Starting phenix.real_space_refine
on Tue Mar  3 17:50:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sfk_25091/03_2026/7sfk_25091.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sfk_25091/03_2026/7sfk_25091.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sfk_25091/03_2026/7sfk_25091.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sfk_25091/03_2026/7sfk_25091.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sfk_25091/03_2026/7sfk_25091.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sfk_25091/03_2026/7sfk_25091.map"
  }
  resolution = 2.74
  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=   0.202
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       3      5.49       5
     S      48      5.16       5
     C    4971      2.51       5
     N    1098      2.21       5
     O    1299      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  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: 7419
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2299
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 8, 'TRANS': 275}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'AYA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2299
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 8, 'TRANS': 275}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'AYA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2299
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 8, 'TRANS': 275}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'AYA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 155
          Unusual residues: {'PEE': 7, 'RET': 1}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 223
          Unresolved non-hydrogen angles: 255
          Unresolved non-hydrogen dihedrals: 215
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'PEE:plan-2': 3, 'PEE:plan-1': 5, 'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "B"
      Number of atoms: 146
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 146
          Unusual residues: {'PEE': 6, 'RET': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 181
          Unresolved non-hydrogen angles: 207
          Unresolved non-hydrogen dihedrals: 175
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PEE:plan-2': 2, 'PEE:plan-1': 4, 'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "C"
      Number of atoms: 164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 164
          Unusual residues: {'PEE': 8, 'RET': 1}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 265
          Unresolved non-hydrogen angles: 303
          Unresolved non-hydrogen dihedrals: 255
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'PEE:plan-1': 6, 'PEE:plan-2': 4, 'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 41
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 19
          Classifications: {'water': 19}
          Link IDs: {None: 18}
    Chain: "B"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 19
          Classifications: {'water': 19}
          Link IDs: {None: 18}
    Chain: "C"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 19
          Classifications: {'water': 19}
          Link IDs: {None: 18}
  Time building chain proxies: 1.85, per 1000 atoms: 0.25
  Number of scatterers: 7419
  At special positions: 0
  Unit cell: (78.453, 79.59, 88.686, 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       3     15.00
     O    1299      8.00
     N    1098      7.00
     C    4971      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 235.3 milliseconds
  

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1566

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 0 sheets defined
      76.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 21
    Processing helix  chain 'A' and resid 26 through 53
    Processing helix  chain 'A' and resid 63 through 68
    Processing helix  chain 'A' and resid 69 through 71
      No H-bonds generated for 'chain 'A' and resid 69 through 71'
    Processing helix  chain 'A' and resid 72 through 95
      removed outlier: 3.510A  pdb=" N   GLY A  87 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   LYS A  88 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 130
      removed outlier: 3.881A  pdb=" N   THR A 119 " --> pdb=" O   ASP A 115 " (cutoff:3.500A)
      Proline residue:  A 121  - end of helix
      removed outlier: 3.610A  pdb=" N   GLN A 130 " --> pdb=" O   ASP A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 158
      removed outlier: 3.832A  pdb=" N   CYS A 139 " --> pdb=" O   TYR A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 163
    Processing helix  chain 'A' and resid 164 through 200
      removed outlier: 4.025A  pdb=" N   TYR A 168 " --> pdb=" O   ARG A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 222
      removed outlier: 3.736A  pdb=" N   HIS A 210 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   VAL A 211 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LEU A 212 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 233
    Processing helix  chain 'A' and resid 241 through 269
      removed outlier: 3.601A  pdb=" N   GLU A 246 " --> pdb=" O   ASP A 242 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   VAL A 247 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   CYS A 259 " --> pdb=" O   VAL A 255 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   TYR A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 283
      removed outlier: 3.705A  pdb=" N   GLY A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 21
    Processing helix  chain 'B' and resid 26 through 53
    Processing helix  chain 'B' and resid 63 through 68
    Processing helix  chain 'B' and resid 69 through 71
      No H-bonds generated for 'chain 'B' and resid 69 through 71'
    Processing helix  chain 'B' and resid 72 through 95
      removed outlier: 3.511A  pdb=" N   GLY B  87 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   LYS B  88 " --> pdb=" O   SER B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 130
      removed outlier: 3.881A  pdb=" N   THR B 119 " --> pdb=" O   ASP B 115 " (cutoff:3.500A)
      Proline residue:  B 121  - end of helix
      removed outlier: 3.610A  pdb=" N   GLN B 130 " --> pdb=" O   ASP B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 158
      removed outlier: 3.831A  pdb=" N   CYS B 139 " --> pdb=" O   TYR B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 163
    Processing helix  chain 'B' and resid 164 through 200
      removed outlier: 4.026A  pdb=" N   TYR B 168 " --> pdb=" O   ARG B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 222
      removed outlier: 3.736A  pdb=" N   HIS B 210 " --> pdb=" O   GLU B 206 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   VAL B 211 " --> pdb=" O   HIS B 207 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   LEU B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 233
    Processing helix  chain 'B' and resid 241 through 269
      removed outlier: 3.600A  pdb=" N   GLU B 246 " --> pdb=" O   ASP B 242 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   VAL B 247 " --> pdb=" O   ASN B 243 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   CYS B 259 " --> pdb=" O   VAL B 255 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   TYR B 260 " --> pdb=" O   ALA B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 283
      removed outlier: 3.706A  pdb=" N   GLY B 283 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 21
    Processing helix  chain 'C' and resid 26 through 53
    Processing helix  chain 'C' and resid 63 through 68
    Processing helix  chain 'C' and resid 69 through 71
      No H-bonds generated for 'chain 'C' and resid 69 through 71'
    Processing helix  chain 'C' and resid 72 through 95
      removed outlier: 3.510A  pdb=" N   GLY C  87 " --> pdb=" O   LEU C  83 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   LYS C  88 " --> pdb=" O   SER C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 130
      removed outlier: 3.881A  pdb=" N   THR C 119 " --> pdb=" O   ASP C 115 " (cutoff:3.500A)
      Proline residue:  C 121  - end of helix
      removed outlier: 3.610A  pdb=" N   GLN C 130 " --> pdb=" O   ASP C 126 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 135 through 158
      removed outlier: 3.832A  pdb=" N   CYS C 139 " --> pdb=" O   TYR C 135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 163
    Processing helix  chain 'C' and resid 164 through 200
      removed outlier: 4.025A  pdb=" N   TYR C 168 " --> pdb=" O   ARG C 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 222
      removed outlier: 3.736A  pdb=" N   HIS C 210 " --> pdb=" O   GLU C 206 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   VAL C 211 " --> pdb=" O   HIS C 207 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   LEU C 212 " --> pdb=" O   SER C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 233
    Processing helix  chain 'C' and resid 241 through 269
      removed outlier: 3.600A  pdb=" N   GLU C 246 " --> pdb=" O   ASP C 242 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   VAL C 247 " --> pdb=" O   ASN C 243 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   CYS C 259 " --> pdb=" O   VAL C 255 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   TYR C 260 " --> pdb=" O   ALA C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 283
      removed outlier: 3.706A  pdb=" N   GLY C 283 " --> pdb=" O   LEU C 279 " (cutoff:3.500A)

    450 hydrogen bonds defined for protein.
    1323 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.03

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2059
        1.34 -     1.45: 1517
        1.45 -     1.57: 3918
        1.57 -     1.69: 3
        1.69 -     1.81: 75
  Bond restraints: 7572
  Sorted by residual:
  bond pdb=" C30 PEE B 404 "
       pdb=" O5  PEE B 404 "
    ideal  model  delta    sigma   weight residual
    1.206  1.353 -0.147 2.00e-02 2.50e+03 5.40e+01
  bond pdb=" C30 PEE A 404 "
       pdb=" O5  PEE A 404 "
    ideal  model  delta    sigma   weight residual
    1.206  1.353 -0.147 2.00e-02 2.50e+03 5.40e+01
  bond pdb=" C30 PEE C 405 "
       pdb=" O5  PEE C 405 "
    ideal  model  delta    sigma   weight residual
    1.206  1.352 -0.146 2.00e-02 2.50e+03 5.34e+01
  bond pdb=" C30 PEE B 402 "
       pdb=" O5  PEE B 402 "
    ideal  model  delta    sigma   weight residual
    1.206  1.352 -0.146 2.00e-02 2.50e+03 5.34e+01
  bond pdb=" C30 PEE C 403 "
       pdb=" O5  PEE C 403 "
    ideal  model  delta    sigma   weight residual
    1.206  1.352 -0.146 2.00e-02 2.50e+03 5.33e+01
  ... (remaining 7567 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 9808
        2.45 -     4.90: 315
        4.90 -     7.34: 20
        7.34 -     9.79: 15
        9.79 -    12.24: 9
  Bond angle restraints: 10167
  Sorted by residual:
  angle pdb=" C11 PEE C 402 "
        pdb=" C10 PEE C 402 "
        pdb=" O2  PEE C 402 "
      ideal   model   delta    sigma   weight residual
     111.70  123.94  -12.24 3.00e+00 1.11e-01 1.66e+01
  angle pdb=" C11 PEE B 401 "
        pdb=" C10 PEE B 401 "
        pdb=" O2  PEE B 401 "
      ideal   model   delta    sigma   weight residual
     111.70  123.93  -12.23 3.00e+00 1.11e-01 1.66e+01
  angle pdb=" C11 PEE A 401 "
        pdb=" C10 PEE A 401 "
        pdb=" O2  PEE A 401 "
      ideal   model   delta    sigma   weight residual
     111.70  123.92  -12.22 3.00e+00 1.11e-01 1.66e+01
  angle pdb=" C31 PEE B 404 "
        pdb=" C30 PEE B 404 "
        pdb=" O3  PEE B 404 "
      ideal   model   delta    sigma   weight residual
     111.87  123.95  -12.08 3.00e+00 1.11e-01 1.62e+01
  angle pdb=" C31 PEE A 404 "
        pdb=" C30 PEE A 404 "
        pdb=" O3  PEE A 404 "
      ideal   model   delta    sigma   weight residual
     111.87  123.91  -12.04 3.00e+00 1.11e-01 1.61e+01
  ... (remaining 10162 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.68: 4197
       35.68 -    71.36: 99
       71.36 -   107.04: 12
      107.04 -   142.72: 6
      142.72 -   178.40: 6
  Dihedral angle restraints: 4320
    sinusoidal: 1845
      harmonic: 2475
  Sorted by residual:
  dihedral pdb=" C32 PEE C 404 "
           pdb=" C30 PEE C 404 "
           pdb=" C31 PEE C 404 "
           pdb=" O3  PEE C 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     161.16  -20.44 -178.40     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C32 PEE B 403 "
           pdb=" C30 PEE B 403 "
           pdb=" C31 PEE B 403 "
           pdb=" O3  PEE B 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     161.16  -20.49 -178.35     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C32 PEE A 403 "
           pdb=" C30 PEE A 403 "
           pdb=" C31 PEE A 403 "
           pdb=" O3  PEE A 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     161.16  -20.54 -178.30     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 4317 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 633
       0.033 -    0.065: 282
       0.065 -    0.098: 78
       0.098 -    0.130: 15
       0.130 -    0.163: 3
  Chirality restraints: 1011
  Sorted by residual:
  chirality pdb=" C2  PEE A 406 "
            pdb=" C1  PEE A 406 "
            pdb=" C3  PEE A 406 "
            pdb=" O2  PEE A 406 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.49    0.16 2.00e-01 2.50e+01 6.63e-01
  chirality pdb=" C2  PEE B 406 "
            pdb=" C1  PEE B 406 "
            pdb=" C3  PEE B 406 "
            pdb=" O2  PEE B 406 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.49    0.16 2.00e-01 2.50e+01 6.52e-01
  chirality pdb=" C2  PEE C 408 "
            pdb=" C1  PEE C 408 "
            pdb=" C3  PEE C 408 "
            pdb=" O2  PEE C 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.48    0.16 2.00e-01 2.50e+01 6.16e-01
  ... (remaining 1008 not shown)

  Planarity restraints: 1242
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 160 "    0.033 5.00e-02 4.00e+02   4.97e-02 3.95e+00
        pdb=" N   PRO B 161 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B 161 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 161 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 160 "    0.033 5.00e-02 4.00e+02   4.96e-02 3.94e+00
        pdb=" N   PRO A 161 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 161 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 161 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 160 "   -0.033 5.00e-02 4.00e+02   4.95e-02 3.93e+00
        pdb=" N   PRO C 161 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO C 161 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 161 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1239 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1868
        2.79 -     3.32: 6599
        3.32 -     3.85: 12571
        3.85 -     4.37: 15095
        4.37 -     4.90: 26074
  Nonbonded interactions: 62207
  Sorted by model distance:
  nonbonded pdb=" O   GLY C 107 "
            pdb=" O   HOH C 501 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   GLY B 107 "
            pdb=" O   HOH B 501 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   GLY A 107 "
            pdb=" O   HOH A 501 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OD1 ASN A 110 "
            pdb=" O   HOH A 502 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" OD1 ASN B 110 "
            pdb=" O   HOH B 502 "
     model   vdw
     2.323 3.040
  ... (remaining 62202 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 285 or (resid 403 through 404 and (name C30 or n \ 
ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37  \ 
or name C38 or name C39 or name C40 or name C41 or name C42 or name O3 or name O \ 
5 )) or (resid 405 and (name C36 or name C37 or name C38 or name C39 or name C40 \ 
 or name C41 or name C42)) or (resid 406 and (name C36 or name C37 or name C38 o \ 
r name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name C \ 
45 or name C46 or name C47))))
  selection = (chain 'B' and (resid 2 through 285 or (resid 403 through 404 and (name C30 or n \ 
ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37  \ 
or name C38 or name C39 or name C40 or name C41 or name C42 or name O3 or name O \ 
5 )) or (resid 405 and (name C36 or name C37 or name C38 or name C39 or name C40 \ 
 or name C41 or name C42)) or (resid 406 and (name C36 or name C37 or name C38 o \ 
r name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name C \ 
45 or name C46 or name C47))))
  selection = (chain 'C' and (resid 2 through 285 or (resid 403 through 404 and (name C30 or n \ 
ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37  \ 
or name C38 or name C39 or name C40 or name C41 or name C42 or name O3 or name O \ 
5 )) or (resid 405 and (name C36 or name C37 or name C38 or name C39 or name C40 \ 
 or name C41 or name C42)) or resid 406))
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.040
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.000
  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:             0.010
  Load rotamer database and sin/cos tables:6.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
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      :  0.008   0.147   7575  Z= 0.387
  Angle     :  0.966  12.239  10167  Z= 0.401
  Chirality :  0.039   0.163   1011
  Planarity :  0.005   0.050   1242
  Dihedral  : 18.398 178.399   2754
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  1.71 %
    Favored  : 97.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.37 (0.28), residues: 843
  helix:  1.80 (0.20), residues: 576
  sheet:  None (None), residues: 0
  loop :  1.31 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 132 
 TYR   0.013   0.002   TYR B 271 
 PHE   0.016   0.001   PHE B 176 
 TRP   0.009   0.001   TRP A 177 
 HIS   0.003   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00777 ( 7572)
  covalent geometry    : angle       0.96555 (10167)
  hydrogen bonds       : bond        0.14819 (  450)
  hydrogen bonds       : angle       4.67821 ( 1323)
  Misc. bond           : bond        0.00059 (    3)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.8415 (mp10) cc_final: 0.8188 (mp10)
REVERT: A  148 MET cc_start: 0.7948 (ttp) cc_final: 0.7508 (ttp)
REVERT: A  180 PHE cc_start: 0.8039 (t80) cc_final: 0.7823 (t80)
REVERT: B  148 MET cc_start: 0.7888 (ttp) cc_final: 0.7637 (ttp)
REVERT: C  148 MET cc_start: 0.8100 (ttp) cc_final: 0.7876 (ttp)
  outliers start: 3
  outliers final: 1
  residues processed: 101
  average time/residue: 0.4421
  time to fit residues: 47.6446
Evaluate side-chains
  81 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.3980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN
B 192 GLN
C   9 GLN
C 192 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.147683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.126553 restraints weight = 7030.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 0.96
r_work: 0.3191 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.3076 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7575  Z= 0.120
  Angle     :  0.478   4.858  10167  Z= 0.254
  Chirality :  0.038   0.125   1011
  Planarity :  0.004   0.045   1242
  Dihedral  : 15.072 139.002   1301
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  5.13 %
    Favored  : 93.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  3.11 (0.29), residues: 843
  helix:  2.24 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop :  1.81 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 268 
 TYR   0.013   0.001   TYR B 271 
 PHE   0.013   0.002   PHE C 173 
 TRP   0.014   0.001   TRP A  19 
 HIS   0.003   0.000   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7572)
  covalent geometry    : angle       0.47798 (10167)
  hydrogen bonds       : bond        0.05261 (  450)
  hydrogen bonds       : angle       3.35180 ( 1323)
  Misc. bond           : bond        0.00037 (    3)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.8035 (mtpp) cc_final: 0.7513 (mmtm)
REVERT: A   68 GLN cc_start: 0.8174 (mp10) cc_final: 0.7683 (mp10)
REVERT: A  148 MET cc_start: 0.8438 (ttp) cc_final: 0.8068 (ttp)
REVERT: A  221 MET cc_start: 0.7232 (tmm) cc_final: 0.6964 (tmm)
REVERT: A  277 ARG cc_start: 0.6711 (ptp90) cc_final: 0.6486 (ptp90)
REVERT: B   50 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7556 (tt0)
REVERT: B  148 MET cc_start: 0.8246 (ttp) cc_final: 0.8028 (ttp)
REVERT: B  272 ASP cc_start: 0.7217 (p0) cc_final: 0.6836 (p0)
  outliers start: 7
  outliers final: 3
  residues processed: 103
  average time/residue: 0.4631
  time to fit residues: 50.7404
Evaluate side-chains
  92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain C residue  194 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 40 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
B  78 ASN
C   9 GLN
C  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.135338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.114534 restraints weight = 7160.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 1.07
r_work: 0.3173 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   7575  Z= 0.272
  Angle     :  0.657   5.713  10167  Z= 0.348
  Chirality :  0.047   0.129   1011
  Planarity :  0.005   0.055   1242
  Dihedral  : 15.446 116.260   1299
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  :  8.26 %
    Favored  : 89.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.17 (0.28), residues: 843
  helix:  1.63 (0.21), residues: 597
  sheet:  None (None), residues: 0
  loop :  1.26 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 268 
 TYR   0.031   0.003   TYR A 271 
 PHE   0.046   0.003   PHE C 155 
 TRP   0.017   0.003   TRP C  19 
 HIS   0.009   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00673 ( 7572)
  covalent geometry    : angle       0.65686 (10167)
  hydrogen bonds       : bond        0.07908 (  450)
  hydrogen bonds       : angle       3.79896 ( 1323)
  Misc. bond           : bond        0.00044 (    3)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.8164 (mtpp) cc_final: 0.7615 (mmtm)
REVERT: A   68 GLN cc_start: 0.8503 (mp10) cc_final: 0.7956 (mp10)
REVERT: A  118 LEU cc_start: 0.8836 (tp) cc_final: 0.8623 (mt)
REVERT: A  148 MET cc_start: 0.8554 (ttp) cc_final: 0.8219 (ttp)
REVERT: A  272 ASP cc_start: 0.7523 (p0) cc_final: 0.7248 (p0)
REVERT: A  277 ARG cc_start: 0.7053 (ptp90) cc_final: 0.6788 (ptt-90)
REVERT: B    9 GLN cc_start: 0.8347 (tt0) cc_final: 0.8082 (tt0)
REVERT: B   50 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7798 (tt0)
REVERT: B  272 ASP cc_start: 0.7883 (p0) cc_final: 0.7496 (p0)
REVERT: C   50 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7581 (tt0)
REVERT: C  221 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7151 (tmm)
  outliers start: 18
  outliers final: 8
  residues processed: 111
  average time/residue: 0.6148
  time to fit residues: 71.6272
Evaluate side-chains
  109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  186 MET
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain C residue   50 GLU
Chi-restraints excluded: chain C residue  194 SER
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  271 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
C   9 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.138713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.114829 restraints weight = 7283.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 1.18
r_work: 0.3208 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7575  Z= 0.122
  Angle     :  0.473   5.235  10167  Z= 0.254
  Chirality :  0.038   0.125   1011
  Planarity :  0.004   0.052   1242
  Dihedral  : 13.501 113.336   1299
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  9.40 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.65 (0.28), residues: 843
  helix:  2.00 (0.21), residues: 603
  sheet:  None (None), residues: 0
  loop :  1.34 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 268 
 TYR   0.012   0.001   TYR A 271 
 PHE   0.012   0.001   PHE C 173 
 TRP   0.013   0.001   TRP C  19 
 HIS   0.004   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7572)
  covalent geometry    : angle       0.47348 (10167)
  hydrogen bonds       : bond        0.05376 (  450)
  hydrogen bonds       : angle       3.34655 ( 1323)
  Misc. bond           : bond        0.00029 (    3)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.8275 (mp10) cc_final: 0.7663 (mp10)
REVERT: A  148 MET cc_start: 0.8411 (ttp) cc_final: 0.8121 (ttp)
REVERT: A  272 ASP cc_start: 0.7359 (p0) cc_final: 0.7125 (p0)
REVERT: B    9 GLN cc_start: 0.8275 (tt0) cc_final: 0.8052 (tt0)
REVERT: B   92 ASP cc_start: 0.8158 (m-30) cc_final: 0.7914 (m-30)
REVERT: B  272 ASP cc_start: 0.7644 (p0) cc_final: 0.7247 (p0)
  outliers start: 12
  outliers final: 10
  residues processed: 102
  average time/residue: 0.5167
  time to fit residues: 55.8227
Evaluate side-chains
  105 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  194 SER
Chi-restraints excluded: chain C residue  224 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 81 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
C   9 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.131252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.107195 restraints weight = 7340.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 1.13
r_work: 0.3005 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7575  Z= 0.202
  Angle     :  0.562   5.118  10167  Z= 0.300
  Chirality :  0.042   0.126   1011
  Planarity :  0.005   0.055   1242
  Dihedral  : 14.289 115.313   1299
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 10.40 %
    Favored  : 87.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.37 (0.28), residues: 843
  helix:  1.84 (0.21), residues: 597
  sheet:  None (None), residues: 0
  loop :  1.12 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 268 
 TYR   0.023   0.002   TYR A 271 
 PHE   0.014   0.002   PHE A 155 
 TRP   0.016   0.002   TRP C  19 
 HIS   0.006   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 ( 7572)
  covalent geometry    : angle       0.56211 (10167)
  hydrogen bonds       : bond        0.06874 (  450)
  hydrogen bonds       : angle       3.57249 ( 1323)
  Misc. bond           : bond        0.00019 (    3)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A   50 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7827 (tm-30)
REVERT: A   68 GLN cc_start: 0.8184 (mp10) cc_final: 0.7592 (mp10)
REVERT: A  148 MET cc_start: 0.8429 (ttp) cc_final: 0.8152 (ttp)
REVERT: A  272 ASP cc_start: 0.7371 (p0) cc_final: 0.7130 (p0)
REVERT: B    9 GLN cc_start: 0.8304 (tt0) cc_final: 0.8039 (tt0)
REVERT: B  272 ASP cc_start: 0.7681 (p0) cc_final: 0.7327 (p0)
REVERT: C  221 MET cc_start: 0.7266 (tmt) cc_final: 0.6970 (tmm)
  outliers start: 14
  outliers final: 10
  residues processed: 110
  average time/residue: 0.5401
  time to fit residues: 62.7580
Evaluate side-chains
  108 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  194 SER
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  271 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 38 optimal weight:    0.2980
   chunk 83 optimal weight:    4.9990
   chunk 39 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 75 optimal weight:    4.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
C   9 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.136045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.112436 restraints weight = 7251.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 1.14
r_work: 0.3042 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7575  Z= 0.140
  Angle     :  0.492   5.160  10167  Z= 0.264
  Chirality :  0.039   0.127   1011
  Planarity :  0.005   0.053   1242
  Dihedral  : 13.396 114.459   1299
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 11.40 %
    Favored  : 86.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.56 (0.28), residues: 843
  helix:  2.00 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop :  1.12 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 268 
 TYR   0.014   0.002   TYR A 271 
 PHE   0.011   0.002   PHE C 219 
 TRP   0.013   0.001   TRP C  19 
 HIS   0.004   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7572)
  covalent geometry    : angle       0.49175 (10167)
  hydrogen bonds       : bond        0.05719 (  450)
  hydrogen bonds       : angle       3.36885 ( 1323)
  Misc. bond           : bond        0.00012 (    3)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.8078 (mp10) cc_final: 0.7445 (mp10)
REVERT: A  148 MET cc_start: 0.8468 (ttp) cc_final: 0.8191 (ttp)
REVERT: A  272 ASP cc_start: 0.7342 (p0) cc_final: 0.7114 (p0)
REVERT: B    9 GLN cc_start: 0.8298 (tt0) cc_final: 0.8024 (tt0)
REVERT: B  272 ASP cc_start: 0.7610 (p0) cc_final: 0.7269 (p0)
REVERT: C  221 MET cc_start: 0.7209 (tmt) cc_final: 0.6940 (tmm)
  outliers start: 14
  outliers final: 10
  residues processed: 106
  average time/residue: 0.4900
  time to fit residues: 55.0988
Evaluate side-chains
  103 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  194 SER
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  271 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
C   9 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.135745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.112174 restraints weight = 7243.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 1.14
r_work: 0.3048 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7575  Z= 0.142
  Angle     :  0.496   5.250  10167  Z= 0.266
  Chirality :  0.039   0.126   1011
  Planarity :  0.005   0.053   1242
  Dihedral  : 13.228 114.650   1299
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 11.40 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.65 (0.28), residues: 843
  helix:  2.07 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop :  1.15 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 164 
 TYR   0.015   0.002   TYR A 271 
 PHE   0.011   0.002   PHE A 173 
 TRP   0.013   0.002   TRP C  19 
 HIS   0.004   0.001   HIS A  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 7572)
  covalent geometry    : angle       0.49640 (10167)
  hydrogen bonds       : bond        0.05813 (  450)
  hydrogen bonds       : angle       3.35495 ( 1323)
  Misc. bond           : bond        0.00009 (    3)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   50 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7679 (tm-30)
REVERT: A   68 GLN cc_start: 0.8131 (mp10) cc_final: 0.7495 (mp10)
REVERT: A  148 MET cc_start: 0.8441 (ttp) cc_final: 0.8173 (ttp)
REVERT: B    9 GLN cc_start: 0.8326 (tt0) cc_final: 0.8053 (tt0)
REVERT: B  272 ASP cc_start: 0.7649 (p0) cc_final: 0.7312 (p0)
REVERT: C  221 MET cc_start: 0.7310 (tmt) cc_final: 0.7027 (tmm)
  outliers start: 17
  outliers final: 11
  residues processed: 110
  average time/residue: 0.4952
  time to fit residues: 57.8011
Evaluate side-chains
  107 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  186 MET
Chi-restraints excluded: chain C residue  194 SER
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  271 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 80 optimal weight:    0.6980
   chunk 52 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 76 optimal weight:    8.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
C   9 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.133993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.110153 restraints weight = 7332.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 1.17
r_work: 0.3141 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7575  Z= 0.201
  Angle     :  0.565   5.264  10167  Z= 0.301
  Chirality :  0.042   0.130   1011
  Planarity :  0.005   0.054   1242
  Dihedral  : 13.992 115.271   1299
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 12.11 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.40 (0.28), residues: 843
  helix:  1.89 (0.21), residues: 597
  sheet:  None (None), residues: 0
  loop :  1.04 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 164 
 TYR   0.021   0.002   TYR A 271 
 PHE   0.013   0.002   PHE C 219 
 TRP   0.016   0.002   TRP C  19 
 HIS   0.006   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 ( 7572)
  covalent geometry    : angle       0.56483 (10167)
  hydrogen bonds       : bond        0.06820 (  450)
  hydrogen bonds       : angle       3.54006 ( 1323)
  Misc. bond           : bond        0.00025 (    3)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A   50 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7771 (tm-30)
REVERT: A   59 LYS cc_start: 0.8067 (mtpp) cc_final: 0.7534 (mmtm)
REVERT: A   68 GLN cc_start: 0.8232 (mp10) cc_final: 0.7589 (mp10)
REVERT: A  148 MET cc_start: 0.8448 (ttp) cc_final: 0.8140 (ttp)
REVERT: A  191 LYS cc_start: 0.8427 (tttm) cc_final: 0.8064 (tttm)
REVERT: B    9 GLN cc_start: 0.8326 (tt0) cc_final: 0.8094 (tt0)
REVERT: B  122 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8221 (mtm)
REVERT: B  272 ASP cc_start: 0.7797 (p0) cc_final: 0.7465 (p0)
REVERT: C   70 GLU cc_start: 0.7638 (mp0) cc_final: 0.7281 (mp0)
REVERT: C  221 MET cc_start: 0.7373 (tmt) cc_final: 0.7053 (tmm)
  outliers start: 16
  outliers final: 12
  residues processed: 108
  average time/residue: 0.4959
  time to fit residues: 56.7566
Evaluate side-chains
  110 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  271 TYR
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  186 MET
Chi-restraints excluded: chain C residue  194 SER
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  271 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 41 optimal weight:    0.4980
   chunk 49 optimal weight:    3.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
C   9 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.133815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.110362 restraints weight = 7209.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 1.13
r_work: 0.3015 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7575  Z= 0.178
  Angle     :  0.540   5.173  10167  Z= 0.289
  Chirality :  0.041   0.128   1011
  Planarity :  0.005   0.054   1242
  Dihedral  : 13.841 115.136   1299
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 12.54 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.43 (0.28), residues: 843
  helix:  1.92 (0.21), residues: 597
  sheet:  None (None), residues: 0
  loop :  1.03 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 164 
 TYR   0.019   0.002   TYR A 271 
 PHE   0.014   0.002   PHE C 219 
 TRP   0.015   0.002   TRP C  19 
 HIS   0.005   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 7572)
  covalent geometry    : angle       0.53967 (10167)
  hydrogen bonds       : bond        0.06384 (  450)
  hydrogen bonds       : angle       3.48782 ( 1323)
  Misc. bond           : bond        0.00012 (    3)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A   50 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7704 (tm-30)
REVERT: A   59 LYS cc_start: 0.7975 (mtpp) cc_final: 0.7449 (mmtm)
REVERT: A  148 MET cc_start: 0.8363 (ttp) cc_final: 0.8065 (ttp)
REVERT: A  191 LYS cc_start: 0.8315 (tttm) cc_final: 0.7946 (tttm)
REVERT: B    9 GLN cc_start: 0.8242 (tt0) cc_final: 0.8001 (tt0)
REVERT: B  122 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8111 (mtm)
REVERT: B  272 ASP cc_start: 0.7675 (p0) cc_final: 0.7354 (p0)
REVERT: C   70 GLU cc_start: 0.7553 (mp0) cc_final: 0.7125 (mp0)
REVERT: C  221 MET cc_start: 0.7274 (tmt) cc_final: 0.6963 (tmm)
  outliers start: 15
  outliers final: 12
  residues processed: 106
  average time/residue: 0.5057
  time to fit residues: 56.8539
Evaluate side-chains
  109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  271 TYR
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  186 MET
Chi-restraints excluded: chain C residue  194 SER
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  271 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
C   9 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.138028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.114584 restraints weight = 7147.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 1.14
r_work: 0.3043 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7575  Z= 0.121
  Angle     :  0.476   5.388  10167  Z= 0.256
  Chirality :  0.039   0.159   1011
  Planarity :  0.004   0.053   1242
  Dihedral  : 12.912 113.776   1299
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.96 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.73 (0.28), residues: 843
  helix:  2.12 (0.21), residues: 603
  sheet:  None (None), residues: 0
  loop :  1.18 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 268 
 TYR   0.012   0.001   TYR A 271 
 PHE   0.011   0.001   PHE B 173 
 TRP   0.013   0.002   TRP A  52 
 HIS   0.003   0.000   HIS A  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7572)
  covalent geometry    : angle       0.47622 (10167)
  hydrogen bonds       : bond        0.05229 (  450)
  hydrogen bonds       : angle       3.29695 ( 1323)
  Misc. bond           : bond        0.00024 (    3)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7427 (mmtm)
REVERT: B    9 GLN cc_start: 0.8223 (tt0) cc_final: 0.7937 (tt0)
REVERT: B  272 ASP cc_start: 0.7555 (p0) cc_final: 0.7256 (p0)
REVERT: C   70 GLU cc_start: 0.7519 (mp0) cc_final: 0.7062 (mp0)
REVERT: C  221 MET cc_start: 0.7216 (tmt) cc_final: 0.6944 (tmm)
  outliers start: 12
  outliers final: 10
  residues processed: 103
  average time/residue: 0.4761
  time to fit residues: 52.1254
Evaluate side-chains
  104 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  194 SER
Chi-restraints excluded: chain C residue  224 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 69 optimal weight:    0.0970
   chunk 40 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 20 optimal weight:    8.9990
   chunk 14 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
C   9 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.139875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.116353 restraints weight = 7086.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 1.15
r_work: 0.3066 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7575  Z= 0.109
  Angle     :  0.455   5.586  10167  Z= 0.243
  Chirality :  0.038   0.222   1011
  Planarity :  0.004   0.053   1242
  Dihedral  : 12.082 113.262   1299
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 13.11 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.91 (0.28), residues: 843
  helix:  2.27 (0.21), residues: 603
  sheet:  None (None), residues: 0
  loop :  1.22 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 277 
 TYR   0.011   0.001   TYR A 271 
 PHE   0.011   0.001   PHE B 173 
 TRP   0.011   0.001   TRP C  19 
 HIS   0.002   0.000   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 7572)
  covalent geometry    : angle       0.45535 (10167)
  hydrogen bonds       : bond        0.04850 (  450)
  hydrogen bonds       : angle       3.20680 ( 1323)
  Misc. bond           : bond        0.00027 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2104.74 seconds
wall clock time: 36 minutes 35.49 seconds (2195.49 seconds total)