Starting phenix.real_space_refine
on Wed Apr 30 21:21:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8blp_16112/04_2025/8blp_16112.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8blp_16112/04_2025/8blp_16112.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8blp_16112/04_2025/8blp_16112.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8blp_16112/04_2025/8blp_16112.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8blp_16112/04_2025/8blp_16112.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8blp_16112/04_2025/8blp_16112.cif"
  }
  resolution = 2.6
  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=   0.004 sd=   0.119
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      87      5.16       5
     C    6351      2.51       5
     N    1287      2.21       5
     O    1647      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9378
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 355, 2699
          Classifications: {'peptide': 355}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 20, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 2699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 355, 2699
          Classifications: {'peptide': 355}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 20, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "C"
      Number of atoms: 2699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 355, 2699
          Classifications: {'peptide': 355}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 20, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "A"
      Number of atoms: 405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 405
          Unusual residues: {'5D3': 2, 'LMT': 17, 'PTY': 2, 'Y01': 1}
          Classifications: {'undetermined': 22}
          Link IDs: {None: 21}
          Unresolved non-hydrogen bonds: 415
          Unresolved non-hydrogen angles: 595
          Unresolved non-hydrogen dihedrals: 819
          Unresolved non-hydrogen chiralities: 150
    Chain: "B"
      Number of atoms: 405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 405
          Unusual residues: {'5D3': 2, 'LMT': 17, 'PTY': 2, 'Y01': 1}
          Classifications: {'undetermined': 22}
          Link IDs: {None: 21}
          Unresolved non-hydrogen bonds: 415
          Unresolved non-hydrogen angles: 595
          Unresolved non-hydrogen dihedrals: 819
          Unresolved non-hydrogen chiralities: 150
    Chain: "C"
      Number of atoms: 405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 405
          Unusual residues: {'5D3': 2, 'LMT': 17, 'PTY': 2, 'Y01': 1}
          Classifications: {'undetermined': 22}
          Link IDs: {None: 21}
          Unresolved non-hydrogen bonds: 415
          Unresolved non-hydrogen angles: 595
          Unresolved non-hydrogen dihedrals: 819
          Unresolved non-hydrogen chiralities: 150
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 22
          Classifications: {'water': 22}
          Link IDs: {None: 21}
    Chain: "B"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 22
          Classifications: {'water': 22}
          Link IDs: {None: 21}
    Chain: "C"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 22
          Classifications: {'water': 22}
          Link IDs: {None: 21}
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" CAA 5D3 A 420 " occ=0.40
      ... (28 atoms not shown)
      pdb=" SBD 5D3 A 420 " occ=0.40
    residue:
      pdb=" CAA 5D3 B 422 " occ=0.40
      ... (28 atoms not shown)
      pdb=" SBD 5D3 B 422 " occ=0.40
    residue:
      pdb=" CAA 5D3 C 422 " occ=0.40
      ... (28 atoms not shown)
      pdb=" SBD 5D3 C 422 " occ=0.40
  Time building chain proxies: 6.18, per 1000 atoms: 0.66
  Number of scatterers: 9378
  At special positions: 0
  Unit cell: (103.32, 97.58, 72.98, 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      87     16.00
     P       6     15.00
     O    1647      8.00
     N    1287      7.00
     C    6351      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=0, symmetry=0
  Time building additional restraints: 2.40
  Conformation dependent library (CDL) restraints added in 956.5 milliseconds
  

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1956

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 0 sheets defined
      79.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 39
    Processing helix  chain 'A' and resid 42 through 52
    Processing helix  chain 'A' and resid 53 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 74 through 89
    Processing helix  chain 'A' and resid 89 through 110
    Processing helix  chain 'A' and resid 113 through 119
    Processing helix  chain 'A' and resid 123 through 136
      removed outlier: 3.713A  pdb=" N   ALA A 134 " --> pdb=" O   GLY A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 145
      No H-bonds generated for 'chain 'A' and resid 143 through 145'
    Processing helix  chain 'A' and resid 146 through 171
      Proline residue:  A 158  - end of helix
      removed outlier: 4.267A  pdb=" N   TRP A 171 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 192
    Processing helix  chain 'A' and resid 213 through 217
      removed outlier: 3.540A  pdb=" N   LEU A 217 " --> pdb=" O   TRP A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 233
      removed outlier: 4.023A  pdb=" N   ILE A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      Proline residue:  A 227  - end of helix
      removed outlier: 3.628A  pdb=" N   VAL A 230 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 253
    Processing helix  chain 'A' and resid 253 through 274
    Processing helix  chain 'A' and resid 277 through 283
      removed outlier: 3.516A  pdb=" N   ILE A 281 " --> pdb=" O   PRO A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 298
    Processing helix  chain 'A' and resid 305 through 331
    Processing helix  chain 'A' and resid 339 through 352
    Processing helix  chain 'A' and resid 363 through 367
      removed outlier: 3.643A  pdb=" N   VAL A 367 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 385
    Processing helix  chain 'B' and resid 32 through 39
    Processing helix  chain 'B' and resid 42 through 52
    Processing helix  chain 'B' and resid 53 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 74 through 89
    Processing helix  chain 'B' and resid 89 through 110
    Processing helix  chain 'B' and resid 113 through 119
    Processing helix  chain 'B' and resid 123 through 136
      removed outlier: 3.714A  pdb=" N   ALA B 134 " --> pdb=" O   GLY B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 145
      No H-bonds generated for 'chain 'B' and resid 143 through 145'
    Processing helix  chain 'B' and resid 146 through 171
      Proline residue:  B 158  - end of helix
      removed outlier: 4.267A  pdb=" N   TRP B 171 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 192
    Processing helix  chain 'B' and resid 213 through 217
      removed outlier: 3.540A  pdb=" N   LEU B 217 " --> pdb=" O   TRP B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 218 through 233
      removed outlier: 4.022A  pdb=" N   ILE B 226 " --> pdb=" O   LEU B 222 " (cutoff:3.500A)
      Proline residue:  B 227  - end of helix
      removed outlier: 3.628A  pdb=" N   VAL B 230 " --> pdb=" O   ILE B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 253
    Processing helix  chain 'B' and resid 253 through 274
    Processing helix  chain 'B' and resid 277 through 283
      removed outlier: 3.516A  pdb=" N   ILE B 281 " --> pdb=" O   PRO B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 298
    Processing helix  chain 'B' and resid 305 through 331
    Processing helix  chain 'B' and resid 339 through 352
    Processing helix  chain 'B' and resid 363 through 367
      removed outlier: 3.643A  pdb=" N   VAL B 367 " --> pdb=" O   LEU B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 385
    Processing helix  chain 'C' and resid 32 through 39
    Processing helix  chain 'C' and resid 42 through 52
    Processing helix  chain 'C' and resid 53 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 74 through 89
    Processing helix  chain 'C' and resid 89 through 110
    Processing helix  chain 'C' and resid 113 through 119
    Processing helix  chain 'C' and resid 123 through 136
      removed outlier: 3.714A  pdb=" N   ALA C 134 " --> pdb=" O   GLY C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 143 through 145
      No H-bonds generated for 'chain 'C' and resid 143 through 145'
    Processing helix  chain 'C' and resid 146 through 171
      Proline residue:  C 158  - end of helix
      removed outlier: 4.267A  pdb=" N   TRP C 171 " --> pdb=" O   VAL C 167 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 192
    Processing helix  chain 'C' and resid 213 through 217
      removed outlier: 3.540A  pdb=" N   LEU C 217 " --> pdb=" O   TRP C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 218 through 233
      removed outlier: 4.022A  pdb=" N   ILE C 226 " --> pdb=" O   LEU C 222 " (cutoff:3.500A)
      Proline residue:  C 227  - end of helix
      removed outlier: 3.629A  pdb=" N   VAL C 230 " --> pdb=" O   ILE C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 253
    Processing helix  chain 'C' and resid 253 through 274
    Processing helix  chain 'C' and resid 277 through 283
      removed outlier: 3.516A  pdb=" N   ILE C 281 " --> pdb=" O   PRO C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 298
    Processing helix  chain 'C' and resid 305 through 331
    Processing helix  chain 'C' and resid 339 through 352
    Processing helix  chain 'C' and resid 363 through 367
      removed outlier: 3.644A  pdb=" N   VAL C 367 " --> pdb=" O   LEU C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 369 through 385

    571 hydrogen bonds defined for protein.
    1695 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: 2.35

  Time building geometry restraints manager: 2.81 seconds

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

  Histogram of bond lengths:
        1.17 -     1.29: 1245
        1.29 -     1.42: 2433
        1.42 -     1.55: 5681
        1.55 -     1.68: 22
        1.68 -     1.81: 150
  Bond restraints: 9531
  Sorted by residual:
  bond pdb=" C1' LMT B 404 "
       pdb=" O5' LMT B 404 "
    ideal  model  delta    sigma   weight residual
    1.408  1.488 -0.080 2.00e-02 2.50e+03 1.60e+01
  bond pdb=" C1' LMT A 402 "
       pdb=" O5' LMT A 402 "
    ideal  model  delta    sigma   weight residual
    1.408  1.487 -0.079 2.00e-02 2.50e+03 1.58e+01
  bond pdb=" C1' LMT C 404 "
       pdb=" O5' LMT C 404 "
    ideal  model  delta    sigma   weight residual
    1.408  1.487 -0.079 2.00e-02 2.50e+03 1.55e+01
  bond pdb=" C30 PTY C 403 "
       pdb=" O4  PTY C 403 "
    ideal  model  delta    sigma   weight residual
    1.331  1.408 -0.077 2.00e-02 2.50e+03 1.47e+01
  bond pdb=" C30 PTY B 403 "
       pdb=" O4  PTY B 403 "
    ideal  model  delta    sigma   weight residual
    1.331  1.407 -0.076 2.00e-02 2.50e+03 1.45e+01
  ... (remaining 9526 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.30: 12245
        3.30 -     6.60: 442
        6.60 -     9.90: 100
        9.90 -    13.20: 5
       13.20 -    16.51: 3
  Bond angle restraints: 12795
  Sorted by residual:
  angle pdb=" C   CYS A 338 "
        pdb=" CA  CYS A 338 "
        pdb=" CB  CYS A 338 "
      ideal   model   delta    sigma   weight residual
     116.63  110.06    6.57 1.16e+00 7.43e-01 3.21e+01
  angle pdb=" C   CYS C 338 "
        pdb=" CA  CYS C 338 "
        pdb=" CB  CYS C 338 "
      ideal   model   delta    sigma   weight residual
     116.63  110.07    6.56 1.16e+00 7.43e-01 3.20e+01
  angle pdb=" C   CYS B 338 "
        pdb=" CA  CYS B 338 "
        pdb=" CB  CYS B 338 "
      ideal   model   delta    sigma   weight residual
     116.63  110.08    6.55 1.16e+00 7.43e-01 3.19e+01
  angle pdb=" O11 PTY A 401 "
        pdb=" P1  PTY A 401 "
        pdb=" O14 PTY A 401 "
      ideal   model   delta    sigma   weight residual
      92.90  109.41  -16.51 3.00e+00 1.11e-01 3.03e+01
  angle pdb=" O11 PTY B 403 "
        pdb=" P1  PTY B 403 "
        pdb=" O14 PTY B 403 "
      ideal   model   delta    sigma   weight residual
      92.90  109.38  -16.48 3.00e+00 1.11e-01 3.02e+01
  ... (remaining 12790 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.69: 5638
       34.69 -    69.39: 371
       69.39 -   104.08: 9
      104.08 -   138.77: 3
      138.77 -   173.47: 3
  Dihedral angle restraints: 6024
    sinusoidal: 2970
      harmonic: 3054
  Sorted by residual:
  dihedral pdb=" CBA 5D3 B 422 "
           pdb=" CAY 5D3 B 422 "
           pdb=" CAZ 5D3 B 422 "
           pdb=" NAX 5D3 B 422 "
      ideal   model   delta sinusoidal    sigma   weight residual
     111.34  -75.19 -173.47     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" CBA 5D3 C 422 "
           pdb=" CAY 5D3 C 422 "
           pdb=" CAZ 5D3 C 422 "
           pdb=" NAX 5D3 C 422 "
      ideal   model   delta sinusoidal    sigma   weight residual
     111.34  -75.21 -173.45     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" CBA 5D3 A 420 "
           pdb=" CAY 5D3 A 420 "
           pdb=" CAZ 5D3 A 420 "
           pdb=" NAX 5D3 A 420 "
      ideal   model   delta sinusoidal    sigma   weight residual
     111.34  -75.23 -173.43     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 6021 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 721
       0.033 -    0.065: 466
       0.065 -    0.098: 156
       0.098 -    0.130: 75
       0.130 -    0.163: 10
  Chirality restraints: 1428
  Sorted by residual:
  chirality pdb=" CA  PRO A 370 "
            pdb=" N   PRO A 370 "
            pdb=" C   PRO A 370 "
            pdb=" CB  PRO A 370 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.63e-01
  chirality pdb=" CA  PRO C 370 "
            pdb=" N   PRO C 370 "
            pdb=" C   PRO C 370 "
            pdb=" CB  PRO C 370 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.50e-01
  chirality pdb=" CA  PRO B 370 "
            pdb=" N   PRO B 370 "
            pdb=" C   PRO B 370 "
            pdb=" CB  PRO B 370 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.46e-01
  ... (remaining 1425 not shown)

  Planarity restraints: 1425
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAY 5D3 B 421 "    0.111 2.00e-02 2.50e+03   9.52e-02 1.36e+02
        pdb=" CAZ 5D3 B 421 "   -0.037 2.00e-02 2.50e+03
        pdb=" CBA 5D3 B 421 "   -0.131 2.00e-02 2.50e+03
        pdb=" CBB 5D3 B 421 "    0.070 2.00e-02 2.50e+03
        pdb=" CBC 5D3 B 421 "    0.090 2.00e-02 2.50e+03
        pdb=" SBD 5D3 B 421 "   -0.103 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAY 5D3 A 419 "    0.111 2.00e-02 2.50e+03   9.51e-02 1.36e+02
        pdb=" CAZ 5D3 A 419 "   -0.037 2.00e-02 2.50e+03
        pdb=" CBA 5D3 A 419 "   -0.130 2.00e-02 2.50e+03
        pdb=" CBB 5D3 A 419 "    0.070 2.00e-02 2.50e+03
        pdb=" CBC 5D3 A 419 "    0.090 2.00e-02 2.50e+03
        pdb=" SBD 5D3 A 419 "   -0.103 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAY 5D3 C 421 "   -0.110 2.00e-02 2.50e+03   9.51e-02 1.36e+02
        pdb=" CAZ 5D3 C 421 "    0.037 2.00e-02 2.50e+03
        pdb=" CBA 5D3 C 421 "    0.131 2.00e-02 2.50e+03
        pdb=" CBB 5D3 C 421 "   -0.070 2.00e-02 2.50e+03
        pdb=" CBC 5D3 C 421 "   -0.090 2.00e-02 2.50e+03
        pdb=" SBD 5D3 C 421 "    0.103 2.00e-02 2.50e+03
  ... (remaining 1422 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1343
        2.75 -     3.28: 8789
        3.28 -     3.82: 16704
        3.82 -     4.36: 22613
        4.36 -     4.90: 36200
  Nonbonded interactions: 85649
  Sorted by model distance:
  nonbonded pdb=" O   LYS B 366 "
            pdb=" O   HOH B 501 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   LYS A 366 "
            pdb=" O   HOH A 501 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   LYS C 366 "
            pdb=" O   HOH C 501 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   CYS A 157 "
            pdb=" OG  SER A 161 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   CYS C 157 "
            pdb=" OG  SER C 161 "
     model   vdw
     2.272 3.040
  ... (remaining 85644 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 31 through 385 or (resid 402 and (name C1 or name C10 or n \ 
ame C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ 
 C9 or name O1')) or resid 404 through 406 or (resid 408 and (name C1 or name C2 \ 
 or name C3 or name C4 or name C5 or name C6 or name C7 or name O1')) or resid 4 \ 
10 through 412 or (resid 413 through 414 and (name C1 or name C2 or name C3 or n \ 
ame C4 or name C5 or name C6 or name C7 or name O1')) or (resid 415 and (name C1 \ 
 or name C10 or name C11 or name C2 or name C3 or name C4 or name C5 or name C6  \ 
or name C7 or name C8 or name C9 or name O1')) or (resid 416 and (name C1 or nam \ 
e C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name O1')) or res \ 
id 417 through 418))
  selection = (chain 'B' and (resid 31 through 385 or resid 402 or (resid 404 and (name C1 or  \ 
name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name O1')) or  \ 
(resid 405 and (name C1 or name C10 or name C2 or name C3 or name C4 or name C5  \ 
or name C6 or name C7 or name C8 or name C9 or name O1')) or resid 406 or resid  \ 
408 or (resid 410 and (name C1 or name C10 or name C2 or name C3 or name C4 or n \ 
ame C5 or name C6 or name C7 or name C8 or name C9 or name O1')) or (resid 411 t \ 
hrough 414 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 o \ 
r name C7 or name O1')) or resid 415 through 417 or (resid 418 and (name C1 or n \ 
ame C2 or name C3 or name C4 or name C5 or name C6 or name O1'))))
  selection = (chain 'C' and (resid 31 through 385 or resid 402 or (resid 404 and (name C1 or  \ 
name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name O1')) or  \ 
(resid 405 and (name C1 or name C10 or name C2 or name C3 or name C4 or name C5  \ 
or name C6 or name C7 or name C8 or name C9 or name O1')) or resid 406 or resid  \ 
408 or (resid 410 and (name C1 or name C10 or name C2 or name C3 or name C4 or n \ 
ame C5 or name C6 or name C7 or name C8 or name C9 or name O1')) or (resid 411 t \ 
hrough 414 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 o \ 
r name C7 or name O1')) or resid 415 through 417 or (resid 418 and (name C1 or n \ 
ame C2 or name C3 or name C4 or name C5 or name C6 or name O1'))))
}

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=0.40 max=1.00 mean=0.99
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:             1.510
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.030
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.040
  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:10.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.080   9531  Z= 0.436
  Angle     :  1.371  16.505  12795  Z= 0.543
  Chirality :  0.049   0.163   1428
  Planarity :  0.008   0.095   1425
  Dihedral  : 19.492 173.468   4068
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  8.30 %
    Favored  : 91.35 %
  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: -1.57 (0.23), residues: 1059
  helix: -1.06 (0.16), residues: 780
  sheet:  None (None), residues: 0
  loop : -0.37 (0.39), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 306 
 HIS   0.005   0.001   HIS B 259 
 PHE   0.017   0.002   PHE C 288 
 TYR   0.014   0.002   TYR B 234 
 ARG   0.002   0.001   ARG C 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13767 (  571)
  hydrogen bonds       : angle       6.65787 ( 1695)
  covalent geometry    : bond        0.00977 ( 9531)
  covalent geometry    : angle       1.37150 (12795)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 105
  time to evaluate  : 1.133 
Fit side-chains
REVERT: A  115 SER cc_start: 0.8429 (m) cc_final: 0.8069 (p)
REVERT: B   60 ASP cc_start: 0.7941 (t70) cc_final: 0.7659 (t70)
  outliers start: 3
  outliers final: 2
  residues processed: 108
  average time/residue: 1.1524
  time to fit residues: 135.1337
Evaluate side-chains
  103 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 101
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain C residue  129 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.8980
   chunk 79 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 82 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN
B 165 ASN
C 165 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.115270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.093363 restraints weight = 9972.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 1.09
r_work: 0.2910 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2790 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.1102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9531  Z= 0.135
  Angle     :  0.556   7.977  12795  Z= 0.267
  Chirality :  0.039   0.156   1428
  Planarity :  0.005   0.046   1425
  Dihedral  : 18.931 177.023   2330
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  6.69 %
    Favored  : 90.77 %
  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:  0.77 (0.25), residues: 1059
  helix:  0.62 (0.17), residues: 780
  sheet:  None (None), residues: 0
  loop :  0.60 (0.42), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 306 
 HIS   0.003   0.001   HIS A 259 
 PHE   0.014   0.001   PHE A  71 
 TYR   0.012   0.001   TYR B 369 
 ARG   0.001   0.000   ARG C 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04684 (  571)
  hydrogen bonds       : angle       4.50456 ( 1695)
  covalent geometry    : bond        0.00294 ( 9531)
  covalent geometry    : angle       0.55629 (12795)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A  115 SER cc_start: 0.7817 (OUTLIER) cc_final: 0.7575 (p)
REVERT: A  220 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8014 (mp)
REVERT: B  115 SER cc_start: 0.7994 (OUTLIER) cc_final: 0.7680 (p)
REVERT: B  206 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8134 (mm)
REVERT: C  115 SER cc_start: 0.7854 (OUTLIER) cc_final: 0.7561 (p)
REVERT: C  212 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7353 (mp)
  outliers start: 22
  outliers final: 7
  residues processed: 116
  average time/residue: 0.9273
  time to fit residues: 117.6825
Evaluate side-chains
  115 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  206 ILE
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  357 SER
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  352 MET
Chi-restraints excluded: chain C residue  357 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 77 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0060
   chunk 65 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
B 358 ASN
C 165 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.116617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.094502 restraints weight = 9912.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 1.09
r_work: 0.2918 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9531  Z= 0.125
  Angle     :  0.526   8.084  12795  Z= 0.253
  Chirality :  0.039   0.154   1428
  Planarity :  0.004   0.044   1425
  Dihedral  : 16.206 179.954   2328
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  :  7.84 %
    Favored  : 89.97 %
  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:  1.79 (0.25), residues: 1059
  helix:  1.39 (0.17), residues: 780
  sheet:  None (None), residues: 0
  loop :  0.90 (0.42), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 306 
 HIS   0.004   0.001   HIS A 259 
 PHE   0.012   0.001   PHE A 288 
 TYR   0.011   0.001   TYR A 369 
 ARG   0.001   0.000   ARG C 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04495 (  571)
  hydrogen bonds       : angle       4.17484 ( 1695)
  covalent geometry    : bond        0.00278 ( 9531)
  covalent geometry    : angle       0.52627 (12795)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.880 
Fit side-chains
REVERT: A  115 SER cc_start: 0.7787 (OUTLIER) cc_final: 0.7514 (p)
REVERT: A  220 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8052 (mp)
REVERT: B  115 SER cc_start: 0.7924 (OUTLIER) cc_final: 0.7590 (p)
REVERT: B  212 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7322 (mp)
REVERT: C  115 SER cc_start: 0.7869 (OUTLIER) cc_final: 0.7567 (p)
REVERT: C  206 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8174 (tp)
  outliers start: 19
  outliers final: 7
  residues processed: 114
  average time/residue: 1.0260
  time to fit residues: 127.3223
Evaluate side-chains
  117 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  357 SER
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  352 MET
Chi-restraints excluded: chain C residue  357 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 83 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   chunk 63 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
C 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.115555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.093199 restraints weight = 9901.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 1.10
r_work: 0.2888 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2750
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9531  Z= 0.139
  Angle     :  0.545   8.546  12795  Z= 0.261
  Chirality :  0.040   0.157   1428
  Planarity :  0.005   0.045   1425
  Dihedral  : 15.557 179.679   2328
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  7.96 %
    Favored  : 89.50 %
  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:  2.06 (0.25), residues: 1059
  helix:  1.58 (0.17), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.02 (0.43), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 306 
 HIS   0.004   0.001   HIS A 259 
 PHE   0.013   0.001   PHE A 288 
 TYR   0.012   0.001   TYR B 369 
 ARG   0.001   0.000   ARG C 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04690 (  571)
  hydrogen bonds       : angle       4.17592 ( 1695)
  covalent geometry    : bond        0.00319 ( 9531)
  covalent geometry    : angle       0.54491 (12795)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.986 
Fit side-chains
REVERT: A  115 SER cc_start: 0.7817 (OUTLIER) cc_final: 0.7512 (p)
REVERT: A  220 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8076 (mp)
REVERT: B  115 SER cc_start: 0.7962 (OUTLIER) cc_final: 0.7604 (p)
REVERT: B  204 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7395 (mp)
REVERT: B  212 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7391 (mp)
REVERT: C  115 SER cc_start: 0.7889 (OUTLIER) cc_final: 0.7554 (p)
REVERT: C  206 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8194 (tp)
REVERT: C  212 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7260 (mp)
  outliers start: 22
  outliers final: 10
  residues processed: 112
  average time/residue: 1.0395
  time to fit residues: 126.3403
Evaluate side-chains
  123 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  357 SER
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  302 MET
Chi-restraints excluded: chain C residue  352 MET
Chi-restraints excluded: chain C residue  357 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0060
   chunk 56 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.6996

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

Flipped N/Q/H residues before XYZ refinement:
C 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.116928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.094655 restraints weight = 9844.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 1.09
r_work: 0.2910 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2790 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2764
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2764 r_free = 0.2764    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2764 r_free = 0.2764    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2764
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9531  Z= 0.123
  Angle     :  0.523   8.036  12795  Z= 0.251
  Chirality :  0.039   0.153   1428
  Planarity :  0.004   0.043   1425
  Dihedral  : 15.053 179.446   2328
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  :  8.42 %
    Favored  : 89.27 %
  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:  2.31 (0.26), residues: 1059
  helix:  1.77 (0.17), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.10 (0.43), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 340 
 HIS   0.004   0.001   HIS A 259 
 PHE   0.012   0.001   PHE A  71 
 TYR   0.011   0.001   TYR B 369 
 ARG   0.001   0.000   ARG C 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04481 (  571)
  hydrogen bonds       : angle       4.07443 ( 1695)
  covalent geometry    : bond        0.00273 ( 9531)
  covalent geometry    : angle       0.52266 (12795)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 1.322 
Fit side-chains
REVERT: A  115 SER cc_start: 0.7788 (OUTLIER) cc_final: 0.7482 (p)
REVERT: A  220 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8064 (mp)
REVERT: A  256 MET cc_start: 0.8780 (mtp) cc_final: 0.8573 (mtm)
REVERT: B  115 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7604 (p)
REVERT: B  204 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7390 (mp)
REVERT: B  212 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7359 (mp)
REVERT: C  115 SER cc_start: 0.7854 (OUTLIER) cc_final: 0.7530 (p)
REVERT: C  206 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8161 (tp)
REVERT: C  212 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7240 (mp)
  outliers start: 20
  outliers final: 9
  residues processed: 114
  average time/residue: 1.1418
  time to fit residues: 142.1624
Evaluate side-chains
  121 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  357 SER
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  352 MET
Chi-restraints excluded: chain C residue  357 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 77 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 1 optimal weight:    6.9990
   chunk 20 optimal weight:    0.5980
   chunk 96 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 88 optimal weight:    0.0980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
C 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.118011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.095763 restraints weight = 9853.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 1.10
r_work: 0.2949 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2801
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2801 r_free = 0.2801    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2801 r_free = 0.2801    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2801
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9531  Z= 0.115
  Angle     :  0.513   7.863  12795  Z= 0.247
  Chirality :  0.039   0.151   1428
  Planarity :  0.004   0.043   1425
  Dihedral  : 14.637 179.741   2328
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  :  8.42 %
    Favored  : 88.93 %
  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:  2.51 (0.26), residues: 1059
  helix:  1.92 (0.17), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.15 (0.43), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 340 
 HIS   0.004   0.001   HIS A 259 
 PHE   0.012   0.001   PHE A  71 
 TYR   0.011   0.001   TYR B 369 
 ARG   0.001   0.000   ARG C 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04373 (  571)
  hydrogen bonds       : angle       4.00467 ( 1695)
  covalent geometry    : bond        0.00252 ( 9531)
  covalent geometry    : angle       0.51269 (12795)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.879 
Fit side-chains
REVERT: A  115 SER cc_start: 0.7776 (OUTLIER) cc_final: 0.7410 (p)
REVERT: A  220 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8063 (mp)
REVERT: B  115 SER cc_start: 0.7931 (OUTLIER) cc_final: 0.7600 (p)
REVERT: B  204 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7309 (mp)
REVERT: B  212 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7356 (mp)
REVERT: C  115 SER cc_start: 0.7817 (OUTLIER) cc_final: 0.7497 (p)
REVERT: C  206 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8154 (tp)
REVERT: C  212 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7228 (mp)
  outliers start: 23
  outliers final: 8
  residues processed: 114
  average time/residue: 1.2658
  time to fit residues: 156.1071
Evaluate side-chains
  121 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  357 SER
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  352 MET
Chi-restraints excluded: chain C residue  357 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0030
   chunk 16 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   overall best weight:    1.1794

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

Flipped N/Q/H residues before XYZ refinement:
C 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.115116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.092503 restraints weight = 9992.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 1.12
r_work: 0.2888 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2766 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2721
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2721 r_free = 0.2721    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2721 r_free = 0.2721    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2721
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9531  Z= 0.158
  Angle     :  0.570   8.942  12795  Z= 0.272
  Chirality :  0.041   0.158   1428
  Planarity :  0.005   0.044   1425
  Dihedral  : 14.975 179.691   2328
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  9.00 %
    Favored  : 88.47 %
  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:  2.25 (0.25), residues: 1059
  helix:  1.70 (0.17), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.16 (0.43), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 171 
 HIS   0.005   0.001   HIS A 259 
 PHE   0.014   0.001   PHE A 288 
 TYR   0.013   0.001   TYR C 369 
 ARG   0.001   0.000   ARG C 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04846 (  571)
  hydrogen bonds       : angle       4.18005 ( 1695)
  covalent geometry    : bond        0.00370 ( 9531)
  covalent geometry    : angle       0.57007 (12795)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.959 
Fit side-chains
REVERT: A  115 SER cc_start: 0.7801 (OUTLIER) cc_final: 0.7471 (p)
REVERT: A  220 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8063 (mp)
REVERT: B  115 SER cc_start: 0.7993 (OUTLIER) cc_final: 0.7592 (p)
REVERT: B  204 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7412 (mp)
REVERT: B  212 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7394 (mp)
REVERT: C  206 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8206 (tp)
REVERT: C  212 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7287 (mp)
  outliers start: 22
  outliers final: 11
  residues processed: 115
  average time/residue: 1.0075
  time to fit residues: 126.5121
Evaluate side-chains
  121 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  357 SER
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  352 MET
Chi-restraints excluded: chain C residue  357 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 95 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
C 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.116396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.093890 restraints weight = 10104.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 1.11
r_work: 0.2920 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2763
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2763 r_free = 0.2763    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2763 r_free = 0.2763    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2763
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9531  Z= 0.133
  Angle     :  0.542   8.881  12795  Z= 0.259
  Chirality :  0.040   0.154   1428
  Planarity :  0.004   0.043   1425
  Dihedral  : 14.690 179.534   2328
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  :  9.11 %
    Favored  : 88.58 %
  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:  2.38 (0.25), residues: 1059
  helix:  1.80 (0.17), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.17 (0.43), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 171 
 HIS   0.005   0.001   HIS A 259 
 PHE   0.013   0.001   PHE A  71 
 TYR   0.012   0.001   TYR B 369 
 ARG   0.001   0.000   ARG C 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04591 (  571)
  hydrogen bonds       : angle       4.10409 ( 1695)
  covalent geometry    : bond        0.00302 ( 9531)
  covalent geometry    : angle       0.54154 (12795)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.884 
Fit side-chains
REVERT: A  115 SER cc_start: 0.7762 (OUTLIER) cc_final: 0.7375 (p)
REVERT: A  220 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8048 (mp)
REVERT: A  256 MET cc_start: 0.8755 (mtp) cc_final: 0.8544 (mtm)
REVERT: B  115 SER cc_start: 0.7959 (OUTLIER) cc_final: 0.7562 (p)
REVERT: B  204 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7335 (mp)
REVERT: B  212 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7357 (mp)
REVERT: C  115 SER cc_start: 0.7832 (OUTLIER) cc_final: 0.7474 (p)
REVERT: C  206 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8147 (tp)
REVERT: C  212 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7237 (mp)
  outliers start: 20
  outliers final: 8
  residues processed: 114
  average time/residue: 1.0983
  time to fit residues: 136.0669
Evaluate side-chains
  121 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  357 SER
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  352 MET
Chi-restraints excluded: chain C residue  357 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
C 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.115554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.093133 restraints weight = 9923.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 1.10
r_work: 0.2907 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2786 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2751
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2751
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9531  Z= 0.147
  Angle     :  0.559   8.912  12795  Z= 0.268
  Chirality :  0.041   0.156   1428
  Planarity :  0.005   0.044   1425
  Dihedral  : 14.713 179.712   2328
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  :  9.23 %
    Favored  : 88.35 %
  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:  2.29 (0.25), residues: 1059
  helix:  1.73 (0.17), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.17 (0.43), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 171 
 HIS   0.005   0.001   HIS A 259 
 PHE   0.014   0.001   PHE A  71 
 TYR   0.013   0.001   TYR C 369 
 ARG   0.001   0.000   ARG C 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04740 (  571)
  hydrogen bonds       : angle       4.15648 ( 1695)
  covalent geometry    : bond        0.00342 ( 9531)
  covalent geometry    : angle       0.55926 (12795)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.890 
Fit side-chains
REVERT: A  115 SER cc_start: 0.7769 (OUTLIER) cc_final: 0.7375 (p)
REVERT: A  220 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8049 (mp)
REVERT: A  256 MET cc_start: 0.8779 (mtp) cc_final: 0.8564 (mtm)
REVERT: B  115 SER cc_start: 0.7961 (OUTLIER) cc_final: 0.7548 (p)
REVERT: B  204 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7327 (mp)
REVERT: B  212 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7368 (mp)
REVERT: C  206 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8159 (tp)
REVERT: C  212 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7256 (mp)
  outliers start: 21
  outliers final: 12
  residues processed: 115
  average time/residue: 1.0066
  time to fit residues: 125.7918
Evaluate side-chains
  124 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  357 SER
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  352 MET
Chi-restraints excluded: chain C residue  357 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 104 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
C 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.116438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.094040 restraints weight = 9981.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 1.10
r_work: 0.2912 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2790 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2765
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2765 r_free = 0.2765    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2765 r_free = 0.2765    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2765
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9531  Z= 0.135
  Angle     :  0.545   8.850  12795  Z= 0.261
  Chirality :  0.040   0.155   1428
  Planarity :  0.005   0.045   1425
  Dihedral  : 14.515 179.527   2328
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  8.88 %
    Favored  : 88.58 %
  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 (0.25), residues: 1059
  helix:  1.80 (0.17), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.15 (0.43), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 171 
 HIS   0.005   0.001   HIS A 259 
 PHE   0.013   0.001   PHE A  71 
 TYR   0.012   0.001   TYR B 369 
 ARG   0.001   0.000   ARG C 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04603 (  571)
  hydrogen bonds       : angle       4.10883 ( 1695)
  covalent geometry    : bond        0.00308 ( 9531)
  covalent geometry    : angle       0.54530 (12795)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.957 
Fit side-chains
REVERT: A  115 SER cc_start: 0.7731 (OUTLIER) cc_final: 0.7334 (p)
REVERT: A  220 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8012 (mp)
REVERT: A  256 MET cc_start: 0.8745 (mtp) cc_final: 0.8540 (mtm)
REVERT: B  115 SER cc_start: 0.7954 (OUTLIER) cc_final: 0.7547 (p)
REVERT: B  204 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7323 (mp)
REVERT: B  212 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7358 (mp)
REVERT: C  115 SER cc_start: 0.7831 (OUTLIER) cc_final: 0.7475 (p)
REVERT: C  206 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8153 (tp)
REVERT: C  212 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7243 (mp)
  outliers start: 22
  outliers final: 11
  residues processed: 115
  average time/residue: 1.0935
  time to fit residues: 137.2622
Evaluate side-chains
  124 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 1.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  357 SER
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  352 MET
Chi-restraints excluded: chain C residue  357 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 67 optimal weight:    0.0770
   chunk 89 optimal weight:    0.8980
   chunk 36 optimal weight:    6.9990
   chunk 78 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9980
   chunk 88 optimal weight:    0.8980
   chunk 104 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
C 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.117852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.095470 restraints weight = 9905.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 1.10
r_work: 0.2943 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2823 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2793
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2793 r_free = 0.2793    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2793 r_free = 0.2793    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2793
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9531  Z= 0.119
  Angle     :  0.527   8.613  12795  Z= 0.253
  Chirality :  0.039   0.152   1428
  Planarity :  0.004   0.044   1425
  Dihedral  : 14.192 179.526   2328
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  :  9.23 %
    Favored  : 88.47 %
  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:  2.49 (0.25), residues: 1059
  helix:  1.90 (0.17), residues: 780
  sheet:  None (None), residues: 0
  loop :  1.15 (0.43), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 171 
 HIS   0.005   0.001   HIS A 259 
 PHE   0.014   0.001   PHE A  71 
 TYR   0.011   0.001   TYR B 369 
 ARG   0.001   0.000   ARG C 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04419 (  571)
  hydrogen bonds       : angle       4.03726 ( 1695)
  covalent geometry    : bond        0.00265 ( 9531)
  covalent geometry    : angle       0.52705 (12795)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6434.84 seconds
wall clock time: 113 minutes 16.88 seconds (6796.88 seconds total)