    1.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.100185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.071359 restraints weight = 25128.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.073798 restraints weight = 11188.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.075222 restraints weight = 7303.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.3326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9828  Z= 0.210
  Angle     :  0.617   6.753  13308  Z= 0.323
  Chirality :  0.038   0.126   1524
  Planarity :  0.004   0.029   1608
  Dihedral  :  3.927  15.587   1266
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 22.63 %
    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:  2.43 (0.26), residues: 1152
  helix:  2.56 (0.18), residues: 834
  sheet:  1.70 (0.67), residues: 60
  loop : -1.82 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  25 
 HIS   0.001   0.000   HIS E  74 
 PHE   0.014   0.001   PHE F 229 
 TYR   0.016   0.001   TYR D 177 
 ARG   0.003   0.000   ARG E 101 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2834.35 seconds
wall clock time: 51 minutes 44.89 seconds (3104.89 seconds total)