Starting phenix.real_space_refine
on Wed Sep 17 15:39:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xqi_33397/09_2025/7xqi_33397.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xqi_33397/09_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_33397/09_2025/7xqi_33397.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xqi_33397/09_2025/7xqi_33397.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xqi_33397/09_2025/7xqi_33397.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xqi_33397/09_2025/7xqi_33397.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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:
    B, C, D, E, F
  Time building chain proxies: 1.20, per 1000 atoms: 0.13
  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 B  54 " - pdb=" SG  CYS B 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  54 " - pdb=" SG  CYS C 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  54 " - pdb=" SG  CYS D 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  54 " - pdb=" SG  CYS E 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  54 " - pdb=" SG  CYS F 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  61 " - pdb=" SG  CYS B 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  61 " - pdb=" SG  CYS C 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  61 " - pdb=" SG  CYS D 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  61 " - pdb=" SG  CYS E 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  61 " - pdb=" SG  CYS F 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  65 " - pdb=" SG  CYS B 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  65 " - pdb=" SG  CYS C 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  65 " - pdb=" SG  CYS D 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  65 " - pdb=" SG  CYS E 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  65 " - pdb=" SG  CYS F 187 " distance=2.03

  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: 0.67
  Conformation dependent library (CDL) restraints added in 386.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.26
  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: 1.36

  Time building geometry restraints manager: 0.94 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.490
  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:             0.020
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.300
  Find NCS groups from input model:        0.050
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.0000

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

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

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG D 202 
 TYR   0.016   0.002   TYR C  17 
 PHE   0.011   0.001   PHE C  52 
 TRP   0.006   0.001   TRP C  25 
 HIS   0.001   0.000   HIS F  95 

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

*********************** 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  : 0.345 
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: 0.9034 (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: 0.1021
  time to fit residues: 28.6680
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  : 0.409 
-------------------------------------------------------------------------------
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 108 optimal weight:    0.1980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0570
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    1.0300

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.102206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.073476 restraints weight = 24477.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.076036 restraints weight = 10963.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.077495 restraints weight = 7107.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.078276 restraints weight = 5739.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.078581 restraints weight = 5178.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9846  Z= 0.123
  Angle     :  0.577   5.848  13344  Z= 0.300
  Chirality :  0.038   0.180   1524
  Planarity :  0.003   0.024   1608
  Dihedral  :  5.117  40.525   1280
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 13.26 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.25), residues: 1152
  helix:  1.28 (0.18), residues: 828
  sheet:  2.93 (0.60), residues: 60
  loop : -2.97 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 101 
 TYR   0.009   0.001   TYR A 177 
 PHE   0.005   0.001   PHE E  52 
 TRP   0.011   0.001   TRP E  25 
 HIS   0.001   0.000   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 9828)
  covalent geometry    : angle       0.56344 (13308)
  SS BOND              : bond        0.00319 (   18)
  SS BOND              : angle       2.49898 (   36)
  hydrogen bonds       : bond        0.03903 (  643)
  hydrogen bonds       : angle       2.92084 ( 1911)

*********************** 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
  203 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 175
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.8333 (tmm) cc_final: 0.7945 (tmm)
REVERT: A  148 ARG cc_start: 0.4057 (mtt-85) cc_final: 0.2953 (tpt170)
REVERT: A  227 GLU cc_start: 0.8722 (tp30) cc_final: 0.8253 (tm-30)
REVERT: B   47 ASP cc_start: 0.8244 (p0) cc_final: 0.8041 (p0)
REVERT: B  148 ARG cc_start: 0.4566 (mtt-85) cc_final: 0.3223 (tpt170)
REVERT: C   47 ASP cc_start: 0.8199 (p0) cc_final: 0.7980 (p0)
REVERT: C  104 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8311 (tm-30)
REVERT: C  148 ARG cc_start: 0.4607 (mtt-85) cc_final: 0.3538 (tpt170)
REVERT: C  166 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8636 (tp30)
REVERT: C  213 MET cc_start: 0.9124 (mmm) cc_final: 0.8860 (mmm)
REVERT: C  227 GLU cc_start: 0.8773 (tp30) cc_final: 0.8430 (tm-30)
REVERT: D  166 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8669 (tp30)
REVERT: D  227 GLU cc_start: 0.8855 (tp30) cc_final: 0.8389 (tm-30)
REVERT: E   47 ASP cc_start: 0.8354 (p0) cc_final: 0.8117 (p0)
REVERT: E  148 ARG cc_start: 0.4378 (mtt-85) cc_final: 0.3252 (tpt170)
REVERT: F  148 ARG cc_start: 0.4652 (mtt-85) cc_final: 0.3493 (tpt170)
  outliers start: 28
  outliers final: 19
  residues processed: 199
  average time/residue: 0.0931
  time to fit residues: 26.1432
Evaluate side-chains
  152 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
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  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 79 optimal weight:    5.9990
   chunk 95 optimal weight:   40.0000
   chunk 74 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9980
   chunk 38 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 108 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   chunk 100 optimal weight:    0.9980
   overall best weight:    2.5986

-------------------------------------------------------------------------------
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 = 0.3668 r_free = 0.3668 target = 0.098915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.069943 restraints weight = 25009.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.072372 restraints weight = 11490.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.073832 restraints weight = 7564.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.074486 restraints weight = 6119.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.074927 restraints weight = 5558.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9846  Z= 0.185
  Angle     :  0.621   8.267  13344  Z= 0.327
  Chirality :  0.040   0.205   1524
  Planarity :  0.004   0.027   1608
  Dihedral  :  5.250  41.896   1280
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 16.29 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.70 (0.26), residues: 1152
  helix:  2.02 (0.19), residues: 834
  sheet:  1.77 (0.59), residues: 72
  loop : -2.37 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 101 
 TYR   0.011   0.001   TYR A 177 
 PHE   0.008   0.001   PHE F 209 
 TRP   0.016   0.001   TRP B  25 
 HIS   0.001   0.000   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 9828)
  covalent geometry    : angle       0.61189 (13308)
  SS BOND              : bond        0.00649 (   18)
  SS BOND              : angle       2.14560 (   36)
  hydrogen bonds       : bond        0.04524 (  643)
  hydrogen bonds       : angle       3.00036 ( 1911)

*********************** 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
  198 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 151
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A   47 ASP cc_start: 0.8337 (p0) cc_final: 0.8118 (p0)
REVERT: A  148 ARG cc_start: 0.4100 (mtt-85) cc_final: 0.2985 (tpt170)
REVERT: B   31 ILE cc_start: 0.9414 (tp) cc_final: 0.9173 (tt)
REVERT: B  100 MET cc_start: 0.8360 (tmm) cc_final: 0.8118 (tmm)
REVERT: B  101 ARG cc_start: 0.8494 (tpp-160) cc_final: 0.8157 (tpp-160)
REVERT: C   48 GLU cc_start: 0.8755 (tp30) cc_final: 0.8487 (tp30)
REVERT: C  166 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8856 (mm-30)
REVERT: C  213 MET cc_start: 0.9121 (mmm) cc_final: 0.8857 (mmm)
REVERT: D   31 ILE cc_start: 0.9383 (tp) cc_final: 0.9172 (tt)
REVERT: E  148 ARG cc_start: 0.4296 (mtt-85) cc_final: 0.3161 (tpt170)
REVERT: F  100 MET cc_start: 0.8314 (tmm) cc_final: 0.8019 (tmm)
REVERT: F  101 ARG cc_start: 0.8569 (tpp-160) cc_final: 0.8256 (tpp-160)
REVERT: F  148 ARG cc_start: 0.4520 (mtt-85) cc_final: 0.3442 (tpt170)
  outliers start: 47
  outliers final: 30
  residues processed: 192
  average time/residue: 0.0868
  time to fit residues: 24.1412
Evaluate side-chains
  159 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 129
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  233 PHE
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue   98 TYR
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  231 VAL
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  233 PHE
Chi-restraints excluded: chain E residue   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 E residue  233 PHE
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain F residue   89 THR
Chi-restraints excluded: chain F residue   98 TYR
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  231 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9980
   chunk 102 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   chunk 106 optimal weight:    7.9990
   chunk 113 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.3668 r_free = 0.3668 target = 0.098228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.069308 restraints weight = 25217.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.071712 restraints weight = 11421.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.073118 restraints weight = 7497.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.073881 restraints weight = 6091.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.074154 restraints weight = 5507.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9846  Z= 0.182
  Angle     :  0.618   8.921  13344  Z= 0.325
  Chirality :  0.039   0.192   1524
  Planarity :  0.003   0.024   1608
  Dihedral  :  5.183  41.943   1280
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.28 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.26), residues: 1152
  helix:  2.25 (0.19), residues: 840
  sheet:  2.67 (0.62), residues: 60
  loop : -2.37 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 101 
 TYR   0.007   0.001   TYR B 155 
 PHE   0.020   0.001   PHE F 229 
 TRP   0.018   0.001   TRP B  25 
 HIS   0.001   0.000   HIS D  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 9828)
  covalent geometry    : angle       0.61139 (13308)
  SS BOND              : bond        0.00625 (   18)
  SS BOND              : angle       1.87800 (   36)
  hydrogen bonds       : bond        0.04387 (  643)
  hydrogen bonds       : angle       2.99931 ( 1911)

*********************** 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
  184 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 151
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.8314 (tmm) cc_final: 0.7964 (tmm)
REVERT: A  148 ARG cc_start: 0.4145 (mtt-85) cc_final: 0.2997 (tpt170)
REVERT: B   31 ILE cc_start: 0.9397 (tp) cc_final: 0.9162 (tt)
REVERT: B  100 MET cc_start: 0.8375 (tmm) cc_final: 0.8022 (tmm)
REVERT: C  148 ARG cc_start: 0.4613 (mtt-85) cc_final: 0.3484 (tpt170)
REVERT: C  166 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8830 (mm-30)
REVERT: C  213 MET cc_start: 0.9131 (mmm) cc_final: 0.8930 (mmm)
REVERT: E  148 ARG cc_start: 0.4409 (mtt-85) cc_final: 0.3213 (tpt170)
REVERT: F  100 MET cc_start: 0.8329 (tmm) cc_final: 0.7956 (tmm)
REVERT: F  148 ARG cc_start: 0.4486 (mtt-85) cc_final: 0.3421 (tpt170)
  outliers start: 33
  outliers final: 27
  residues processed: 181
  average time/residue: 0.0823
  time to fit residues: 22.0487
Evaluate side-chains
  166 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 139
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
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   89 THR
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   89 THR
Chi-restraints excluded: chain C residue   98 TYR
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  233 PHE
Chi-restraints excluded: chain E residue   15 GLN
Chi-restraints excluded: chain E residue   32 PHE
Chi-restraints excluded: chain E residue   89 THR
Chi-restraints excluded: chain E residue   98 TYR
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  226 ILE
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain F residue   89 THR
Chi-restraints excluded: chain F residue   98 TYR
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  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 23 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 75 optimal weight:   10.0000
   chunk 0 optimal weight:   50.0000
   chunk 85 optimal weight:    7.9990
   chunk 76 optimal weight:   40.0000
   chunk 7 optimal weight:    2.9990
   chunk 105 optimal weight:   10.0000
   chunk 81 optimal weight:    0.0870
   chunk 58 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   overall best weight:    1.1562

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.100696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.071916 restraints weight = 24748.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.074369 restraints weight = 11125.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.075794 restraints weight = 7295.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.076301 restraints weight = 5908.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.076852 restraints weight = 5454.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.2886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9846  Z= 0.118
  Angle     :  0.561   6.745  13344  Z= 0.296
  Chirality :  0.036   0.120   1524
  Planarity :  0.003   0.027   1608
  Dihedral  :  4.822  40.011   1278
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 21.12 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.25 (0.26), residues: 1152
  helix:  2.43 (0.19), residues: 834
  sheet:  1.50 (0.59), residues: 72
  loop : -2.01 (0.35), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 101 
 TYR   0.008   0.001   TYR D 177 
 PHE   0.015   0.001   PHE F 229 
 TRP   0.020   0.001   TRP B  25 
 HIS   0.001   0.000   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9828)
  covalent geometry    : angle       0.55780 (13308)
  SS BOND              : bond        0.00611 (   18)
  SS BOND              : angle       1.33787 (   36)
  hydrogen bonds       : bond        0.03392 (  643)
  hydrogen bonds       : angle       2.79226 ( 1911)

*********************** 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
  167 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.8339 (tmm) cc_final: 0.7965 (tmm)
REVERT: A  148 ARG cc_start: 0.4142 (mtt-85) cc_final: 0.3172 (tpt170)
REVERT: B   31 ILE cc_start: 0.9384 (tp) cc_final: 0.9107 (tt)
REVERT: B  100 MET cc_start: 0.8417 (tmm) cc_final: 0.8013 (tmm)
REVERT: B  148 ARG cc_start: 0.4657 (mtt-85) cc_final: 0.3350 (tpt170)
REVERT: C  148 ARG cc_start: 0.4557 (mtt-85) cc_final: 0.3496 (tpt170)
REVERT: C  166 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8525 (tp30)
REVERT: D  148 ARG cc_start: 0.4083 (mtt-85) cc_final: 0.3064 (tpt170)
REVERT: D  197 ASP cc_start: 0.8227 (m-30) cc_final: 0.7673 (p0)
REVERT: E  148 ARG cc_start: 0.4469 (mtt-85) cc_final: 0.3203 (tpt170)
REVERT: F  148 ARG cc_start: 0.4510 (mtt-85) cc_final: 0.3443 (tpt170)
  outliers start: 18
  outliers final: 17
  residues processed: 167
  average time/residue: 0.0967
  time to fit residues: 22.9495
Evaluate side-chains
  155 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
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   98 TYR
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   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 69 optimal weight:    0.8980
   chunk 112 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 100 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 83 optimal weight:    0.6980
   chunk 13 optimal weight:    0.3980
   chunk 105 optimal weight:    7.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3745 r_free = 0.3745 target = 0.102480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.072482 restraints weight = 25718.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.074935 restraints weight = 11578.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.076407 restraints weight = 7704.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.077139 restraints weight = 6313.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.077304 restraints weight = 5765.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9846  Z= 0.108
  Angle     :  0.549   5.941  13344  Z= 0.288
  Chirality :  0.035   0.120   1524
  Planarity :  0.003   0.029   1608
  Dihedral  :  4.480  39.138   1276
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 21.50 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.41 (0.26), residues: 1152
  helix:  2.56 (0.18), residues: 834
  sheet:  1.29 (0.59), residues: 72
  loop : -1.93 (0.35), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 101 
 TYR   0.013   0.001   TYR A 177 
 PHE   0.013   0.001   PHE F 229 
 TRP   0.026   0.001   TRP B  25 
 HIS   0.003   0.000   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 9828)
  covalent geometry    : angle       0.54717 (13308)
  SS BOND              : bond        0.00462 (   18)
  SS BOND              : angle       1.09870 (   36)
  hydrogen bonds       : bond        0.02953 (  643)
  hydrogen bonds       : angle       2.67854 ( 1911)

*********************** 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
  161 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 ARG cc_start: 0.4110 (mtt-85) cc_final: 0.3169 (tpt170)
REVERT: A  227 GLU cc_start: 0.8792 (tp30) cc_final: 0.8547 (tp30)
REVERT: B   31 ILE cc_start: 0.9363 (tp) cc_final: 0.9104 (tt)
REVERT: B  100 MET cc_start: 0.8329 (tmm) cc_final: 0.7874 (tmm)
REVERT: B  148 ARG cc_start: 0.4532 (mtt-85) cc_final: 0.3322 (tpt170)
REVERT: B  213 MET cc_start: 0.9169 (mmm) cc_final: 0.8945 (mmm)
REVERT: C  148 ARG cc_start: 0.4453 (mtt-85) cc_final: 0.3506 (tpt170)
REVERT: C  166 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8509 (tp30)
REVERT: D  148 ARG cc_start: 0.4123 (mtt-85) cc_final: 0.3170 (tpt170)
REVERT: E  148 ARG cc_start: 0.4356 (mtt-85) cc_final: 0.3231 (tpt170)
REVERT: E  213 MET cc_start: 0.9127 (mmm) cc_final: 0.8860 (mmm)
REVERT: F  100 MET cc_start: 0.8313 (tmm) cc_final: 0.7934 (tmm)
REVERT: F  148 ARG cc_start: 0.4351 (mtt-85) cc_final: 0.3530 (tpt170)
  outliers start: 17
  outliers final: 13
  residues processed: 161
  average time/residue: 0.0925
  time to fit residues: 21.2899
Evaluate side-chains
  145 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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  233 PHE
Chi-restraints excluded: chain C residue   85 VAL
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   98 TYR
Chi-restraints excluded: chain E residue  231 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   chunk 113 optimal weight:    7.9990
   chunk 77 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 73 optimal weight:    3.9990
   chunk 105 optimal weight:   50.0000
   chunk 2 optimal weight:    5.9990
   overall best weight:    2.1986

-------------------------------------------------------------------------------
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 = 0.099425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.070531 restraints weight = 25220.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.072953 restraints weight = 11324.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.074392 restraints weight = 7376.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.074766 restraints weight = 5970.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.075368 restraints weight = 5571.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9846  Z= 0.159
  Angle     :  0.605   5.991  13344  Z= 0.315
  Chirality :  0.038   0.129   1524
  Planarity :  0.004   0.029   1608
  Dihedral  :  4.145  40.371   1268
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 21.21 %
    Favored  : 76.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.26), residues: 1152
  helix:  2.56 (0.19), residues: 834
  sheet:  1.24 (0.60), residues: 72
  loop : -1.66 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 101 
 TYR   0.013   0.001   TYR C  66 
 PHE   0.012   0.001   PHE A 229 
 TRP   0.025   0.001   TRP D  25 
 HIS   0.001   0.000   HIS F  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 9828)
  covalent geometry    : angle       0.60154 (13308)
  SS BOND              : bond        0.00593 (   18)
  SS BOND              : angle       1.31447 (   36)
  hydrogen bonds       : bond        0.04126 (  643)
  hydrogen bonds       : angle       2.83837 ( 1911)

*********************** 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
  156 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.477 
Fit side-chains
REVERT: A   84 PHE cc_start: 0.8835 (m-80) cc_final: 0.8621 (m-10)
REVERT: A  100 MET cc_start: 0.8391 (tmm) cc_final: 0.8114 (tmm)
REVERT: A  148 ARG cc_start: 0.4103 (mtt-85) cc_final: 0.3131 (tpt170)
REVERT: A  227 GLU cc_start: 0.8820 (tp30) cc_final: 0.8608 (tp30)
REVERT: B   31 ILE cc_start: 0.9367 (tp) cc_final: 0.9153 (tt)
REVERT: B  100 MET cc_start: 0.8318 (tmm) cc_final: 0.7855 (tmm)
REVERT: B  148 ARG cc_start: 0.4511 (mtt-85) cc_final: 0.3282 (tpt170)
REVERT: B  213 MET cc_start: 0.9157 (mmm) cc_final: 0.8912 (mmm)
REVERT: C  148 ARG cc_start: 0.4495 (mtt-85) cc_final: 0.3502 (tpt170)
REVERT: C  166 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8783 (mm-30)
REVERT: D   84 PHE cc_start: 0.8834 (m-80) cc_final: 0.8607 (m-10)
REVERT: D  100 MET cc_start: 0.8227 (tmm) cc_final: 0.7781 (tmm)
REVERT: D  148 ARG cc_start: 0.3806 (mtt-85) cc_final: 0.3002 (tpt170)
REVERT: E  148 ARG cc_start: 0.4434 (mtt-85) cc_final: 0.3284 (tpt170)
REVERT: E  166 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8842 (mm-30)
REVERT: F  148 ARG cc_start: 0.4400 (mtt-85) cc_final: 0.3564 (tpt170)
  outliers start: 22
  outliers final: 19
  residues processed: 155
  average time/residue: 0.0857
  time to fit residues: 19.4556
Evaluate side-chains
  149 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
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   98 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain D residue  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   89 THR
Chi-restraints excluded: chain F residue   98 TYR
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  231 VAL
Chi-restraints excluded: chain F residue  233 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 104 optimal weight:   10.0000
   chunk 68 optimal weight:    7.9990
   chunk 5 optimal weight:    0.0370
   chunk 8 optimal weight:    2.9990
   chunk 84 optimal weight:    7.9990
   chunk 96 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 107 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0370
   overall best weight:    1.8142

-------------------------------------------------------------------------------
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 = 0.3712 r_free = 0.3712 target = 0.100199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.070080 restraints weight = 26115.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.072513 restraints weight = 11882.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.073940 restraints weight = 7904.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.074417 restraints weight = 6502.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.074927 restraints weight = 6046.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9846  Z= 0.144
  Angle     :  0.596   5.538  13344  Z= 0.312
  Chirality :  0.037   0.127   1524
  Planarity :  0.003   0.029   1608
  Dihedral  :  4.106  39.763   1268
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 21.59 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.26), residues: 1152
  helix:  2.56 (0.18), residues: 834
  sheet:  1.15 (0.62), residues: 72
  loop : -1.57 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 101 
 TYR   0.015   0.001   TYR D 177 
 PHE   0.011   0.001   PHE F 229 
 TRP   0.027   0.001   TRP B  25 
 HIS   0.003   0.000   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 9828)
  covalent geometry    : angle       0.59253 (13308)
  SS BOND              : bond        0.00544 (   18)
  SS BOND              : angle       1.40691 (   36)
  hydrogen bonds       : bond        0.03748 (  643)
  hydrogen bonds       : angle       2.76949 ( 1911)

*********************** 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
  151 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A   84 PHE cc_start: 0.8827 (m-80) cc_final: 0.8610 (m-10)
REVERT: A  100 MET cc_start: 0.8363 (tmm) cc_final: 0.8110 (tmm)
REVERT: A  148 ARG cc_start: 0.4098 (mtt-85) cc_final: 0.3136 (tpt170)
REVERT: A  227 GLU cc_start: 0.8813 (tp30) cc_final: 0.8610 (tp30)
REVERT: B   31 ILE cc_start: 0.9361 (tp) cc_final: 0.9150 (tt)
REVERT: B  100 MET cc_start: 0.8276 (tmm) cc_final: 0.7807 (tmm)
REVERT: B  148 ARG cc_start: 0.4475 (mtt-85) cc_final: 0.3209 (tpt170)
REVERT: B  213 MET cc_start: 0.9147 (mmm) cc_final: 0.8902 (mmm)
REVERT: C  148 ARG cc_start: 0.4456 (mtt-85) cc_final: 0.3462 (tpt170)
REVERT: C  166 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8769 (mm-30)
REVERT: D   84 PHE cc_start: 0.8820 (m-80) cc_final: 0.8582 (m-10)
REVERT: D  100 MET cc_start: 0.8252 (tmm) cc_final: 0.7808 (tmm)
REVERT: D  148 ARG cc_start: 0.3788 (mtt-85) cc_final: 0.3011 (tpt170)
REVERT: E  148 ARG cc_start: 0.4429 (mtt-85) cc_final: 0.3263 (tpt170)
REVERT: F  148 ARG cc_start: 0.4380 (mtt-85) cc_final: 0.3538 (tpt170)
  outliers start: 23
  outliers final: 21
  residues processed: 151
  average time/residue: 0.0854
  time to fit residues: 18.7414
Evaluate side-chains
  150 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 THR
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   89 THR
Chi-restraints excluded: chain B residue  233 PHE
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  233 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 E residue  233 PHE
Chi-restraints excluded: chain F residue   98 TYR
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  231 VAL
Chi-restraints excluded: chain F residue  233 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0010
   chunk 67 optimal weight:   40.0000
   chunk 10 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 14 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.7388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.102568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.072679 restraints weight = 25783.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.075139 restraints weight = 11571.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.076614 restraints weight = 7709.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.077091 restraints weight = 6324.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.077662 restraints weight = 5884.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9846  Z= 0.112
  Angle     :  0.571   6.593  13344  Z= 0.298
  Chirality :  0.035   0.117   1524
  Planarity :  0.003   0.030   1608
  Dihedral  :  3.868  37.469   1268
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 22.35 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.51 (0.26), residues: 1152
  helix:  2.61 (0.18), residues: 834
  sheet:  1.96 (0.65), residues: 60
  loop : -1.83 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 101 
 TYR   0.017   0.001   TYR D 177 
 PHE   0.011   0.001   PHE A 229 
 TRP   0.029   0.002   TRP D  25 
 HIS   0.002   0.000   HIS F  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9828)
  covalent geometry    : angle       0.56794 (13308)
  SS BOND              : bond        0.00514 (   18)
  SS BOND              : angle       1.23859 (   36)
  hydrogen bonds       : bond        0.02889 (  643)
  hydrogen bonds       : angle       2.63310 ( 1911)

*********************** 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
  145 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A  100 MET cc_start: 0.8364 (tmm) cc_final: 0.8104 (tmm)
REVERT: A  148 ARG cc_start: 0.4039 (mtt-85) cc_final: 0.3135 (tpt170)
REVERT: A  227 GLU cc_start: 0.8807 (tp30) cc_final: 0.8592 (tp30)
REVERT: B  100 MET cc_start: 0.8273 (tmm) cc_final: 0.8032 (tmm)
REVERT: B  148 ARG cc_start: 0.4494 (mtt-85) cc_final: 0.3287 (tpt170)
REVERT: B  213 MET cc_start: 0.9165 (mmm) cc_final: 0.8934 (mmm)
REVERT: C  148 ARG cc_start: 0.4493 (mtt-85) cc_final: 0.3573 (tpt170)
REVERT: C  166 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8493 (tp30)
REVERT: D   84 PHE cc_start: 0.8783 (m-80) cc_final: 0.8531 (m-10)
REVERT: D  100 MET cc_start: 0.8117 (tmm) cc_final: 0.7681 (tmm)
REVERT: D  148 ARG cc_start: 0.4036 (mtt-85) cc_final: 0.3142 (tpt170)
REVERT: E  148 ARG cc_start: 0.4405 (mtt-85) cc_final: 0.3328 (tpt170)
REVERT: F  148 ARG cc_start: 0.4335 (mtt-85) cc_final: 0.3530 (tpt170)
  outliers start: 14
  outliers final: 13
  residues processed: 145
  average time/residue: 0.0848
  time to fit residues: 17.8394
Evaluate side-chains
  137 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
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   37 LEU
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  231 VAL
Chi-restraints excluded: chain F residue  233 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.2980
   chunk 109 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 57 optimal weight:    0.2980
   chunk 12 optimal weight:    0.7980
   chunk 63 optimal weight:    0.1980
   chunk 0 optimal weight:   50.0000
   chunk 78 optimal weight:    6.9990
   chunk 50 optimal weight:    0.8980
   chunk 48 optimal weight:   40.0000
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3694 r_free = 0.3694 target = 0.101514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.071491 restraints weight = 25268.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.074069 restraints weight = 11512.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.075428 restraints weight = 7651.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.076391 restraints weight = 6322.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.076655 restraints weight = 5666.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.3593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9846  Z= 0.110
  Angle     :  0.576   7.124  13344  Z= 0.299
  Chirality :  0.035   0.117   1524
  Planarity :  0.004   0.032   1608
  Dihedral  :  3.595  13.864   1266
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.58 (0.26), residues: 1152
  helix:  2.66 (0.18), residues: 834
  sheet:  1.89 (0.66), residues: 60
  loop : -1.79 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 101 
 TYR   0.017   0.001   TYR A 177 
 PHE   0.011   0.001   PHE F 229 
 TRP   0.035   0.002   TRP B  25 
 HIS   0.001   0.000   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9828)
  covalent geometry    : angle       0.57314 (13308)
  SS BOND              : bond        0.00477 (   18)
  SS BOND              : angle       1.15982 (   36)
  hydrogen bonds       : bond        0.02628 (  643)
  hydrogen bonds       : angle       2.55237 ( 1911)

********************** 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
  145 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A   84 PHE cc_start: 0.8858 (m-80) cc_final: 0.8603 (m-10)
REVERT: A  100 MET cc_start: 0.8311 (tmm) cc_final: 0.8062 (tmm)
REVERT: A  148 ARG cc_start: 0.3992 (mtt-85) cc_final: 0.3167 (tpt170)
REVERT: A  166 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8888 (mm-30)
REVERT: A  227 GLU cc_start: 0.8795 (tp30) cc_final: 0.8588 (tp30)
REVERT: B  148 ARG cc_start: 0.4406 (mtt-85) cc_final: 0.3243 (tpt170)
REVERT: B  213 MET cc_start: 0.9108 (mmm) cc_final: 0.8890 (mmm)
REVERT: C  148 ARG cc_start: 0.4463 (mtt-85) cc_final: 0.3564 (tpt170)
REVERT: C  166 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8429 (tp30)
REVERT: D  100 MET cc_start: 0.8015 (tmm) cc_final: 0.7692 (tmm)
REVERT: D  148 ARG cc_start: 0.3954 (mtt-85) cc_final: 0.3080 (tpt170)
REVERT: D  227 GLU cc_start: 0.8883 (tp30) cc_final: 0.8221 (tm-30)
REVERT: D  231 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7153 (p)
REVERT: E  148 ARG cc_start: 0.4362 (mtt-85) cc_final: 0.3291 (tpt170)
REVERT: F  148 ARG cc_start: 0.4257 (mtt-85) cc_final: 0.3482 (tpt170)
REVERT: F  227 GLU cc_start: 0.8841 (tp30) cc_final: 0.8151 (tm-30)
REVERT: F  231 VAL cc_start: 0.8053 (OUTLIER) cc_final: 0.7175 (p)
  outliers start: 16
  outliers final: 10
  residues processed: 145
  average time/residue: 0.0927
  time to fit residues: 19.6112
Evaluate side-chains
  137 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
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  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  231 VAL
Chi-restraints excluded: chain F residue  233 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3667 r_free = 0.3667 target = 0.099978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.069715 restraints weight = 25336.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.072265 restraints weight = 11804.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.073804 restraints weight = 7852.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.074563 restraints weight = 6378.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.074847 restraints weight = 5781.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.3509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9846  Z= 0.121
  Angle     :  0.601   8.076  13344  Z= 0.311
  Chirality :  0.036   0.113   1524
  Planarity :  0.004   0.032   1608
  Dihedral  :  3.617  14.201   1266
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 22.44 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.63 (0.26), residues: 1152
  helix:  2.70 (0.18), residues: 834
  sheet:  1.88 (0.67), residues: 60
  loop : -1.77 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 101 
 TYR   0.016   0.001   TYR D 177 
 PHE   0.011   0.001   PHE F 229 
 TRP   0.031   0.002   TRP B  25 
 HIS   0.001   0.000   HIS F  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9828)
  covalent geometry    : angle       0.59839 (13308)
  SS BOND              : bond        0.00475 (   18)
  SS BOND              : angle       1.17901 (   36)
  hydrogen bonds       : bond        0.03142 (  643)
  hydrogen bonds       : angle       2.57199 ( 1911)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1472.64 seconds
wall clock time: 26 minutes 12.22 seconds (1572.22 seconds total)