Starting phenix.real_space_refine
on Sat Aug 23 04:22:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xqh_33396/08_2025/7xqh_33396.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xqh_33396/08_2025/7xqh_33396.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xqh_33396/08_2025/7xqh_33396.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xqh_33396/08_2025/7xqh_33396.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xqh_33396/08_2025/7xqh_33396.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xqh_33396/08_2025/7xqh_33396.cif"
  }
  resolution = 3.8
  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    6516      2.51       5
     N    1548      2.21       5
     O    1662      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9774
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1629
          Classifications: {'peptide': 200}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 193}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 1.22, per 1000 atoms: 0.12
  Number of scatterers: 9774
  At special positions: 0
  Unit cell: (102.608, 106, 102.608, 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    1662      8.00
     N    1548      7.00
     C    6516      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 332.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2268

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 6 sheets defined
      72.0% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 15
    Processing helix  chain 'A' and resid 20 through 25
    Processing helix  chain 'A' and resid 27 through 32
    Processing helix  chain 'A' and resid 33 through 40
    Processing helix  chain 'A' and resid 40 through 45
      removed outlier: 3.801A  pdb=" N   ALA A  44 " --> pdb=" O   ALA A  40 " (cutoff:3.500A)
      removed outlier: 3.854A  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: 3.972A  pdb=" N   VAL A  64 " --> pdb=" O   GLY A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 107
      removed outlier: 3.535A  pdb=" N   VAL A  87 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      Proline residue:  A  88  - end of helix
    Processing helix  chain 'A' and resid 149 through 177
      removed outlier: 4.059A  pdb=" N   ARG A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 235
      removed outlier: 3.848A  pdb=" N   LYS A 206 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLU A 227 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A 228 " --> pdb=" O   ASN A 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 15
    Processing helix  chain 'B' and resid 20 through 25
    Processing helix  chain 'B' and resid 27 through 32
    Processing helix  chain 'B' and resid 33 through 40
    Processing helix  chain 'B' and resid 40 through 45
      removed outlier: 3.800A  pdb=" N   ALA B  44 " --> pdb=" O   ALA B  40 " (cutoff:3.500A)
      removed outlier: 3.855A  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: 3.972A  pdb=" N   VAL B  64 " --> pdb=" O   GLY B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 107
      removed outlier: 3.535A  pdb=" N   VAL B  87 " --> pdb=" O   ILE B  83 " (cutoff:3.500A)
      Proline residue:  B  88  - end of helix
    Processing helix  chain 'B' and resid 149 through 177
      removed outlier: 4.058A  pdb=" N   ARG B 153 " --> pdb=" O   GLY B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 235
      removed outlier: 3.848A  pdb=" N   LYS B 206 " --> pdb=" O   ARG B 202 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLU B 227 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU B 228 " --> pdb=" O   ASN B 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 15
    Processing helix  chain 'C' and resid 20 through 25
    Processing helix  chain 'C' and resid 27 through 32
    Processing helix  chain 'C' and resid 33 through 40
    Processing helix  chain 'C' and resid 40 through 45
      removed outlier: 3.801A  pdb=" N   ALA C  44 " --> pdb=" O   ALA C  40 " (cutoff:3.500A)
      removed outlier: 3.854A  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: 3.972A  pdb=" N   VAL C  64 " --> pdb=" O   GLY C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 107
      removed outlier: 3.535A  pdb=" N   VAL C  87 " --> pdb=" O   ILE C  83 " (cutoff:3.500A)
      Proline residue:  C  88  - end of helix
    Processing helix  chain 'C' and resid 149 through 177
      removed outlier: 4.059A  pdb=" N   ARG C 153 " --> pdb=" O   GLY C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 235
      removed outlier: 3.848A  pdb=" N   LYS C 206 " --> pdb=" O   ARG C 202 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLU C 227 " --> pdb=" O   LEU C 223 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU C 228 " --> pdb=" O   ASN C 224 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 15
    Processing helix  chain 'D' and resid 20 through 25
    Processing helix  chain 'D' and resid 27 through 32
    Processing helix  chain 'D' and resid 33 through 40
    Processing helix  chain 'D' and resid 40 through 45
      removed outlier: 3.801A  pdb=" N   ALA D  44 " --> pdb=" O   ALA D  40 " (cutoff:3.500A)
      removed outlier: 3.854A  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: 3.972A  pdb=" N   VAL D  64 " --> pdb=" O   GLY D  60 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 107
      removed outlier: 3.535A  pdb=" N   VAL D  87 " --> pdb=" O   ILE D  83 " (cutoff:3.500A)
      Proline residue:  D  88  - end of helix
    Processing helix  chain 'D' and resid 149 through 177
      removed outlier: 4.059A  pdb=" N   ARG D 153 " --> pdb=" O   GLY D 149 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 235
      removed outlier: 3.848A  pdb=" N   LYS D 206 " --> pdb=" O   ARG D 202 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLU D 227 " --> pdb=" O   LEU D 223 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU D 228 " --> pdb=" O   ASN D 224 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 7 through 15
    Processing helix  chain 'E' and resid 20 through 25
    Processing helix  chain 'E' and resid 27 through 32
    Processing helix  chain 'E' and resid 33 through 40
    Processing helix  chain 'E' and resid 40 through 45
      removed outlier: 3.801A  pdb=" N   ALA E  44 " --> pdb=" O   ALA E  40 " (cutoff:3.500A)
      removed outlier: 3.853A  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: 3.972A  pdb=" N   VAL E  64 " --> pdb=" O   GLY E  60 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 73 through 107
      removed outlier: 3.535A  pdb=" N   VAL E  87 " --> pdb=" O   ILE E  83 " (cutoff:3.500A)
      Proline residue:  E  88  - end of helix
    Processing helix  chain 'E' and resid 149 through 177
      removed outlier: 4.059A  pdb=" N   ARG E 153 " --> pdb=" O   GLY E 149 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 202 through 235
      removed outlier: 3.848A  pdb=" N   LYS E 206 " --> pdb=" O   ARG E 202 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLU E 227 " --> pdb=" O   LEU E 223 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU E 228 " --> pdb=" O   ASN E 224 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 7 through 15
    Processing helix  chain 'F' and resid 20 through 25
    Processing helix  chain 'F' and resid 27 through 32
    Processing helix  chain 'F' and resid 33 through 40
    Processing helix  chain 'F' and resid 40 through 45
      removed outlier: 3.801A  pdb=" N   ALA F  44 " --> pdb=" O   ALA F  40 " (cutoff:3.500A)
      removed outlier: 3.854A  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: 3.972A  pdb=" N   VAL F  64 " --> pdb=" O   GLY F  60 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 73 through 107
      removed outlier: 3.535A  pdb=" N   VAL F  87 " --> pdb=" O   ILE F  83 " (cutoff:3.500A)
      Proline residue:  F  88  - end of helix
    Processing helix  chain 'F' and resid 149 through 177
      removed outlier: 4.059A  pdb=" N   ARG F 153 " --> pdb=" O   GLY F 149 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 202 through 235
      removed outlier: 3.848A  pdb=" N   LYS F 206 " --> pdb=" O   ARG F 202 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLU F 227 " --> pdb=" O   LEU F 223 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU F 228 " --> pdb=" O   ASN F 224 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54
      removed outlier: 3.623A  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: 3.623A  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: 3.623A  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: 3.623A  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: 3.623A  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: 3.623A  pdb=" N   ARG F  53 " --> pdb=" O   PHE F 199 " (cutoff:3.500A)

    612 hydrogen bonds defined for protein.
    1818 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: 1.03

  Time building geometry restraints manager: 0.90 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: 2898
        1.34 -     1.46: 2154
        1.46 -     1.57: 4920
        1.57 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 10032
  Sorted by residual:
  bond pdb=" CA  VAL B  87 "
       pdb=" C   VAL B  87 "
    ideal  model  delta    sigma   weight residual
    1.520  1.538 -0.018 8.80e-03 1.29e+04 4.35e+00
  bond pdb=" CA  VAL E  87 "
       pdb=" C   VAL E  87 "
    ideal  model  delta    sigma   weight residual
    1.520  1.538 -0.018 8.80e-03 1.29e+04 4.28e+00
  bond pdb=" CA  VAL F  87 "
       pdb=" C   VAL F  87 "
    ideal  model  delta    sigma   weight residual
    1.520  1.538 -0.018 8.80e-03 1.29e+04 4.25e+00
  bond pdb=" CA  VAL C  87 "
       pdb=" C   VAL C  87 "
    ideal  model  delta    sigma   weight residual
    1.520  1.538 -0.018 8.80e-03 1.29e+04 4.25e+00
  bond pdb=" CA  VAL A  87 "
       pdb=" C   VAL A  87 "
    ideal  model  delta    sigma   weight residual
    1.520  1.538 -0.018 8.80e-03 1.29e+04 4.20e+00
  ... (remaining 10027 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 12981
        1.59 -     3.17: 481
        3.17 -     4.76: 80
        4.76 -     6.34: 36
        6.34 -     7.93: 12
  Bond angle restraints: 13590
  Sorted by residual:
  angle pdb=" C   SER D  86 "
        pdb=" N   VAL D  87 "
        pdb=" CA  VAL D  87 "
      ideal   model   delta    sigma   weight residual
     120.24  124.52   -4.28 6.30e-01 2.52e+00 4.63e+01
  angle pdb=" C   SER B  86 "
        pdb=" N   VAL B  87 "
        pdb=" CA  VAL B  87 "
      ideal   model   delta    sigma   weight residual
     120.24  124.52   -4.28 6.30e-01 2.52e+00 4.62e+01
  angle pdb=" C   SER A  86 "
        pdb=" N   VAL A  87 "
        pdb=" CA  VAL A  87 "
      ideal   model   delta    sigma   weight residual
     120.24  124.51   -4.27 6.30e-01 2.52e+00 4.60e+01
  angle pdb=" C   SER C  86 "
        pdb=" N   VAL C  87 "
        pdb=" CA  VAL C  87 "
      ideal   model   delta    sigma   weight residual
     120.24  124.51   -4.27 6.30e-01 2.52e+00 4.60e+01
  angle pdb=" C   SER F  86 "
        pdb=" N   VAL F  87 "
        pdb=" CA  VAL F  87 "
      ideal   model   delta    sigma   weight residual
     120.24  124.50   -4.26 6.30e-01 2.52e+00 4.58e+01
  ... (remaining 13585 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.78: 4992
       13.78 -    27.56: 534
       27.56 -    41.33: 222
       41.33 -    55.11: 90
       55.11 -    68.89: 36
  Dihedral angle restraints: 5874
    sinusoidal: 2364
      harmonic: 3510
  Sorted by residual:
  dihedral pdb=" CA  TYR E 177 "
           pdb=" C   TYR E 177 "
           pdb=" N   GLY E 178 "
           pdb=" CA  GLY E 178 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.31  -16.69     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  TYR A 177 "
           pdb=" C   TYR A 177 "
           pdb=" N   GLY A 178 "
           pdb=" CA  GLY A 178 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.34  -16.66     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  TYR B 177 "
           pdb=" C   TYR B 177 "
           pdb=" N   GLY B 178 "
           pdb=" CA  GLY B 178 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.35  -16.65     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 5871 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1119
       0.044 -    0.088: 334
       0.088 -    0.132: 83
       0.132 -    0.176: 0
       0.176 -    0.220: 6
  Chirality restraints: 1542
  Sorted by residual:
  chirality pdb=" CA  HIS A 194 "
            pdb=" N   HIS A 194 "
            pdb=" C   HIS A 194 "
            pdb=" CB  HIS A 194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  HIS D 194 "
            pdb=" N   HIS D 194 "
            pdb=" C   HIS D 194 "
            pdb=" CB  HIS D 194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  HIS E 194 "
            pdb=" N   HIS E 194 "
            pdb=" C   HIS E 194 "
            pdb=" CB  HIS E 194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1539 not shown)

  Planarity restraints: 1644
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  87 "   -0.031 5.00e-02 4.00e+02   4.67e-02 3.48e+00
        pdb=" N   PRO B  88 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B  88 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B  88 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E  87 "    0.031 5.00e-02 4.00e+02   4.66e-02 3.48e+00
        pdb=" N   PRO E  88 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO E  88 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO E  88 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C  87 "    0.031 5.00e-02 4.00e+02   4.66e-02 3.47e+00
        pdb=" N   PRO C  88 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO C  88 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C  88 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1641 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 3398
        2.85 -     3.36: 8833
        3.36 -     3.87: 15659
        3.87 -     4.39: 15479
        4.39 -     4.90: 27451
  Nonbonded interactions: 70820
  Sorted by model distance:
  nonbonded pdb=" O   LEU C  35 "
            pdb=" OG1 THR C  39 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" O   LEU B  35 "
            pdb=" OG1 THR B  39 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" O   LEU E  35 "
            pdb=" OG1 THR E  39 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" O   LEU A  35 "
            pdb=" OG1 THR A  39 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" O   LEU D  35 "
            pdb=" OG1 THR D  39 "
     model   vdw
     2.338 3.040
  ... (remaining 70815 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:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     7.260
  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:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
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      :  0.005   0.053  10050  Z= 0.235
  Angle     :  0.782   7.929  13626  Z= 0.475
  Chirality :  0.042   0.220   1542
  Planarity :  0.006   0.047   1644
  Dihedral  : 15.527  68.889   3552
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  3.57 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 15.08 %
    Favored  : 82.68 %
  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: -2.01 (0.21), residues: 1176
  helix: -1.31 (0.15), residues: 774
  sheet:  2.72 (0.64), residues: 66
  loop : -1.88 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG F 202 
 TYR   0.010   0.002   TYR F  92 
 PHE   0.011   0.001   PHE D  52 
 TRP   0.007   0.001   TRP C  78 
 HIS   0.001   0.000   HIS D  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 (10032)
  covalent geometry    : angle       0.78132 (13590)
  SS BOND              : bond        0.00166 (   18)
  SS BOND              : angle       0.85593 (   36)
  hydrogen bonds       : bond        0.13365 (  612)
  hydrogen bonds       : angle       5.37252 ( 1818)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 227
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8384 (p0) cc_final: 0.8140 (p0)
REVERT: A  100 MET cc_start: 0.8239 (ttt) cc_final: 0.7884 (ttt)
REVERT: A  104 GLU cc_start: 0.9259 (tt0) cc_final: 0.9014 (pt0)
REVERT: A  190 ASP cc_start: 0.8872 (m-30) cc_final: 0.8636 (t0)
REVERT: B  212 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8340 (t80)
REVERT: C   47 ASP cc_start: 0.8435 (p0) cc_final: 0.8194 (p0)
REVERT: C  100 MET cc_start: 0.8139 (ttt) cc_final: 0.7809 (ttt)
REVERT: C  104 GLU cc_start: 0.9281 (tt0) cc_final: 0.9011 (pt0)
REVERT: C  190 ASP cc_start: 0.8807 (m-30) cc_final: 0.8514 (t0)
REVERT: D   47 ASP cc_start: 0.8393 (p0) cc_final: 0.8178 (p0)
REVERT: D  100 MET cc_start: 0.8246 (ttt) cc_final: 0.7944 (ttt)
REVERT: D  104 GLU cc_start: 0.9301 (tt0) cc_final: 0.9029 (pt0)
REVERT: D  190 ASP cc_start: 0.8852 (m-30) cc_final: 0.8558 (t0)
REVERT: E  100 MET cc_start: 0.8083 (ttt) cc_final: 0.7604 (tmm)
REVERT: E  104 GLU cc_start: 0.9378 (tt0) cc_final: 0.8963 (pt0)
REVERT: E  212 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8288 (t80)
REVERT: F   47 ASP cc_start: 0.8452 (p0) cc_final: 0.8201 (p0)
REVERT: F  100 MET cc_start: 0.8186 (ttt) cc_final: 0.7883 (ttt)
REVERT: F  104 GLU cc_start: 0.9277 (tt0) cc_final: 0.9015 (pt0)
REVERT: F  190 ASP cc_start: 0.8832 (m-30) cc_final: 0.8526 (t0)
  outliers start: 24
  outliers final: 16
  residues processed: 239
  average time/residue: 0.0684
  time to fit residues: 24.0307
Evaluate side-chains
  176 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 ASP
Chi-restraints excluded: chain A residue  197 ASP
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain B residue    3 ASP
Chi-restraints excluded: chain B residue  197 ASP
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain C residue    3 ASP
Chi-restraints excluded: chain C residue  197 ASP
Chi-restraints excluded: chain C residue  212 PHE
Chi-restraints excluded: chain D residue    3 ASP
Chi-restraints excluded: chain D residue  197 ASP
Chi-restraints excluded: chain D residue  212 PHE
Chi-restraints excluded: chain E residue    3 ASP
Chi-restraints excluded: chain E residue  197 ASP
Chi-restraints excluded: chain E residue  212 PHE
Chi-restraints excluded: chain F residue    3 ASP
Chi-restraints excluded: chain F residue  197 ASP
Chi-restraints excluded: chain F residue  212 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 117 optimal weight:    4.9990
   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  81 GLN
A 224 ASN
B  81 GLN
B 224 ASN
C  81 GLN
** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 GLN
D 224 ASN
E  81 GLN
E 224 ASN
F  81 GLN
** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.094622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.071738 restraints weight = 30440.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.074016 restraints weight = 13823.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.075584 restraints weight = 8514.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.076329 restraints weight = 6330.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.076507 restraints weight = 5453.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10050  Z= 0.180
  Angle     :  0.663   9.250  13626  Z= 0.339
  Chirality :  0.041   0.188   1542
  Planarity :  0.004   0.022   1644
  Dihedral  :  6.887  59.524   1326
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  3.57 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  9.50 %
    Allowed  : 14.80 %
    Favored  : 75.70 %
  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:  0.58 (0.24), residues: 1176
  helix:  0.99 (0.18), residues: 780
  sheet:  3.90 (0.69), residues: 60
  loop : -1.71 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  53 
 TYR   0.011   0.001   TYR B 177 
 PHE   0.014   0.001   PHE E 233 
 TRP   0.020   0.001   TRP B   4 
 HIS   0.003   0.001   HIS E 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (10032)
  covalent geometry    : angle       0.64995 (13590)
  SS BOND              : bond        0.00739 (   18)
  SS BOND              : angle       2.67444 (   36)
  hydrogen bonds       : bond        0.04317 (  612)
  hydrogen bonds       : angle       3.77133 ( 1818)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 102
    poor density    : 132
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.6745 (t80)
REVERT: A  100 MET cc_start: 0.8360 (ttt) cc_final: 0.7996 (ttt)
REVERT: A  104 GLU cc_start: 0.9295 (tt0) cc_final: 0.9025 (pt0)
REVERT: B   47 ASP cc_start: 0.8277 (p0) cc_final: 0.7960 (p0)
REVERT: C   47 ASP cc_start: 0.8349 (p0) cc_final: 0.7781 (p0)
REVERT: C  100 MET cc_start: 0.8343 (ttt) cc_final: 0.8006 (ttt)
REVERT: C  104 GLU cc_start: 0.9293 (tt0) cc_final: 0.9041 (pt0)
REVERT: C  202 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8075 (mtm180)
REVERT: D   47 ASP cc_start: 0.8323 (p0) cc_final: 0.8107 (p0)
REVERT: D  100 MET cc_start: 0.8322 (ttt) cc_final: 0.8008 (ttt)
REVERT: D  104 GLU cc_start: 0.9306 (tt0) cc_final: 0.9027 (pt0)
REVERT: E   47 ASP cc_start: 0.8196 (p0) cc_final: 0.7910 (p0)
REVERT: E  100 MET cc_start: 0.8267 (ttt) cc_final: 0.7906 (ttp)
REVERT: E  104 GLU cc_start: 0.9415 (tt0) cc_final: 0.9198 (pt0)
REVERT: E  213 MET cc_start: 0.8949 (mmp) cc_final: 0.8566 (mmp)
REVERT: F   47 ASP cc_start: 0.8349 (p0) cc_final: 0.7808 (p0)
REVERT: F  100 MET cc_start: 0.8359 (ttt) cc_final: 0.8015 (ttt)
REVERT: F  104 GLU cc_start: 0.9275 (tt0) cc_final: 0.9031 (pt0)
REVERT: F  202 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8045 (mtm180)
  outliers start: 102
  outliers final: 67
  residues processed: 204
  average time/residue: 0.0845
  time to fit residues: 24.0400
Evaluate side-chains
  191 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 121
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  197 ASP
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  197 ASP
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  224 ASN
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue    7 LEU
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  197 ASP
Chi-restraints excluded: chain C residue  202 ARG
Chi-restraints excluded: chain C residue  212 PHE
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain D residue   32 PHE
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   96 VAL
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  167 VAL
Chi-restraints excluded: chain D residue  197 ASP
Chi-restraints excluded: chain D residue  212 PHE
Chi-restraints excluded: chain D residue  224 ASN
Chi-restraints excluded: chain D residue  226 ILE
Chi-restraints excluded: chain E residue   32 PHE
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  106 LEU
Chi-restraints excluded: chain E residue  167 VAL
Chi-restraints excluded: chain E residue  197 ASP
Chi-restraints excluded: chain E residue  212 PHE
Chi-restraints excluded: chain E residue  224 ASN
Chi-restraints excluded: chain E residue  226 ILE
Chi-restraints excluded: chain F residue    7 LEU
Chi-restraints excluded: chain F residue   32 PHE
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   96 VAL
Chi-restraints excluded: chain F residue  106 LEU
Chi-restraints excluded: chain F residue  167 VAL
Chi-restraints excluded: chain F residue  197 ASP
Chi-restraints excluded: chain F residue  202 ARG
Chi-restraints excluded: chain F residue  212 PHE
Chi-restraints excluded: chain F residue  226 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 60 optimal weight:    0.4980
   chunk 95 optimal weight:    9.9990
   chunk 76 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   chunk 0 optimal weight:   50.0000
   chunk 119 optimal weight:    7.9990
   chunk 110 optimal weight:   20.0000
   chunk 83 optimal weight:    0.0770
   overall best weight:    0.8942

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

Flipped N/Q/H residues before XYZ refinement:
A 224 ASN
B 224 ASN
C 224 ASN
D 224 ASN
F 224 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.094768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.071623 restraints weight = 32148.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.073874 restraints weight = 14720.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.075347 restraints weight = 9190.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.075935 restraints weight = 6986.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.076450 restraints weight = 6142.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10050  Z= 0.122
  Angle     :  0.650  10.677  13626  Z= 0.317
  Chirality :  0.040   0.230   1542
  Planarity :  0.003   0.025   1644
  Dihedral  :  6.361  59.683   1314
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  2.98 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 18.72 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.31 (0.25), residues: 1176
  helix:  1.46 (0.18), residues: 816
  sheet:  3.75 (0.73), residues: 60
  loop : -1.40 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 189 
 TYR   0.011   0.001   TYR B 177 
 PHE   0.007   0.001   PHE C 233 
 TRP   0.011   0.001   TRP A   4 
 HIS   0.003   0.001   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10032)
  covalent geometry    : angle       0.63754 (13590)
  SS BOND              : bond        0.00667 (   18)
  SS BOND              : angle       2.50341 (   36)
  hydrogen bonds       : bond        0.03582 (  612)
  hydrogen bonds       : angle       3.64867 ( 1818)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 153
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.8376 (ttt) cc_final: 0.7931 (ttt)
REVERT: A  104 GLU cc_start: 0.9308 (tt0) cc_final: 0.9045 (pt0)
REVERT: A  223 LEU cc_start: 0.9431 (tp) cc_final: 0.9084 (tt)
REVERT: B   91 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8856 (tt)
REVERT: B  212 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8199 (t80)
REVERT: D  100 MET cc_start: 0.8368 (ttt) cc_final: 0.7950 (ttt)
REVERT: D  104 GLU cc_start: 0.9324 (tt0) cc_final: 0.9046 (pt0)
REVERT: E  100 MET cc_start: 0.8299 (ttt) cc_final: 0.7906 (ttp)
REVERT: E  104 GLU cc_start: 0.9461 (tt0) cc_final: 0.9208 (pt0)
REVERT: F  100 MET cc_start: 0.8359 (ttt) cc_final: 0.7995 (ttt)
REVERT: F  104 GLU cc_start: 0.9343 (tt0) cc_final: 0.9066 (pt0)
  outliers start: 58
  outliers final: 40
  residues processed: 185
  average time/residue: 0.0773
  time to fit residues: 20.8598
Evaluate side-chains
  183 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 141
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  212 PHE
Chi-restraints excluded: chain C residue  224 ASN
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   32 PHE
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  212 PHE
Chi-restraints excluded: chain E residue   32 PHE
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  212 PHE
Chi-restraints excluded: chain E residue  226 ILE
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   32 PHE
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue  212 PHE
Chi-restraints excluded: chain F residue  224 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 19 optimal weight:    9.9990
   chunk 11 optimal weight:    8.9990
   chunk 94 optimal weight:    0.3980
   chunk 69 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 111 optimal weight:    5.9990
   chunk 100 optimal weight:    0.0010
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.6792

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

Flipped N/Q/H residues before XYZ refinement:
A 224 ASN
B 224 ASN
C  49 GLN
D  49 GLN
D 224 ASN
** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.093945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.070592 restraints weight = 33064.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.072916 restraints weight = 15162.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.074250 restraints weight = 9453.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.075226 restraints weight = 7218.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.075499 restraints weight = 6172.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.3005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10050  Z= 0.132
  Angle     :  0.624  10.462  13626  Z= 0.305
  Chirality :  0.039   0.154   1542
  Planarity :  0.003   0.024   1644
  Dihedral  :  5.789  59.812   1302
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  3.06 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 18.99 %
    Favored  : 74.39 %
  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:  1.82 (0.26), residues: 1176
  helix:  1.91 (0.19), residues: 816
  sheet:  3.34 (0.75), residues: 60
  loop : -1.27 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  53 
 TYR   0.014   0.001   TYR C  66 
 PHE   0.007   0.001   PHE F 209 
 TRP   0.006   0.001   TRP B   4 
 HIS   0.004   0.001   HIS F  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10032)
  covalent geometry    : angle       0.61665 (13590)
  SS BOND              : bond        0.00519 (   18)
  SS BOND              : angle       1.93440 (   36)
  hydrogen bonds       : bond        0.03411 (  612)
  hydrogen bonds       : angle       3.59687 ( 1818)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 137
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8247 (p0) cc_final: 0.8021 (p0)
REVERT: B   91 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8865 (tt)
REVERT: B  212 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8242 (t80)
REVERT: C  223 LEU cc_start: 0.9445 (tp) cc_final: 0.9188 (tt)
REVERT: E   47 ASP cc_start: 0.8260 (p0) cc_final: 0.7998 (p0)
REVERT: E  100 MET cc_start: 0.8346 (ttt) cc_final: 0.8058 (ttt)
REVERT: E  104 GLU cc_start: 0.9450 (tt0) cc_final: 0.9222 (pt0)
REVERT: F  223 LEU cc_start: 0.9447 (tp) cc_final: 0.9189 (tt)
  outliers start: 71
  outliers final: 58
  residues processed: 182
  average time/residue: 0.0594
  time to fit residues: 16.7707
Evaluate side-chains
  183 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 123
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  224 ASN
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue    7 LEU
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  212 PHE
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   32 PHE
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  212 PHE
Chi-restraints excluded: chain D residue  226 ILE
Chi-restraints excluded: chain E residue   32 PHE
Chi-restraints excluded: chain E residue   54 CYS
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue   89 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  106 LEU
Chi-restraints excluded: chain E residue  212 PHE
Chi-restraints excluded: chain E residue  226 ILE
Chi-restraints excluded: chain F residue    7 LEU
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   32 PHE
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue  106 LEU
Chi-restraints excluded: chain F residue  212 PHE
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  226 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   chunk 49 optimal weight:   10.0000
   chunk 113 optimal weight:    0.0030
   chunk 96 optimal weight:    3.9990
   chunk 117 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.1994

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

Flipped N/Q/H residues before XYZ refinement:
A 224 ASN
D 224 ASN
E  49 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.094616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.071310 restraints weight = 32549.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.073555 restraints weight = 15373.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.074990 restraints weight = 9679.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.075600 restraints weight = 7354.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.076194 restraints weight = 6496.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.3218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10050  Z= 0.115
  Angle     :  0.614  11.337  13626  Z= 0.296
  Chirality :  0.038   0.150   1542
  Planarity :  0.003   0.025   1644
  Dihedral  :  5.692  59.668   1302
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  2.47 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 20.95 %
    Favored  : 73.28 %
  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:  1.87 (0.26), residues: 1176
  helix:  1.93 (0.19), residues: 834
  sheet:  2.89 (0.76), residues: 60
  loop : -1.29 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  53 
 TYR   0.013   0.001   TYR D  66 
 PHE   0.007   0.001   PHE F 233 
 TRP   0.004   0.001   TRP F  78 
 HIS   0.003   0.001   HIS F  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10032)
  covalent geometry    : angle       0.60813 (13590)
  SS BOND              : bond        0.00612 (   18)
  SS BOND              : angle       1.77117 (   36)
  hydrogen bonds       : bond        0.03205 (  612)
  hydrogen bonds       : angle       3.55372 ( 1818)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 133
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8242 (p0) cc_final: 0.8035 (p0)
REVERT: A   92 TYR cc_start: 0.8697 (t80) cc_final: 0.8161 (t80)
REVERT: B   91 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8859 (tt)
REVERT: B  212 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8202 (t80)
REVERT: B  223 LEU cc_start: 0.9476 (tp) cc_final: 0.9181 (tt)
REVERT: E  100 MET cc_start: 0.8362 (ttt) cc_final: 0.8038 (ttt)
REVERT: E  104 GLU cc_start: 0.9431 (tt0) cc_final: 0.9211 (pt0)
  outliers start: 62
  outliers final: 50
  residues processed: 172
  average time/residue: 0.0557
  time to fit residues: 15.1016
Evaluate side-chains
  178 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 126
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain C residue    7 LEU
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  212 PHE
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   32 PHE
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  100 MET
Chi-restraints excluded: chain D residue  212 PHE
Chi-restraints excluded: chain D residue  226 ILE
Chi-restraints excluded: chain E residue   32 PHE
Chi-restraints excluded: chain E residue   54 CYS
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   95 HIS
Chi-restraints excluded: chain E residue  212 PHE
Chi-restraints excluded: chain E residue  226 ILE
Chi-restraints excluded: chain F residue    7 LEU
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   32 PHE
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue  100 MET
Chi-restraints excluded: chain F residue  212 PHE
Chi-restraints excluded: chain F residue  226 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 109 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 117 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0670
   overall best weight:    0.9920

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

Flipped N/Q/H residues before XYZ refinement:
A 224 ASN
D 224 ASN
E 224 ASN
F  49 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.095762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.072640 restraints weight = 32455.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.074926 restraints weight = 15319.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.076397 restraints weight = 9599.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.076992 restraints weight = 7279.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.077417 restraints weight = 6407.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.3407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10050  Z= 0.107
  Angle     :  0.610  12.080  13626  Z= 0.288
  Chirality :  0.038   0.150   1542
  Planarity :  0.003   0.027   1644
  Dihedral  :  5.562  59.838   1302
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  1.96 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 21.32 %
    Favored  : 73.28 %
  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:  2.05 (0.26), residues: 1176
  helix:  2.11 (0.19), residues: 834
  sheet:  2.68 (0.78), residues: 60
  loop : -1.31 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  53 
 TYR   0.009   0.001   TYR D  66 
 PHE   0.007   0.001   PHE B  52 
 TRP   0.004   0.000   TRP C  78 
 HIS   0.002   0.001   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (10032)
  covalent geometry    : angle       0.60449 (13590)
  SS BOND              : bond        0.00589 (   18)
  SS BOND              : angle       1.64307 (   36)
  hydrogen bonds       : bond        0.02999 (  612)
  hydrogen bonds       : angle       3.50620 ( 1818)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 139
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8247 (p0) cc_final: 0.8022 (p0)
REVERT: A   92 TYR cc_start: 0.8665 (t80) cc_final: 0.8109 (t80)
REVERT: B   91 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8848 (tt)
REVERT: B  212 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8210 (t80)
REVERT: C   92 TYR cc_start: 0.8635 (t80) cc_final: 0.8052 (t80)
REVERT: D   92 TYR cc_start: 0.8610 (t80) cc_final: 0.8046 (t80)
REVERT: E  100 MET cc_start: 0.8315 (ttt) cc_final: 0.8099 (ttt)
REVERT: E  104 GLU cc_start: 0.9463 (tt0) cc_final: 0.9146 (pt0)
REVERT: F   92 TYR cc_start: 0.8648 (t80) cc_final: 0.8062 (t80)
  outliers start: 58
  outliers final: 48
  residues processed: 179
  average time/residue: 0.0662
  time to fit residues: 18.4785
Evaluate side-chains
  185 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 135
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue    7 LEU
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   54 CYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  212 PHE
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   32 PHE
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   54 CYS
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  212 PHE
Chi-restraints excluded: chain D residue  226 ILE
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   32 PHE
Chi-restraints excluded: chain E residue   54 CYS
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   95 HIS
Chi-restraints excluded: chain E residue  212 PHE
Chi-restraints excluded: chain E residue  224 ASN
Chi-restraints excluded: chain F residue    7 LEU
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   32 PHE
Chi-restraints excluded: chain F residue   54 CYS
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  212 PHE
Chi-restraints excluded: chain F residue  226 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0970
   chunk 116 optimal weight:    0.9980
   chunk 19 optimal weight:    9.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    0.8178

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

Flipped N/Q/H residues before XYZ refinement:
A 224 ASN
D 224 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.095849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.073225 restraints weight = 32203.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.075505 restraints weight = 15043.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.076919 restraints weight = 9345.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.077568 restraints weight = 7029.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.078002 restraints weight = 6129.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.3540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10050  Z= 0.102
  Angle     :  0.617  12.566  13626  Z= 0.287
  Chirality :  0.037   0.152   1542
  Planarity :  0.003   0.027   1644
  Dihedral  :  5.515  59.970   1302
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  1.96 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 21.51 %
    Favored  : 73.18 %
  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:  2.13 (0.26), residues: 1176
  helix:  2.20 (0.19), residues: 834
  sheet:  2.63 (0.79), residues: 60
  loop : -1.41 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  53 
 TYR   0.010   0.001   TYR E  66 
 PHE   0.006   0.001   PHE C 233 
 TRP   0.003   0.000   TRP F  78 
 HIS   0.002   0.001   HIS E  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (10032)
  covalent geometry    : angle       0.61292 (13590)
  SS BOND              : bond        0.00524 (   18)
  SS BOND              : angle       1.51432 (   36)
  hydrogen bonds       : bond        0.02870 (  612)
  hydrogen bonds       : angle       3.47953 ( 1818)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 139
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8218 (p0) cc_final: 0.8001 (p0)
REVERT: A   92 TYR cc_start: 0.8670 (t80) cc_final: 0.8364 (t80)
REVERT: B   91 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8865 (tt)
REVERT: B  212 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8194 (t80)
REVERT: C   92 TYR cc_start: 0.8641 (t80) cc_final: 0.8313 (t80)
REVERT: D   92 TYR cc_start: 0.8640 (t80) cc_final: 0.8301 (t80)
REVERT: E  100 MET cc_start: 0.8362 (ttt) cc_final: 0.8037 (ttt)
REVERT: E  104 GLU cc_start: 0.9461 (tt0) cc_final: 0.9207 (pt0)
REVERT: E  223 LEU cc_start: 0.9473 (tp) cc_final: 0.9240 (tt)
REVERT: F   92 TYR cc_start: 0.8647 (t80) cc_final: 0.8326 (t80)
  outliers start: 57
  outliers final: 46
  residues processed: 178
  average time/residue: 0.0611
  time to fit residues: 17.0868
Evaluate side-chains
  185 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 137
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue    7 LEU
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   54 CYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  212 PHE
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   32 PHE
Chi-restraints excluded: chain D residue   54 CYS
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue  212 PHE
Chi-restraints excluded: chain D residue  226 ILE
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   32 PHE
Chi-restraints excluded: chain E residue   54 CYS
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   95 HIS
Chi-restraints excluded: chain E residue  212 PHE
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  226 ILE
Chi-restraints excluded: chain F residue    7 LEU
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   32 PHE
Chi-restraints excluded: chain F residue   54 CYS
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  212 PHE
Chi-restraints excluded: chain F residue  226 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 224 ASN
D 224 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.095330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.072247 restraints weight = 32612.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.074557 restraints weight = 15236.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.076005 restraints weight = 9491.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.076698 restraints weight = 7179.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.077085 restraints weight = 6266.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.3695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10050  Z= 0.104
  Angle     :  0.611  12.544  13626  Z= 0.283
  Chirality :  0.038   0.148   1542
  Planarity :  0.003   0.027   1644
  Dihedral  :  5.478  59.849   1302
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  1.87 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 22.81 %
    Favored  : 72.44 %
  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:  2.40 (0.26), residues: 1176
  helix:  2.59 (0.18), residues: 804
  sheet:  2.58 (0.80), residues: 60
  loop : -1.48 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  53 
 TYR   0.015   0.001   TYR B  17 
 PHE   0.006   0.001   PHE E 169 
 TRP   0.003   0.000   TRP F  78 
 HIS   0.002   0.001   HIS F  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (10032)
  covalent geometry    : angle       0.60693 (13590)
  SS BOND              : bond        0.00508 (   18)
  SS BOND              : angle       1.44969 (   36)
  hydrogen bonds       : bond        0.02805 (  612)
  hydrogen bonds       : angle       3.46617 ( 1818)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 139
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8244 (p0) cc_final: 0.8029 (p0)
REVERT: B   91 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8866 (tt)
REVERT: B   92 TYR cc_start: 0.8290 (t80) cc_final: 0.7771 (t80)
REVERT: B  212 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8214 (t80)
REVERT: E  100 MET cc_start: 0.8340 (ttt) cc_final: 0.8035 (ttt)
REVERT: E  104 GLU cc_start: 0.9477 (tt0) cc_final: 0.9182 (pt0)
  outliers start: 51
  outliers final: 43
  residues processed: 174
  average time/residue: 0.0644
  time to fit residues: 17.1675
Evaluate side-chains
  180 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 135
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue    7 LEU
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   54 CYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  212 PHE
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   32 PHE
Chi-restraints excluded: chain D residue   54 CYS
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue  212 PHE
Chi-restraints excluded: chain D residue  226 ILE
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   32 PHE
Chi-restraints excluded: chain E residue   54 CYS
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   95 HIS
Chi-restraints excluded: chain E residue  212 PHE
Chi-restraints excluded: chain F residue    7 LEU
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   32 PHE
Chi-restraints excluded: chain F residue   54 CYS
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  212 PHE
Chi-restraints excluded: chain F residue  226 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 34 optimal weight:    7.9990
   chunk 77 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   chunk 88 optimal weight:    0.8980
   chunk 1 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0980
   chunk 117 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
D 224 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.095616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.072695 restraints weight = 32460.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.075004 restraints weight = 15172.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.076118 restraints weight = 9415.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.077217 restraints weight = 7420.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.077547 restraints weight = 6221.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.3839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10050  Z= 0.100
  Angle     :  0.612  12.245  13626  Z= 0.282
  Chirality :  0.037   0.151   1542
  Planarity :  0.003   0.027   1644
  Dihedral  :  5.446  59.898   1302
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  1.62 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 23.65 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.43 (0.26), residues: 1176
  helix:  2.64 (0.18), residues: 804
  sheet:  2.53 (0.81), residues: 60
  loop : -1.53 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  53 
 TYR   0.012   0.001   TYR B  92 
 PHE   0.006   0.001   PHE C 233 
 TRP   0.003   0.000   TRP F  78 
 HIS   0.002   0.001   HIS D  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 (10032)
  covalent geometry    : angle       0.60905 (13590)
  SS BOND              : bond        0.00491 (   18)
  SS BOND              : angle       1.37777 (   36)
  hydrogen bonds       : bond        0.02693 (  612)
  hydrogen bonds       : angle       3.42379 ( 1818)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 138
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8258 (p0) cc_final: 0.8046 (p0)
REVERT: A   92 TYR cc_start: 0.8580 (t80) cc_final: 0.8238 (t80)
REVERT: B   91 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8865 (tt)
REVERT: B   92 TYR cc_start: 0.8308 (t80) cc_final: 0.7815 (t80)
REVERT: B  212 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8226 (t80)
REVERT: C   92 TYR cc_start: 0.8475 (t80) cc_final: 0.8127 (t80)
REVERT: D   92 TYR cc_start: 0.8499 (t80) cc_final: 0.8231 (t80)
REVERT: E  100 MET cc_start: 0.8328 (ttt) cc_final: 0.8017 (ttt)
REVERT: E  104 GLU cc_start: 0.9482 (tt0) cc_final: 0.9197 (pt0)
REVERT: F   92 TYR cc_start: 0.8488 (t80) cc_final: 0.8133 (t80)
  outliers start: 48
  outliers final: 42
  residues processed: 171
  average time/residue: 0.0599
  time to fit residues: 16.0029
Evaluate side-chains
  180 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 136
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   54 CYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  212 PHE
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   32 PHE
Chi-restraints excluded: chain D residue   54 CYS
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue  212 PHE
Chi-restraints excluded: chain D residue  226 ILE
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   32 PHE
Chi-restraints excluded: chain E residue   54 CYS
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  212 PHE
Chi-restraints excluded: chain E residue  226 ILE
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   32 PHE
Chi-restraints excluded: chain F residue   54 CYS
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  212 PHE
Chi-restraints excluded: chain F residue  226 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 40 optimal weight:   30.0000
   chunk 14 optimal weight:    0.9990
   chunk 86 optimal weight:    0.5980
   chunk 54 optimal weight:    5.9990
   chunk 24 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 117 optimal weight:    5.9990
   chunk 102 optimal weight:    7.9990
   chunk 41 optimal weight:   30.0000
   chunk 7 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
D 224 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.095933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.073334 restraints weight = 31934.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.075614 restraints weight = 14970.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.077024 restraints weight = 9313.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.077722 restraints weight = 7027.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.078012 restraints weight = 6084.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.3904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10050  Z= 0.105
  Angle     :  0.617  12.356  13626  Z= 0.283
  Chirality :  0.038   0.150   1542
  Planarity :  0.003   0.028   1644
  Dihedral  :  5.437  59.815   1302
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  1.87 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 24.58 %
    Favored  : 71.23 %
  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:  2.45 (0.26), residues: 1176
  helix:  2.68 (0.18), residues: 804
  sheet:  2.38 (0.80), residues: 60
  loop : -1.56 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  53 
 TYR   0.013   0.001   TYR B  92 
 PHE   0.006   0.001   PHE A  70 
 TRP   0.003   0.000   TRP B  78 
 HIS   0.002   0.001   HIS F  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (10032)
  covalent geometry    : angle       0.61416 (13590)
  SS BOND              : bond        0.00489 (   18)
  SS BOND              : angle       1.38522 (   36)
  hydrogen bonds       : bond        0.02755 (  612)
  hydrogen bonds       : angle       3.44348 ( 1818)

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

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

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2352 Ramachandran restraints generated.
    1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 134
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8272 (p0) cc_final: 0.8060 (p0)
REVERT: A   92 TYR cc_start: 0.8543 (t80) cc_final: 0.8200 (t80)
REVERT: B   91 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8866 (tt)
REVERT: B   92 TYR cc_start: 0.8364 (t80) cc_final: 0.7872 (t80)
REVERT: B  212 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8228 (t80)
REVERT: C   92 TYR cc_start: 0.8489 (t80) cc_final: 0.8125 (t80)
REVERT: D   92 TYR cc_start: 0.8507 (t80) cc_final: 0.8205 (t80)
REVERT: E  100 MET cc_start: 0.8372 (ttt) cc_final: 0.8057 (ttt)
REVERT: E  104 GLU cc_start: 0.9481 (tt0) cc_final: 0.9179 (pt0)
REVERT: E  212 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8210 (t80)
REVERT: F   92 TYR cc_start: 0.8508 (t80) cc_final: 0.8145 (t80)
  outliers start: 45
  outliers final: 41
  residues processed: 164
  average time/residue: 0.0599
  time to fit residues: 15.8581
Evaluate side-chains
  179 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 135
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   54 CYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  212 PHE
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   32 PHE
Chi-restraints excluded: chain D residue   54 CYS
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue  212 PHE
Chi-restraints excluded: chain D residue  226 ILE
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   32 PHE
Chi-restraints excluded: chain E residue   54 CYS
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   95 HIS
Chi-restraints excluded: chain E residue  212 PHE
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   32 PHE
Chi-restraints excluded: chain F residue   54 CYS
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  212 PHE
Chi-restraints excluded: chain F residue  226 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0870
   chunk 94 optimal weight:    0.9980
   chunk 95 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 69 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.7962

-------------------------------------------------------------------------------
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 = 0.3766 r_free = 0.3766 target = 0.096085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.073658 restraints weight = 32064.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.075901 restraints weight = 15151.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.077014 restraints weight = 9454.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.078062 restraints weight = 7415.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.078408 restraints weight = 6193.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.3973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10050  Z= 0.099
  Angle     :  0.609  12.303  13626  Z= 0.277
  Chirality :  0.037   0.149   1542
  Planarity :  0.003   0.028   1644
  Dihedral  :  5.426  59.728   1302
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  1.45 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 24.58 %
    Favored  : 71.42 %
  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:  2.41 (0.26), residues: 1176
  helix:  2.69 (0.18), residues: 804
  sheet:  2.10 (0.76), residues: 60
  loop : -1.65 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  53 
 TYR   0.012   0.001   TYR B  92 
 PHE   0.006   0.001   PHE E  70 
 TRP   0.003   0.000   TRP F  78 
 HIS   0.002   0.001   HIS F  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 (10032)
  covalent geometry    : angle       0.60591 (13590)
  SS BOND              : bond        0.00486 (   18)
  SS BOND              : angle       1.33716 (   36)
  hydrogen bonds       : bond        0.02644 (  612)
  hydrogen bonds       : angle       3.39271 ( 1818)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1241.97 seconds
wall clock time: 22 minutes 15.20 seconds (1335.20 seconds total)