Starting phenix.real_space_refine
on Tue Mar  3 17:55:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sfj_25079/03_2026/7sfj_25079.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sfj_25079/03_2026/7sfj_25079.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sfj_25079/03_2026/7sfj_25079.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sfj_25079/03_2026/7sfj_25079.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sfj_25079/03_2026/7sfj_25079.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sfj_25079/03_2026/7sfj_25079.map"
  }
  resolution = 2.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.175
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      48      5.16       5
     C    4983      2.51       5
     N    1098      2.21       5
     O    1245      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7377
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2299
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 8, 'TRANS': 275}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'AYA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2299
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 8, 'TRANS': 275}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'AYA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2299
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 8, 'TRANS': 275}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'AYA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 168
          Unusual residues: {'PEE': 8, 'RET': 1}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 261
          Unresolved non-hydrogen angles: 299
          Unresolved non-hydrogen dihedrals: 251
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'PEE:plan-2': 4, 'PEE:plan-1': 6, 'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 41
    Chain: "B"
      Number of atoms: 159
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 159
          Unusual residues: {'PEE': 7, 'RET': 1}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 219
          Unresolved non-hydrogen angles: 251
          Unresolved non-hydrogen dihedrals: 211
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'PEE:plan-2': 3, 'PEE:plan-1': 5, 'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "C"
      Number of atoms: 150
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 150
          Unusual residues: {'PEE': 6, 'RET': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 177
          Unresolved non-hydrogen angles: 203
          Unresolved non-hydrogen dihedrals: 171
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PEE:plan-1': 4, 'PEE:plan-2': 2, 'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 1.74, per 1000 atoms: 0.24
  Number of scatterers: 7377
  At special positions: 0
  Unit cell: (78.453, 77.316, 88.686, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     P       3     15.00
     O    1245      8.00
     N    1098      7.00
     C    4983      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 223.9 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 3 sheets defined
      74.3% alpha, 1.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 21
    Processing helix  chain 'A' and resid 26 through 53
    Processing helix  chain 'A' and resid 63 through 68
      removed outlier: 3.597A  pdb=" N   TYR A  67 " --> pdb=" O   PHE A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 71
      No H-bonds generated for 'chain 'A' and resid 69 through 71'
    Processing helix  chain 'A' and resid 72 through 95
      removed outlier: 3.515A  pdb=" N   GLY A  87 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   LYS A  88 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 130
      removed outlier: 3.748A  pdb=" N   THR A 119 " --> pdb=" O   ASP A 115 " (cutoff:3.500A)
      Proline residue:  A 121  - end of helix
    Processing helix  chain 'A' and resid 136 through 158
    Processing helix  chain 'A' and resid 160 through 163
    Processing helix  chain 'A' and resid 164 through 200
      removed outlier: 3.936A  pdb=" N   TYR A 168 " --> pdb=" O   ARG A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 222
      removed outlier: 3.711A  pdb=" N   LEU A 209 " --> pdb=" O   ALA A 205 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   HIS A 210 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   VAL A 211 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 233
    Processing helix  chain 'A' and resid 244 through 268
      removed outlier: 3.884A  pdb=" N   CYS A 259 " --> pdb=" O   VAL A 255 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   TYR A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 283
      removed outlier: 3.739A  pdb=" N   GLY A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 21
    Processing helix  chain 'B' and resid 26 through 53
    Processing helix  chain 'B' and resid 63 through 68
      removed outlier: 3.596A  pdb=" N   TYR B  67 " --> pdb=" O   PHE B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 71
      No H-bonds generated for 'chain 'B' and resid 69 through 71'
    Processing helix  chain 'B' and resid 72 through 95
      removed outlier: 3.515A  pdb=" N   GLY B  87 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   LYS B  88 " --> pdb=" O   SER B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 130
      removed outlier: 3.749A  pdb=" N   THR B 119 " --> pdb=" O   ASP B 115 " (cutoff:3.500A)
      Proline residue:  B 121  - end of helix
    Processing helix  chain 'B' and resid 136 through 158
    Processing helix  chain 'B' and resid 160 through 163
    Processing helix  chain 'B' and resid 164 through 200
      removed outlier: 3.936A  pdb=" N   TYR B 168 " --> pdb=" O   ARG B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 222
      removed outlier: 3.710A  pdb=" N   LEU B 209 " --> pdb=" O   ALA B 205 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   HIS B 210 " --> pdb=" O   GLU B 206 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   VAL B 211 " --> pdb=" O   HIS B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 233
    Processing helix  chain 'B' and resid 244 through 268
      removed outlier: 3.884A  pdb=" N   CYS B 259 " --> pdb=" O   VAL B 255 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   TYR B 260 " --> pdb=" O   ALA B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 283
      removed outlier: 3.739A  pdb=" N   GLY B 283 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 21
    Processing helix  chain 'C' and resid 26 through 53
    Processing helix  chain 'C' and resid 63 through 68
      removed outlier: 3.596A  pdb=" N   TYR C  67 " --> pdb=" O   PHE C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 71
      No H-bonds generated for 'chain 'C' and resid 69 through 71'
    Processing helix  chain 'C' and resid 72 through 95
      removed outlier: 3.515A  pdb=" N   GLY C  87 " --> pdb=" O   LEU C  83 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   LYS C  88 " --> pdb=" O   SER C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 130
      removed outlier: 3.748A  pdb=" N   THR C 119 " --> pdb=" O   ASP C 115 " (cutoff:3.500A)
      Proline residue:  C 121  - end of helix
    Processing helix  chain 'C' and resid 136 through 158
    Processing helix  chain 'C' and resid 160 through 163
    Processing helix  chain 'C' and resid 164 through 200
      removed outlier: 3.935A  pdb=" N   TYR C 168 " --> pdb=" O   ARG C 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 222
      removed outlier: 3.711A  pdb=" N   LEU C 209 " --> pdb=" O   ALA C 205 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   HIS C 210 " --> pdb=" O   GLU C 206 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   VAL C 211 " --> pdb=" O   HIS C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 233
    Processing helix  chain 'C' and resid 244 through 268
      removed outlier: 3.883A  pdb=" N   CYS C 259 " --> pdb=" O   VAL C 255 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   TYR C 260 " --> pdb=" O   ALA C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 283
      removed outlier: 3.739A  pdb=" N   GLY C 283 " --> pdb=" O   LEU C 279 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4
      removed outlier: 4.573A  pdb=" N   ALA A   4 " --> pdb=" O   THR A   7 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR A   7 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 4
      removed outlier: 4.572A  pdb=" N   ALA B   4 " --> pdb=" O   THR B   7 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR B   7 " --> pdb=" O   ALA B   4 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 4
      removed outlier: 4.572A  pdb=" N   ALA C   4 " --> pdb=" O   THR C   7 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR C   7 " --> pdb=" O   ALA C   4 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3

    444 hydrogen bonds defined for protein.
    1305 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: 0.86

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2079
        1.34 -     1.46: 1569
        1.46 -     1.57: 3858
        1.57 -     1.69: 3
        1.69 -     1.81: 75
  Bond restraints: 7584
  Sorted by residual:
  bond pdb=" C30 PEE B 403 "
       pdb=" O5  PEE B 403 "
    ideal  model  delta    sigma   weight residual
    1.206  1.353 -0.147 2.00e-02 2.50e+03 5.37e+01
  bond pdb=" C30 PEE A 403 "
       pdb=" O5  PEE A 403 "
    ideal  model  delta    sigma   weight residual
    1.206  1.352 -0.146 2.00e-02 2.50e+03 5.34e+01
  bond pdb=" C10 PEE A 401 "
       pdb=" O4  PEE A 401 "
    ideal  model  delta    sigma   weight residual
    1.206  1.352 -0.146 2.00e-02 2.50e+03 5.32e+01
  bond pdb=" C10 PEE C 403 "
       pdb=" O4  PEE C 403 "
    ideal  model  delta    sigma   weight residual
    1.206  1.352 -0.146 2.00e-02 2.50e+03 5.32e+01
  bond pdb=" C30 PEE C 405 "
       pdb=" O5  PEE C 405 "
    ideal  model  delta    sigma   weight residual
    1.206  1.352 -0.146 2.00e-02 2.50e+03 5.32e+01
  ... (remaining 7579 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.44: 9797
        2.44 -     4.88: 346
        4.88 -     7.32: 18
        7.32 -     9.76: 12
        9.76 -    12.20: 6
  Bond angle restraints: 10179
  Sorted by residual:
  angle pdb=" C11 PEE C 403 "
        pdb=" C10 PEE C 403 "
        pdb=" O2  PEE C 403 "
      ideal   model   delta    sigma   weight residual
     111.70  123.90  -12.20 3.00e+00 1.11e-01 1.65e+01
  angle pdb=" C11 PEE B 401 "
        pdb=" C10 PEE B 401 "
        pdb=" O2  PEE B 401 "
      ideal   model   delta    sigma   weight residual
     111.70  123.87  -12.17 3.00e+00 1.11e-01 1.65e+01
  angle pdb=" C11 PEE A 401 "
        pdb=" C10 PEE A 401 "
        pdb=" O2  PEE A 401 "
      ideal   model   delta    sigma   weight residual
     111.70  123.86  -12.16 3.00e+00 1.11e-01 1.64e+01
  angle pdb=" C31 PEE B 403 "
        pdb=" C30 PEE B 403 "
        pdb=" O3  PEE B 403 "
      ideal   model   delta    sigma   weight residual
     111.87  123.93  -12.06 3.00e+00 1.11e-01 1.62e+01
  angle pdb=" C31 PEE A 403 "
        pdb=" C30 PEE A 403 "
        pdb=" O3  PEE A 403 "
      ideal   model   delta    sigma   weight residual
     111.87  123.88  -12.01 3.00e+00 1.11e-01 1.60e+01
  ... (remaining 10174 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.46: 4127
       30.46 -    60.91: 175
       60.91 -    91.37: 12
       91.37 -   121.83: 9
      121.83 -   152.28: 9
  Dihedral angle restraints: 4332
    sinusoidal: 1857
      harmonic: 2475
  Sorted by residual:
  dihedral pdb=" C32 PEE B 406 "
           pdb=" C30 PEE B 406 "
           pdb=" C31 PEE B 406 "
           pdb=" O3  PEE B 406 "
      ideal   model   delta sinusoidal    sigma   weight residual
     161.16    8.88  152.28     1      3.00e+01 1.11e-03 2.01e+01
  dihedral pdb=" C32 PEE A 407 "
           pdb=" C30 PEE A 407 "
           pdb=" C31 PEE A 407 "
           pdb=" O3  PEE A 407 "
      ideal   model   delta sinusoidal    sigma   weight residual
     161.16    8.88  152.28     1      3.00e+01 1.11e-03 2.01e+01
  dihedral pdb=" C32 PEE C 401 "
           pdb=" C30 PEE C 401 "
           pdb=" C31 PEE C 401 "
           pdb=" O3  PEE C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     161.16    8.93  152.23     1      3.00e+01 1.11e-03 2.01e+01
  ... (remaining 4329 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 707
       0.037 -    0.074: 237
       0.074 -    0.111: 52
       0.111 -    0.147: 12
       0.147 -    0.184: 3
  Chirality restraints: 1011
  Sorted by residual:
  chirality pdb=" CB  ILE B 224 "
            pdb=" CA  ILE B 224 "
            pdb=" CG1 ILE B 224 "
            pdb=" CG2 ILE B 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.50e-01
  chirality pdb=" CB  ILE A 224 "
            pdb=" CA  ILE A 224 "
            pdb=" CG1 ILE A 224 "
            pdb=" CG2 ILE A 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.12e-01
  chirality pdb=" CB  ILE C 224 "
            pdb=" CA  ILE C 224 "
            pdb=" CG1 ILE C 224 "
            pdb=" CG2 ILE C 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.10e-01
  ... (remaining 1008 not shown)

  Planarity restraints: 1242
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 233 "    0.031 5.00e-02 4.00e+02   4.68e-02 3.50e+00
        pdb=" N   PRO A 234 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 234 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 234 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C 233 "   -0.031 5.00e-02 4.00e+02   4.67e-02 3.49e+00
        pdb=" N   PRO C 234 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO C 234 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 234 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 233 "    0.031 5.00e-02 4.00e+02   4.66e-02 3.47e+00
        pdb=" N   PRO B 234 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B 234 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 234 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1239 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2269
        2.83 -     3.34: 6885
        3.34 -     3.86: 12038
        3.86 -     4.38: 14221
        4.38 -     4.90: 24644
  Nonbonded interactions: 60057
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 195 "
            pdb=" O   LEU A 282 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" NH1 ARG C 195 "
            pdb=" O   LEU C 282 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" NH1 ARG B 195 "
            pdb=" O   LEU B 282 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" OG  SER B  51 "
            pdb=" OD1 ASN B  72 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OG  SER A  51 "
            pdb=" OD1 ASN A  72 "
     model   vdw
     2.314 3.040
  ... (remaining 60052 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 285 or (resid 402 and (name C36 or name C37 or n \ 
ame C38 or name C39 or name C40 or name C41 or name C42)) or (resid 404 and (nam \ 
e C39 or name C40 or name C41 or name C42))))
  selection = (chain 'B' and (resid 2 through 285 or (resid 402 and (name C36 or name C37 or n \ 
ame C38 or name C39 or name C40 or name C41 or name C42)) or (resid 404 and (nam \ 
e C39 or name C40 or name C41 or name C42))))
  selection = (chain 'C' and (resid 2 through 285 or (resid 402 and (name C36 or name C37 or n \ 
ame C38 or name C39 or name C40 or name C41 or name C42)) or (resid 404 and (nam \ 
e C39 or name C40 or name C41 or name C42))))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.890
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.370
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:7.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
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      :  0.007   0.147   7587  Z= 0.345
  Angle     :  0.940  12.201  10179  Z= 0.400
  Chirality :  0.040   0.184   1011
  Planarity :  0.005   0.047   1242
  Dihedral  : 18.487 152.281   2766
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  1.28 %
    Favored  : 97.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.20 (0.28), residues: 843
  helix:  1.78 (0.21), residues: 579
  sheet:  None (None), residues: 0
  loop :  0.95 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 266 
 TYR   0.012   0.001   TYR A 271 
 PHE   0.010   0.001   PHE A 173 
 TRP   0.009   0.001   TRP C 177 
 HIS   0.003   0.001   HIS B  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00685 ( 7584)
  covalent geometry    : angle       0.94045 (10179)
  hydrogen bonds       : bond        0.12550 (  444)
  hydrogen bonds       : angle       5.18080 ( 1305)
  Misc. bond           : bond        0.00027 (    3)

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

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: B  117 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8402 (ttp)
REVERT: B  122 MET cc_start: 0.8558 (mtt) cc_final: 0.8329 (mtm)
REVERT: C  117 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8299 (ttm)
  outliers start: 9
  outliers final: 0
  residues processed: 90
  average time/residue: 0.6761
  time to fit residues: 63.4889
Evaluate side-chains
  64 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain C residue  117 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
B   3 HIS
C 192 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.137705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.112132 restraints weight = 8385.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.05
r_work: 0.3328 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7587  Z= 0.154
  Angle     :  0.513   5.018  10179  Z= 0.267
  Chirality :  0.039   0.125   1011
  Planarity :  0.004   0.048   1242
  Dihedral  : 15.874 121.719   1317
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  7.83 %
    Favored  : 90.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.92 (0.29), residues: 843
  helix:  2.36 (0.21), residues: 585
  sheet:  None (None), residues: 0
  loop :  1.08 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 195 
 TYR   0.017   0.002   TYR C 271 
 PHE   0.017   0.002   PHE B 173 
 TRP   0.022   0.002   TRP C  19 
 HIS   0.003   0.001   HIS C   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7584)
  covalent geometry    : angle       0.51275 (10179)
  hydrogen bonds       : bond        0.05578 (  444)
  hydrogen bonds       : angle       3.40944 ( 1305)
  Misc. bond           : bond        0.00008 (    3)

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

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6334 (OUTLIER) cc_final: 0.5949 (mm-40)
REVERT: A  260 TYR cc_start: 0.8059 (t80) cc_final: 0.7529 (t80)
REVERT: B   24 LYS cc_start: 0.6969 (mttt) cc_final: 0.6750 (mttp)
REVERT: B   68 GLN cc_start: 0.6651 (OUTLIER) cc_final: 0.6321 (mt0)
REVERT: C  117 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8686 (ttm)
  outliers start: 10
  outliers final: 1
  residues processed: 65
  average time/residue: 0.7222
  time to fit residues: 48.9651
Evaluate side-chains
  60 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  271 TYR
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain C residue  117 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    1.0586

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.136524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.111333 restraints weight = 8377.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.03
r_work: 0.3319 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7587  Z= 0.143
  Angle     :  0.482   4.738  10179  Z= 0.252
  Chirality :  0.039   0.125   1011
  Planarity :  0.004   0.048   1242
  Dihedral  : 14.236 111.609   1314
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 10.97 %
    Favored  : 86.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.04 (0.29), residues: 843
  helix:  2.49 (0.22), residues: 585
  sheet:  None (None), residues: 0
  loop :  1.01 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 235 
 TYR   0.019   0.001   TYR B 271 
 PHE   0.013   0.001   PHE A 173 
 TRP   0.017   0.001   TRP C  19 
 HIS   0.003   0.001   HIS C  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 7584)
  covalent geometry    : angle       0.48223 (10179)
  hydrogen bonds       : bond        0.05291 (  444)
  hydrogen bonds       : angle       3.29658 ( 1305)
  Misc. bond           : bond        0.00009 (    3)

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

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6322 (OUTLIER) cc_final: 0.5978 (mm-40)
REVERT: B  117 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8648 (ttp)
REVERT: C   68 GLN cc_start: 0.6634 (OUTLIER) cc_final: 0.6431 (mm-40)
  outliers start: 17
  outliers final: 3
  residues processed: 64
  average time/residue: 0.8070
  time to fit residues: 53.6313
Evaluate side-chains
  62 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLN
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  271 TYR
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue   68 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 78 optimal weight:    0.3980
   chunk 35 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 28 optimal weight:    0.3980
   chunk 2 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.138611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.113793 restraints weight = 8437.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 2.01
r_work: 0.3356 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7587  Z= 0.111
  Angle     :  0.439   4.663  10179  Z= 0.229
  Chirality :  0.037   0.121   1011
  Planarity :  0.003   0.047   1242
  Dihedral  : 12.881 111.139   1311
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 12.96 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.18 (0.29), residues: 843
  helix:  2.67 (0.21), residues: 585
  sheet:  None (None), residues: 0
  loop :  0.86 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 277 
 TYR   0.012   0.001   TYR C 271 
 PHE   0.011   0.001   PHE B 173 
 TRP   0.013   0.001   TRP C  19 
 HIS   0.002   0.001   HIS C   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 7584)
  covalent geometry    : angle       0.43940 (10179)
  hydrogen bonds       : bond        0.04587 (  444)
  hydrogen bonds       : angle       3.15647 ( 1305)
  Misc. bond           : bond        0.00018 (    3)

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

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6385 (mt0) cc_final: 0.6050 (mm-40)
REVERT: A  269 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7277 (mttm)
REVERT: B  117 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8621 (ttp)
REVERT: B  164 ARG cc_start: 0.6852 (tmt170) cc_final: 0.6426 (tmt170)
REVERT: B  269 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7223 (mttm)
REVERT: C   68 GLN cc_start: 0.6498 (OUTLIER) cc_final: 0.6285 (mm-40)
  outliers start: 9
  outliers final: 2
  residues processed: 61
  average time/residue: 0.7856
  time to fit residues: 49.8912
Evaluate side-chains
  64 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLN
Chi-restraints excluded: chain A residue  269 LYS
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain B residue  269 LYS
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue   68 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 36 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0270
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.5038

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.140323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.115191 restraints weight = 8339.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 2.04
r_work: 0.3373 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   7587  Z= 0.097
  Angle     :  0.418   4.654  10179  Z= 0.217
  Chirality :  0.036   0.119   1011
  Planarity :  0.003   0.045   1242
  Dihedral  : 12.356 111.312   1311
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 13.68 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.34 (0.29), residues: 843
  helix:  2.79 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop :  0.89 (0.40), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 277 
 TYR   0.010   0.001   TYR C 271 
 PHE   0.010   0.001   PHE B 173 
 TRP   0.011   0.001   TRP C 177 
 HIS   0.002   0.000   HIS C  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 7584)
  covalent geometry    : angle       0.41808 (10179)
  hydrogen bonds       : bond        0.04262 (  444)
  hydrogen bonds       : angle       3.07239 ( 1305)
  Misc. bond           : bond        0.00018 (    3)

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

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6125 (OUTLIER) cc_final: 0.5795 (mm-40)
REVERT: A  269 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7188 (mttm)
REVERT: B  117 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8578 (ttp)
REVERT: B  164 ARG cc_start: 0.6804 (tmt170) cc_final: 0.6338 (tmt170)
REVERT: B  269 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7157 (mttm)
REVERT: C   68 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.6271 (mm-40)
  outliers start: 9
  outliers final: 2
  residues processed: 59
  average time/residue: 0.7880
  time to fit residues: 48.4596
Evaluate side-chains
  62 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLN
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  269 LYS
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain B residue  269 LYS
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue   68 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 = 0.3710 r_free = 0.3710 target = 0.134846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.110263 restraints weight = 8427.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.00
r_work: 0.3311 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7587  Z= 0.149
  Angle     :  0.476   4.751  10179  Z= 0.248
  Chirality :  0.039   0.124   1011
  Planarity :  0.004   0.047   1242
  Dihedral  : 13.188 112.256   1311
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.11 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.11 (0.29), residues: 843
  helix:  2.62 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop :  0.80 (0.39), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 277 
 TYR   0.018   0.001   TYR C 271 
 PHE   0.014   0.001   PHE A 173 
 TRP   0.016   0.001   TRP C  19 
 HIS   0.002   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7584)
  covalent geometry    : angle       0.47601 (10179)
  hydrogen bonds       : bond        0.05297 (  444)
  hydrogen bonds       : angle       3.20915 ( 1305)
  Misc. bond           : bond        0.00004 (    3)

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

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6428 (OUTLIER) cc_final: 0.6066 (mm-40)
REVERT: A  269 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7337 (mttm)
REVERT: B   10 MET cc_start: 0.8167 (mtm) cc_final: 0.7828 (mtp)
REVERT: B  117 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8646 (ttp)
REVERT: B  269 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7281 (mttm)
REVERT: C   68 GLN cc_start: 0.6634 (OUTLIER) cc_final: 0.6389 (mm-40)
  outliers start: 18
  outliers final: 4
  residues processed: 70
  average time/residue: 0.7911
  time to fit residues: 57.5179
Evaluate side-chains
  68 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  269 LYS
Chi-restraints excluded: chain A residue  271 TYR
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain B residue  269 LYS
Chi-restraints excluded: chain B residue  271 TYR
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue   68 GLN
Chi-restraints excluded: chain C residue  186 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 76 optimal weight:   20.0000
   chunk 49 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0070
   chunk 51 optimal weight:    0.4980
   chunk 67 optimal weight:    0.1980
   overall best weight:    0.4798

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.139371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.114673 restraints weight = 8462.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.03
r_work: 0.3367 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   7587  Z= 0.096
  Angle     :  0.417   4.669  10179  Z= 0.217
  Chirality :  0.036   0.119   1011
  Planarity :  0.003   0.046   1242
  Dihedral  : 12.198 111.153   1311
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 14.53 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.33 (0.29), residues: 843
  helix:  2.80 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop :  0.84 (0.40), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 277 
 TYR   0.009   0.001   TYR A 193 
 PHE   0.010   0.001   PHE C 173 
 TRP   0.011   0.001   TRP C  19 
 HIS   0.002   0.000   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 7584)
  covalent geometry    : angle       0.41735 (10179)
  hydrogen bonds       : bond        0.04193 (  444)
  hydrogen bonds       : angle       3.07652 ( 1305)
  Misc. bond           : bond        0.00021 (    3)

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

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6028 (OUTLIER) cc_final: 0.5690 (mm-40)
REVERT: A  269 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7215 (mttm)
REVERT: B   10 MET cc_start: 0.8097 (mtm) cc_final: 0.7769 (mtp)
REVERT: B  117 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8541 (ttp)
REVERT: B  221 MET cc_start: 0.6335 (mtm) cc_final: 0.5495 (pp-130)
REVERT: B  269 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7221 (mttm)
REVERT: C   68 GLN cc_start: 0.6404 (mt0) cc_final: 0.6163 (mm-40)
  outliers start: 8
  outliers final: 2
  residues processed: 64
  average time/residue: 0.7747
  time to fit residues: 51.7030
Evaluate side-chains
  63 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  269 LYS
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain B residue  269 LYS
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue  152 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN
A 192 GLN
B 192 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.134536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.110468 restraints weight = 8548.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.00
r_work: 0.3310 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7587  Z= 0.143
  Angle     :  0.471   4.712  10179  Z= 0.245
  Chirality :  0.038   0.122   1011
  Planarity :  0.004   0.047   1242
  Dihedral  : 12.857 112.884   1311
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.39 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.12 (0.29), residues: 843
  helix:  2.64 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop :  0.78 (0.40), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 277 
 TYR   0.016   0.001   TYR A 271 
 PHE   0.014   0.001   PHE A 173 
 TRP   0.017   0.001   TRP C  19 
 HIS   0.003   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 7584)
  covalent geometry    : angle       0.47055 (10179)
  hydrogen bonds       : bond        0.05159 (  444)
  hydrogen bonds       : angle       3.18061 ( 1305)
  Misc. bond           : bond        0.00007 (    3)

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

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6223 (OUTLIER) cc_final: 0.5874 (mm-40)
REVERT: A  269 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7284 (mttm)
REVERT: B   10 MET cc_start: 0.8156 (mtm) cc_final: 0.7819 (mtp)
REVERT: B  117 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8633 (ttp)
REVERT: B  164 ARG cc_start: 0.6907 (tmt170) cc_final: 0.6425 (tmt170)
REVERT: B  221 MET cc_start: 0.6620 (mtm) cc_final: 0.5695 (pp-130)
REVERT: C   68 GLN cc_start: 0.6361 (OUTLIER) cc_final: 0.6117 (mm-40)
  outliers start: 15
  outliers final: 4
  residues processed: 66
  average time/residue: 0.8121
  time to fit residues: 55.7426
Evaluate side-chains
  67 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLN
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  269 LYS
Chi-restraints excluded: chain A residue  271 TYR
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue   68 GLN
Chi-restraints excluded: chain C residue  152 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 38 optimal weight:    0.4980
   chunk 10 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.133454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.109633 restraints weight = 8430.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 1.98
r_work: 0.3298 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7587  Z= 0.155
  Angle     :  0.495   5.280  10179  Z= 0.257
  Chirality :  0.039   0.143   1011
  Planarity :  0.004   0.049   1242
  Dihedral  : 13.114 113.038   1311
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 14.67 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.95 (0.29), residues: 843
  helix:  2.46 (0.21), residues: 591
  sheet:  None (None), residues: 0
  loop :  0.83 (0.40), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 277 
 TYR   0.018   0.002   TYR A 271 
 PHE   0.014   0.001   PHE B 173 
 TRP   0.018   0.001   TRP C  19 
 HIS   0.003   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 7584)
  covalent geometry    : angle       0.49477 (10179)
  hydrogen bonds       : bond        0.05356 (  444)
  hydrogen bonds       : angle       3.27311 ( 1305)
  Misc. bond           : bond        0.00005 (    3)

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

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6315 (OUTLIER) cc_final: 0.5929 (mm-40)
REVERT: A  269 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7352 (mttm)
REVERT: B   10 MET cc_start: 0.8158 (mtm) cc_final: 0.7820 (mtp)
REVERT: B  117 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8608 (ttp)
REVERT: B  152 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7257 (mm)
REVERT: B  221 MET cc_start: 0.6498 (mtm) cc_final: 0.5732 (pp-130)
REVERT: C   68 GLN cc_start: 0.6585 (OUTLIER) cc_final: 0.6316 (mm-40)
  outliers start: 13
  outliers final: 5
  residues processed: 66
  average time/residue: 0.7806
  time to fit residues: 53.5591
Evaluate side-chains
  67 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLN
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  269 LYS
Chi-restraints excluded: chain A residue  271 TYR
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue   68 GLN
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  271 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.134601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.110842 restraints weight = 8436.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.97
r_work: 0.3323 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7587  Z= 0.127
  Angle     :  0.468   5.248  10179  Z= 0.241
  Chirality :  0.039   0.236   1011
  Planarity :  0.004   0.047   1242
  Dihedral  : 12.784 112.912   1311
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 15.67 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.02 (0.29), residues: 843
  helix:  2.57 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop :  0.74 (0.40), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 277 
 TYR   0.014   0.001   TYR A 271 
 PHE   0.012   0.001   PHE B 173 
 TRP   0.015   0.001   TRP C  19 
 HIS   0.003   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7584)
  covalent geometry    : angle       0.46813 (10179)
  hydrogen bonds       : bond        0.04882 (  444)
  hydrogen bonds       : angle       3.21272 ( 1305)
  Misc. bond           : bond        0.00016 (    3)

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

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6142 (OUTLIER) cc_final: 0.5786 (mm-40)
REVERT: A  269 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7292 (mttm)
REVERT: B   10 MET cc_start: 0.8129 (mtm) cc_final: 0.7808 (mtp)
REVERT: B  117 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8560 (ttp)
REVERT: B  152 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7137 (mm)
REVERT: B  221 MET cc_start: 0.6539 (mtm) cc_final: 0.5760 (pp-130)
REVERT: C   68 GLN cc_start: 0.6296 (OUTLIER) cc_final: 0.6047 (mm-40)
  outliers start: 9
  outliers final: 4
  residues processed: 63
  average time/residue: 0.8146
  time to fit residues: 53.3937
Evaluate side-chains
  67 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLN
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  269 LYS
Chi-restraints excluded: chain A residue  271 TYR
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue   68 GLN
Chi-restraints excluded: chain C residue  152 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 76 optimal weight:   20.0000
   chunk 72 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 70 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.136806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.112401 restraints weight = 8406.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.98
r_work: 0.3337 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7587  Z= 0.117
  Angle     :  0.456   5.198  10179  Z= 0.234
  Chirality :  0.038   0.231   1011
  Planarity :  0.004   0.047   1242
  Dihedral  : 12.395 112.857   1311
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 15.67 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.07 (0.29), residues: 843
  helix:  2.64 (0.21), residues: 585
  sheet:  None (None), residues: 0
  loop :  0.67 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 277 
 TYR   0.013   0.001   TYR A 271 
 PHE   0.011   0.001   PHE B 173 
 TRP   0.014   0.001   TRP C  19 
 HIS   0.002   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7584)
  covalent geometry    : angle       0.45636 (10179)
  hydrogen bonds       : bond        0.04687 (  444)
  hydrogen bonds       : angle       3.16570 ( 1305)
  Misc. bond           : bond        0.00018 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2189.45 seconds
wall clock time: 38 minutes 1.03 seconds (2281.03 seconds total)