Starting phenix.real_space_refine
on Fri Dec 19 16:47:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sfj_25079/12_2025/7sfj_25079.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sfj_25079/12_2025/7sfj_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sfj_25079/12_2025/7sfj_25079.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sfj_25079/12_2025/7sfj_25079.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sfj_25079/12_2025/7sfj_25079.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sfj_25079/12_2025/7sfj_25079.cif"
  }
  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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7377
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2299
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 8, 'TRANS': 275}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'AYA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2299
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 8, 'TRANS': 275}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'AYA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 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: 108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 108
          Unusual residues: {'PEE': 4, 'RET': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 112
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'RET:plan-5': 1, 'PEE:plan-1': 3, 'PEE:plan-2': 2}
          Unresolved non-hydrogen planarities: 21
    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}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.07, per 1000 atoms: 0.28
  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=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  36 " - pdb=" SG  CYS B  36 " distance=0.00
    Simple disulfide: pdb=" SG  CYS B 120 " - pdb=" SG  CYS B 120 " distance=0.00
    Simple disulfide: pdb=" SG  CYS B 139 " - pdb=" SG  CYS B 139 " distance=0.00
    Simple disulfide: pdb=" SG  CYS B 175 " - pdb=" SG  CYS B 175 " distance=0.00
    Simple disulfide: pdb=" SG  CYS B 233 " - pdb=" SG  CYS B 233 " distance=0.00
    Simple disulfide: pdb=" SG  CYS B 250 " - pdb=" SG  CYS B 250 " distance=0.00
    Simple disulfide: pdb=" SG  CYS B 252 " - pdb=" SG  CYS B 252 " distance=0.00
    Simple disulfide: pdb=" SG  CYS B 259 " - pdb=" SG  CYS B 259 " distance=0.00

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 361.1 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: 0.21
  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: 1.15

  Time building geometry restraints manager: 0.89 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: 4143
       30.46 -    60.91: 175
       60.91 -    91.37: 12
       91.37 -   121.83: 9
      121.83 -   152.28: 9
  Dihedral angle restraints: 4348
    sinusoidal: 1873
      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 4345 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:             0.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.760
  Find NCS groups from input model:        0.160
  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:             0.000
  Load rotamer database and sin/cos tables:6.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.450
-------------------------------------------------------------------------------
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  10187  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)
  SS BOND              : angle       0.00000 (    8)
  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  : 0.260 
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: 0.7280
  time to fit residues: 68.6129
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  : 0.260 
-------------------------------------------------------------------------------
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 = 35)----------------|
| 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: 2.83 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
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  10187  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)
  SS BOND              : angle       0.00000 (    8)
  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  : 0.256 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6339 (OUTLIER) cc_final: 0.5954 (mm-40)
REVERT: A  260 TYR cc_start: 0.8061 (t80) cc_final: 0.7530 (t80)
REVERT: B   24 LYS cc_start: 0.6970 (mttt) cc_final: 0.6750 (mttp)
REVERT: B   68 GLN cc_start: 0.6657 (OUTLIER) cc_final: 0.6327 (mt0)
REVERT: C  117 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8686 (ttm)
  outliers start: 10
  outliers final: 1
  residues processed: 65
  average time/residue: 0.8256
  time to fit residues: 56.0262
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  : 0.255 
-------------------------------------------------------------------------------
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:    1.9990
   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:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.133065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.108184 restraints weight = 8440.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.03
r_work: 0.3280 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7587  Z= 0.192
  Angle     :  0.542   4.765  10187  Z= 0.283
  Chirality :  0.041   0.130   1011
  Planarity :  0.004   0.051   1242
  Dihedral  : 15.321 112.852   1314
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 11.68 %
    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:  2.78 (0.29), residues: 843
  helix:  2.25 (0.22), residues: 588
  sheet:  None (None), residues: 0
  loop :  1.02 (0.40), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 235 
 TYR   0.028   0.002   TYR B 271 
 PHE   0.016   0.002   PHE A 173 
 TRP   0.021   0.002   TRP C  19 
 HIS   0.003   0.001   HIS C  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 7584)
  covalent geometry    : angle       0.54247 (10179)
  SS BOND              : angle       0.00000 (    8)
  hydrogen bonds       : bond        0.06100 (  444)
  hydrogen bonds       : angle       3.46712 ( 1305)
  Misc. bond           : bond        0.00006 (    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
  81 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6359 (OUTLIER) cc_final: 0.6000 (mm-40)
REVERT: A  277 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.5839 (mpt-90)
REVERT: B   24 LYS cc_start: 0.7012 (mttt) cc_final: 0.6805 (mttm)
REVERT: B  117 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8687 (ttp)
REVERT: C   68 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6373 (mm-40)
REVERT: C  260 TYR cc_start: 0.8028 (t80) cc_final: 0.7729 (t80)
REVERT: C  277 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.5620 (mpt-90)
  outliers start: 18
  outliers final: 2
  residues processed: 70
  average time/residue: 0.8413
  time to fit residues: 61.3432
Evaluate side-chains
  66 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  271 TYR
Chi-restraints excluded: chain A residue  277 ARG
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  277 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 71 optimal weight:    0.0970
   chunk 78 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0270
   chunk 2 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.139309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.114801 restraints weight = 8450.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.03
r_work: 0.3364 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7587  Z= 0.098
  Angle     :  0.427   4.677  10187  Z= 0.222
  Chirality :  0.036   0.118   1011
  Planarity :  0.003   0.047   1242
  Dihedral  : 13.009 111.422   1311
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 13.25 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.16 (0.29), residues: 843
  helix:  2.66 (0.21), residues: 585
  sheet:  None (None), residues: 0
  loop :  0.85 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 277 
 TYR   0.009   0.001   TYR C 271 
 PHE   0.010   0.001   PHE C 173 
 TRP   0.012   0.001   TRP C 177 
 HIS   0.002   0.000   HIS C   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 7584)
  covalent geometry    : angle       0.42709 (10179)
  SS BOND              : angle       0.00000 (    8)
  hydrogen bonds       : bond        0.04311 (  444)
  hydrogen bonds       : angle       3.18047 ( 1305)
  Misc. bond           : bond        0.00023 (    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
  67 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6326 (mt0) cc_final: 0.5947 (mm-40)
REVERT: A  269 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7237 (mttm)
REVERT: B  117 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8631 (ttp)
REVERT: B  164 ARG cc_start: 0.6849 (tmt170) cc_final: 0.6424 (tmt170)
REVERT: C   68 GLN cc_start: 0.6631 (mt0) cc_final: 0.6394 (mm-40)
  outliers start: 9
  outliers final: 2
  residues processed: 59
  average time/residue: 0.9150
  time to fit residues: 56.1072
Evaluate side-chains
  58 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
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 C residue  138 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 36 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0000
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.6784

-------------------------------------------------------------------------------
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 = 0.3736 r_free = 0.3736 target = 0.137498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.113086 restraints weight = 8395.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.02
r_work: 0.3348 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.2275

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= 0.110
  Angle     :  0.436   4.613  10187  Z= 0.227
  Chirality :  0.037   0.122   1011
  Planarity :  0.003   0.046   1242
  Dihedral  : 12.813 111.762   1311
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.25 %
    Favored  : 83.76 %
  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:  3.23 (0.29), residues: 843
  helix:  2.75 (0.21), residues: 585
  sheet:  None (None), residues: 0
  loop :  0.77 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 277 
 TYR   0.012   0.001   TYR B 271 
 PHE   0.012   0.001   PHE B 173 
 TRP   0.012   0.001   TRP C  19 
 HIS   0.002   0.001   HIS C  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 7584)
  covalent geometry    : angle       0.43584 (10179)
  SS BOND              : angle       0.00000 (    8)
  hydrogen bonds       : bond        0.04666 (  444)
  hydrogen bonds       : angle       3.12938 ( 1305)
  Misc. bond           : bond        0.00016 (    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
  75 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6270 (mt0) cc_final: 0.5909 (mm-40)
REVERT: A  269 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7269 (mttm)
REVERT: B   10 MET cc_start: 0.8031 (mtm) cc_final: 0.7682 (mtp)
REVERT: B  117 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8610 (ttp)
REVERT: C   68 GLN cc_start: 0.6561 (OUTLIER) cc_final: 0.6345 (mm-40)
  outliers start: 14
  outliers final: 3
  residues processed: 68
  average time/residue: 0.8849
  time to fit residues: 62.5695
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  : 0.260 
-------------------------------------------------------------------------------
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 C residue   61 THR
Chi-restraints excluded: chain C residue   68 GLN
Chi-restraints excluded: chain C residue  138 SER
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:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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
C  78 ASN
C 165 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.130966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.106838 restraints weight = 8548.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.97
r_work: 0.3270 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7587  Z= 0.209
  Angle     :  0.542   4.811  10187  Z= 0.282
  Chirality :  0.041   0.130   1011
  Planarity :  0.004   0.050   1242
  Dihedral  : 14.135 113.528   1311
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 14.53 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.78 (0.29), residues: 843
  helix:  2.35 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop :  0.73 (0.39), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 136 
 TYR   0.027   0.002   TYR B 271 
 PHE   0.017   0.002   PHE B 173 
 TRP   0.021   0.002   TRP C  19 
 HIS   0.003   0.001   HIS A  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 7584)
  covalent geometry    : angle       0.54180 (10179)
  SS BOND              : angle       0.00000 (    8)
  hydrogen bonds       : bond        0.06095 (  444)
  hydrogen bonds       : angle       3.40174 ( 1305)
  Misc. bond           : bond        0.00013 (    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
  79 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6340 (OUTLIER) cc_final: 0.5948 (mm-40)
REVERT: A  277 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.5849 (mpt-90)
REVERT: B   10 MET cc_start: 0.8215 (mtm) cc_final: 0.7881 (mtp)
REVERT: B  117 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8692 (ttp)
REVERT: B  164 ARG cc_start: 0.6977 (tmt170) cc_final: 0.6502 (tmt170)
REVERT: C   68 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.6385 (mm-40)
REVERT: C  260 TYR cc_start: 0.8121 (t80) cc_final: 0.7826 (t80)
  outliers start: 16
  outliers final: 7
  residues processed: 72
  average time/residue: 0.8349
  time to fit residues: 62.7330
Evaluate side-chains
  72 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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  189 VAL
Chi-restraints excluded: chain A residue  271 TYR
Chi-restraints excluded: chain A residue  277 ARG
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
Chi-restraints excluded: chain C residue  138 SER
Chi-restraints excluded: chain C residue  152 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 76 optimal weight:   20.0000
   chunk 49 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3706 r_free = 0.3706 target = 0.134165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.109765 restraints weight = 8527.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.99
r_work: 0.3303 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.2540

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= 0.142
  Angle     :  0.476   4.710  10187  Z= 0.247
  Chirality :  0.038   0.124   1011
  Planarity :  0.004   0.050   1242
  Dihedral  : 13.386 112.761   1311
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.39 %
    Favored  : 82.62 %
  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:  2.90 (0.29), residues: 843
  helix:  2.41 (0.21), residues: 591
  sheet:  None (None), residues: 0
  loop :  0.87 (0.40), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 277 
 TYR   0.017   0.001   TYR B 271 
 PHE   0.013   0.001   PHE B 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       0.47593 (10179)
  SS BOND              : angle       0.00000 (    8)
  hydrogen bonds       : bond        0.05117 (  444)
  hydrogen bonds       : angle       3.27367 ( 1305)
  Misc. bond           : bond        0.00010 (    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
  83 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6356 (OUTLIER) cc_final: 0.5995 (mm-40)
REVERT: A  164 ARG cc_start: 0.7429 (ptt90) cc_final: 0.6749 (ptp-170)
REVERT: A  269 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7359 (mttm)
REVERT: B   10 MET cc_start: 0.8190 (mtm) cc_final: 0.7867 (mtp)
REVERT: B  152 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7219 (mm)
REVERT: C   68 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.6400 (mm-40)
  outliers start: 21
  outliers final: 8
  residues processed: 74
  average time/residue: 0.8528
  time to fit residues: 65.7573
Evaluate side-chains
  71 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
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  189 VAL
Chi-restraints excluded: chain A residue  269 LYS
Chi-restraints excluded: chain A residue  271 TYR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  269 LYS
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue   68 GLN
Chi-restraints excluded: chain C residue  138 SER
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:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 76 optimal weight:   20.0000
   chunk 44 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.3704 r_free = 0.3704 target = 0.133914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.109793 restraints weight = 8530.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 1.97
r_work: 0.3306 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.2574

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= 0.137
  Angle     :  0.473   4.658  10187  Z= 0.246
  Chirality :  0.038   0.140   1011
  Planarity :  0.004   0.050   1242
  Dihedral  : 13.267 113.066   1311
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 14.67 %
    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:  2.92 (0.29), residues: 843
  helix:  2.48 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop :  0.72 (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 B 271 
 PHE   0.013   0.001   PHE C 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        0.00321 ( 7584)
  covalent geometry    : angle       0.47355 (10179)
  SS BOND              : angle       0.00000 (    8)
  hydrogen bonds       : bond        0.05084 (  444)
  hydrogen bonds       : angle       3.24677 ( 1305)
  Misc. bond           : bond        0.00009 (    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
  78 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6217 (OUTLIER) cc_final: 0.5854 (mm-40)
REVERT: A  164 ARG cc_start: 0.7536 (ptt90) cc_final: 0.6797 (ptp-170)
REVERT: A  269 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7384 (mttm)
REVERT: B   10 MET cc_start: 0.8189 (mtm) cc_final: 0.7867 (mtp)
REVERT: B  152 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7246 (mm)
REVERT: B  221 MET cc_start: 0.6300 (mtm) cc_final: 0.5579 (pp-130)
REVERT: C   68 GLN cc_start: 0.6400 (OUTLIER) cc_final: 0.6170 (mm-40)
  outliers start: 16
  outliers final: 8
  residues processed: 72
  average time/residue: 0.8753
  time to fit residues: 65.6896
Evaluate side-chains
  71 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
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  189 VAL
Chi-restraints excluded: chain A residue  269 LYS
Chi-restraints excluded: chain A residue  271 TYR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  269 LYS
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue   68 GLN
Chi-restraints excluded: chain C residue  138 SER
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:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3734 r_free = 0.3734 target = 0.136558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.112208 restraints weight = 8370.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 1.97
r_work: 0.3337 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7587  Z= 0.110
  Angle     :  0.445   4.611  10187  Z= 0.231
  Chirality :  0.038   0.220   1011
  Planarity :  0.004   0.050   1242
  Dihedral  : 12.778 112.762   1311
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.67 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.08 (0.29), residues: 843
  helix:  2.65 (0.21), residues: 585
  sheet:  None (None), residues: 0
  loop :  0.68 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 277 
 TYR   0.012   0.001   TYR B 271 
 PHE   0.011   0.001   PHE C 173 
 TRP   0.013   0.001   TRP C  19 
 HIS   0.002   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7584)
  covalent geometry    : angle       0.44564 (10179)
  SS BOND              : angle       0.00000 (    8)
  hydrogen bonds       : bond        0.04530 (  444)
  hydrogen bonds       : angle       3.17481 ( 1305)
  Misc. bond           : bond        0.00016 (    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
  76 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6226 (OUTLIER) cc_final: 0.5895 (mm-40)
REVERT: A  164 ARG cc_start: 0.7434 (ptt90) cc_final: 0.6733 (ptp-170)
REVERT: A  269 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7346 (mttm)
REVERT: B   10 MET cc_start: 0.8177 (mtm) cc_final: 0.7852 (mtp)
REVERT: B  152 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7206 (mm)
REVERT: B  164 ARG cc_start: 0.6900 (tmt170) cc_final: 0.6286 (tmt170)
REVERT: B  221 MET cc_start: 0.6343 (mtm) cc_final: 0.5576 (pp-130)
REVERT: C   68 GLN cc_start: 0.6565 (OUTLIER) cc_final: 0.6323 (mm-40)
  outliers start: 15
  outliers final: 7
  residues processed: 70
  average time/residue: 0.8474
  time to fit residues: 61.8565
Evaluate side-chains
  69 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
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  189 VAL
Chi-restraints excluded: chain A residue  269 LYS
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  269 LYS
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue   68 GLN
Chi-restraints excluded: chain C residue  138 SER
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 18 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 16 optimal weight:    0.2980
   chunk 78 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3701 r_free = 0.3701 target = 0.133869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.110046 restraints weight = 8432.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 1.98
r_work: 0.3306 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.2640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7587  Z= 0.139
  Angle     :  0.488   6.129  10187  Z= 0.252
  Chirality :  0.039   0.247   1011
  Planarity :  0.004   0.050   1242
  Dihedral  : 13.114 113.109   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 :  1.71 %
    Allowed  : 14.81 %
    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:  2.99 (0.29), residues: 843
  helix:  2.56 (0.21), residues: 585
  sheet:  None (None), residues: 0
  loop :  0.69 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 164 
 TYR   0.016   0.001   TYR B 271 
 PHE   0.014   0.001   PHE C 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        0.00325 ( 7584)
  covalent geometry    : angle       0.48851 (10179)
  SS BOND              : angle       0.00000 (    8)
  hydrogen bonds       : bond        0.05076 (  444)
  hydrogen bonds       : angle       3.25064 ( 1305)
  Misc. bond           : bond        0.00009 (    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
  73 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.6375 (OUTLIER) cc_final: 0.6031 (mm-40)
REVERT: A  164 ARG cc_start: 0.7515 (ptt90) cc_final: 0.6779 (ptp-170)
REVERT: A  269 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7340 (mttm)
REVERT: B   10 MET cc_start: 0.8178 (mtm) cc_final: 0.7864 (mtp)
REVERT: B  152 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7250 (mm)
REVERT: B  164 ARG cc_start: 0.6958 (tmt170) cc_final: 0.6355 (tmt170)
REVERT: B  221 MET cc_start: 0.6299 (mtm) cc_final: 0.5557 (pp-130)
REVERT: C   68 GLN cc_start: 0.6398 (OUTLIER) cc_final: 0.6175 (mm-40)
  outliers start: 12
  outliers final: 7
  residues processed: 68
  average time/residue: 0.8693
  time to fit residues: 61.3745
Evaluate side-chains
  70 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
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  189 VAL
Chi-restraints excluded: chain A residue  269 LYS
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  269 LYS
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue   68 GLN
Chi-restraints excluded: chain C residue  138 SER
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:    0.9990
   chunk 76 optimal weight:   20.0000
   chunk 72 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 20 optimal weight:   20.0000
   chunk 5 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3728 r_free = 0.3728 target = 0.135889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.111455 restraints weight = 8412.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 2.00
r_work: 0.3326 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.2636

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= 0.120
  Angle     :  0.473   7.962  10187  Z= 0.241
  Chirality :  0.038   0.235   1011
  Planarity :  0.004   0.050   1242
  Dihedral  : 12.541 112.905   1311
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.53 %
    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:  3.06 (0.29), residues: 843
  helix:  2.62 (0.21), residues: 585
  sheet:  None (None), residues: 0
  loop :  0.70 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 164 
 TYR   0.013   0.001   TYR B 271 
 PHE   0.012   0.001   PHE C 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        0.00273 ( 7584)
  covalent geometry    : angle       0.47306 (10179)
  SS BOND              : angle       0.00000 (    8)
  hydrogen bonds       : bond        0.04695 (  444)
  hydrogen bonds       : angle       3.21374 ( 1305)
  Misc. bond           : bond        0.00017 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2390.62 seconds
wall clock time: 41 minutes 37.36 seconds (2497.36 seconds total)