Starting phenix.real_space_refine
on Wed Mar 12 01:25:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r0c_14221/03_2025/7r0c_14221.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r0c_14221/03_2025/7r0c_14221.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r0c_14221/03_2025/7r0c_14221.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r0c_14221/03_2025/7r0c_14221.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r0c_14221/03_2025/7r0c_14221.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r0c_14221/03_2025/7r0c_14221.cif"
  }
  resolution = 4.73
  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=  -0.001 sd=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      39      5.16       5
     C    4365      2.51       5
     N    1158      2.21       5
     O    1248      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6816
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2181
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 15, 'TRANS': 268}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'TPO:plan-1': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 41
    Chain: "B"
      Number of atoms: 74
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 74
          Classifications: {'peptide': 9}
          Link IDs: {'PTRANS': 1, 'TRANS': 7}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 2810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 353, 2810
          Classifications: {'peptide': 353}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 324}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1750
          Classifications: {'peptide': 229}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 220}
          Chain breaks: 1
  Time building chain proxies: 4.32, per 1000 atoms: 0.63
  Number of scatterers: 6816
  At special positions: 0
  Unit cell: (83.2, 99.84, 139.52, 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      39     16.00
     P       6     15.00
     O    1248      8.00
     N    1158      7.00
     C    4365      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 112 " - pdb=" SG  CYS A 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   1 " - pdb=" SG  CYS B   6 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  26 " - pdb=" SG  CYS D  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 103 " - pdb=" SG  CYS D 170 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 148 " - pdb=" SG  CYS D 222 " distance=2.03

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.47
  Conformation dependent library (CDL) restraints added in 804.4 milliseconds
  

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1660

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 11 sheets defined
      29.0% alpha, 26.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 69
    Processing helix  chain 'A' and resid 72 through 103
      removed outlier: 3.924A  pdb=" N   ILE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   LEU A  94 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
      Proline residue:  A  95  - end of helix
    Processing helix  chain 'A' and resid 109 through 140
      removed outlier: 4.001A  pdb=" N   ARG A 113 " --> pdb=" O   ASP A 109 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   GLY A 122 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   MET A 123 " --> pdb=" O   GLN A 119 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER A 127 " --> pdb=" O   MET A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 171
    Processing helix  chain 'A' and resid 173 through 178
      removed outlier: 3.582A  pdb=" N   PHE A 178 " --> pdb=" O   GLN A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 228
      removed outlier: 5.019A  pdb=" N   ALA A 216 " --> pdb=" O   MET A 212 " (cutoff:3.500A)
      Proline residue:  A 217  - end of helix
      removed outlier: 3.938A  pdb=" N   ILE A 228 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 296
      Proline residue:  A 286  - end of helix
    Processing helix  chain 'A' and resid 304 through 311
      removed outlier: 3.583A  pdb=" N   VAL A 308 " --> pdb=" O   GLY A 304 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU A 309 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU A 310 " --> pdb=" O   PRO A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 319
      removed outlier: 5.570A  pdb=" N   SER A 315 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ASN A 317 " --> pdb=" O   ALA A 314 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   CYS A 319 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 329
      removed outlier: 3.574A  pdb=" N   PHE A 328 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 339
    Processing helix  chain 'C' and resid 98 through 109
    Processing helix  chain 'C' and resid 159 through 161
      No H-bonds generated for 'chain 'C' and resid 159 through 161'
    Processing helix  chain 'C' and resid 277 through 282
      removed outlier: 3.663A  pdb=" N   ASN C 280 " --> pdb=" O   PHE C 277 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ARG C 282 " --> pdb=" O   ALA C 279 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 82 through 86
      removed outlier: 3.529A  pdb=" N   PHE D  86 " --> pdb=" O   PRO D  83 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 154 through 157
    Processing helix  chain 'D' and resid 188 through 191
    Processing helix  chain 'D' and resid 213 through 217
    Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 363
    Processing sheet with id=AA2, first strand: chain 'C' and resid 26 through 28
      removed outlier: 6.102A  pdb=" N   PHE C  27 " --> pdb=" O   VAL C 171 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   LYS C 170 " --> pdb=" O   VAL C 142 " (cutoff:3.500A)
      removed outlier: 10.265A  pdb=" N   VAL C 142 " --> pdb=" O   LYS C 170 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   VAL C  53 " --> pdb=" O   SER C  86 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   PHE C  61 " --> pdb=" O   ASP C  78 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   ASP C  78 " --> pdb=" O   PHE C  61 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 67
    Processing sheet with id=AA4, first strand: chain 'C' and resid 127 through 129
    Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 188
    Processing sheet with id=AA6, first strand: chain 'C' and resid 207 through 208
      removed outlier: 4.128A  pdb=" N   TYR C 321 " --> pdb=" O   PHE C 349 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   LEU C 351 " --> pdb=" O   VAL C 319 " (cutoff:3.500A)
      removed outlier: 9.194A  pdb=" N   VAL C 319 " --> pdb=" O   LEU C 351 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   ILE C 318 " --> pdb=" O   ALA C 239 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ALA C 239 " --> pdb=" O   ILE C 318 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   SER C 320 " --> pdb=" O   GLN C 237 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   GLN C 237 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   LYS C 322 " --> pdb=" O   VAL C 235 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   VAL C 235 " --> pdb=" O   LYS C 322 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   LYS C 324 " --> pdb=" O   ILE C 233 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   ILE C 233 " --> pdb=" O   LYS C 324 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   LYS C 326 " --> pdb=" O   ILE C 231 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ILE C 231 " --> pdb=" O   LYS C 326 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   VAL C 328 " --> pdb=" O   LYS C 229 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ILE C 231 " --> pdb=" O   GLU C 257 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   GLU C 257 " --> pdb=" O   ILE C 231 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ILE C 233 " --> pdb=" O   MET C 255 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   MET C 255 " --> pdb=" O   ILE C 233 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   VAL C 235 " --> pdb=" O   VAL C 253 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLN C 237 " --> pdb=" O   CYS C 251 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   CYS C 251 " --> pdb=" O   GLN C 237 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA C 239 " --> pdb=" O   TYR C 249 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 7 through 9
    Processing sheet with id=AA8, first strand: chain 'D' and resid 56 through 57
      removed outlier: 6.413A  pdb=" N   TRP D  38 " --> pdb=" O   LEU D  50 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   TYR D  52 " --> pdb=" O   VAL D  36 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   VAL D  36 " --> pdb=" O   TYR D  52 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 129 through 133
    Processing sheet with id=AB1, first strand: chain 'D' and resid 136 through 138
      removed outlier: 6.376A  pdb=" N   GLY D 136 " --> pdb=" O   THR D 243 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ILE D 160 " --> pdb=" O   SER D 176 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   SER D 176 " --> pdb=" O   ILE D 160 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   TRP D 162 " --> pdb=" O   VAL D 174 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLU D 172 " --> pdb=" O   ARG D 164 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 136 through 138
      removed outlier: 6.376A  pdb=" N   GLY D 136 " --> pdb=" O   THR D 243 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   TYR D 235 " --> pdb=" O   ARG D 224 " (cutoff:3.500A)

    305 hydrogen bonds defined for protein.
    828 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: 1.93

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1179
        1.32 -     1.45: 1796
        1.45 -     1.57: 3926
        1.57 -     1.69: 22
        1.69 -     1.81: 52
  Bond restraints: 6975
  Sorted by residual:
  bond pdb=" OG1 TPO A 360 "
       pdb=" P   TPO A 360 "
    ideal  model  delta    sigma   weight residual
    1.717  1.607  0.110 2.00e-02 2.50e+03 3.00e+01
  bond pdb=" OG1 TPO A 359 "
       pdb=" P   TPO A 359 "
    ideal  model  delta    sigma   weight residual
    1.717  1.620  0.097 2.00e-02 2.50e+03 2.37e+01
  bond pdb=" O1P TPO A 359 "
       pdb=" P   TPO A 359 "
    ideal  model  delta    sigma   weight residual
    1.525  1.610 -0.085 2.00e-02 2.50e+03 1.80e+01
  bond pdb=" O1P TPO A 360 "
       pdb=" P   TPO A 360 "
    ideal  model  delta    sigma   weight residual
    1.525  1.609 -0.084 2.00e-02 2.50e+03 1.75e+01
  bond pdb=" O3P TPO A 359 "
       pdb=" P   TPO A 359 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.70e+01
  ... (remaining 6970 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 9271
        2.56 -     5.11: 193
        5.11 -     7.67: 27
        7.67 -    10.23: 6
       10.23 -    12.78: 1
  Bond angle restraints: 9498
  Sorted by residual:
  angle pdb=" N   ILE A  74 "
        pdb=" CA  ILE A  74 "
        pdb=" C   ILE A  74 "
      ideal   model   delta    sigma   weight residual
     110.42  101.79    8.63 9.60e-01 1.09e+00 8.08e+01
  angle pdb=" N   VAL A  76 "
        pdb=" CA  VAL A  76 "
        pdb=" C   VAL A  76 "
      ideal   model   delta    sigma   weight residual
     110.62  104.23    6.39 1.02e+00 9.61e-01 3.93e+01
  angle pdb=" N   PRO A  73 "
        pdb=" CA  PRO A  73 "
        pdb=" C   PRO A  73 "
      ideal   model   delta    sigma   weight residual
     113.84  107.29    6.55 1.30e+00 5.92e-01 2.53e+01
  angle pdb=" CA  LYS D 202 "
        pdb=" CB  LYS D 202 "
        pdb=" CG  LYS D 202 "
      ideal   model   delta    sigma   weight residual
     114.10  122.95   -8.85 2.00e+00 2.50e-01 1.96e+01
  angle pdb=" C   LEU C  68 "
        pdb=" N   ASP C  69 "
        pdb=" CA  ASP C  69 "
      ideal   model   delta    sigma   weight residual
     122.61  129.40   -6.79 1.56e+00 4.11e-01 1.89e+01
  ... (remaining 9493 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.88: 3812
       16.88 -    33.77: 308
       33.77 -    50.65: 54
       50.65 -    67.54: 9
       67.54 -    84.42: 8
  Dihedral angle restraints: 4191
    sinusoidal: 1628
      harmonic: 2563
  Sorted by residual:
  dihedral pdb=" CB  CYS A 112 "
           pdb=" SG  CYS A 112 "
           pdb=" SG  CYS A 192 "
           pdb=" CB  CYS A 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -141.74   55.74     1      1.00e+01 1.00e-02 4.20e+01
  dihedral pdb=" CB  CYS B   1 "
           pdb=" SG  CYS B   1 "
           pdb=" SG  CYS B   6 "
           pdb=" CB  CYS B   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   45.16   47.84     1      1.00e+01 1.00e-02 3.16e+01
  dihedral pdb=" CA  ARG D 226 "
           pdb=" C   ARG D 226 "
           pdb=" N   GLN D 227 "
           pdb=" CA  GLN D 227 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.86  -27.14     0      5.00e+00 4.00e-02 2.95e+01
  ... (remaining 4188 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.108: 1040
       0.108 -    0.215: 43
       0.215 -    0.323: 1
       0.323 -    0.430: 1
       0.430 -    0.538: 1
  Chirality restraints: 1086
  Sorted by residual:
  chirality pdb=" CA  ILE A  74 "
            pdb=" N   ILE A  74 "
            pdb=" C   ILE A  74 "
            pdb=" CB  ILE A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.97   -0.54 2.00e-01 2.50e+01 7.24e+00
  chirality pdb=" CA  TRP A  71 "
            pdb=" N   TRP A  71 "
            pdb=" C   TRP A  71 "
            pdb=" CB  TRP A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.75e+00
  chirality pdb=" CA  VAL A  76 "
            pdb=" N   VAL A  76 "
            pdb=" C   VAL A  76 "
            pdb=" CB  VAL A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.25 2.00e-01 2.50e+01 1.62e+00
  ... (remaining 1083 not shown)

  Planarity restraints: 1191
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  99 "    0.015 2.00e-02 2.50e+03   1.55e-02 6.01e+00
        pdb=" CG  TRP A  99 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  99 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  99 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  99 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  99 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  99 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  99 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  99 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  99 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  94 "    0.040 5.00e-02 4.00e+02   6.03e-02 5.82e+00
        pdb=" N   PRO A  95 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 359 "    0.039 5.00e-02 4.00e+02   5.92e-02 5.60e+00
        pdb=" N   PRO C 360 "   -0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO C 360 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C 360 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1188 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 180
        2.66 -     3.22: 7059
        3.22 -     3.78: 11171
        3.78 -     4.34: 14375
        4.34 -     4.90: 22454
  Nonbonded interactions: 55239
  Sorted by model distance:
  nonbonded pdb=" O   ASN C 222 "
            pdb=" N   SER C 265 "
     model   vdw
     2.100 3.120
  nonbonded pdb=" OE1 GLN D   9 "
            pdb=" OG1 THR D 105 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OG1 THR C  56 "
            pdb=" O   ALA C  82 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" NZ  LYS C  11 "
            pdb=" O   ARG C 165 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" OD1 ASP C 204 "
            pdb=" OH  TYR C 208 "
     model   vdw
     2.210 3.040
  ... (remaining 55234 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.210
  Find NCS groups from input model:        0.060
  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:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
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   0.110   6975  Z= 0.322
  Angle     :  0.909  12.782   9498  Z= 0.523
  Chirality :  0.052   0.538   1086
  Planarity :  0.005   0.060   1191
  Dihedral  : 13.187  84.422   2516
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 26.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.55 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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: -0.89 (0.28), residues: 846
  helix: -0.59 (0.32), residues: 209
  sheet: -0.36 (0.34), residues: 245
  loop : -0.59 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP A  99 
 HIS   0.006   0.002   HIS C 159 
 PHE   0.023   0.002   PHE D 228 
 TYR   0.020   0.002   TYR A 128 
 ARG   0.008   0.001   ARG D  64 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.9158 (ppp) cc_final: 0.8925 (ppp)
REVERT: A  288 PHE cc_start: 0.8903 (m-80) cc_final: 0.8337 (m-80)
REVERT: C   75 PHE cc_start: 0.6481 (m-80) cc_final: 0.5776 (m-10)
REVERT: C  129 LEU cc_start: 0.9301 (mt) cc_final: 0.9092 (mt)
REVERT: D   48 LYS cc_start: 0.9181 (tmtt) cc_final: 0.8827 (tmtt)
REVERT: D   49 LEU cc_start: 0.8528 (tp) cc_final: 0.8280 (tp)
REVERT: D   50 LEU cc_start: 0.8422 (mt) cc_final: 0.7655 (mt)
REVERT: D   74 PHE cc_start: 0.9063 (m-80) cc_final: 0.8473 (m-80)
REVERT: D  195 THR cc_start: 0.8680 (m) cc_final: 0.8416 (p)
REVERT: D  209 MET cc_start: 0.6815 (mpp) cc_final: 0.6419 (mpp)
  outliers start: 1
  outliers final: 1
  residues processed: 131
  average time/residue: 0.1945
  time to fit residues: 33.5512
Evaluate side-chains
  95 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 22 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   4 GLN
C 122 ASN
C 237 GLN
C 281 ASN
D   9 GLN
D 165 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.113060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.091274 restraints weight = 27311.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.094388 restraints weight = 17154.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.096552 restraints weight = 12272.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.1300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6975  Z= 0.186
  Angle     :  0.647   7.096   9498  Z= 0.330
  Chirality :  0.045   0.177   1086
  Planarity :  0.005   0.057   1191
  Dihedral  :  6.254  72.329    965
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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: -0.64 (0.29), residues: 846
  helix: -0.01 (0.33), residues: 211
  sheet: -0.19 (0.34), residues: 244
  loop : -0.69 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  99 
 HIS   0.007   0.001   HIS A  75 
 PHE   0.024   0.002   PHE D 228 
 TYR   0.013   0.001   TYR A 128 
 ARG   0.003   0.001   ARG D 213 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.9086 (ppp) cc_final: 0.8806 (ppp)
REVERT: A  272 MET cc_start: 0.8508 (ppp) cc_final: 0.8262 (ppp)
REVERT: A  288 PHE cc_start: 0.8958 (m-80) cc_final: 0.8466 (m-80)
REVERT: C   10 LYS cc_start: 0.7611 (pttt) cc_final: 0.7043 (pttt)
REVERT: C   75 PHE cc_start: 0.6398 (m-80) cc_final: 0.5631 (m-10)
REVERT: C  172 GLN cc_start: 0.8746 (mp-120) cc_final: 0.8076 (mp-120)
REVERT: C  315 LEU cc_start: 0.9208 (mm) cc_final: 0.9005 (mm)
REVERT: D   48 LYS cc_start: 0.8799 (tmtt) cc_final: 0.8549 (tptt)
REVERT: D   50 LEU cc_start: 0.8859 (mt) cc_final: 0.8363 (mt)
REVERT: D   74 PHE cc_start: 0.9079 (m-80) cc_final: 0.8466 (m-80)
REVERT: D   75 THR cc_start: 0.8610 (p) cc_final: 0.8298 (p)
REVERT: D  195 THR cc_start: 0.8830 (m) cc_final: 0.8599 (p)
REVERT: D  209 MET cc_start: 0.6905 (mpp) cc_final: 0.6353 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.2021
  time to fit residues: 35.3216
Evaluate side-chains
  93 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0070
   chunk 14 optimal weight:    0.3980
   chunk 39 optimal weight:    0.0070
   chunk 72 optimal weight:    0.9990
   chunk 21 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9990
   chunk 33 optimal weight:    8.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    0.4820

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 122 ASN
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** 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 = 0.3970 r_free = 0.3970 target = 0.114755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.092591 restraints weight = 27497.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.095762 restraints weight = 17072.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.097918 restraints weight = 12142.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.1791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6975  Z= 0.164
  Angle     :  0.619   6.396   9498  Z= 0.314
  Chirality :  0.044   0.177   1086
  Planarity :  0.005   0.057   1191
  Dihedral  :  6.034  72.349    965
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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: -0.42 (0.29), residues: 846
  helix:  0.26 (0.34), residues: 211
  sheet: -0.08 (0.34), residues: 253
  loop : -0.61 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP A  99 
 HIS   0.005   0.001   HIS C 159 
 PHE   0.020   0.001   PHE D 228 
 TYR   0.023   0.001   TYR D  52 
 ARG   0.005   0.000   ARG D  64 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.9118 (ppp) cc_final: 0.8786 (ppp)
REVERT: A  134 THR cc_start: 0.9048 (p) cc_final: 0.8845 (p)
REVERT: A  272 MET cc_start: 0.8570 (ppp) cc_final: 0.8317 (ppp)
REVERT: C   29 ASP cc_start: 0.7995 (t0) cc_final: 0.7523 (t0)
REVERT: C  161 ARG cc_start: 0.8241 (tpt90) cc_final: 0.7896 (tpt90)
REVERT: C  172 GLN cc_start: 0.8734 (mp-120) cc_final: 0.7943 (mp-120)
REVERT: C  315 LEU cc_start: 0.9123 (mm) cc_final: 0.8886 (mm)
REVERT: D   65 PHE cc_start: 0.8199 (m-10) cc_final: 0.7991 (m-80)
REVERT: D   74 PHE cc_start: 0.9094 (m-80) cc_final: 0.8862 (m-80)
REVERT: D  195 THR cc_start: 0.8767 (m) cc_final: 0.8437 (p)
REVERT: D  207 LEU cc_start: 0.9075 (tp) cc_final: 0.8790 (tp)
REVERT: D  209 MET cc_start: 0.7389 (mpp) cc_final: 0.6262 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1944
  time to fit residues: 33.8106
Evaluate side-chains
  95 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0060
   chunk 11 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 67 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 80 optimal weight:    0.9990
   chunk 65 optimal weight:    6.9990
   overall best weight:    1.1802

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

Flipped N/Q/H residues before XYZ refinement:
C 159 HIS
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** 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 = 0.3944 r_free = 0.3944 target = 0.112989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.090943 restraints weight = 27655.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.094137 restraints weight = 16977.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.096336 restraints weight = 12017.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6975  Z= 0.187
  Angle     :  0.617   6.836   9498  Z= 0.312
  Chirality :  0.044   0.160   1086
  Planarity :  0.005   0.057   1191
  Dihedral  :  5.972  74.583    965
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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: -0.39 (0.29), residues: 846
  helix:  0.42 (0.34), residues: 211
  sheet: -0.24 (0.33), residues: 266
  loop : -0.53 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP D 173 
 HIS   0.004   0.001   HIS C 159 
 PHE   0.021   0.002   PHE A 166 
 TYR   0.010   0.001   TYR A 280 
 ARG   0.003   0.000   ARG C  76 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.7360 (mmp) cc_final: 0.7134 (mmp)
REVERT: A  130 ILE cc_start: 0.9726 (mm) cc_final: 0.9518 (mm)
REVERT: A  288 PHE cc_start: 0.8813 (m-80) cc_final: 0.8482 (m-80)
REVERT: C   29 ASP cc_start: 0.8079 (t0) cc_final: 0.7579 (t0)
REVERT: C  172 GLN cc_start: 0.8724 (mp-120) cc_final: 0.7744 (mp-120)
REVERT: C  223 ASN cc_start: 0.8058 (m-40) cc_final: 0.7722 (p0)
REVERT: D   65 PHE cc_start: 0.8160 (m-10) cc_final: 0.7904 (m-80)
REVERT: D   74 PHE cc_start: 0.9025 (m-80) cc_final: 0.8725 (m-80)
REVERT: D  195 THR cc_start: 0.8657 (m) cc_final: 0.8428 (p)
REVERT: D  209 MET cc_start: 0.7088 (mpp) cc_final: 0.6586 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1881
  time to fit residues: 31.3390
Evaluate side-chains
  94 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0670
   chunk 74 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 46 optimal weight:    7.9990
   chunk 54 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   chunk 10 optimal weight:    0.6980
   chunk 63 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    1.3322

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

Flipped N/Q/H residues before XYZ refinement:
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** 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 = 0.3932 r_free = 0.3932 target = 0.112456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.090194 restraints weight = 28409.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.093344 restraints weight = 17357.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.095481 restraints weight = 12261.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6975  Z= 0.193
  Angle     :  0.627   6.767   9498  Z= 0.317
  Chirality :  0.044   0.147   1086
  Planarity :  0.005   0.056   1191
  Dihedral  :  6.001  76.725    965
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 16.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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: -0.34 (0.29), residues: 846
  helix:  0.39 (0.34), residues: 209
  sheet: -0.32 (0.33), residues: 264
  loop : -0.34 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.003   TRP A  99 
 HIS   0.004   0.001   HIS A  75 
 PHE   0.018   0.001   PHE D 228 
 TYR   0.027   0.001   TYR D  52 
 ARG   0.005   0.000   ARG D 213 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 PHE cc_start: 0.8143 (m-10) cc_final: 0.7935 (m-80)
REVERT: A  133 MET cc_start: 0.9161 (ppp) cc_final: 0.8893 (ppp)
REVERT: A  272 MET cc_start: 0.8448 (ppp) cc_final: 0.8230 (ppp)
REVERT: A  288 PHE cc_start: 0.8806 (m-80) cc_final: 0.8426 (m-80)
REVERT: C   29 ASP cc_start: 0.8120 (t0) cc_final: 0.7663 (t0)
REVERT: C  142 VAL cc_start: 0.7992 (t) cc_final: 0.7789 (t)
REVERT: C  172 GLN cc_start: 0.8578 (mp-120) cc_final: 0.7747 (mp-120)
REVERT: C  212 GLU cc_start: 0.8499 (mp0) cc_final: 0.8205 (mp0)
REVERT: C  223 ASN cc_start: 0.8086 (m-40) cc_final: 0.7770 (p0)
REVERT: C  306 LEU cc_start: 0.9378 (mt) cc_final: 0.9161 (mt)
REVERT: D   65 PHE cc_start: 0.8147 (m-10) cc_final: 0.7926 (m-80)
REVERT: D   74 PHE cc_start: 0.9011 (m-80) cc_final: 0.8715 (m-80)
REVERT: D   75 THR cc_start: 0.8525 (p) cc_final: 0.8314 (p)
REVERT: D  193 ARG cc_start: 0.8168 (ttt180) cc_final: 0.7941 (ttt180)
REVERT: D  195 THR cc_start: 0.8703 (m) cc_final: 0.8453 (p)
REVERT: D  209 MET cc_start: 0.7235 (mpp) cc_final: 0.6718 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1939
  time to fit residues: 33.3981
Evaluate side-chains
  101 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 81 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 37 optimal weight:    0.2980
   chunk 33 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 74 optimal weight:    8.9990
   chunk 67 optimal weight:    9.9990
   overall best weight:    2.3584

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

Flipped N/Q/H residues before XYZ refinement:
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** 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 = 0.3890 r_free = 0.3890 target = 0.109262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.088095 restraints weight = 28999.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.091020 restraints weight = 18165.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.093076 restraints weight = 13001.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6975  Z= 0.267
  Angle     :  0.673   7.337   9498  Z= 0.347
  Chirality :  0.045   0.142   1086
  Planarity :  0.006   0.074   1191
  Dihedral  :  6.340  79.470    965
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 21.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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: -0.36 (0.30), residues: 846
  helix:  0.46 (0.35), residues: 202
  sheet: -0.54 (0.33), residues: 261
  loop : -0.23 (0.34), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.003   TRP D  38 
 HIS   0.011   0.002   HIS A  80 
 PHE   0.022   0.002   PHE C  27 
 TYR   0.014   0.002   TYR A 325 
 ARG   0.009   0.001   ARG C 236 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.9134 (ppp) cc_final: 0.8868 (ppp)
REVERT: A  134 THR cc_start: 0.9372 (p) cc_final: 0.9164 (p)
REVERT: A  212 MET cc_start: 0.8929 (ppp) cc_final: 0.8723 (ppp)
REVERT: A  272 MET cc_start: 0.8499 (ppp) cc_final: 0.8286 (ppp)
REVERT: A  288 PHE cc_start: 0.8870 (m-80) cc_final: 0.8331 (m-80)
REVERT: C   29 ASP cc_start: 0.8125 (t0) cc_final: 0.7682 (t0)
REVERT: C  129 LEU cc_start: 0.9286 (mt) cc_final: 0.9057 (mt)
REVERT: C  142 VAL cc_start: 0.8056 (t) cc_final: 0.7848 (t)
REVERT: C  172 GLN cc_start: 0.8478 (mp-120) cc_final: 0.7784 (mp-120)
REVERT: C  212 GLU cc_start: 0.8516 (mp0) cc_final: 0.8312 (mp0)
REVERT: D   50 LEU cc_start: 0.8612 (mm) cc_final: 0.8271 (mp)
REVERT: D   74 PHE cc_start: 0.9000 (m-80) cc_final: 0.8582 (m-80)
REVERT: D  193 ARG cc_start: 0.8176 (ttt180) cc_final: 0.7943 (ttt180)
REVERT: D  195 THR cc_start: 0.8812 (m) cc_final: 0.8600 (p)
REVERT: D  209 MET cc_start: 0.7020 (mpp) cc_final: 0.6171 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1949
  time to fit residues: 32.9178
Evaluate side-chains
  99 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   chunk 67 optimal weight:    0.4980
   chunk 28 optimal weight:    9.9990
   chunk 10 optimal weight:    0.0870
   chunk 8 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 58 optimal weight:    0.8980
   chunk 22 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 299 ASN
** D   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** 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 = 0.3939 r_free = 0.3939 target = 0.112841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.090892 restraints weight = 27677.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.094057 restraints weight = 17132.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.096209 restraints weight = 12116.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6975  Z= 0.174
  Angle     :  0.641   6.955   9498  Z= 0.321
  Chirality :  0.045   0.151   1086
  Planarity :  0.005   0.065   1191
  Dihedral  :  6.048  77.502    965
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 15.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.19 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 (0.30), residues: 846
  helix:  0.60 (0.36), residues: 202
  sheet: -0.14 (0.35), residues: 241
  loop : -0.43 (0.33), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP D  38 
 HIS   0.004   0.001   HIS D 161 
 PHE   0.022   0.002   PHE A 166 
 TYR   0.027   0.002   TYR D  52 
 ARG   0.005   0.000   ARG C 236 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.7355 (mmp) cc_final: 0.7098 (mmp)
REVERT: A  133 MET cc_start: 0.9037 (ppp) cc_final: 0.8815 (ppp)
REVERT: A  288 PHE cc_start: 0.8865 (m-80) cc_final: 0.8350 (m-80)
REVERT: C   29 ASP cc_start: 0.8060 (t0) cc_final: 0.7632 (t0)
REVERT: C  142 VAL cc_start: 0.7976 (t) cc_final: 0.7751 (t)
REVERT: C  166 LEU cc_start: 0.8000 (tt) cc_final: 0.7516 (tp)
REVERT: C  167 VAL cc_start: 0.8403 (p) cc_final: 0.8194 (p)
REVERT: C  172 GLN cc_start: 0.8539 (mp-120) cc_final: 0.7896 (mp-120)
REVERT: C  212 GLU cc_start: 0.8519 (mp0) cc_final: 0.8150 (mp0)
REVERT: C  315 LEU cc_start: 0.9178 (mm) cc_final: 0.8976 (mm)
REVERT: D   57 LEU cc_start: 0.8860 (pp) cc_final: 0.8537 (pp)
REVERT: D   65 PHE cc_start: 0.7533 (m-80) cc_final: 0.7319 (m-80)
REVERT: D  193 ARG cc_start: 0.8172 (ttt180) cc_final: 0.7748 (ttt-90)
REVERT: D  195 THR cc_start: 0.8767 (m) cc_final: 0.8562 (p)
REVERT: D  209 MET cc_start: 0.7046 (mpp) cc_final: 0.6516 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2047
  time to fit residues: 36.0218
Evaluate side-chains
  104 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 57 optimal weight:    8.9990
   chunk 52 optimal weight:    0.8980
   chunk 27 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0570
   chunk 34 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   overall best weight:    0.9502

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

Flipped N/Q/H residues before XYZ refinement:
A 119 GLN
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** 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 = 0.3951 r_free = 0.3951 target = 0.113453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.091794 restraints weight = 28169.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.094926 restraints weight = 17454.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.096994 restraints weight = 12377.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6975  Z= 0.181
  Angle     :  0.647   6.914   9498  Z= 0.325
  Chirality :  0.045   0.162   1086
  Planarity :  0.005   0.059   1191
  Dihedral  :  6.005  77.491    965
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 16.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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: -0.28 (0.30), residues: 846
  helix:  0.47 (0.35), residues: 203
  sheet: -0.04 (0.36), residues: 235
  loop : -0.50 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.070   0.003   TRP A  99 
 HIS   0.002   0.001   HIS A  75 
 PHE   0.022   0.002   PHE D 228 
 TYR   0.015   0.001   TYR A 280 
 ARG   0.012   0.001   ARG D 213 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.9128 (ppp) cc_final: 0.8765 (ppp)
REVERT: A  272 MET cc_start: 0.8437 (ppp) cc_final: 0.8236 (ppp)
REVERT: A  280 TYR cc_start: 0.8894 (t80) cc_final: 0.8609 (t80)
REVERT: A  284 TRP cc_start: 0.8263 (m-10) cc_final: 0.7631 (m100)
REVERT: A  288 PHE cc_start: 0.8863 (m-80) cc_final: 0.7692 (m-80)
REVERT: A  325 TYR cc_start: 0.9300 (t80) cc_final: 0.9072 (t80)
REVERT: C   29 ASP cc_start: 0.7916 (t0) cc_final: 0.7497 (t0)
REVERT: C  166 LEU cc_start: 0.7838 (tt) cc_final: 0.7258 (tp)
REVERT: C  172 GLN cc_start: 0.8566 (mp-120) cc_final: 0.7867 (mp-120)
REVERT: C  315 LEU cc_start: 0.9134 (mm) cc_final: 0.8927 (mm)
REVERT: D   48 LYS cc_start: 0.8423 (tmtt) cc_final: 0.8203 (tptt)
REVERT: D   65 PHE cc_start: 0.7587 (m-80) cc_final: 0.7304 (m-80)
REVERT: D   73 ASP cc_start: 0.8740 (m-30) cc_final: 0.8421 (m-30)
REVERT: D  193 ARG cc_start: 0.8068 (ttt180) cc_final: 0.7863 (ttt180)
REVERT: D  209 MET cc_start: 0.6962 (mpp) cc_final: 0.6459 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1826
  time to fit residues: 30.6246
Evaluate side-chains
  99 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 58 optimal weight:   10.0000
   chunk 64 optimal weight:    8.9990
   chunk 20 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0870
   chunk 5 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.8960

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

Flipped N/Q/H residues before XYZ refinement:
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** 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 = 0.3950 r_free = 0.3950 target = 0.113571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.091633 restraints weight = 28548.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.094776 restraints weight = 17698.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.096854 restraints weight = 12543.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6975  Z= 0.177
  Angle     :  0.643   7.017   9498  Z= 0.323
  Chirality :  0.044   0.147   1086
  Planarity :  0.005   0.058   1191
  Dihedral  :  5.919  77.329    965
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 (0.30), residues: 846
  helix:  0.50 (0.35), residues: 202
  sheet:  0.02 (0.35), residues: 239
  loop : -0.51 (0.33), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.003   TRP A  99 
 HIS   0.003   0.001   HIS D 161 
 PHE   0.023   0.002   PHE A 307 
 TYR   0.017   0.001   TYR D  52 
 ARG   0.007   0.001   ARG C  76 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ILE cc_start: 0.6715 (pt) cc_final: 0.6460 (pt)
REVERT: A  133 MET cc_start: 0.9045 (ppp) cc_final: 0.8760 (ppp)
REVERT: A  272 MET cc_start: 0.8366 (ppp) cc_final: 0.8163 (ppp)
REVERT: A  280 TYR cc_start: 0.8927 (t80) cc_final: 0.8661 (t80)
REVERT: A  284 TRP cc_start: 0.8285 (m-10) cc_final: 0.7811 (m100)
REVERT: A  288 PHE cc_start: 0.8878 (m-80) cc_final: 0.8008 (m-80)
REVERT: A  325 TYR cc_start: 0.9358 (t80) cc_final: 0.9081 (t80)
REVERT: C   29 ASP cc_start: 0.7955 (t0) cc_final: 0.7522 (t0)
REVERT: C   75 PHE cc_start: 0.5017 (m-10) cc_final: 0.4543 (m-10)
REVERT: C  166 LEU cc_start: 0.7832 (tt) cc_final: 0.7240 (tp)
REVERT: C  172 GLN cc_start: 0.8560 (mp-120) cc_final: 0.7856 (mp-120)
REVERT: C  315 LEU cc_start: 0.9123 (mm) cc_final: 0.8916 (mm)
REVERT: D   65 PHE cc_start: 0.7586 (m-80) cc_final: 0.7301 (m-80)
REVERT: D   73 ASP cc_start: 0.8696 (m-30) cc_final: 0.8325 (m-30)
REVERT: D   74 PHE cc_start: 0.9075 (m-80) cc_final: 0.8345 (m-80)
REVERT: D  193 ARG cc_start: 0.8068 (ttt180) cc_final: 0.7689 (ttt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1842
  time to fit residues: 30.7476
Evaluate side-chains
  97 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 65 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 57 optimal weight:    8.9990
   chunk 69 optimal weight:    8.9990
   chunk 16 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B   5 ASN
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** 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 = 0.3950 r_free = 0.3950 target = 0.113569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.091590 restraints weight = 28208.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.094738 restraints weight = 17412.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.096933 restraints weight = 12271.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6975  Z= 0.183
  Angle     :  0.643   7.023   9498  Z= 0.323
  Chirality :  0.045   0.146   1086
  Planarity :  0.005   0.058   1191
  Dihedral  :  5.884  77.383    965
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 16.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 (0.30), residues: 846
  helix:  0.50 (0.35), residues: 205
  sheet:  0.05 (0.36), residues: 239
  loop : -0.54 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP A  99 
 HIS   0.002   0.001   HIS A  80 
 PHE   0.020   0.002   PHE D 228 
 TYR   0.018   0.001   TYR A 325 
 ARG   0.007   0.000   ARG C  76 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 TYR cc_start: 0.6386 (t80) cc_final: 0.6174 (t80)
REVERT: A  133 MET cc_start: 0.9069 (ppp) cc_final: 0.8767 (ppp)
REVERT: A  272 MET cc_start: 0.8372 (ppp) cc_final: 0.8166 (ppp)
REVERT: A  280 TYR cc_start: 0.8958 (t80) cc_final: 0.8625 (t80)
REVERT: A  284 TRP cc_start: 0.8286 (m-10) cc_final: 0.7788 (m100)
REVERT: A  288 PHE cc_start: 0.8880 (m-80) cc_final: 0.7919 (m-80)
REVERT: A  325 TYR cc_start: 0.9326 (t80) cc_final: 0.9048 (t80)
REVERT: C   29 ASP cc_start: 0.7932 (t0) cc_final: 0.7520 (t0)
REVERT: C  172 GLN cc_start: 0.8602 (mp-120) cc_final: 0.7923 (mp-120)
REVERT: C  223 ASN cc_start: 0.8604 (m-40) cc_final: 0.8051 (p0)
REVERT: C  315 LEU cc_start: 0.9121 (mm) cc_final: 0.8916 (mm)
REVERT: D   65 PHE cc_start: 0.7594 (m-80) cc_final: 0.7297 (m-80)
REVERT: D   73 ASP cc_start: 0.8775 (m-30) cc_final: 0.8384 (m-30)
REVERT: D   74 PHE cc_start: 0.9147 (m-80) cc_final: 0.8369 (m-80)
REVERT: D  193 ARG cc_start: 0.8164 (ttt180) cc_final: 0.7941 (ttt180)
REVERT: D  226 ARG cc_start: 0.8889 (ttp80) cc_final: 0.7920 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1987
  time to fit residues: 32.9874
Evaluate side-chains
  96 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 78 optimal weight:   20.0000
   chunk 76 optimal weight:    0.3980
   chunk 1 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 69 optimal weight:    8.9990
   chunk 66 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 37 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   4 GLN
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** 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 = 0.3903 r_free = 0.3903 target = 0.110325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.088628 restraints weight = 28574.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.091634 restraints weight = 17843.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.093621 restraints weight = 12731.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6975  Z= 0.234
  Angle     :  0.671   6.972   9498  Z= 0.343
  Chirality :  0.046   0.229   1086
  Planarity :  0.005   0.058   1191
  Dihedral  :  6.115  78.727    965
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 19.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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: -0.32 (0.30), residues: 846
  helix:  0.43 (0.35), residues: 205
  sheet: -0.15 (0.35), residues: 239
  loop : -0.48 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.003   TRP A  99 
 HIS   0.004   0.001   HIS C  30 
 PHE   0.021   0.002   PHE D 228 
 TYR   0.022   0.002   TYR D  52 
 ARG   0.006   0.001   ARG C  76 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2335.17 seconds
wall clock time: 41 minutes 37.11 seconds (2497.11 seconds total)