Starting phenix.real_space_refine
on Wed Mar  4 03:37:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xqg_33395/03_2026/7xqg_33395.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xqg_33395/03_2026/7xqg_33395.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/7xqg_33395/03_2026/7xqg_33395.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xqg_33395/03_2026/7xqg_33395.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xqg_33395/03_2026/7xqg_33395.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xqg_33395/03_2026/7xqg_33395.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: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      48      5.16       5
     C    6846      2.51       5
     N    1566      2.21       5
     O    1740      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10206
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1636
          Classifications: {'peptide': 201}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 65
          Unusual residues: {'PTY': 1, 'Y01': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 20
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 1.53, per 1000 atoms: 0.15
  Number of scatterers: 10206
  At special positions: 0
  Unit cell: (106, 111.088, 99.216, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     P       6     15.00
     O    1740      8.00
     N    1566      7.00
     C    6846      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: 0.79
  Conformation dependent library (CDL) restraints added in 433.9 milliseconds
  

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2280

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 6 sheets defined
      74.6% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 15
      removed outlier: 3.512A  pdb=" N   GLN A  15 " --> pdb=" O   LEU A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 40
      removed outlier: 3.535A  pdb=" N   TRP A  25 " --> pdb=" O   GLY A  21 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 45
      removed outlier: 3.603A  pdb=" N   ALA A  44 " --> pdb=" O   ALA A  40 " (cutoff:3.500A)
      removed outlier: 3.751A  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: 3.797A  pdb=" N   VAL A  64 " --> pdb=" O   GLY A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 110
      Proline residue:  A  88  - end of helix
    Processing helix  chain 'A' and resid 151 through 177
    Processing helix  chain 'A' and resid 202 through 237
      removed outlier: 3.584A  pdb=" N   LYS A 237 " --> pdb=" O   PHE A 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 15
      removed outlier: 3.512A  pdb=" N   GLN B  15 " --> pdb=" O   LEU B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 40
      removed outlier: 3.535A  pdb=" N   TRP B  25 " --> pdb=" O   GLY B  21 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ALA B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 45
      removed outlier: 3.603A  pdb=" N   ALA B  44 " --> pdb=" O   ALA B  40 " (cutoff:3.500A)
      removed outlier: 3.751A  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: 3.796A  pdb=" N   VAL B  64 " --> pdb=" O   GLY B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 110
      Proline residue:  B  88  - end of helix
    Processing helix  chain 'B' and resid 151 through 177
    Processing helix  chain 'B' and resid 202 through 237
      removed outlier: 3.583A  pdb=" N   LYS B 237 " --> pdb=" O   PHE B 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 15
      removed outlier: 3.512A  pdb=" N   GLN C  15 " --> pdb=" O   LEU C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 40
      removed outlier: 3.535A  pdb=" N   TRP C  25 " --> pdb=" O   GLY C  21 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ALA C  40 " --> pdb=" O   LEU C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 45
      removed outlier: 3.603A  pdb=" N   ALA C  44 " --> pdb=" O   ALA C  40 " (cutoff:3.500A)
      removed outlier: 3.751A  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: 3.797A  pdb=" N   VAL C  64 " --> pdb=" O   GLY C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 110
      Proline residue:  C  88  - end of helix
    Processing helix  chain 'C' and resid 151 through 177
    Processing helix  chain 'C' and resid 202 through 237
      removed outlier: 3.584A  pdb=" N   LYS C 237 " --> pdb=" O   PHE C 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 4 through 15
      removed outlier: 3.512A  pdb=" N   GLN D  15 " --> pdb=" O   LEU D  11 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 21 through 40
      removed outlier: 3.535A  pdb=" N   TRP D  25 " --> pdb=" O   GLY D  21 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ALA D  40 " --> pdb=" O   LEU D  36 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 45
      removed outlier: 3.602A  pdb=" N   ALA D  44 " --> pdb=" O   ALA D  40 " (cutoff:3.500A)
      removed outlier: 3.751A  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: 3.796A  pdb=" N   VAL D  64 " --> pdb=" O   GLY D  60 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 110
      Proline residue:  D  88  - end of helix
    Processing helix  chain 'D' and resid 151 through 177
    Processing helix  chain 'D' and resid 202 through 237
      removed outlier: 3.583A  pdb=" N   LYS D 237 " --> pdb=" O   PHE D 233 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 4 through 15
      removed outlier: 3.512A  pdb=" N   GLN E  15 " --> pdb=" O   LEU E  11 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 21 through 40
      removed outlier: 3.534A  pdb=" N   TRP E  25 " --> pdb=" O   GLY E  21 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ALA E  40 " --> pdb=" O   LEU E  36 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 40 through 45
      removed outlier: 3.603A  pdb=" N   ALA E  44 " --> pdb=" O   ALA E  40 " (cutoff:3.500A)
      removed outlier: 3.751A  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: 3.795A  pdb=" N   VAL E  64 " --> pdb=" O   GLY E  60 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 73 through 110
      Proline residue:  E  88  - end of helix
    Processing helix  chain 'E' and resid 151 through 177
    Processing helix  chain 'E' and resid 202 through 237
      removed outlier: 3.584A  pdb=" N   LYS E 237 " --> pdb=" O   PHE E 233 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 4 through 15
      removed outlier: 3.511A  pdb=" N   GLN F  15 " --> pdb=" O   LEU F  11 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 21 through 40
      removed outlier: 3.535A  pdb=" N   TRP F  25 " --> pdb=" O   GLY F  21 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ALA F  40 " --> pdb=" O   LEU F  36 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 40 through 45
      removed outlier: 3.603A  pdb=" N   ALA F  44 " --> pdb=" O   ALA F  40 " (cutoff:3.500A)
      removed outlier: 3.752A  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: 3.796A  pdb=" N   VAL F  64 " --> pdb=" O   GLY F  60 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 73 through 110
      Proline residue:  F  88  - end of helix
    Processing helix  chain 'F' and resid 151 through 177
    Processing helix  chain 'F' and resid 202 through 237
      removed outlier: 3.584A  pdb=" N   LYS F 237 " --> pdb=" O   PHE F 233 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54
      removed outlier: 3.745A  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: 3.745A  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: 3.744A  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: 3.745A  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: 3.744A  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: 3.745A  pdb=" N   ARG F  53 " --> pdb=" O   PHE F 199 " (cutoff:3.500A)

    702 hydrogen bonds defined for protein.
    2088 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: 1.54

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1597
        1.33 -     1.45: 2897
        1.45 -     1.57: 5910
        1.57 -     1.69: 12
        1.69 -     1.81: 60
  Bond restraints: 10476
  Sorted by residual:
  bond pdb=" C   VAL D  87 "
       pdb=" N   PRO D  88 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.011 1.36e-02 5.41e+03 6.20e-01
  bond pdb=" C   VAL F  87 "
       pdb=" N   PRO F  88 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.011 1.36e-02 5.41e+03 6.20e-01
  bond pdb=" C   VAL B  87 "
       pdb=" N   PRO B  88 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.010 1.36e-02 5.41e+03 5.95e-01
  bond pdb=" C   VAL A  87 "
       pdb=" N   PRO A  88 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.010 1.36e-02 5.41e+03 5.90e-01
  bond pdb=" C   VAL C  87 "
       pdb=" N   PRO C  88 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.010 1.36e-02 5.41e+03 5.82e-01
  ... (remaining 10471 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 13864
        1.22 -     2.44: 244
        2.44 -     3.66: 52
        3.66 -     4.88: 12
        4.88 -     6.10: 18
  Bond angle restraints: 14190
  Sorted by residual:
  angle pdb=" C   SER C 201 "
        pdb=" N   ARG C 202 "
        pdb=" CA  ARG C 202 "
      ideal   model   delta    sigma   weight residual
     121.80  127.27   -5.47 2.44e+00 1.68e-01 5.02e+00
  angle pdb=" C   SER F 201 "
        pdb=" N   ARG F 202 "
        pdb=" CA  ARG F 202 "
      ideal   model   delta    sigma   weight residual
     121.80  127.26   -5.46 2.44e+00 1.68e-01 5.01e+00
  angle pdb=" C   SER E 201 "
        pdb=" N   ARG E 202 "
        pdb=" CA  ARG E 202 "
      ideal   model   delta    sigma   weight residual
     121.80  127.25   -5.45 2.44e+00 1.68e-01 4.99e+00
  angle pdb=" C   SER A 201 "
        pdb=" N   ARG A 202 "
        pdb=" CA  ARG A 202 "
      ideal   model   delta    sigma   weight residual
     121.80  127.24   -5.44 2.44e+00 1.68e-01 4.98e+00
  angle pdb=" C   SER D 201 "
        pdb=" N   ARG D 202 "
        pdb=" CA  ARG D 202 "
      ideal   model   delta    sigma   weight residual
     121.80  127.24   -5.44 2.44e+00 1.68e-01 4.98e+00
  ... (remaining 14185 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.74: 6026
       16.74 -    33.48: 303
       33.48 -    50.22: 97
       50.22 -    66.97: 24
       66.97 -    83.71: 12
  Dihedral angle restraints: 6462
    sinusoidal: 2934
      harmonic: 3528
  Sorted by residual:
  dihedral pdb=" N   PHE A 212 "
           pdb=" CA  PHE A 212 "
           pdb=" CB  PHE A 212 "
           pdb=" CG  PHE A 212 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -126.50  -53.50     3      1.50e+01 4.44e-03 9.21e+00
  dihedral pdb=" N   PHE C 212 "
           pdb=" CA  PHE C 212 "
           pdb=" CB  PHE C 212 "
           pdb=" CG  PHE C 212 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -126.52  -53.48     3      1.50e+01 4.44e-03 9.21e+00
  dihedral pdb=" N   PHE B 212 "
           pdb=" CA  PHE B 212 "
           pdb=" CB  PHE B 212 "
           pdb=" CG  PHE B 212 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -126.53  -53.47     3      1.50e+01 4.44e-03 9.21e+00
  ... (remaining 6459 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.021: 878
       0.021 -    0.041: 409
       0.041 -    0.062: 227
       0.062 -    0.083: 53
       0.083 -    0.103: 35
  Chirality restraints: 1602
  Sorted by residual:
  chirality pdb=" CA  PRO B 203 "
            pdb=" N   PRO B 203 "
            pdb=" C   PRO B 203 "
            pdb=" CB  PRO B 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.62    0.10 2.00e-01 2.50e+01 2.66e-01
  chirality pdb=" CA  PRO E 203 "
            pdb=" N   PRO E 203 "
            pdb=" C   PRO E 203 "
            pdb=" CB  PRO E 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.62    0.10 2.00e-01 2.50e+01 2.64e-01
  chirality pdb=" CA  VAL C 184 "
            pdb=" N   VAL C 184 "
            pdb=" C   VAL C 184 "
            pdb=" CB  VAL C 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.54   -0.10 2.00e-01 2.50e+01 2.63e-01
  ... (remaining 1599 not shown)

  Planarity restraints: 1674
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 190 "    0.014 5.00e-02 4.00e+02   2.13e-02 7.24e-01
        pdb=" N   PRO E 191 "   -0.037 5.00e-02 4.00e+02
        pdb=" CA  PRO E 191 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO E 191 "    0.011 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 190 "   -0.014 5.00e-02 4.00e+02   2.12e-02 7.20e-01
        pdb=" N   PRO C 191 "    0.037 5.00e-02 4.00e+02
        pdb=" CA  PRO C 191 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO C 191 "   -0.011 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP F 190 "    0.014 5.00e-02 4.00e+02   2.12e-02 7.20e-01
        pdb=" N   PRO F 191 "   -0.037 5.00e-02 4.00e+02
        pdb=" CA  PRO F 191 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO F 191 "    0.011 5.00e-02 4.00e+02
  ... (remaining 1671 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 2430
        2.79 -     3.32: 10217
        3.32 -     3.85: 16371
        3.85 -     4.37: 16449
        4.37 -     4.90: 30061
  Nonbonded interactions: 75528
  Sorted by model distance:
  nonbonded pdb=" O   LEU C  35 "
            pdb=" OG1 THR C  39 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   LEU F  35 "
            pdb=" OG1 THR F  39 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   LEU D  35 "
            pdb=" OG1 THR D  39 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   LEU A  35 "
            pdb=" OG1 THR A  39 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   LEU B  35 "
            pdb=" OG1 THR B  39 "
     model   vdw
     2.268 3.040
  ... (remaining 75523 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: 0.03
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:             1.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     9.510
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
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      :  0.002   0.018  10494  Z= 0.099
  Angle     :  0.459   6.101  14226  Z= 0.234
  Chirality :  0.032   0.103   1602
  Planarity :  0.002   0.021   1674
  Dihedral  : 12.111  83.707   4128
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  1.52 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  :  3.89 %
    Favored  : 91.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.98 (0.24), residues: 1182
  helix:  2.75 (0.17), residues: 834
  sheet:  3.07 (0.70), residues: 66
  loop : -0.84 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 153 
 TYR   0.008   0.001   TYR C 155 
 PHE   0.006   0.001   PHE E  32 
 TRP   0.003   0.001   TRP A  78 
 HIS   0.001   0.000   HIS F 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 (10476)
  covalent geometry    : angle       0.45865 (14190)
  SS BOND              : bond        0.00163 (   18)
  SS BOND              : angle       0.50849 (   36)
  hydrogen bonds       : bond        0.08910 (  702)
  hydrogen bonds       : angle       2.97157 ( 2088)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 296
  time to evaluate  : 0.253 
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: symmetry clash
REVERT: A   47 ASP cc_start: 0.8362 (p0) cc_final: 0.8145 (p0)
REVERT: A  173 GLN cc_start: 0.9564 (tt0) cc_final: 0.8945 (tm-30)
REVERT: B   47 ASP cc_start: 0.8327 (p0) cc_final: 0.8048 (p0)
REVERT: B   92 TYR cc_start: 0.9254 (t80) cc_final: 0.9052 (t80)
REVERT: B  103 GLU cc_start: 0.9494 (mm-30) cc_final: 0.9290 (mm-30)
REVERT: B  173 GLN cc_start: 0.9582 (tt0) cc_final: 0.8986 (tm-30)
REVERT: C   47 ASP cc_start: 0.8056 (p0) cc_final: 0.7755 (p0)
REVERT: C   92 TYR cc_start: 0.9306 (t80) cc_final: 0.9097 (t80)
REVERT: C  173 GLN cc_start: 0.9550 (tt0) cc_final: 0.9013 (tm-30)
REVERT: D   47 ASP cc_start: 0.8142 (p0) cc_final: 0.7876 (p0)
REVERT: D  103 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9096 (tp30)
REVERT: E   47 ASP cc_start: 0.8197 (p0) cc_final: 0.7834 (p0)
REVERT: E  101 ARG cc_start: 0.8875 (mtp85) cc_final: 0.8595 (tpt170)
REVERT: E  173 GLN cc_start: 0.9563 (tt0) cc_final: 0.8999 (tm-30)
REVERT: F   47 ASP cc_start: 0.8159 (p0) cc_final: 0.7888 (p0)
REVERT: F  101 ARG cc_start: 0.8930 (mtp85) cc_final: 0.8688 (tpt170)
REVERT: F  173 GLN cc_start: 0.9563 (tt0) cc_final: 0.9033 (tm-30)
REVERT: F  202 ARG cc_start: 0.8823 (ptp-170) cc_final: 0.8539 (ptp90)
  outliers start: 54
  outliers final: 19
  residues processed: 340
  average time/residue: 0.1099
  time to fit residues: 49.8065
Evaluate side-chains
  205 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 186
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  194 HIS
Chi-restraints excluded: chain D residue   84 PHE
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  194 HIS
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  194 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    9.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
B  49 GLN
C  49 GLN
C 107 ASN
C 224 ASN
D  49 GLN
D 224 ASN
E 107 ASN
E 224 ASN
F 107 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.071020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.055587 restraints weight = 41143.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.057526 restraints weight = 20285.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.058882 restraints weight = 12929.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.059654 restraints weight = 9418.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.060208 restraints weight = 7808.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  10494  Z= 0.164
  Angle     :  0.741  10.002  14226  Z= 0.372
  Chirality :  0.041   0.279   1602
  Planarity :  0.004   0.026   1674
  Dihedral  : 11.555  85.910   1884
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  2.88 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 12.31 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.66 (0.24), residues: 1182
  helix:  2.59 (0.18), residues: 828
  sheet:  2.36 (0.69), residues: 66
  loop : -0.98 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 189 
 TYR   0.012   0.001   TYR D  66 
 PHE   0.007   0.001   PHE E  97 
 TRP   0.002   0.000   TRP C  78 
 HIS   0.001   0.001   HIS F  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (10476)
  covalent geometry    : angle       0.70675 (14190)
  SS BOND              : bond        0.01048 (   18)
  SS BOND              : angle       4.47501 (   36)
  hydrogen bonds       : bond        0.04546 (  702)
  hydrogen bonds       : angle       3.03891 ( 2088)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 184
  time to evaluate  : 0.362 
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: 0.8234 (p0) cc_final: 0.7931 (p0)
REVERT: A  173 GLN cc_start: 0.9583 (tt0) cc_final: 0.8961 (tm-30)
REVERT: B   92 TYR cc_start: 0.9270 (t80) cc_final: 0.8678 (t80)
REVERT: B  173 GLN cc_start: 0.9592 (tt0) cc_final: 0.9002 (tm-30)
REVERT: C   92 TYR cc_start: 0.9293 (t80) cc_final: 0.8585 (t80)
REVERT: C  173 GLN cc_start: 0.9555 (tt0) cc_final: 0.9019 (tm-30)
REVERT: D   47 ASP cc_start: 0.7972 (p0) cc_final: 0.7711 (p0)
REVERT: D  103 GLU cc_start: 0.9387 (mm-30) cc_final: 0.9167 (tp30)
REVERT: D  155 TYR cc_start: 0.8556 (t80) cc_final: 0.8112 (t80)
REVERT: D  173 GLN cc_start: 0.9636 (tt0) cc_final: 0.9064 (tm-30)
REVERT: E   48 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7282 (mt-10)
REVERT: E  101 ARG cc_start: 0.8958 (mtp85) cc_final: 0.8690 (tpt170)
REVERT: E  173 GLN cc_start: 0.9566 (tt0) cc_final: 0.9059 (tm-30)
REVERT: F   47 ASP cc_start: 0.8151 (p0) cc_final: 0.7895 (p0)
REVERT: F   53 ARG cc_start: 0.8861 (ptp-110) cc_final: 0.8640 (mtm110)
REVERT: F  101 ARG cc_start: 0.9031 (mtp85) cc_final: 0.8814 (tpt170)
REVERT: F  173 GLN cc_start: 0.9565 (tt0) cc_final: 0.9018 (tm-30)
  outliers start: 49
  outliers final: 35
  residues processed: 221
  average time/residue: 0.0877
  time to fit residues: 27.3024
Evaluate side-chains
  202 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 166
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   84 PHE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  194 HIS
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain D residue   84 PHE
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain D residue  198 CYS
Chi-restraints excluded: chain D residue  224 ASN
Chi-restraints excluded: chain E residue   48 GLU
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  194 HIS
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   84 PHE
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain F residue  194 HIS
Chi-restraints excluded: chain F residue  198 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9980
   chunk 5 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 90 optimal weight:    5.9990
   chunk 64 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
C 224 ASN
E  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.071354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.055816 restraints weight = 42153.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.057711 restraints weight = 20831.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.059066 restraints weight = 13256.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.059966 restraints weight = 9603.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.060428 restraints weight = 7748.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  10494  Z= 0.163
  Angle     :  0.724  11.706  14226  Z= 0.366
  Chirality :  0.040   0.251   1602
  Planarity :  0.004   0.032   1674
  Dihedral  : 11.318  87.936   1884
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  2.37 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 14.35 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.51 (0.24), residues: 1182
  helix:  2.50 (0.18), residues: 834
  sheet:  1.90 (0.70), residues: 66
  loop : -1.10 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 189 
 TYR   0.010   0.001   TYR D  66 
 PHE   0.006   0.001   PHE D  32 
 TRP   0.002   0.000   TRP D  45 
 HIS   0.001   0.000   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (10476)
  covalent geometry    : angle       0.69912 (14190)
  SS BOND              : bond        0.00860 (   18)
  SS BOND              : angle       3.80995 (   36)
  hydrogen bonds       : bond        0.04541 (  702)
  hydrogen bonds       : angle       3.02073 ( 2088)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 167
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 GLN cc_start: 0.9583 (tt0) cc_final: 0.8980 (tm-30)
REVERT: B   92 TYR cc_start: 0.9273 (t80) cc_final: 0.8702 (t80)
REVERT: B  173 GLN cc_start: 0.9596 (tt0) cc_final: 0.9020 (tm-30)
REVERT: C   92 TYR cc_start: 0.9305 (t80) cc_final: 0.8628 (t80)
REVERT: C  173 GLN cc_start: 0.9580 (tt0) cc_final: 0.9015 (tm-30)
REVERT: D  103 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9213 (tp30)
REVERT: D  155 TYR cc_start: 0.8716 (t80) cc_final: 0.8356 (t80)
REVERT: E  101 ARG cc_start: 0.8936 (mtp85) cc_final: 0.8684 (tpt170)
REVERT: E  173 GLN cc_start: 0.9575 (tt0) cc_final: 0.9052 (tm-30)
REVERT: F  101 ARG cc_start: 0.8990 (mtp85) cc_final: 0.8774 (tpt170)
REVERT: F  173 GLN cc_start: 0.9579 (tt0) cc_final: 0.9009 (tm-30)
  outliers start: 45
  outliers final: 33
  residues processed: 207
  average time/residue: 0.0881
  time to fit residues: 26.2632
Evaluate side-chains
  190 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 157
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   84 PHE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue   98 TYR
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  194 HIS
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain D residue   84 PHE
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  194 HIS
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   84 PHE
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain F residue  194 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 5 optimal weight:    8.9990
   chunk 86 optimal weight:    0.8980
   chunk 96 optimal weight:    7.9990
   chunk 39 optimal weight:    0.1980
   chunk 91 optimal weight:    9.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
C 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 = 0.3420 r_free = 0.3420 target = 0.072759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.057201 restraints weight = 42391.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.059148 restraints weight = 21076.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.060334 restraints weight = 13291.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.061294 restraints weight = 10160.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.062015 restraints weight = 8156.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  10494  Z= 0.137
  Angle     :  0.709  12.699  14226  Z= 0.354
  Chirality :  0.039   0.226   1602
  Planarity :  0.004   0.032   1674
  Dihedral  : 11.042  89.981   1884
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  2.37 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 15.74 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.41 (0.24), residues: 1182
  helix:  2.49 (0.18), residues: 834
  sheet:  1.61 (0.71), residues: 66
  loop : -1.29 (0.31), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  53 
 TYR   0.009   0.001   TYR A  66 
 PHE   0.008   0.001   PHE A  32 
 TRP   0.007   0.000   TRP F  45 
 HIS   0.001   0.000   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (10476)
  covalent geometry    : angle       0.69045 (14190)
  SS BOND              : bond        0.00891 (   18)
  SS BOND              : angle       3.29524 (   36)
  hydrogen bonds       : bond        0.04273 (  702)
  hydrogen bonds       : angle       2.97588 ( 2088)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 178
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 GLN cc_start: 0.9545 (tt0) cc_final: 0.8967 (tm-30)
REVERT: B   42 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8304 (tm-30)
REVERT: B   92 TYR cc_start: 0.9231 (t80) cc_final: 0.8650 (t80)
REVERT: B  173 GLN cc_start: 0.9568 (tt0) cc_final: 0.9049 (tm-30)
REVERT: C   92 TYR cc_start: 0.9276 (t80) cc_final: 0.8610 (t80)
REVERT: C  173 GLN cc_start: 0.9530 (tt0) cc_final: 0.9003 (tm-30)
REVERT: D  103 GLU cc_start: 0.9416 (mm-30) cc_final: 0.9198 (tp30)
REVERT: D  155 TYR cc_start: 0.8668 (t80) cc_final: 0.8271 (t80)
REVERT: E   42 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8337 (tm-30)
REVERT: E   47 ASP cc_start: 0.7819 (p0) cc_final: 0.7608 (p0)
REVERT: E  101 ARG cc_start: 0.8964 (mtp85) cc_final: 0.8748 (tpt170)
REVERT: E  173 GLN cc_start: 0.9547 (tt0) cc_final: 0.9046 (tm-30)
REVERT: F  173 GLN cc_start: 0.9532 (tt0) cc_final: 0.8985 (tm-30)
  outliers start: 54
  outliers final: 38
  residues processed: 221
  average time/residue: 0.0848
  time to fit residues: 27.0845
Evaluate side-chains
  194 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 156
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   98 TYR
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   84 PHE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  194 HIS
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   84 PHE
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain D residue  224 ASN
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  194 HIS
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain E residue  221 LEU
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   84 PHE
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain F residue  194 HIS
Chi-restraints excluded: chain F residue  198 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9980
   chunk 46 optimal weight:    0.2980
   chunk 113 optimal weight:    0.7980
   chunk 31 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 86 optimal weight:    4.9990
   chunk 100 optimal weight:    8.9990
   chunk 110 optimal weight:    6.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.6184

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.071929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.056225 restraints weight = 42630.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.058149 restraints weight = 21397.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.059521 restraints weight = 13635.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.060480 restraints weight = 10073.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.060832 restraints weight = 8126.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  10494  Z= 0.147
  Angle     :  0.727  11.472  14226  Z= 0.363
  Chirality :  0.039   0.235   1602
  Planarity :  0.004   0.042   1674
  Dihedral  : 10.849  87.665   1884
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  2.45 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 17.31 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.38 (0.24), residues: 1182
  helix:  2.47 (0.17), residues: 846
  sheet:  1.23 (0.71), residues: 66
  loop : -1.35 (0.31), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  53 
 TYR   0.010   0.001   TYR C  66 
 PHE   0.007   0.001   PHE A  32 
 TRP   0.024   0.000   TRP F  45 
 HIS   0.003   0.001   HIS E 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (10476)
  covalent geometry    : angle       0.70879 (14190)
  SS BOND              : bond        0.00872 (   18)
  SS BOND              : angle       3.30070 (   36)
  hydrogen bonds       : bond        0.04274 (  702)
  hydrogen bonds       : angle       3.05083 ( 2088)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 166
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 GLN cc_start: 0.9543 (tt0) cc_final: 0.8985 (tm-30)
REVERT: B   92 TYR cc_start: 0.9266 (t80) cc_final: 0.8677 (t80)
REVERT: B  173 GLN cc_start: 0.9573 (tt0) cc_final: 0.9068 (tm-30)
REVERT: B  205 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8535 (mt-10)
REVERT: C   92 TYR cc_start: 0.9309 (t80) cc_final: 0.8647 (t80)
REVERT: C  173 GLN cc_start: 0.9538 (tt0) cc_final: 0.8999 (tm-30)
REVERT: D  155 TYR cc_start: 0.8715 (t80) cc_final: 0.8365 (t80)
REVERT: E   47 ASP cc_start: 0.7875 (p0) cc_final: 0.7627 (p0)
REVERT: E  101 ARG cc_start: 0.8988 (mtp85) cc_final: 0.8784 (tpt170)
REVERT: E  173 GLN cc_start: 0.9546 (tt0) cc_final: 0.9058 (tm-30)
REVERT: F  173 GLN cc_start: 0.9529 (tt0) cc_final: 0.8999 (tm-30)
  outliers start: 48
  outliers final: 36
  residues processed: 207
  average time/residue: 0.0820
  time to fit residues: 24.8752
Evaluate side-chains
  194 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 158
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   98 TYR
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain B residue  224 ASN
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   84 PHE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  194 HIS
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   84 PHE
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  194 HIS
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   84 PHE
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain F residue  194 HIS
Chi-restraints excluded: chain F residue  198 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 115 optimal weight:    0.1980
   chunk 60 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 105 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 79 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 111 optimal weight:   10.0000
   overall best weight:    4.6388

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.068254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.052495 restraints weight = 44119.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.054301 restraints weight = 22376.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.055560 restraints weight = 14466.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.056399 restraints weight = 10762.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.056972 restraints weight = 8885.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  10494  Z= 0.259
  Angle     :  0.789  11.256  14226  Z= 0.405
  Chirality :  0.042   0.225   1602
  Planarity :  0.004   0.047   1674
  Dihedral  : 10.834  87.192   1884
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 17.04 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.05 (0.24), residues: 1182
  helix:  2.26 (0.17), residues: 834
  sheet:  1.68 (0.71), residues: 60
  loop : -1.55 (0.31), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  53 
 TYR   0.014   0.002   TYR A  92 
 PHE   0.015   0.001   PHE B 169 
 TRP   0.016   0.001   TRP F  45 
 HIS   0.004   0.001   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00592 (10476)
  covalent geometry    : angle       0.76945 (14190)
  SS BOND              : bond        0.00747 (   18)
  SS BOND              : angle       3.56567 (   36)
  hydrogen bonds       : bond        0.05143 (  702)
  hydrogen bonds       : angle       3.34381 ( 2088)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 145
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8681 (pm20)
REVERT: B   42 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8301 (tm-30)
REVERT: B   92 TYR cc_start: 0.9334 (t80) cc_final: 0.8697 (t80)
REVERT: B  205 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8682 (mt-10)
REVERT: C  195 GLN cc_start: 0.9248 (mt0) cc_final: 0.8815 (pp30)
REVERT: D  205 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8637 (mt-10)
REVERT: E   42 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8353 (tm-30)
REVERT: E   47 ASP cc_start: 0.8112 (p0) cc_final: 0.7834 (p0)
REVERT: E  101 ARG cc_start: 0.8908 (mtp85) cc_final: 0.8684 (tpt170)
  outliers start: 55
  outliers final: 39
  residues processed: 194
  average time/residue: 0.0879
  time to fit residues: 24.3709
Evaluate side-chains
  178 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 139
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 CYS
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   84 PHE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  194 HIS
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   84 PHE
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain D residue  224 ASN
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  194 HIS
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   84 PHE
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain F residue  194 HIS
Chi-restraints excluded: chain F residue  198 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9990
   chunk 112 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 92 optimal weight:    4.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
C 224 ASN
E 224 ASN
F 224 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.071442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.055926 restraints weight = 43043.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.057854 restraints weight = 21450.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.059257 restraints weight = 13576.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.060174 restraints weight = 9861.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.060815 restraints weight = 7974.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10494  Z= 0.139
  Angle     :  0.757  11.227  14226  Z= 0.373
  Chirality :  0.039   0.214   1602
  Planarity :  0.004   0.050   1674
  Dihedral  : 10.508  86.459   1882
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 17.87 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.24), residues: 1182
  helix:  2.43 (0.17), residues: 834
  sheet:  1.55 (0.73), residues: 60
  loop : -1.67 (0.30), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  53 
 TYR   0.008   0.001   TYR C  66 
 PHE   0.009   0.001   PHE F  32 
 TRP   0.005   0.000   TRP F  25 
 HIS   0.001   0.000   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (10476)
  covalent geometry    : angle       0.74387 (14190)
  SS BOND              : bond        0.00887 (   18)
  SS BOND              : angle       2.90831 (   36)
  hydrogen bonds       : bond        0.04414 (  702)
  hydrogen bonds       : angle       3.12664 ( 2088)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 173
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 GLN cc_start: 0.9547 (tt0) cc_final: 0.9032 (tm-30)
REVERT: A  195 GLN cc_start: 0.9250 (mt0) cc_final: 0.8611 (pp30)
REVERT: B   92 TYR cc_start: 0.9260 (t80) cc_final: 0.8665 (t80)
REVERT: B  173 GLN cc_start: 0.9584 (tt0) cc_final: 0.9073 (tm-30)
REVERT: C   92 TYR cc_start: 0.9281 (t80) cc_final: 0.8653 (t80)
REVERT: C  173 GLN cc_start: 0.9549 (tt0) cc_final: 0.9022 (tm-30)
REVERT: C  195 GLN cc_start: 0.9171 (mt0) cc_final: 0.8625 (pp30)
REVERT: D  155 TYR cc_start: 0.8822 (t80) cc_final: 0.8601 (t80)
REVERT: D  195 GLN cc_start: 0.9181 (mt0) cc_final: 0.8463 (pp30)
REVERT: D  205 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8504 (mt-10)
REVERT: E   42 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8347 (tm-30)
REVERT: E   47 ASP cc_start: 0.7959 (p0) cc_final: 0.7693 (p0)
REVERT: E  173 GLN cc_start: 0.9555 (tt0) cc_final: 0.9072 (tm-30)
REVERT: E  205 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8504 (mt-10)
REVERT: F   48 GLU cc_start: 0.8083 (mp0) cc_final: 0.7875 (mp0)
REVERT: F  173 GLN cc_start: 0.9554 (tt0) cc_final: 0.9008 (tm-30)
  outliers start: 48
  outliers final: 35
  residues processed: 214
  average time/residue: 0.0842
  time to fit residues: 26.1166
Evaluate side-chains
  193 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 158
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   84 PHE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  194 HIS
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   84 PHE
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  194 HIS
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   84 PHE
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain F residue  194 HIS
Chi-restraints excluded: chain F residue  198 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 28 optimal weight:    0.0370
   chunk 3 optimal weight:    0.9980
   chunk 107 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   chunk 75 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.9860

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.071798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.056176 restraints weight = 43230.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.058079 restraints weight = 21867.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.059417 restraints weight = 14011.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.060344 restraints weight = 10391.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.060994 restraints weight = 8385.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.3266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10494  Z= 0.136
  Angle     :  0.733  11.625  14226  Z= 0.367
  Chirality :  0.039   0.187   1602
  Planarity :  0.004   0.060   1674
  Dihedral  : 10.408  88.853   1882
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 17.50 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.24), residues: 1182
  helix:  2.37 (0.17), residues: 834
  sheet:  1.46 (0.75), residues: 60
  loop : -1.67 (0.30), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  53 
 TYR   0.009   0.001   TYR D  66 
 PHE   0.008   0.001   PHE F  32 
 TRP   0.009   0.001   TRP F  45 
 HIS   0.002   0.000   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10476)
  covalent geometry    : angle       0.72100 (14190)
  SS BOND              : bond        0.00902 (   18)
  SS BOND              : angle       2.76401 (   36)
  hydrogen bonds       : bond        0.04231 (  702)
  hydrogen bonds       : angle       3.13083 ( 2088)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 167
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 GLN cc_start: 0.9519 (tt0) cc_final: 0.9049 (tm-30)
REVERT: A  195 GLN cc_start: 0.9214 (mt0) cc_final: 0.8692 (pp30)
REVERT: B   42 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8296 (tm-30)
REVERT: B   92 TYR cc_start: 0.9280 (t80) cc_final: 0.8686 (t80)
REVERT: B  173 GLN cc_start: 0.9546 (tt0) cc_final: 0.9062 (tm-30)
REVERT: B  195 GLN cc_start: 0.9105 (mt0) cc_final: 0.8542 (pp30)
REVERT: C  173 GLN cc_start: 0.9507 (tt0) cc_final: 0.9015 (tm-30)
REVERT: C  195 GLN cc_start: 0.9155 (mt0) cc_final: 0.8626 (pp30)
REVERT: D  155 TYR cc_start: 0.8807 (t80) cc_final: 0.8578 (t80)
REVERT: D  195 GLN cc_start: 0.9184 (mt0) cc_final: 0.8501 (pp30)
REVERT: D  205 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8511 (mt-10)
REVERT: E   47 ASP cc_start: 0.7957 (p0) cc_final: 0.7680 (p0)
REVERT: E  173 GLN cc_start: 0.9521 (tt0) cc_final: 0.9067 (tm-30)
REVERT: E  195 GLN cc_start: 0.9109 (mt0) cc_final: 0.8793 (pp30)
REVERT: E  205 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8556 (mt-10)
REVERT: F  173 GLN cc_start: 0.9520 (tt0) cc_final: 0.9020 (tm-30)
  outliers start: 45
  outliers final: 39
  residues processed: 206
  average time/residue: 0.0837
  time to fit residues: 25.1769
Evaluate side-chains
  196 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 157
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   84 PHE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  194 HIS
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain C residue  224 ASN
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   84 PHE
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain D residue  224 ASN
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  194 HIS
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain E residue  224 ASN
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   84 PHE
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain F residue  194 HIS
Chi-restraints excluded: chain F residue  198 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 33 optimal weight:    8.9990
   chunk 104 optimal weight:    2.9990
   chunk 73 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 110 optimal weight:    5.9990
   chunk 115 optimal weight:    0.7980
   chunk 119 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9980
   chunk 50 optimal weight:    7.9990
   chunk 8 optimal weight:    0.4980
   overall best weight:    1.4584

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.071787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.056326 restraints weight = 43160.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.058205 restraints weight = 21904.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.059517 restraints weight = 14132.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.060444 restraints weight = 10452.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.060890 restraints weight = 8435.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10494  Z= 0.142
  Angle     :  0.742  10.875  14226  Z= 0.370
  Chirality :  0.039   0.187   1602
  Planarity :  0.004   0.054   1674
  Dihedral  : 10.297  88.531   1882
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 18.06 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.24), residues: 1182
  helix:  2.36 (0.17), residues: 834
  sheet:  1.46 (0.76), residues: 60
  loop : -1.65 (0.30), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B  53 
 TYR   0.009   0.001   TYR B  66 
 PHE   0.008   0.001   PHE F  32 
 TRP   0.011   0.001   TRP F  45 
 HIS   0.001   0.000   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (10476)
  covalent geometry    : angle       0.73006 (14190)
  SS BOND              : bond        0.00813 (   18)
  SS BOND              : angle       2.74054 (   36)
  hydrogen bonds       : bond        0.04228 (  702)
  hydrogen bonds       : angle       3.12271 ( 2088)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 156
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 GLN cc_start: 0.9521 (tt0) cc_final: 0.9059 (tm-30)
REVERT: A  195 GLN cc_start: 0.9194 (mt0) cc_final: 0.8690 (pp30)
REVERT: B   42 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8358 (tm-30)
REVERT: B   92 TYR cc_start: 0.9303 (t80) cc_final: 0.8708 (t80)
REVERT: B  173 GLN cc_start: 0.9552 (tt0) cc_final: 0.9068 (tm-30)
REVERT: B  195 GLN cc_start: 0.9050 (mt0) cc_final: 0.8517 (pp30)
REVERT: C  173 GLN cc_start: 0.9519 (tt0) cc_final: 0.9045 (tm-30)
REVERT: C  195 GLN cc_start: 0.9109 (mt0) cc_final: 0.8623 (pp30)
REVERT: D   42 GLU cc_start: 0.8573 (pp20) cc_final: 0.8322 (tm-30)
REVERT: D  155 TYR cc_start: 0.8874 (t80) cc_final: 0.8606 (t80)
REVERT: D  195 GLN cc_start: 0.9145 (mt0) cc_final: 0.8505 (pp30)
REVERT: D  205 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8516 (mt-10)
REVERT: E   47 ASP cc_start: 0.7972 (p0) cc_final: 0.7694 (p0)
REVERT: E  173 GLN cc_start: 0.9519 (tt0) cc_final: 0.9067 (tm-30)
REVERT: E  195 GLN cc_start: 0.9080 (mt0) cc_final: 0.8724 (pp30)
REVERT: E  205 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8545 (mt-10)
REVERT: F  173 GLN cc_start: 0.9513 (tt0) cc_final: 0.9030 (tm-30)
  outliers start: 43
  outliers final: 39
  residues processed: 195
  average time/residue: 0.0855
  time to fit residues: 24.3830
Evaluate side-chains
  195 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 156
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   84 PHE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  194 HIS
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   84 PHE
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  224 ASN
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  194 HIS
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   84 PHE
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain F residue  187 CYS
Chi-restraints excluded: chain F residue  194 HIS
Chi-restraints excluded: chain F residue  198 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   chunk 59 optimal weight:    8.9990
   chunk 26 optimal weight:    0.0670
   chunk 65 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   chunk 42 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.7520

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.072774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.057267 restraints weight = 42710.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.059198 restraints weight = 21642.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.060525 restraints weight = 13942.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.061449 restraints weight = 10257.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.061970 restraints weight = 8278.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.3443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10494  Z= 0.133
  Angle     :  0.745  10.069  14226  Z= 0.369
  Chirality :  0.039   0.180   1602
  Planarity :  0.004   0.057   1674
  Dihedral  : 10.151  89.180   1882
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 18.61 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.24), residues: 1182
  helix:  2.26 (0.17), residues: 852
  sheet:  1.48 (0.77), residues: 60
  loop : -1.71 (0.32), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  53 
 TYR   0.006   0.001   TYR C  66 
 PHE   0.009   0.001   PHE F  32 
 TRP   0.010   0.001   TRP F  45 
 HIS   0.001   0.000   HIS D 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (10476)
  covalent geometry    : angle       0.73557 (14190)
  SS BOND              : bond        0.00781 (   18)
  SS BOND              : angle       2.48255 (   36)
  hydrogen bonds       : bond        0.04095 (  702)
  hydrogen bonds       : angle       3.16279 ( 2088)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 166
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 TYR cc_start: 0.8662 (t80) cc_final: 0.8422 (t80)
REVERT: A  173 GLN cc_start: 0.9480 (tt0) cc_final: 0.9056 (tm-30)
REVERT: A  195 GLN cc_start: 0.9112 (mt0) cc_final: 0.8670 (pp30)
REVERT: B   92 TYR cc_start: 0.9261 (t80) cc_final: 0.8690 (t80)
REVERT: B  173 GLN cc_start: 0.9521 (tt0) cc_final: 0.9063 (tm-30)
REVERT: B  195 GLN cc_start: 0.9090 (mt0) cc_final: 0.8502 (pp30)
REVERT: C   92 TYR cc_start: 0.9194 (t80) cc_final: 0.8752 (t80)
REVERT: C  173 GLN cc_start: 0.9482 (tt0) cc_final: 0.9053 (tm-30)
REVERT: C  195 GLN cc_start: 0.9040 (mt0) cc_final: 0.8596 (pp30)
REVERT: D   42 GLU cc_start: 0.8611 (pp20) cc_final: 0.8389 (tm-30)
REVERT: D  155 TYR cc_start: 0.8830 (t80) cc_final: 0.8499 (t80)
REVERT: D  173 GLN cc_start: 0.9521 (tt0) cc_final: 0.9069 (tm-30)
REVERT: D  195 GLN cc_start: 0.9152 (mt0) cc_final: 0.8535 (pp30)
REVERT: D  205 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8484 (mt-10)
REVERT: E   47 ASP cc_start: 0.7929 (p0) cc_final: 0.7641 (p0)
REVERT: E   53 ARG cc_start: 0.8843 (ttm110) cc_final: 0.8516 (ptp-110)
REVERT: E   92 TYR cc_start: 0.9102 (t80) cc_final: 0.8795 (t80)
REVERT: E  173 GLN cc_start: 0.9493 (tt0) cc_final: 0.9092 (tm-30)
REVERT: E  195 GLN cc_start: 0.9037 (mt0) cc_final: 0.8724 (pp30)
REVERT: E  205 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8525 (mt-10)
REVERT: F   92 TYR cc_start: 0.9125 (t80) cc_final: 0.8755 (t80)
REVERT: F  173 GLN cc_start: 0.9492 (tt0) cc_final: 0.9055 (tm-30)
REVERT: F  195 GLN cc_start: 0.9152 (mt0) cc_final: 0.8770 (pp30)
  outliers start: 40
  outliers final: 37
  residues processed: 201
  average time/residue: 0.0811
  time to fit residues: 23.9193
Evaluate side-chains
  200 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 163
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   84 PHE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  194 HIS
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain C residue  224 ASN
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   84 PHE
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   98 TYR
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  224 ASN
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain E residue  224 ASN
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   84 PHE
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain F residue  187 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 93 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 99 optimal weight:    6.9990
   chunk 47 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 88 optimal weight:    0.0010
   chunk 59 optimal weight:    7.9990
   chunk 48 optimal weight:    0.0000
   chunk 11 optimal weight:    0.0770
   chunk 31 optimal weight:   10.0000
   overall best weight:    2.4152

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.071616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.056100 restraints weight = 43841.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.058011 restraints weight = 22154.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.059344 restraints weight = 14218.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.060269 restraints weight = 10444.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.060886 restraints weight = 8413.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.3448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  10494  Z= 0.169
  Angle     :  0.771  12.282  14226  Z= 0.388
  Chirality :  0.040   0.227   1602
  Planarity :  0.004   0.049   1674
  Dihedral  : 10.086  88.429   1878
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.35 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.24), residues: 1182
  helix:  2.38 (0.17), residues: 834
  sheet:  1.51 (0.76), residues: 60
  loop : -1.67 (0.30), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  53 
 TYR   0.005   0.001   TYR D  92 
 PHE   0.008   0.001   PHE F 209 
 TRP   0.010   0.001   TRP F  45 
 HIS   0.001   0.000   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (10476)
  covalent geometry    : angle       0.75958 (14190)
  SS BOND              : bond        0.00828 (   18)
  SS BOND              : angle       2.73793 (   36)
  hydrogen bonds       : bond        0.04262 (  702)
  hydrogen bonds       : angle       3.17878 ( 2088)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1435.50 seconds
wall clock time: 25 minutes 38.28 seconds (1538.28 seconds total)