Starting phenix.real_space_refine
on Tue Feb 11 14:16:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ji3_22343/02_2025/7ji3_22343.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ji3_22343/02_2025/7ji3_22343.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ji3_22343/02_2025/7ji3_22343.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ji3_22343/02_2025/7ji3_22343.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ji3_22343/02_2025/7ji3_22343.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ji3_22343/02_2025/7ji3_22343.cif"
  }
  resolution = 3.46
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    3837      2.51       5
     N    1005      2.21       5
     O    1122      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6000
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2000
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 2000
          Classifications: {'peptide': 259}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 12, 'TRANS': 246}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 118
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 43
    Chain: "B"
      Number of atoms: 2000
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 2000
          Classifications: {'peptide': 259}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 12, 'TRANS': 246}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 118
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 43
    Chain: "C"
      Number of atoms: 2000
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 2000
          Classifications: {'peptide': 259}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 12, 'TRANS': 246}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 118
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 43
  Time building chain proxies: 4.10, per 1000 atoms: 0.68
  Number of scatterers: 6000
  At special positions: 0
  Unit cell: (84.7, 81.4, 127.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1122      8.00
     N    1005      7.00
     C    3837      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 225 " - pdb=" SG  CYS A 229 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 225 " - pdb=" SG  CYS B 229 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 225 " - pdb=" SG  CYS C 229 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.40
  Conformation dependent library (CDL) restraints added in 873.8 milliseconds
  

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 12 sheets defined
      34.0% alpha, 32.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 66 through 99
      removed outlier: 3.755A  pdb=" N   ILE A  90 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ASN A  99 " --> pdb=" O   GLU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 182
    Processing helix  chain 'A' and resid 209 through 214
      removed outlier: 3.524A  pdb=" N   ILE A 213 " --> pdb=" O   PHE A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 229
      removed outlier: 3.946A  pdb=" N   PHE A 221 " --> pdb=" O   ASN A 217 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   THR A 227 " --> pdb=" O   GLY A 223 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ASN A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 332
      removed outlier: 3.928A  pdb=" N   PHE A 319 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA A 322 " --> pdb=" O   LEU A 318 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLN A 330 " --> pdb=" O   LYS A 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 99
      removed outlier: 3.755A  pdb=" N   ILE B  90 " --> pdb=" O   ALA B  86 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ASN B  99 " --> pdb=" O   GLU B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 182
    Processing helix  chain 'B' and resid 209 through 214
      removed outlier: 3.525A  pdb=" N   ILE B 213 " --> pdb=" O   PHE B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 229
      removed outlier: 3.947A  pdb=" N   PHE B 221 " --> pdb=" O   ASN B 217 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   THR B 227 " --> pdb=" O   GLY B 223 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ASN B 228 " --> pdb=" O   GLU B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 332
      removed outlier: 3.927A  pdb=" N   PHE B 319 " --> pdb=" O   PHE B 315 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA B 322 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLN B 330 " --> pdb=" O   LYS B 326 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 99
      removed outlier: 3.754A  pdb=" N   ILE C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ASN C  99 " --> pdb=" O   GLU C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 182
    Processing helix  chain 'C' and resid 209 through 214
      removed outlier: 3.525A  pdb=" N   ILE C 213 " --> pdb=" O   PHE C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 217 through 229
      removed outlier: 3.947A  pdb=" N   PHE C 221 " --> pdb=" O   ASN C 217 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   THR C 227 " --> pdb=" O   GLY C 223 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ASN C 228 " --> pdb=" O   GLU C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 303 through 332
      removed outlier: 3.928A  pdb=" N   PHE C 319 " --> pdb=" O   PHE C 315 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA C 322 " --> pdb=" O   LEU C 318 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLN C 330 " --> pdb=" O   LYS C 326 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 108
      removed outlier: 13.982A  pdb=" N   TYR A 292 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 9.848A  pdb=" N   MET A 244 " --> pdb=" O   TYR A 292 " (cutoff:3.500A)
      removed outlier: 9.713A  pdb=" N   GLN A 294 " --> pdb=" O   MET A 244 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   LEU A 246 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   ASN A 296 " --> pdb=" O   LEU A 246 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LYS A 248 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 8.132A  pdb=" N   MET A 298 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LYS A 243 " --> pdb=" O   GLU A 262 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 132
      removed outlier: 6.336A  pdb=" N   GLN A 188 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   CYS A 129 " --> pdb=" O   PHE A 186 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   PHE A 186 " --> pdb=" O   CYS A 129 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   HIS A 131 " --> pdb=" O   MET A 184 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   MET A 184 " --> pdb=" O   HIS A 131 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   PHE A 286 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   PHE A 238 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   PHE A 283 " --> pdb=" O   PHE A 238 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 152 through 156
      removed outlier: 3.671A  pdb=" N   GLU A 155 " --> pdb=" O   ALA A 170 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU A 119 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 203
    Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 108
      removed outlier: 13.980A  pdb=" N   TYR B 292 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 9.847A  pdb=" N   MET B 244 " --> pdb=" O   TYR B 292 " (cutoff:3.500A)
      removed outlier: 9.713A  pdb=" N   GLN B 294 " --> pdb=" O   MET B 244 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   LEU B 246 " --> pdb=" O   GLN B 294 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   ASN B 296 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LYS B 248 " --> pdb=" O   ASN B 296 " (cutoff:3.500A)
      removed outlier: 8.132A  pdb=" N   MET B 298 " --> pdb=" O   LYS B 248 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 132
      removed outlier: 6.335A  pdb=" N   GLN B 188 " --> pdb=" O   LEU B 127 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   CYS B 129 " --> pdb=" O   PHE B 186 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   PHE B 186 " --> pdb=" O   CYS B 129 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   HIS B 131 " --> pdb=" O   MET B 184 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   MET B 184 " --> pdb=" O   HIS B 131 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   PHE B 286 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   PHE B 238 " --> pdb=" O   LEU B 281 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   PHE B 283 " --> pdb=" O   PHE B 238 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 156
      removed outlier: 3.671A  pdb=" N   GLU B 155 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU B 119 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 200 through 203
    Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 108
      removed outlier: 13.981A  pdb=" N   TYR C 292 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
      removed outlier: 9.847A  pdb=" N   MET C 244 " --> pdb=" O   TYR C 292 " (cutoff:3.500A)
      removed outlier: 9.713A  pdb=" N   GLN C 294 " --> pdb=" O   MET C 244 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   LEU C 246 " --> pdb=" O   GLN C 294 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   ASN C 296 " --> pdb=" O   LEU C 246 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LYS C 248 " --> pdb=" O   ASN C 296 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   MET C 298 " --> pdb=" O   LYS C 248 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LYS C 243 " --> pdb=" O   GLU C 262 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 132
      removed outlier: 6.335A  pdb=" N   GLN C 188 " --> pdb=" O   LEU C 127 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   CYS C 129 " --> pdb=" O   PHE C 186 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   PHE C 186 " --> pdb=" O   CYS C 129 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   HIS C 131 " --> pdb=" O   MET C 184 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   MET C 184 " --> pdb=" O   HIS C 131 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   PHE C 286 " --> pdb=" O   VAL C 185 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   PHE C 238 " --> pdb=" O   LEU C 281 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   PHE C 283 " --> pdb=" O   PHE C 238 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 152 through 156
      removed outlier: 3.672A  pdb=" N   GLU C 155 " --> pdb=" O   ALA C 170 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU C 119 " --> pdb=" O   LEU C 171 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 200 through 203

    311 hydrogen bonds defined for protein.
    861 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: 1.63

  Time building geometry restraints manager: 1.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1947
        1.35 -     1.48: 1562
        1.48 -     1.61: 2566
        1.61 -     1.74: 0
        1.74 -     1.86: 60
  Bond restraints: 6135
  Sorted by residual:
  bond pdb=" N   ILE C 299 "
       pdb=" CA  ILE C 299 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.14e-02 7.69e+03 1.14e+01
  bond pdb=" N   ILE A 299 "
       pdb=" CA  ILE A 299 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.14e-02 7.69e+03 1.07e+01
  bond pdb=" N   ILE B 299 "
       pdb=" CA  ILE B 299 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.14e-02 7.69e+03 1.06e+01
  bond pdb=" N   ILE C 308 "
       pdb=" CA  ILE C 308 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.19e-02 7.06e+03 8.14e+00
  bond pdb=" N   ILE B 308 "
       pdb=" CA  ILE B 308 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 8.11e+00
  ... (remaining 6130 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 7549
        1.29 -     2.57: 641
        2.57 -     3.86: 107
        3.86 -     5.14: 28
        5.14 -     6.43: 6
  Bond angle restraints: 8331
  Sorted by residual:
  angle pdb=" N   GLY B 223 "
        pdb=" CA  GLY B 223 "
        pdb=" C   GLY B 223 "
      ideal   model   delta    sigma   weight residual
     112.50  107.99    4.51 1.16e+00 7.43e-01 1.51e+01
  angle pdb=" N   GLY A 223 "
        pdb=" CA  GLY A 223 "
        pdb=" C   GLY A 223 "
      ideal   model   delta    sigma   weight residual
     112.50  108.00    4.50 1.16e+00 7.43e-01 1.51e+01
  angle pdb=" N   CYS C 225 "
        pdb=" CA  CYS C 225 "
        pdb=" C   CYS C 225 "
      ideal   model   delta    sigma   weight residual
     112.54  116.65   -4.11 1.22e+00 6.72e-01 1.14e+01
  angle pdb=" N   MET A 316 "
        pdb=" CA  MET A 316 "
        pdb=" C   MET A 316 "
      ideal   model   delta    sigma   weight residual
     112.45  107.77    4.68 1.39e+00 5.18e-01 1.13e+01
  angle pdb=" N   CYS B 225 "
        pdb=" CA  CYS B 225 "
        pdb=" C   CYS B 225 "
      ideal   model   delta    sigma   weight residual
     112.54  116.65   -4.11 1.22e+00 6.72e-01 1.13e+01
  ... (remaining 8326 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.48: 3332
       16.48 -    32.97: 266
       32.97 -    49.45: 60
       49.45 -    65.94: 7
       65.94 -    82.42: 10
  Dihedral angle restraints: 3675
    sinusoidal: 1386
      harmonic: 2289
  Sorted by residual:
  dihedral pdb=" CB  CYS C 225 "
           pdb=" SG  CYS C 225 "
           pdb=" SG  CYS C 229 "
           pdb=" CB  CYS C 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -123.22   37.22     1      1.00e+01 1.00e-02 1.96e+01
  dihedral pdb=" CB  CYS A 225 "
           pdb=" SG  CYS A 225 "
           pdb=" SG  CYS A 229 "
           pdb=" CB  CYS A 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -123.22   37.22     1      1.00e+01 1.00e-02 1.95e+01
  dihedral pdb=" CB  CYS B 225 "
           pdb=" SG  CYS B 225 "
           pdb=" SG  CYS B 229 "
           pdb=" CB  CYS B 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -123.20   37.20     1      1.00e+01 1.00e-02 1.95e+01
  ... (remaining 3672 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 623
       0.043 -    0.085: 182
       0.085 -    0.127: 92
       0.127 -    0.170: 28
       0.170 -    0.212: 8
  Chirality restraints: 933
  Sorted by residual:
  chirality pdb=" CA  MET B 316 "
            pdb=" N   MET B 316 "
            pdb=" C   MET B 316 "
            pdb=" CB  MET B 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  MET A 316 "
            pdb=" N   MET A 316 "
            pdb=" C   MET A 316 "
            pdb=" CB  MET A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  MET C 316 "
            pdb=" N   MET C 316 "
            pdb=" C   MET C 316 "
            pdb=" CB  MET C 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 930 not shown)

  Planarity restraints: 1077
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 142 "    0.045 5.00e-02 4.00e+02   6.80e-02 7.39e+00
        pdb=" N   PRO A 143 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A 143 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 143 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 142 "    0.045 5.00e-02 4.00e+02   6.78e-02 7.36e+00
        pdb=" N   PRO C 143 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO C 143 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO C 143 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 142 "    0.045 5.00e-02 4.00e+02   6.77e-02 7.33e+00
        pdb=" N   PRO B 143 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO B 143 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 143 "    0.037 5.00e-02 4.00e+02
  ... (remaining 1074 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.87: 2164
        2.87 -     3.38: 4914
        3.38 -     3.89: 9427
        3.89 -     4.39: 9936
        4.39 -     4.90: 18361
  Nonbonded interactions: 44802
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 324 "
            pdb=" OG1 THR A 328 "
     model   vdw
     2.365 3.040
  nonbonded pdb=" O   PHE C 324 "
            pdb=" OG1 THR C 328 "
     model   vdw
     2.365 3.040
  nonbonded pdb=" O   PHE B 324 "
            pdb=" OG1 THR B 328 "
     model   vdw
     2.366 3.040
  nonbonded pdb=" O   PRO B 176 "
            pdb=" NE1 TRP B 288 "
     model   vdw
     2.416 3.120
  nonbonded pdb=" O   PRO A 176 "
            pdb=" NE1 TRP A 288 "
     model   vdw
     2.416 3.120
  ... (remaining 44797 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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:             0.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.450
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
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      :  0.005   0.056   6135  Z= 0.347
  Angle     :  0.793   6.426   8331  Z= 0.511
  Chirality :  0.055   0.212    933
  Planarity :  0.008   0.068   1077
  Dihedral  : 13.456  82.424   2172
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 14.74 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.13 (0.22), residues: 759
  helix: -3.58 (0.21), residues: 255
  sheet: -2.95 (0.22), residues: 312
  loop : -2.99 (0.32), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 241 
 HIS   0.002   0.001   HIS A 134 
 PHE   0.030   0.003   PHE C 234 
 TYR   0.021   0.002   TYR C 282 
 ARG   0.006   0.001   ARG A 239 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.6077 (p0) cc_final: 0.5719 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.2418
  time to fit residues: 40.9651
Evaluate side-chains
  76 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 58 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  88 GLN
A  99 ASN
A 107 GLN
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 135 ASN
A 188 GLN
** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 280 GLN
B  88 GLN
B  99 ASN
B 107 GLN
B 135 ASN
B 188 GLN
** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 280 GLN
C  88 GLN
C 107 GLN
** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 135 ASN
C 188 GLN
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 280 GLN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.068751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.049658 restraints weight = 21600.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 4.45
r_work: 0.2705 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6135  Z= 0.245
  Angle     :  0.589   9.896   8331  Z= 0.297
  Chirality :  0.043   0.202    933
  Planarity :  0.005   0.051   1077
  Dihedral  :  4.604  23.434    831
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.79 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.65 (0.27), residues: 759
  helix: -0.45 (0.31), residues: 252
  sheet: -2.07 (0.25), residues: 306
  loop : -2.46 (0.37), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 241 
 HIS   0.003   0.001   HIS A 131 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.015   0.002   TYR B 292 
 ARG   0.002   0.000   ARG C 271 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.9356 (mmmm) cc_final: 0.8858 (mmtm)
REVERT: A  102 MET cc_start: 0.8113 (tpp) cc_final: 0.7885 (mmp)
REVERT: A  218 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8168 (mmtt)
REVERT: A  290 ASP cc_start: 0.8643 (p0) cc_final: 0.7990 (p0)
REVERT: A  292 TYR cc_start: 0.9156 (m-80) cc_final: 0.8849 (m-80)
REVERT: B   96 LYS cc_start: 0.8600 (mptt) cc_final: 0.8384 (mmtp)
REVERT: B   98 LYS cc_start: 0.9426 (tppp) cc_final: 0.9210 (ttmm)
REVERT: B  150 ASP cc_start: 0.8764 (m-30) cc_final: 0.8428 (m-30)
REVERT: B  184 MET cc_start: 0.9602 (ptp) cc_final: 0.9385 (ptp)
REVERT: B  187 MET cc_start: 0.9066 (ptp) cc_final: 0.8862 (ptp)
REVERT: B  218 LYS cc_start: 0.8509 (mmtt) cc_final: 0.8213 (mmtt)
REVERT: B  290 ASP cc_start: 0.8776 (p0) cc_final: 0.8159 (p0)
REVERT: C   96 LYS cc_start: 0.8599 (mptt) cc_final: 0.8286 (mmtp)
REVERT: C   98 LYS cc_start: 0.9487 (mmmm) cc_final: 0.9064 (mmtm)
REVERT: C  150 ASP cc_start: 0.8831 (m-30) cc_final: 0.8580 (m-30)
REVERT: C  218 LYS cc_start: 0.8420 (mmtt) cc_final: 0.7802 (mmtt)
  outliers start: 13
  outliers final: 6
  residues processed: 100
  average time/residue: 0.2353
  time to fit residues: 29.1819
Evaluate side-chains
  92 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  303 ASN
Chi-restraints excluded: chain C residue  179 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0060
   chunk 64 optimal weight:    0.0870
   chunk 66 optimal weight:    4.9990
   chunk 50 optimal weight:   40.0000
   chunk 63 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    1.4180

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

Flipped N/Q/H residues before XYZ refinement:
** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 134 HIS
C 134 HIS
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.068628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.049657 restraints weight = 21864.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 4.48
r_work: 0.2705 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6135  Z= 0.196
  Angle     :  0.555  10.433   8331  Z= 0.273
  Chirality :  0.041   0.138    933
  Planarity :  0.004   0.042   1077
  Dihedral  :  4.263  22.202    831
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 18.27 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.30), residues: 759
  helix:  1.03 (0.33), residues: 252
  sheet: -1.61 (0.27), residues: 306
  loop : -2.13 (0.40), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 305 
 HIS   0.002   0.001   HIS A 131 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.011   0.001   TYR B 282 
 ARG   0.001   0.000   ARG A 145 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.9422 (mmmm) cc_final: 0.8926 (mmtm)
REVERT: A  218 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8190 (mmtt)
REVERT: A  290 ASP cc_start: 0.8630 (p0) cc_final: 0.8029 (p0)
REVERT: A  292 TYR cc_start: 0.9130 (m-80) cc_final: 0.8884 (m-10)
REVERT: A  298 MET cc_start: 0.9332 (tpp) cc_final: 0.9005 (mmm)
REVERT: B   96 LYS cc_start: 0.8579 (mptt) cc_final: 0.8253 (mmtp)
REVERT: B  150 ASP cc_start: 0.8785 (m-30) cc_final: 0.8484 (m-30)
REVERT: B  218 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8241 (mmtt)
REVERT: B  290 ASP cc_start: 0.8670 (p0) cc_final: 0.8232 (p0)
REVERT: C   98 LYS cc_start: 0.9487 (mmmm) cc_final: 0.9017 (mmtm)
REVERT: C  150 ASP cc_start: 0.8836 (m-30) cc_final: 0.8610 (m-30)
REVERT: C  171 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8783 (tt)
REVERT: C  218 LYS cc_start: 0.8527 (mmtt) cc_final: 0.7943 (mmtt)
  outliers start: 5
  outliers final: 3
  residues processed: 90
  average time/residue: 0.2509
  time to fit residues: 28.1041
Evaluate side-chains
  83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  179 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 69 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 49 optimal weight:    8.9990
   chunk 34 optimal weight:    5.9990
   chunk 4 optimal weight:    0.5980
   overall best weight:    3.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 131 HIS
** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.066188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.047432 restraints weight = 22466.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 4.44
r_work: 0.2648 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   6135  Z= 0.350
  Angle     :  0.608  10.845   8331  Z= 0.303
  Chirality :  0.042   0.200    933
  Planarity :  0.004   0.044   1077
  Dihedral  :  4.339  22.281    831
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 16.67 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.30), residues: 759
  helix:  1.60 (0.33), residues: 252
  sheet: -1.39 (0.27), residues: 306
  loop : -2.01 (0.41), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 305 
 HIS   0.002   0.001   HIS A 131 
 PHE   0.016   0.001   PHE B 234 
 TYR   0.015   0.002   TYR B 282 
 ARG   0.001   0.000   ARG C 180 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8372 (mmtt)
REVERT: A  290 ASP cc_start: 0.8676 (p0) cc_final: 0.7960 (p0)
REVERT: A  292 TYR cc_start: 0.9076 (m-80) cc_final: 0.8699 (m-80)
REVERT: B  187 MET cc_start: 0.9141 (ptp) cc_final: 0.8904 (ptp)
REVERT: B  218 LYS cc_start: 0.8754 (mmtt) cc_final: 0.8491 (mmtt)
REVERT: B  290 ASP cc_start: 0.8715 (p0) cc_final: 0.7953 (p0)
REVERT: B  292 TYR cc_start: 0.9022 (m-10) cc_final: 0.8722 (m-10)
REVERT: C   98 LYS cc_start: 0.9510 (mmmm) cc_final: 0.9072 (mmtm)
REVERT: C  171 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8796 (tt)
REVERT: C  218 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8055 (mmtt)
  outliers start: 10
  outliers final: 6
  residues processed: 88
  average time/residue: 0.2218
  time to fit residues: 24.6883
Evaluate side-chains
  81 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  179 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   chunk 28 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 73 optimal weight:    0.6980
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 131 HIS
A 188 GLN
** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.066750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.047987 restraints weight = 22206.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.2831 rms_B_bonded: 4.43
r_work: 0.2663 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   6135  Z= 0.247
  Angle     :  0.576  11.608   8331  Z= 0.282
  Chirality :  0.042   0.175    933
  Planarity :  0.004   0.044   1077
  Dihedral  :  4.214  21.130    831
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.63 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.31), residues: 759
  helix:  1.90 (0.34), residues: 252
  sheet: -1.21 (0.27), residues: 306
  loop : -1.85 (0.43), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 305 
 HIS   0.002   0.001   HIS A 131 
 PHE   0.015   0.001   PHE C 234 
 TYR   0.011   0.001   TYR B 282 
 ARG   0.001   0.000   ARG A 272 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.9450 (mmmm) cc_final: 0.8981 (mmtm)
REVERT: A  218 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8352 (mmtt)
REVERT: A  290 ASP cc_start: 0.8642 (p0) cc_final: 0.8006 (p0)
REVERT: A  292 TYR cc_start: 0.9053 (m-80) cc_final: 0.8706 (m-80)
REVERT: B  187 MET cc_start: 0.9158 (ptp) cc_final: 0.8924 (ptp)
REVERT: B  218 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8461 (mmtt)
REVERT: B  290 ASP cc_start: 0.8687 (p0) cc_final: 0.7861 (p0)
REVERT: B  292 TYR cc_start: 0.9033 (m-10) cc_final: 0.8713 (m-10)
REVERT: B  297 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8368 (mmmm)
REVERT: C   98 LYS cc_start: 0.9516 (mmmm) cc_final: 0.9106 (mmtm)
REVERT: C  171 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8787 (tt)
  outliers start: 11
  outliers final: 6
  residues processed: 83
  average time/residue: 0.2390
  time to fit residues: 25.6000
Evaluate side-chains
  77 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  229 CYS
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  229 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 19 optimal weight:    0.4980
   chunk 14 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 71 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   overall best weight:    1.3982

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

Flipped N/Q/H residues before XYZ refinement:
** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.067268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.048325 restraints weight = 21750.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 4.42
r_work: 0.2680 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6135  Z= 0.193
  Angle     :  0.598  12.192   8331  Z= 0.283
  Chirality :  0.044   0.341    933
  Planarity :  0.004   0.043   1077
  Dihedral  :  4.074  20.468    831
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 17.95 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.31), residues: 759
  helix:  2.06 (0.34), residues: 252
  sheet: -1.06 (0.27), residues: 306
  loop : -1.83 (0.43), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 305 
 HIS   0.004   0.001   HIS A 131 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.009   0.001   TYR B 282 
 ARG   0.001   0.000   ARG C 272 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 LYS cc_start: 0.8666 (mptt) cc_final: 0.8421 (mmtp)
REVERT: A   98 LYS cc_start: 0.9492 (mmmm) cc_final: 0.8999 (mmtm)
REVERT: A  244 MET cc_start: 0.9437 (ptt) cc_final: 0.9107 (ptp)
REVERT: A  290 ASP cc_start: 0.8614 (p0) cc_final: 0.7993 (p0)
REVERT: A  292 TYR cc_start: 0.9084 (m-80) cc_final: 0.8724 (m-80)
REVERT: A  315 PHE cc_start: 0.9442 (m-10) cc_final: 0.9111 (t80)
REVERT: B  187 MET cc_start: 0.9111 (ptp) cc_final: 0.8886 (ptp)
REVERT: B  290 ASP cc_start: 0.8628 (p0) cc_final: 0.7787 (p0)
REVERT: C   98 LYS cc_start: 0.9502 (mmmm) cc_final: 0.9095 (mmtm)
REVERT: C  171 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8776 (tt)
REVERT: C  184 MET cc_start: 0.9352 (ptp) cc_final: 0.9090 (ptp)
REVERT: C  218 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8030 (mmmt)
REVERT: C  248 LYS cc_start: 0.9286 (mtpp) cc_final: 0.8903 (ttmm)
  outliers start: 8
  outliers final: 5
  residues processed: 82
  average time/residue: 0.2036
  time to fit residues: 21.7977
Evaluate side-chains
  76 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  311 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:   20.0000
   chunk 59 optimal weight:    0.9980
   chunk 7 optimal weight:    7.9990
   chunk 41 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 131 HIS
** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.067310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.048387 restraints weight = 22116.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 4.42
r_work: 0.2681 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6135  Z= 0.205
  Angle     :  0.605  12.376   8331  Z= 0.284
  Chirality :  0.044   0.306    933
  Planarity :  0.004   0.043   1077
  Dihedral  :  3.997  19.618    831
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 17.95 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.31), residues: 759
  helix:  2.18 (0.33), residues: 252
  sheet: -0.91 (0.27), residues: 306
  loop : -1.82 (0.43), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 305 
 HIS   0.002   0.001   HIS A 131 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.010   0.001   TYR B 282 
 ARG   0.001   0.000   ARG C 272 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 LYS cc_start: 0.8769 (mptt) cc_final: 0.8529 (mmtp)
REVERT: A   98 LYS cc_start: 0.9485 (mmmm) cc_final: 0.8993 (mmtm)
REVERT: A  290 ASP cc_start: 0.8609 (p0) cc_final: 0.8005 (p0)
REVERT: A  292 TYR cc_start: 0.9050 (m-80) cc_final: 0.8700 (m-80)
REVERT: A  315 PHE cc_start: 0.9444 (m-10) cc_final: 0.9106 (t80)
REVERT: B  187 MET cc_start: 0.9116 (ptp) cc_final: 0.8848 (ptp)
REVERT: B  290 ASP cc_start: 0.8651 (p0) cc_final: 0.7797 (p0)
REVERT: B  297 LYS cc_start: 0.8823 (mmmm) cc_final: 0.8467 (mmmm)
REVERT: B  315 PHE cc_start: 0.9381 (m-10) cc_final: 0.8973 (t80)
REVERT: C   98 LYS cc_start: 0.9496 (mmmm) cc_final: 0.9082 (mmtm)
REVERT: C  102 MET cc_start: 0.8743 (tpp) cc_final: 0.8469 (tpp)
REVERT: C  171 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8783 (tt)
REVERT: C  184 MET cc_start: 0.9367 (ptp) cc_final: 0.9114 (ptp)
REVERT: C  248 LYS cc_start: 0.9298 (mtpp) cc_final: 0.8944 (ttmm)
REVERT: C  297 LYS cc_start: 0.8507 (mmmm) cc_final: 0.7869 (mmtm)
  outliers start: 8
  outliers final: 6
  residues processed: 82
  average time/residue: 0.1900
  time to fit residues: 20.5100
Evaluate side-chains
  76 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  229 CYS
Chi-restraints excluded: chain C residue  311 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 25 optimal weight:   40.0000
   chunk 49 optimal weight:    0.5980
   chunk 51 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 46 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.067111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.048271 restraints weight = 21937.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 4.40
r_work: 0.2676 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.3735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6135  Z= 0.214
  Angle     :  0.634  12.358   8331  Z= 0.293
  Chirality :  0.044   0.355    933
  Planarity :  0.004   0.043   1077
  Dihedral  :  4.003  19.783    831
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 18.91 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.31), residues: 759
  helix:  2.25 (0.33), residues: 255
  sheet: -0.82 (0.28), residues: 306
  loop : -1.79 (0.43), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 305 
 HIS   0.006   0.001   HIS A 131 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.010   0.001   TYR B 282 
 ARG   0.001   0.000   ARG A 272 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.765 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8795 (mptt) cc_final: 0.8585 (mmtp)
REVERT: A   98 LYS cc_start: 0.9484 (mmmm) cc_final: 0.9000 (mmtm)
REVERT: A  290 ASP cc_start: 0.8634 (p0) cc_final: 0.8009 (p0)
REVERT: A  292 TYR cc_start: 0.9033 (m-80) cc_final: 0.8686 (m-80)
REVERT: A  297 LYS cc_start: 0.8574 (mmmm) cc_final: 0.8252 (mmtm)
REVERT: A  315 PHE cc_start: 0.9438 (m-10) cc_final: 0.9102 (t80)
REVERT: B  187 MET cc_start: 0.9131 (ptp) cc_final: 0.8899 (ptp)
REVERT: B  290 ASP cc_start: 0.8635 (p0) cc_final: 0.7770 (p0)
REVERT: B  315 PHE cc_start: 0.9358 (m-10) cc_final: 0.8962 (t80)
REVERT: C   98 LYS cc_start: 0.9493 (mmmm) cc_final: 0.9119 (mmtm)
REVERT: C  102 MET cc_start: 0.8726 (tpp) cc_final: 0.8493 (tpp)
REVERT: C  171 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8774 (tt)
REVERT: C  184 MET cc_start: 0.9374 (ptp) cc_final: 0.9133 (ptp)
REVERT: C  204 MET cc_start: 0.9149 (ttp) cc_final: 0.8626 (tmm)
REVERT: C  243 LYS cc_start: 0.9003 (mtpt) cc_final: 0.8600 (mtpp)
  outliers start: 6
  outliers final: 4
  residues processed: 82
  average time/residue: 0.2210
  time to fit residues: 23.1408
Evaluate side-chains
  77 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  311 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 28 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3352 r_free = 0.3352 target = 0.067671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.048891 restraints weight = 21999.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.2858 rms_B_bonded: 4.43
r_work: 0.2694 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.3817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6135  Z= 0.177
  Angle     :  0.630  12.364   8331  Z= 0.290
  Chirality :  0.045   0.363    933
  Planarity :  0.004   0.043   1077
  Dihedral  :  3.955  19.270    831
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 18.91 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.31), residues: 759
  helix:  2.29 (0.33), residues: 255
  sheet: -0.71 (0.28), residues: 300
  loop : -1.53 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 305 
 HIS   0.006   0.001   HIS A 131 
 PHE   0.014   0.001   PHE A 234 
 TYR   0.008   0.001   TYR B 282 
 ARG   0.001   0.000   ARG C 145 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.763 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8753 (mptt) cc_final: 0.8544 (mmtp)
REVERT: A   98 LYS cc_start: 0.9470 (mmmm) cc_final: 0.8982 (mmtm)
REVERT: A  150 ASP cc_start: 0.8873 (m-30) cc_final: 0.8487 (m-30)
REVERT: A  290 ASP cc_start: 0.8620 (p0) cc_final: 0.8014 (p0)
REVERT: A  292 TYR cc_start: 0.9028 (m-80) cc_final: 0.8711 (m-80)
REVERT: A  315 PHE cc_start: 0.9434 (m-10) cc_final: 0.9088 (t80)
REVERT: B  187 MET cc_start: 0.9103 (ptp) cc_final: 0.8819 (ptp)
REVERT: B  290 ASP cc_start: 0.8636 (p0) cc_final: 0.7796 (p0)
REVERT: B  315 PHE cc_start: 0.9358 (m-10) cc_final: 0.8963 (t80)
REVERT: C   98 LYS cc_start: 0.9487 (mmmm) cc_final: 0.9107 (mmtm)
REVERT: C  102 MET cc_start: 0.8756 (tpp) cc_final: 0.8469 (tpp)
REVERT: C  171 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8770 (tt)
REVERT: C  184 MET cc_start: 0.9351 (ptp) cc_final: 0.9104 (ptp)
REVERT: C  218 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8074 (mmmt)
REVERT: C  243 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8581 (mtpp)
REVERT: C  297 LYS cc_start: 0.8433 (mmmm) cc_final: 0.7757 (mmtm)
  outliers start: 7
  outliers final: 5
  residues processed: 88
  average time/residue: 0.1971
  time to fit residues: 22.5362
Evaluate side-chains
  83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  229 CYS
Chi-restraints excluded: chain C residue  311 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 41 optimal weight:    4.9990
   chunk 53 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 44 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9980
   chunk 39 optimal weight:    0.4980
   chunk 38 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 50 optimal weight:   40.0000
   chunk 32 optimal weight:    0.2980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3374 r_free = 0.3374 target = 0.068543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.049729 restraints weight = 21917.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 4.43
r_work: 0.2721 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.3893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6135  Z= 0.160
  Angle     :  0.647  12.582   8331  Z= 0.295
  Chirality :  0.045   0.374    933
  Planarity :  0.004   0.044   1077
  Dihedral  :  3.869  19.194    831
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 19.23 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.31), residues: 759
  helix:  2.39 (0.33), residues: 255
  sheet: -0.56 (0.28), residues: 300
  loop : -1.51 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP C 305 
 HIS   0.005   0.001   HIS A 131 
 PHE   0.014   0.001   PHE A 234 
 TYR   0.007   0.001   TYR C 282 
 ARG   0.001   0.000   ARG C 145 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.9457 (mmmm) cc_final: 0.8961 (mmtm)
REVERT: A  150 ASP cc_start: 0.8831 (m-30) cc_final: 0.8477 (m-30)
REVERT: A  204 MET cc_start: 0.8843 (ttp) cc_final: 0.8515 (tmm)
REVERT: A  218 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8100 (mmtt)
REVERT: A  290 ASP cc_start: 0.8596 (p0) cc_final: 0.8085 (p0)
REVERT: A  292 TYR cc_start: 0.9028 (m-80) cc_final: 0.8764 (m-10)
REVERT: A  297 LYS cc_start: 0.8452 (mmmm) cc_final: 0.8022 (mmtm)
REVERT: A  315 PHE cc_start: 0.9410 (m-10) cc_final: 0.9061 (t80)
REVERT: B  218 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8477 (mmtt)
REVERT: B  290 ASP cc_start: 0.8607 (p0) cc_final: 0.7760 (p0)
REVERT: B  315 PHE cc_start: 0.9337 (m-10) cc_final: 0.8940 (t80)
REVERT: C   98 LYS cc_start: 0.9478 (mmmm) cc_final: 0.9095 (mmtm)
REVERT: C  102 MET cc_start: 0.8883 (tpp) cc_final: 0.8540 (tpp)
REVERT: C  171 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8774 (tt)
REVERT: C  184 MET cc_start: 0.9334 (ptp) cc_final: 0.9065 (ptp)
REVERT: C  197 ASP cc_start: 0.9555 (p0) cc_final: 0.9317 (p0)
REVERT: C  204 MET cc_start: 0.9019 (ttp) cc_final: 0.8804 (tmm)
REVERT: C  243 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8580 (mtpp)
REVERT: C  297 LYS cc_start: 0.8436 (mmmm) cc_final: 0.7915 (mmtm)
  outliers start: 6
  outliers final: 5
  residues processed: 92
  average time/residue: 0.2116
  time to fit residues: 24.9726
Evaluate side-chains
  89 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  229 CYS
Chi-restraints excluded: chain C residue  311 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 57 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 39 optimal weight:    7.9990
   chunk 68 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 GLN
** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  99 ASN
C 188 GLN
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.066942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.048048 restraints weight = 22547.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 4.45
r_work: 0.2671 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.3900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6135  Z= 0.258
  Angle     :  0.656  12.113   8331  Z= 0.307
  Chirality :  0.044   0.344    933
  Planarity :  0.004   0.043   1077
  Dihedral  :  3.959  19.075    831
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 20.03 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.31), residues: 759
  helix:  2.46 (0.33), residues: 255
  sheet: -0.59 (0.28), residues: 300
  loop : -1.50 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 305 
 HIS   0.006   0.001   HIS A 131 
 PHE   0.016   0.001   PHE C 234 
 TYR   0.023   0.002   TYR C 203 
 ARG   0.001   0.000   ARG B 180 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3043.44 seconds
wall clock time: 54 minutes 40.60 seconds (3280.60 seconds total)