Starting phenix.real_space_refine
on Wed Mar 12 10:45:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sfk_25091/03_2025/7sfk_25091.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sfk_25091/03_2025/7sfk_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sfk_25091/03_2025/7sfk_25091.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sfk_25091/03_2025/7sfk_25091.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sfk_25091/03_2025/7sfk_25091.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sfk_25091/03_2025/7sfk_25091.cif"
  }
  resolution = 2.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.202
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7419
  Number of models: 1
  Model: ""
    Number of chains: 7
    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: "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: {'RET:plan-5': 1, 'PEE:plan-1': 5, 'PEE:plan-2': 3}
          Unresolved non-hydrogen planarities: 33
    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: {'RET:plan-5': 1, 'PEE:plan-1': 6, 'PEE:plan-2': 4}
          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}
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.47, per 1000 atoms: 0.74
  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=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  36 " - pdb=" SG  CYS B  36 " distance=0.00
    Simple disulfide: pdb=" SG  CYS B 120 " - pdb=" SG  CYS B 120 " distance=0.00
    Simple disulfide: pdb=" SG  CYS B 139 " - pdb=" SG  CYS B 139 " distance=0.00
    Simple disulfide: pdb=" SG  CYS B 175 " - pdb=" SG  CYS B 175 " distance=0.00
    Simple disulfide: pdb=" SG  CYS B 233 " - pdb=" SG  CYS B 233 " distance=0.00
    Simple disulfide: pdb=" SG  CYS B 250 " - pdb=" SG  CYS B 250 " distance=0.00
    Simple disulfide: pdb=" SG  CYS B 252 " - pdb=" SG  CYS B 252 " distance=0.00
    Simple disulfide: pdb=" SG  CYS B 259 " - pdb=" SG  CYS B 259 " distance=0.00

  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: 2.47
  Conformation dependent library (CDL) restraints added in 961.6 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: 0.62
  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: 1.86

  Time building geometry restraints manager: 2.60 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: 4213
       35.68 -    71.36: 99
       71.36 -   107.04: 12
      107.04 -   142.72: 6
      142.72 -   178.40: 6
  Dihedral angle restraints: 4336
    sinusoidal: 1861
      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 4333 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:             0.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.050
  Find NCS groups from input model:        0.370
  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:15.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.990
-------------------------------------------------------------------------------
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   7572  Z= 0.537
  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 : 3.61
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.37 (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
 TRP   0.009   0.001   TRP A 177 
 HIS   0.003   0.001   HIS B  96 
 PHE   0.016   0.001   PHE B 176 
 TYR   0.013   0.002   TYR B 271 
 ARG   0.002   0.000   ARG B 132 

*********************** 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  : 0.782 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.8415 (mp10) cc_final: 0.8188 (mp10)
REVERT: A  148 MET cc_start: 0.7947 (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: 0.9801
  time to fit residues: 105.8782
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  : 0.689 
-------------------------------------------------------------------------------
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 70 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 76 optimal weight:   10.0000
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3545 r_free = 0.3545 target = 0.139485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.115393 restraints weight = 7059.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.18
r_work: 0.3053 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7572  Z= 0.270
  Angle     :  0.561   5.244  10167  Z= 0.299
  Chirality :  0.042   0.126   1011
  Planarity :  0.005   0.050   1242
  Dihedral  : 15.867 137.359   1301
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  5.84 %
    Favored  : 93.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.72 (0.29), residues: 843
  helix:  2.00 (0.21), residues: 597
  sheet:  None (None), residues: 0
  loop :  1.55 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  19 
 HIS   0.006   0.001   HIS B  96 
 PHE   0.022   0.002   PHE C 155 
 TYR   0.026   0.002   TYR C 125 
 ARG   0.002   0.000   ARG B 268 

*********************** 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  : 0.744 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.8017 (mtpp) cc_final: 0.7483 (mmtm)
REVERT: A   68 GLN cc_start: 0.8206 (mp10) cc_final: 0.7641 (mp10)
REVERT: A  117 MET cc_start: 0.8751 (mtt) cc_final: 0.8546 (mtt)
REVERT: A  148 MET cc_start: 0.8459 (ttp) cc_final: 0.8151 (ttp)
REVERT: A  221 MET cc_start: 0.7298 (tmm) cc_final: 0.6972 (tmm)
REVERT: A  253 ASP cc_start: 0.8641 (m-30) cc_final: 0.8434 (m-30)
REVERT: A  272 ASP cc_start: 0.7165 (p0) cc_final: 0.6893 (p0)
REVERT: B   50 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7735 (tt0)
REVERT: B  272 ASP cc_start: 0.7380 (p0) cc_final: 0.6986 (p0)
  outliers start: 7
  outliers final: 4
  residues processed: 103
  average time/residue: 1.0417
  time to fit residues: 114.4344
Evaluate side-chains
  93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
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 33 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    1.3188

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

Flipped N/Q/H residues before XYZ refinement:
C   9 GLN
C  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.138199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.114161 restraints weight = 7246.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 1.18
r_work: 0.3189 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7572  Z= 0.234
  Angle     :  0.512   5.094  10167  Z= 0.273
  Chirality :  0.040   0.124   1011
  Planarity :  0.005   0.052   1242
  Dihedral  : 13.740 114.510   1301
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  9.26 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.28), residues: 843
  helix:  2.04 (0.21), residues: 597
  sheet:  None (None), residues: 0
  loop :  1.35 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  19 
 HIS   0.005   0.001   HIS B  96 
 PHE   0.023   0.002   PHE C 155 
 TYR   0.017   0.002   TYR A 271 
 ARG   0.002   0.000   ARG B 268 

*********************** 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
  107 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.774 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.7994 (mtpp) cc_final: 0.7469 (mmtm)
REVERT: A   68 GLN cc_start: 0.8299 (mp10) cc_final: 0.7737 (mp10)
REVERT: A  148 MET cc_start: 0.8472 (ttp) cc_final: 0.8186 (ttp)
REVERT: A  221 MET cc_start: 0.7187 (tmm) cc_final: 0.6916 (tmm)
REVERT: A  253 ASP cc_start: 0.8716 (m-30) cc_final: 0.8466 (m-30)
REVERT: A  272 ASP cc_start: 0.7359 (p0) cc_final: 0.7094 (p0)
REVERT: B    9 GLN cc_start: 0.8231 (tt0) cc_final: 0.7930 (tt0)
REVERT: B  272 ASP cc_start: 0.7565 (p0) cc_final: 0.7199 (p0)
  outliers start: 10
  outliers final: 8
  residues processed: 103
  average time/residue: 1.1012
  time to fit residues: 120.7214
Evaluate side-chains
  103 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  186 MET
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain C residue  194 SER
Chi-restraints excluded: chain C residue  221 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.9186

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.131211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.106863 restraints weight = 7372.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 1.15
r_work: 0.3174 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7572  Z= 0.316
  Angle     :  0.567   5.091  10167  Z= 0.302
  Chirality :  0.042   0.128   1011
  Planarity :  0.005   0.055   1242
  Dihedral  : 14.237 115.247   1299
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 10.11 %
    Favored  : 87.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.28), residues: 843
  helix:  1.84 (0.21), residues: 597
  sheet:  None (None), residues: 0
  loop :  1.23 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  19 
 HIS   0.007   0.001   HIS A  96 
 PHE   0.021   0.002   PHE C 155 
 TYR   0.023   0.002   TYR A 271 
 ARG   0.003   0.000   ARG B 268 

*********************** 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
  115 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.712 
Fit side-chains
REVERT: A   50 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7744 (tm-30)
REVERT: A   59 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7459 (mmtm)
REVERT: A   68 GLN cc_start: 0.8271 (mp10) cc_final: 0.7724 (mp10)
REVERT: A  148 MET cc_start: 0.8519 (ttp) cc_final: 0.8187 (ttp)
REVERT: A  221 MET cc_start: 0.7183 (tmm) cc_final: 0.6935 (tmm)
REVERT: A  253 ASP cc_start: 0.8703 (m-30) cc_final: 0.8475 (m-30)
REVERT: A  272 ASP cc_start: 0.7417 (p0) cc_final: 0.7182 (p0)
REVERT: B    9 GLN cc_start: 0.8306 (tt0) cc_final: 0.8082 (tt0)
REVERT: B   50 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7754 (tt0)
REVERT: B  272 ASP cc_start: 0.7744 (p0) cc_final: 0.7366 (p0)
REVERT: C  221 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7055 (tmm)
  outliers start: 15
  outliers final: 9
  residues processed: 108
  average time/residue: 1.1207
  time to fit residues: 128.3697
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  : 0.700 
-------------------------------------------------------------------------------
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   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   89 ILE
Chi-restraints excluded: chain C residue  194 SER
Chi-restraints excluded: chain C residue  221 MET
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 68 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3523 r_free = 0.3523 target = 0.136742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.113046 restraints weight = 7166.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 1.15
r_work: 0.3157 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7572  Z= 0.231
  Angle     :  0.507   5.113  10167  Z= 0.271
  Chirality :  0.040   0.127   1011
  Planarity :  0.005   0.054   1242
  Dihedral  : 13.419 114.460   1299
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 11.11 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.56 (0.28), residues: 843
  helix:  2.00 (0.21), residues: 597
  sheet:  None (None), residues: 0
  loop :  1.14 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  19 
 HIS   0.005   0.001   HIS B  96 
 PHE   0.012   0.002   PHE C 219 
 TYR   0.016   0.002   TYR A 271 
 ARG   0.002   0.000   ARG B 268 

*********************** 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
  110 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 1.681 
Fit side-chains
REVERT: A   50 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7682 (tm-30)
REVERT: A   68 GLN cc_start: 0.8257 (mp10) cc_final: 0.7683 (mp10)
REVERT: A  148 MET cc_start: 0.8501 (ttp) cc_final: 0.8190 (ttp)
REVERT: A  221 MET cc_start: 0.7147 (tmm) cc_final: 0.6922 (tmm)
REVERT: A  272 ASP cc_start: 0.7445 (p0) cc_final: 0.7218 (p0)
REVERT: B    9 GLN cc_start: 0.8303 (tt0) cc_final: 0.8095 (tt0)
REVERT: B   50 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7636 (tt0)
REVERT: B  272 ASP cc_start: 0.7707 (p0) cc_final: 0.7353 (p0)
  outliers start: 13
  outliers final: 10
  residues processed: 105
  average time/residue: 1.2889
  time to fit residues: 143.9179
Evaluate side-chains
  108 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
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   50 GLU
Chi-restraints excluded: chain B residue  186 MET
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  221 MET
Chi-restraints excluded: chain C residue  224 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   chunk 78 optimal weight:    0.8980
   chunk 76 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 80 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3524 r_free = 0.3524 target = 0.137276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.113027 restraints weight = 7221.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 1.19
r_work: 0.3044 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7572  Z= 0.173
  Angle     :  0.463   5.412  10167  Z= 0.248
  Chirality :  0.038   0.125   1011
  Planarity :  0.004   0.053   1242
  Dihedral  : 12.436 113.497   1299
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 11.97 %
    Favored  : 86.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.77 (0.28), residues: 843
  helix:  2.14 (0.21), residues: 603
  sheet:  None (None), residues: 0
  loop :  1.24 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  19 
 HIS   0.003   0.000   HIS A  96 
 PHE   0.011   0.001   PHE B 173 
 TYR   0.012   0.001   TYR A 271 
 ARG   0.001   0.000   ARG B 268 

*********************** 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
  113 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.8056 (mp10) cc_final: 0.7563 (mp10)
REVERT: A  148 MET cc_start: 0.8493 (ttp) cc_final: 0.8197 (ttp)
REVERT: A  253 ASP cc_start: 0.8609 (m-30) cc_final: 0.8343 (m-30)
REVERT: A  272 ASP cc_start: 0.7281 (p0) cc_final: 0.7071 (p0)
REVERT: B    9 GLN cc_start: 0.8264 (tt0) cc_final: 0.7968 (tt0)
REVERT: B  272 ASP cc_start: 0.7562 (p0) cc_final: 0.7225 (p0)
REVERT: C   92 ASP cc_start: 0.8058 (m-30) cc_final: 0.7810 (m-30)
REVERT: C  191 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7803 (tttm)
  outliers start: 12
  outliers final: 9
  residues processed: 108
  average time/residue: 1.0375
  time to fit residues: 119.3486
Evaluate side-chains
  102 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3424 r_free = 0.3424 target = 0.130279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.105443 restraints weight = 7351.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.20
r_work: 0.3080 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7572  Z= 0.322
  Angle     :  0.563   5.273  10167  Z= 0.300
  Chirality :  0.043   0.129   1011
  Planarity :  0.005   0.054   1242
  Dihedral  : 13.696 115.261   1299
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.54 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.43 (0.28), residues: 843
  helix:  1.92 (0.21), residues: 597
  sheet:  None (None), residues: 0
  loop :  1.05 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  19 
 HIS   0.006   0.001   HIS A  96 
 PHE   0.013   0.002   PHE C 173 
 TYR   0.022   0.002   TYR B 271 
 ARG   0.002   0.000   ARG B 268 

*********************** 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
  111 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.726 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.8224 (mp10) cc_final: 0.7591 (mp10)
REVERT: A  148 MET cc_start: 0.8573 (ttp) cc_final: 0.8219 (ttp)
REVERT: A  191 LYS cc_start: 0.8450 (tttm) cc_final: 0.8094 (tttm)
REVERT: A  253 ASP cc_start: 0.8717 (m-30) cc_final: 0.8482 (m-30)
REVERT: B    9 GLN cc_start: 0.8332 (tt0) cc_final: 0.7988 (tt0)
REVERT: B   50 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7811 (tt0)
REVERT: B  272 ASP cc_start: 0.7787 (p0) cc_final: 0.7426 (p0)
REVERT: C  221 MET cc_start: 0.7362 (tmt) cc_final: 0.7084 (tmm)
  outliers start: 14
  outliers final: 8
  residues processed: 108
  average time/residue: 1.2128
  time to fit residues: 138.7413
Evaluate side-chains
  104 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   50 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 83 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 = 0.3429 r_free = 0.3429 target = 0.130609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.105783 restraints weight = 7426.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 1.21
r_work: 0.3148 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7572  Z= 0.293
  Angle     :  0.548   5.156  10167  Z= 0.293
  Chirality :  0.042   0.129   1011
  Planarity :  0.005   0.054   1242
  Dihedral  : 13.658 115.159   1299
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 12.39 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.28), residues: 843
  helix:  1.90 (0.21), residues: 597
  sheet:  None (None), residues: 0
  loop :  1.04 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  19 
 HIS   0.006   0.001   HIS B  96 
 PHE   0.015   0.002   PHE A 219 
 TYR   0.020   0.002   TYR A 271 
 ARG   0.002   0.000   ARG C 164 

*********************** 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
  110 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.707 
Fit side-chains
REVERT: A   50 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7754 (tm-30)
REVERT: A  148 MET cc_start: 0.8530 (ttp) cc_final: 0.8203 (ttp)
REVERT: A  191 LYS cc_start: 0.8426 (tttm) cc_final: 0.8066 (tttm)
REVERT: A  253 ASP cc_start: 0.8706 (m-30) cc_final: 0.8456 (m-30)
REVERT: B    9 GLN cc_start: 0.8243 (tt0) cc_final: 0.7911 (tt0)
REVERT: B   50 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7793 (tt0)
REVERT: B  272 ASP cc_start: 0.7776 (p0) cc_final: 0.7424 (p0)
REVERT: C  221 MET cc_start: 0.7328 (tmt) cc_final: 0.7055 (tmm)
  outliers start: 15
  outliers final: 10
  residues processed: 104
  average time/residue: 1.1684
  time to fit residues: 129.2470
Evaluate side-chains
  105 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
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   50 GLU
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 23 optimal weight:    0.0970
   chunk 4 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 78 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    1.5984

-------------------------------------------------------------------------------
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 = 0.3439 r_free = 0.3439 target = 0.131236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.107022 restraints weight = 7444.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.16
r_work: 0.3164 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7572  Z= 0.269
  Angle     :  0.536   5.148  10167  Z= 0.287
  Chirality :  0.041   0.128   1011
  Planarity :  0.005   0.054   1242
  Dihedral  : 13.579 114.925   1299
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 12.68 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.28), residues: 843
  helix:  1.94 (0.21), residues: 597
  sheet:  None (None), residues: 0
  loop :  1.07 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  52 
 HIS   0.005   0.001   HIS B  96 
 PHE   0.014   0.002   PHE C 219 
 TYR   0.018   0.002   TYR A 271 
 ARG   0.001   0.000   ARG C 164 

*********************** 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
  109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A   50 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7715 (tm-30)
REVERT: A  148 MET cc_start: 0.8507 (ttp) cc_final: 0.8222 (ttp)
REVERT: A  191 LYS cc_start: 0.8452 (tttm) cc_final: 0.8093 (tttm)
REVERT: A  253 ASP cc_start: 0.8708 (m-30) cc_final: 0.8455 (m-30)
REVERT: B    9 GLN cc_start: 0.8254 (tt0) cc_final: 0.7922 (tt0)
REVERT: B   50 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7797 (tt0)
REVERT: B  122 MET cc_start: 0.8454 (mtm) cc_final: 0.8152 (mtm)
REVERT: B  272 ASP cc_start: 0.7775 (p0) cc_final: 0.7444 (p0)
REVERT: C  221 MET cc_start: 0.7341 (tmt) cc_final: 0.7052 (tmm)
  outliers start: 13
  outliers final: 10
  residues processed: 104
  average time/residue: 1.2351
  time to fit residues: 136.3087
Evaluate side-chains
  106 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
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   50 GLU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3514 r_free = 0.3514 target = 0.136129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.112687 restraints weight = 7269.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 1.13
r_work: 0.3214 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7572  Z= 0.203
  Angle     :  0.497   5.231  10167  Z= 0.266
  Chirality :  0.040   0.164   1011
  Planarity :  0.005   0.054   1242
  Dihedral  : 12.961 114.261   1299
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.11 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.28), residues: 843
  helix:  2.03 (0.21), residues: 603
  sheet:  None (None), residues: 0
  loop :  1.17 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  52 
 HIS   0.004   0.001   HIS B  96 
 PHE   0.011   0.002   PHE B 173 
 TYR   0.014   0.002   TYR B 271 
 ARG   0.001   0.000   ARG C 235 

********************** 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
  108 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.781 
Fit side-chains
REVERT: A  148 MET cc_start: 0.8450 (ttp) cc_final: 0.8182 (ttp)
REVERT: A  191 LYS cc_start: 0.8398 (tttm) cc_final: 0.8040 (tttm)
REVERT: B    9 GLN cc_start: 0.8228 (tt0) cc_final: 0.7836 (tt0)
REVERT: B  272 ASP cc_start: 0.7723 (p0) cc_final: 0.7404 (p0)
  outliers start: 11
  outliers final: 10
  residues processed: 103
  average time/residue: 1.1401
  time to fit residues: 125.0285
Evaluate side-chains
  106 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 20 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.9786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.137964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.114361 restraints weight = 7150.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 1.15
r_work: 0.3051 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7572  Z= 0.189
  Angle     :  0.485   5.335  10167  Z= 0.260
  Chirality :  0.039   0.204   1011
  Planarity :  0.005   0.054   1242
  Dihedral  : 12.765 114.029   1299
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.11 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.28), residues: 843
  helix:  2.10 (0.21), residues: 603
  sheet:  None (None), residues: 0
  loop :  1.19 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  52 
 HIS   0.003   0.001   HIS B  96 
 PHE   0.011   0.001   PHE B 173 
 TYR   0.013   0.001   TYR C 125 
 ARG   0.001   0.000   ARG A 268 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5131.64 seconds
wall clock time: 91 minutes 16.24 seconds (5476.24 seconds total)