Starting phenix.real_space_refine
on Thu Jan 16 00:33:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yn9_39419/01_2025/8yn9_39419.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yn9_39419/01_2025/8yn9_39419.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yn9_39419/01_2025/8yn9_39419.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yn9_39419/01_2025/8yn9_39419.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yn9_39419/01_2025/8yn9_39419.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yn9_39419/01_2025/8yn9_39419.cif"
  }
  resolution = 2.3
  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=   0.014
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      58      5.16       5
     C    5853      2.51       5
     N    1490      2.21       5
     O    1647      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 9048
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1770
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 30
          Planarities with less than four sites: {'GLU:plan': 6}
          Unresolved non-hydrogen planarities: 24
    Chain: "B"
      Number of atoms: 2622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 342, 2622
          Classifications: {'peptide': 342}
          Link IDs: {'PTRANS': 5, 'TRANS': 336}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "E"
      Number of atoms: 1779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1779
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2235
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2235
          Classifications: {'peptide': 276}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 9, 'TRANS': 266}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLU:plan': 6}
          Unresolved non-hydrogen planarities: 24
    Chain: "R"
      Number of atoms: 206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 206
          Unusual residues: {'CLR': 7, 'HSM': 1}
          Classifications: {'undetermined': 8, 'water': 2}
          Link IDs: {None: 9}
  Time building chain proxies: 5.47, per 1000 atoms: 0.60
  Number of scatterers: 9048
  At special positions: 0
  Unit cell: (100.58, 118.77, 111.28, 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      58     16.00
     O    1647      8.00
     N    1490      7.00
     C    5853      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  87 " - pdb=" SG  CYS R 164 " 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=0, symmetry=0
  Time building additional restraints: 2.40
  Conformation dependent library (CDL) restraints added in 999.6 milliseconds
  

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2120

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      39.1% alpha, 24.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.539A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.374A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.746A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.625A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 24
      removed outlier: 3.525A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'R' and resid 12 through 43
      removed outlier: 4.019A  pdb=" N   VAL R  36 " --> pdb=" O   GLY R  32 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 48 through 63
    Processing helix  chain 'R' and resid 67 through 78
      Proline residue:  R  74  - end of helix
    Processing helix  chain 'R' and resid 83 through 118
      removed outlier: 3.731A  pdb=" N   VAL R  88 " --> pdb=" O   LYS R  84 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 118 through 125
    Processing helix  chain 'R' and resid 128 through 155
      removed outlier: 3.531A  pdb=" N   TRP R 140 " --> pdb=" O   MET R 136 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ASN R 147 " --> pdb=" O   ALA R 143 " (cutoff:3.500A)
      Proline residue:  R 149  - end of helix
    Processing helix  chain 'R' and resid 156 through 158
      No H-bonds generated for 'chain 'R' and resid 156 through 158'
    Processing helix  chain 'R' and resid 166 through 170
      removed outlier: 3.772A  pdb=" N   SER R 170 " --> pdb=" O   GLY R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 183
      removed outlier: 3.564A  pdb=" N   LEU R 175 " --> pdb=" O   GLU R 171 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 183 through 200
    Processing helix  chain 'R' and resid 292 through 329
      removed outlier: 3.518A  pdb=" N   PHE R 312 " --> pdb=" O   LEU R 308 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
      removed outlier: 3.856A  pdb=" N   ILE R 324 " --> pdb=" O   SER R 320 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 337 through 358
      removed outlier: 3.594A  pdb=" N   GLN R 347 " --> pdb=" O   ALA R 343 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   TRP R 348 " --> pdb=" O   PHE R 344 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASN R 350 " --> pdb=" O   LEU R 346 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   SER R 351 " --> pdb=" O   GLN R 347 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   PHE R 352 " --> pdb=" O   TRP R 348 " (cutoff:3.500A)
      Proline residue:  R 355  - end of helix
    Processing helix  chain 'R' and resid 362 through 374
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.226A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.573A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.737A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 5.986A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.261A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.651A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.784A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.514A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.604A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12
      removed outlier: 5.936A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 4.988A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12
      removed outlier: 4.352A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.499A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148
      removed outlier: 4.015A  pdb=" N   THR E 238 " --> pdb=" O   GLN E 231 " (cutoff:3.500A)

    474 hydrogen bonds defined for protein.
    1314 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.83

  Time building geometry restraints manager: 2.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2829
        1.34 -     1.46: 2014
        1.46 -     1.58: 4341
        1.58 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 9268
  Sorted by residual:
  bond pdb=" CG  HSM R 701 "
       pdb=" ND1 HSM R 701 "
    ideal  model  delta    sigma   weight residual
    1.383  1.336  0.047 2.00e-02 2.50e+03 5.63e+00
  bond pdb=" C5  CLR R 703 "
       pdb=" C6  CLR R 703 "
    ideal  model  delta    sigma   weight residual
    1.332  1.297  0.035 2.00e-02 2.50e+03 3.08e+00
  bond pdb=" C5  CLR R 704 "
       pdb=" C6  CLR R 704 "
    ideal  model  delta    sigma   weight residual
    1.332  1.298  0.034 2.00e-02 2.50e+03 2.93e+00
  bond pdb=" C5  CLR R 705 "
       pdb=" C6  CLR R 705 "
    ideal  model  delta    sigma   weight residual
    1.332  1.298  0.034 2.00e-02 2.50e+03 2.85e+00
  bond pdb=" C5  CLR R 707 "
       pdb=" C6  CLR R 707 "
    ideal  model  delta    sigma   weight residual
    1.332  1.298  0.034 2.00e-02 2.50e+03 2.82e+00
  ... (remaining 9263 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 12320
        1.78 -     3.57: 220
        3.57 -     5.35: 54
        5.35 -     7.13: 13
        7.13 -     8.92: 4
  Bond angle restraints: 12611
  Sorted by residual:
  angle pdb=" C13 CLR R 702 "
        pdb=" C17 CLR R 702 "
        pdb=" C20 CLR R 702 "
      ideal   model   delta    sigma   weight residual
     119.60  110.68    8.92 3.00e+00 1.11e-01 8.84e+00
  angle pdb=" C13 CLR R 707 "
        pdb=" C17 CLR R 707 "
        pdb=" C20 CLR R 707 "
      ideal   model   delta    sigma   weight residual
     119.60  111.81    7.79 3.00e+00 1.11e-01 6.74e+00
  angle pdb=" C   ARG E 191 "
        pdb=" N   MET E 192 "
        pdb=" CA  MET E 192 "
      ideal   model   delta    sigma   weight residual
     121.54  126.49   -4.95 1.91e+00 2.74e-01 6.71e+00
  angle pdb=" C13 CLR R 705 "
        pdb=" C17 CLR R 705 "
        pdb=" C20 CLR R 705 "
      ideal   model   delta    sigma   weight residual
     119.60  111.90    7.70 3.00e+00 1.11e-01 6.59e+00
  angle pdb=" C13 CLR R 703 "
        pdb=" C17 CLR R 703 "
        pdb=" C20 CLR R 703 "
      ideal   model   delta    sigma   weight residual
     119.60  112.03    7.57 3.00e+00 1.11e-01 6.36e+00
  ... (remaining 12606 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 5479
       16.92 -    33.85: 210
       33.85 -    50.77: 63
       50.77 -    67.70: 15
       67.70 -    84.62: 3
  Dihedral angle restraints: 5770
    sinusoidal: 2485
      harmonic: 3285
  Sorted by residual:
  dihedral pdb=" CA  GLN B  75 "
           pdb=" C   GLN B  75 "
           pdb=" N   ASP B  76 "
           pdb=" CA  ASP B  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.36   21.64     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  TRP B 339 "
           pdb=" C   TRP B 339 "
           pdb=" N   ASN B 340 "
           pdb=" CA  ASN B 340 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.74   19.26     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  ARG E 191 "
           pdb=" C   ARG E 191 "
           pdb=" N   MET E 192 "
           pdb=" CA  MET E 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.18   18.82     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 5767 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1340
       0.098 -    0.195: 82
       0.195 -    0.293: 7
       0.293 -    0.390: 7
       0.390 -    0.487: 7
  Chirality restraints: 1443
  Sorted by residual:
  chirality pdb=" C14 CLR R 702 "
            pdb=" C13 CLR R 702 "
            pdb=" C15 CLR R 702 "
            pdb=" C8  CLR R 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.80    0.49 2.00e-01 2.50e+01 5.94e+00
  chirality pdb=" C14 CLR R 705 "
            pdb=" C13 CLR R 705 "
            pdb=" C15 CLR R 705 "
            pdb=" C8  CLR R 705 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.78    0.47 2.00e-01 2.50e+01 5.46e+00
  chirality pdb=" C14 CLR R 707 "
            pdb=" C13 CLR R 707 "
            pdb=" C15 CLR R 707 "
            pdb=" C8  CLR R 707 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.78    0.46 2.00e-01 2.50e+01 5.39e+00
  ... (remaining 1440 not shown)

  Planarity restraints: 1543
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.030 5.00e-02 4.00e+02   4.46e-02 3.19e+00
        pdb=" N   PRO B 236 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "    0.019 5.00e-02 4.00e+02   2.88e-02 1.32e+00
        pdb=" N   PRO B 194 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 106 "   -0.017 5.00e-02 4.00e+02   2.62e-02 1.10e+00
        pdb=" N   PRO B 107 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO B 107 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 107 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1540 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1622
        2.77 -     3.30: 8501
        3.30 -     3.83: 15452
        3.83 -     4.37: 19349
        4.37 -     4.90: 32359
  Nonbonded interactions: 77283
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OE1 GLN A  52 "
            pdb=" ND2 ASN A 331 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" OH  TYR A 230 "
            pdb=" O   SER A 281 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OD1 ASN A 269 "
            pdb=" OG1 THR A 324 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   ALA R 332 "
            pdb=" NZ  LYS R 336 "
     model   vdw
     2.317 3.120
  ... (remaining 77278 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=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:             0.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     22.910
  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:             0.010
  Load rotamer database and sin/cos tables:13.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
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      :  0.004   0.047   9268  Z= 0.232
  Angle     :  0.627   8.918  12611  Z= 0.279
  Chirality :  0.062   0.487   1443
  Planarity :  0.003   0.045   1543
  Dihedral  : 10.628  84.622   3641
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  3.03 %
    Favored  : 96.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.12 (0.24), residues: 1114
  helix:  1.37 (0.24), residues: 415
  sheet:  0.84 (0.29), residues: 293
  loop :  0.17 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.014   0.001   PHE B 151 
 TYR   0.012   0.001   TYR E 190 
 ARG   0.003   0.000   ARG E  72 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 162
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8385 (mttt) cc_final: 0.8025 (mppt)
REVERT: A  261 ASP cc_start: 0.7774 (m-30) cc_final: 0.7523 (m-30)
REVERT: B   79 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8952 (mt)
REVERT: B  137 ARG cc_start: 0.8245 (mmt-90) cc_final: 0.8012 (tpt90)
REVERT: C   21 MET cc_start: 0.8182 (mmm) cc_final: 0.7739 (mpp)
REVERT: R   20 PHE cc_start: 0.8190 (t80) cc_final: 0.7744 (t80)
REVERT: R   24 LEU cc_start: 0.8775 (tp) cc_final: 0.8451 (mm)
REVERT: R   50 SER cc_start: 0.8879 (m) cc_final: 0.8581 (p)
  outliers start: 7
  outliers final: 2
  residues processed: 169
  average time/residue: 1.4082
  time to fit residues: 252.4241
Evaluate side-chains
  134 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 131
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  275 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 84 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 64 optimal weight:    6.9990
   chunk 100 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  22 ASN
B 176 GLN
B 259 GLN
B 266 HIS
E 171 ASN
E 186 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.146026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.101437 restraints weight = 9797.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 1.86
r_work: 0.3015 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.1277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9268  Z= 0.302
  Angle     :  0.593   6.796  12611  Z= 0.320
  Chirality :  0.045   0.187   1443
  Planarity :  0.004   0.045   1543
  Dihedral  :  7.371  59.708   1683
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  :  8.26 %
    Favored  : 89.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.46 (0.25), residues: 1114
  helix:  2.00 (0.25), residues: 419
  sheet:  0.72 (0.29), residues: 297
  loop :  0.15 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 169 
 HIS   0.004   0.001   HIS C  44 
 PHE   0.017   0.002   PHE A 215 
 TYR   0.017   0.002   TYR R 358 
 ARG   0.007   0.001   ARG B  19 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.959 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8515 (mttt) cc_final: 0.7980 (mppt)
REVERT: A  275 GLU cc_start: 0.7717 (pt0) cc_final: 0.7269 (pp20)
REVERT: A  276 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7992 (mt-10)
REVERT: A  328 ASP cc_start: 0.7353 (m-30) cc_final: 0.6951 (m-30)
REVERT: B   23 LYS cc_start: 0.8407 (ttmm) cc_final: 0.7693 (tptt)
REVERT: C   21 MET cc_start: 0.8331 (mmm) cc_final: 0.7163 (ttp)
REVERT: C   42 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7279 (mp0)
REVERT: R   20 PHE cc_start: 0.8223 (t80) cc_final: 0.7935 (t80)
REVERT: R   50 SER cc_start: 0.8823 (m) cc_final: 0.8465 (p)
REVERT: R  342 ILE cc_start: 0.8636 (mm) cc_final: 0.8409 (mm)
REVERT: R  347 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8469 (tt0)
  outliers start: 24
  outliers final: 11
  residues processed: 148
  average time/residue: 1.4351
  time to fit residues: 225.2084
Evaluate side-chains
  136 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  314 VAL
Chi-restraints excluded: chain R residue  320 SER
Chi-restraints excluded: chain R residue  347 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0170
   chunk 63 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    2.5224

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 259 GLN
B 266 HIS
E 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.149474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.110578 restraints weight = 9912.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 1.88
r_work: 0.3151 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.1448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   9268  Z= 0.332
  Angle     :  0.594   6.158  12611  Z= 0.321
  Chirality :  0.045   0.187   1443
  Planarity :  0.004   0.047   1543
  Dihedral  :  6.980  57.292   1679
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  :  9.73 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.34 (0.25), residues: 1114
  helix:  2.07 (0.25), residues: 414
  sheet:  0.63 (0.29), residues: 293
  loop : -0.07 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 169 
 HIS   0.005   0.001   HIS C  44 
 PHE   0.018   0.002   PHE B 151 
 TYR   0.019   0.002   TYR R 358 
 ARG   0.007   0.001   ARG B  19 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 1.011 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8562 (mttt) cc_final: 0.8167 (mppt)
REVERT: A  275 GLU cc_start: 0.7684 (pt0) cc_final: 0.7246 (pp20)
REVERT: A  276 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7921 (mt-10)
REVERT: A  328 ASP cc_start: 0.7376 (m-30) cc_final: 0.7038 (m-30)
REVERT: A  330 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7887 (mtmt)
REVERT: B   23 LYS cc_start: 0.8477 (ttmm) cc_final: 0.7804 (tptt)
REVERT: C   21 MET cc_start: 0.8328 (mmm) cc_final: 0.7143 (ttp)
REVERT: C   42 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7388 (mp0)
REVERT: C   62 ARG cc_start: 0.6683 (mtt90) cc_final: 0.6328 (mtt90)
REVERT: R   50 SER cc_start: 0.8964 (m) cc_final: 0.8645 (p)
REVERT: R  347 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8515 (tt0)
  outliers start: 22
  outliers final: 15
  residues processed: 142
  average time/residue: 1.4540
  time to fit residues: 218.6837
Evaluate side-chains
  139 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  314 VAL
Chi-restraints excluded: chain R residue  320 SER
Chi-restraints excluded: chain R residue  347 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 110 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 266 HIS
E 186 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.151636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.110267 restraints weight = 9964.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 1.76
r_work: 0.3197 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9268  Z= 0.162
  Angle     :  0.493   5.501  12611  Z= 0.267
  Chirality :  0.041   0.172   1443
  Planarity :  0.004   0.045   1543
  Dihedral  :  6.534  55.977   1679
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 10.77 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.50 (0.25), residues: 1114
  helix:  2.37 (0.25), residues: 413
  sheet:  0.61 (0.29), residues: 285
  loop : -0.08 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.012   0.001   PHE B 151 
 TYR   0.014   0.001   TYR E 190 
 ARG   0.008   0.000   ARG B  19 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8477 (mttt) cc_final: 0.8127 (mppt)
REVERT: A  275 GLU cc_start: 0.7872 (pt0) cc_final: 0.7461 (pp20)
REVERT: A  276 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7842 (mt-10)
REVERT: A  328 ASP cc_start: 0.7351 (m-30) cc_final: 0.7013 (m-30)
REVERT: B   23 LYS cc_start: 0.8477 (ttmm) cc_final: 0.7773 (tptt)
REVERT: B  266 HIS cc_start: 0.8223 (t-90) cc_final: 0.8019 (t-170)
REVERT: C   21 MET cc_start: 0.8309 (mmm) cc_final: 0.7153 (ttp)
REVERT: E   18 ARG cc_start: 0.8161 (tpt170) cc_final: 0.7922 (tpt170)
REVERT: R   50 SER cc_start: 0.8786 (m) cc_final: 0.8509 (p)
REVERT: R  165 GLU cc_start: 0.8647 (pt0) cc_final: 0.7863 (pp20)
REVERT: R  342 ILE cc_start: 0.8651 (mm) cc_final: 0.8449 (mm)
  outliers start: 18
  outliers final: 10
  residues processed: 141
  average time/residue: 1.4722
  time to fit residues: 219.4516
Evaluate side-chains
  134 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  320 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 105 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 16 optimal weight:    9.9990
   chunk 66 optimal weight:    1.9990
   chunk 51 optimal weight:    0.2980
   chunk 13 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 155 ASN
B 259 GLN
E 186 GLN
R 362 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.151723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.110220 restraints weight = 9819.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 1.75
r_work: 0.3193 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9268  Z= 0.171
  Angle     :  0.495   5.646  12611  Z= 0.267
  Chirality :  0.041   0.172   1443
  Planarity :  0.004   0.045   1543
  Dihedral  :  6.462  57.238   1678
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 10.88 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.52 (0.25), residues: 1114
  helix:  2.46 (0.25), residues: 413
  sheet:  0.57 (0.29), residues: 282
  loop : -0.11 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS C  44 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.013   0.001   TYR E 190 
 ARG   0.008   0.000   ARG B  19 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.998 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8491 (mttt) cc_final: 0.8131 (mppt)
REVERT: A  275 GLU cc_start: 0.7861 (pt0) cc_final: 0.7425 (pp20)
REVERT: A  276 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7868 (mt-10)
REVERT: A  328 ASP cc_start: 0.7348 (m-30) cc_final: 0.6983 (m-30)
REVERT: B   23 LYS cc_start: 0.8440 (ttmm) cc_final: 0.7735 (tptt)
REVERT: B  172 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7797 (pt0)
REVERT: C   21 MET cc_start: 0.8293 (mmm) cc_final: 0.7124 (ttp)
REVERT: E  160 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.7994 (ttp-110)
REVERT: R   50 SER cc_start: 0.8822 (m) cc_final: 0.8528 (p)
REVERT: R  165 GLU cc_start: 0.8655 (pt0) cc_final: 0.7827 (pp20)
  outliers start: 20
  outliers final: 13
  residues processed: 137
  average time/residue: 1.5301
  time to fit residues: 222.2523
Evaluate side-chains
  133 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  320 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0470
   chunk 53 optimal weight:    4.9990
   chunk 93 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 105 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 259 GLN
E 186 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.153582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.111190 restraints weight = 9784.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.79
r_work: 0.3216 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9268  Z= 0.142
  Angle     :  0.472   5.581  12611  Z= 0.255
  Chirality :  0.040   0.171   1443
  Planarity :  0.003   0.044   1543
  Dihedral  :  6.332  59.127   1678
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.24 %
    Favored  : 86.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.59 (0.25), residues: 1114
  helix:  2.56 (0.25), residues: 413
  sheet:  0.55 (0.29), residues: 270
  loop : -0.05 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS C  44 
 PHE   0.011   0.001   PHE B 151 
 TYR   0.013   0.001   TYR E 190 
 ARG   0.009   0.000   ARG B 219 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8472 (mttt) cc_final: 0.8125 (mppt)
REVERT: A  275 GLU cc_start: 0.7871 (pt0) cc_final: 0.7443 (pp20)
REVERT: A  276 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7875 (mt-10)
REVERT: A  328 ASP cc_start: 0.7372 (m-30) cc_final: 0.6978 (m-30)
REVERT: B   23 LYS cc_start: 0.8444 (ttmm) cc_final: 0.7741 (tptt)
REVERT: B  172 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7757 (tp30)
REVERT: B  219 ARG cc_start: 0.8177 (mtt-85) cc_final: 0.7870 (mmt-90)
REVERT: C   21 MET cc_start: 0.8306 (mmm) cc_final: 0.7139 (ttp)
REVERT: E  160 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7967 (ttp-110)
REVERT: E  194 ASN cc_start: 0.8859 (m-40) cc_final: 0.8501 (m110)
REVERT: R   24 LEU cc_start: 0.8834 (tp) cc_final: 0.8363 (mm)
REVERT: R   50 SER cc_start: 0.8770 (m) cc_final: 0.8512 (p)
REVERT: R  165 GLU cc_start: 0.8611 (pt0) cc_final: 0.7827 (pp20)
  outliers start: 16
  outliers final: 12
  residues processed: 141
  average time/residue: 1.4541
  time to fit residues: 217.0840
Evaluate side-chains
  137 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  320 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 107 optimal weight:    0.0020
   chunk 61 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0060
   chunk 47 optimal weight:    0.4980
   chunk 90 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.4604

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 322 HIS
B 259 GLN
E 171 ASN
E 186 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.154561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.112365 restraints weight = 9917.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.80
r_work: 0.3232 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9268  Z= 0.127
  Angle     :  0.464   5.680  12611  Z= 0.250
  Chirality :  0.040   0.171   1443
  Planarity :  0.003   0.042   1543
  Dihedral  :  6.217  59.316   1678
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 12.03 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.63 (0.25), residues: 1114
  helix:  2.62 (0.25), residues: 414
  sheet:  0.54 (0.29), residues: 270
  loop : -0.05 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.011   0.001   PHE R 328 
 TYR   0.013   0.001   TYR R 173 
 ARG   0.010   0.000   ARG B  19 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8449 (mttt) cc_final: 0.8107 (mppt)
REVERT: A  275 GLU cc_start: 0.7857 (pt0) cc_final: 0.7419 (pp20)
REVERT: A  276 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7849 (mt-10)
REVERT: A  330 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7835 (mtmt)
REVERT: B   23 LYS cc_start: 0.8432 (ttmm) cc_final: 0.7741 (tptt)
REVERT: B  172 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7731 (tp30)
REVERT: C   21 MET cc_start: 0.8293 (mmm) cc_final: 0.7129 (ttp)
REVERT: E  160 ARG cc_start: 0.8278 (mtm-85) cc_final: 0.7981 (ttp-110)
REVERT: E  194 ASN cc_start: 0.8822 (m-40) cc_final: 0.8463 (m110)
REVERT: R   50 SER cc_start: 0.8749 (m) cc_final: 0.8513 (p)
REVERT: R  165 GLU cc_start: 0.8612 (pt0) cc_final: 0.7838 (pp20)
  outliers start: 21
  outliers final: 12
  residues processed: 139
  average time/residue: 1.4694
  time to fit residues: 216.0238
Evaluate side-chains
  139 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  320 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 84 optimal weight:    6.9990
   chunk 64 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 322 HIS
B 259 GLN
E 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.151591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.110035 restraints weight = 10113.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.77
r_work: 0.3193 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9268  Z= 0.199
  Angle     :  0.504   5.652  12611  Z= 0.271
  Chirality :  0.042   0.175   1443
  Planarity :  0.004   0.044   1543
  Dihedral  :  6.271  56.730   1678
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.45 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.58 (0.25), residues: 1114
  helix:  2.55 (0.25), residues: 414
  sheet:  0.48 (0.28), residues: 277
  loop : -0.01 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.014   0.001   PHE A 215 
 TYR   0.013   0.001   TYR R 358 
 ARG   0.009   0.000   ARG B  19 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8486 (mttt) cc_final: 0.8125 (mppt)
REVERT: A  275 GLU cc_start: 0.7881 (pt0) cc_final: 0.7397 (pp20)
REVERT: A  276 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7797 (mt-10)
REVERT: A  330 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7842 (mtmt)
REVERT: B   23 LYS cc_start: 0.8403 (ttmm) cc_final: 0.7742 (tptt)
REVERT: B  172 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7834 (tp30)
REVERT: B  219 ARG cc_start: 0.8173 (mtt-85) cc_final: 0.7854 (mmt-90)
REVERT: C   21 MET cc_start: 0.8225 (mmm) cc_final: 0.7093 (ttp)
REVERT: E  160 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.7972 (ttp-110)
REVERT: R   50 SER cc_start: 0.8863 (m) cc_final: 0.8548 (p)
REVERT: R  165 GLU cc_start: 0.8633 (pt0) cc_final: 0.7770 (pp20)
  outliers start: 20
  outliers final: 14
  residues processed: 136
  average time/residue: 1.4910
  time to fit residues: 214.6681
Evaluate side-chains
  138 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  320 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0060
   chunk 3 optimal weight:    2.9990
   chunk 8 optimal weight:    0.4980
   chunk 79 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 102 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0670
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 322 HIS
B 259 GLN
E 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.153098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.111796 restraints weight = 9868.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 1.76
r_work: 0.3214 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9268  Z= 0.150
  Angle     :  0.485   5.611  12611  Z= 0.260
  Chirality :  0.041   0.173   1443
  Planarity :  0.004   0.043   1543
  Dihedral  :  6.124  56.274   1678
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.87 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.61 (0.25), residues: 1114
  helix:  2.59 (0.25), residues: 414
  sheet:  0.51 (0.29), residues: 270
  loop : -0.03 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS C  44 
 PHE   0.011   0.001   PHE R 328 
 TYR   0.015   0.001   TYR R 173 
 ARG   0.009   0.000   ARG B  19 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8475 (mttt) cc_final: 0.8116 (mppt)
REVERT: A  275 GLU cc_start: 0.7888 (pt0) cc_final: 0.7401 (pp20)
REVERT: A  276 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7799 (mt-10)
REVERT: A  330 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7839 (mtmt)
REVERT: B   23 LYS cc_start: 0.8432 (ttmm) cc_final: 0.7749 (tptt)
REVERT: B  172 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7814 (tp30)
REVERT: B  219 ARG cc_start: 0.8218 (mtt-85) cc_final: 0.7896 (mmt-90)
REVERT: C   21 MET cc_start: 0.8214 (mmm) cc_final: 0.7090 (ttp)
REVERT: E  160 ARG cc_start: 0.8278 (mtm-85) cc_final: 0.7958 (ttp-110)
REVERT: E  194 ASN cc_start: 0.8851 (m-40) cc_final: 0.8496 (m110)
REVERT: R   50 SER cc_start: 0.8814 (m) cc_final: 0.8540 (p)
REVERT: R  165 GLU cc_start: 0.8600 (pt0) cc_final: 0.7719 (pp20)
  outliers start: 18
  outliers final: 12
  residues processed: 141
  average time/residue: 1.4481
  time to fit residues: 216.4591
Evaluate side-chains
  141 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  320 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 108 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0970
   chunk 46 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
E 186 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.153732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.111583 restraints weight = 9949.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.80
r_work: 0.3216 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9268  Z= 0.149
  Angle     :  0.482   5.648  12611  Z= 0.259
  Chirality :  0.041   0.173   1443
  Planarity :  0.003   0.043   1543
  Dihedral  :  5.942  56.766   1678
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 12.97 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.63 (0.25), residues: 1114
  helix:  2.61 (0.25), residues: 414
  sheet:  0.53 (0.29), residues: 270
  loop : -0.02 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS C  44 
 PHE   0.011   0.001   PHE B 151 
 TYR   0.014   0.001   TYR R 173 
 ARG   0.009   0.000   ARG B  19 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8466 (mttt) cc_final: 0.8107 (mppt)
REVERT: A  275 GLU cc_start: 0.7931 (pt0) cc_final: 0.7417 (pp20)
REVERT: A  276 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7870 (mt-10)
REVERT: A  330 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7846 (mtmt)
REVERT: B   23 LYS cc_start: 0.8440 (ttmm) cc_final: 0.7755 (tptt)
REVERT: B  172 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7856 (tp30)
REVERT: B  219 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.7914 (mmt-90)
REVERT: B  254 ASP cc_start: 0.8407 (t70) cc_final: 0.8087 (t70)
REVERT: B  325 MET cc_start: 0.9208 (mmt) cc_final: 0.8887 (tpp)
REVERT: C   21 MET cc_start: 0.8218 (mmm) cc_final: 0.7091 (ttp)
REVERT: E  160 ARG cc_start: 0.8289 (mtm-85) cc_final: 0.7971 (ttp-110)
REVERT: E  194 ASN cc_start: 0.8846 (m-40) cc_final: 0.8496 (m110)
REVERT: R   50 SER cc_start: 0.8787 (m) cc_final: 0.8511 (p)
  outliers start: 17
  outliers final: 13
  residues processed: 140
  average time/residue: 1.4138
  time to fit residues: 210.0960
Evaluate side-chains
  143 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  320 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 44 optimal weight:    5.9990
   chunk 36 optimal weight:    0.1980
   chunk 85 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0470
   chunk 72 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 259 GLN
E 186 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.154945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.112708 restraints weight = 9891.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.79
r_work: 0.3235 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9268  Z= 0.132
  Angle     :  0.468   5.617  12611  Z= 0.250
  Chirality :  0.040   0.172   1443
  Planarity :  0.003   0.042   1543
  Dihedral  :  5.773  57.203   1678
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.87 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.68 (0.25), residues: 1114
  helix:  2.66 (0.25), residues: 414
  sheet:  0.52 (0.29), residues: 270
  loop :  0.02 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.011   0.001   PHE R 328 
 TYR   0.014   0.001   TYR R 173 
 ARG   0.009   0.000   ARG B  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9229.88 seconds
wall clock time: 163 minutes 0.59 seconds (9780.59 seconds total)