Starting phenix.real_space_refine
on Fri Aug 22 17:59:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ge4_29955/08_2025/8ge4_29955.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ge4_29955/08_2025/8ge4_29955.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ge4_29955/08_2025/8ge4_29955.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ge4_29955/08_2025/8ge4_29955.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ge4_29955/08_2025/8ge4_29955.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ge4_29955/08_2025/8ge4_29955.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.036
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      45      5.16       5
     C    4285      2.51       5
     N    1140      2.21       5
     O    1176      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6646
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1746
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 174
          Unresolved non-hydrogen angles: 208
          Unresolved non-hydrogen dihedrals: 141
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'GLU:plan': 12, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 123
    Chain: "B"
      Number of atoms: 2359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2359
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PTRANS': 5, 'TRANS': 325}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 185
          Unresolved non-hydrogen angles: 228
          Unresolved non-hydrogen dihedrals: 142
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 9, 'GLU:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 12}
          Unresolved non-hydrogen planarities: 141
    Chain: "G"
      Number of atoms: 344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 344
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "R"
      Number of atoms: 2181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2181
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 7, 'TRANS': 279}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 131
          Unresolved non-hydrogen angles: 162
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 75
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 1.71, per 1000 atoms: 0.26
  Number of scatterers: 6646
  At special positions: 0
  Unit cell: (68.9, 97.52, 127.2, 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      45     16.00
     O    1176      8.00
     N    1140      7.00
     C    4285      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " 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: 0.69
  Conformation dependent library (CDL) restraints added in 483.5 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1706

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      48.6% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 4.378A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 232 through 239
      removed outlier: 3.786A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.689A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.775A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.554A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 25
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.547A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 12 through 24
      removed outlier: 3.546A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 31 through 61
      removed outlier: 3.561A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 65
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 3.842A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.468A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.609A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ILE R 153 " --> pdb=" O   LYS R 149 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 4.185A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.645A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 4.063A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 341
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.462A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.721A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.555A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.727A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 6.638A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.179A  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: 6.884A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.548A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.843A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)

    389 hydrogen bonds defined for protein.
    1125 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.15

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2136
        1.34 -     1.46: 1611
        1.46 -     1.58: 2983
        1.58 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 6792
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.449 -0.052 2.00e-02 2.50e+03 6.82e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 2.00e-02 2.50e+03 4.85e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.437 -0.043 2.00e-02 2.50e+03 4.63e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.566 -0.043 2.00e-02 2.50e+03 4.60e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" OAK G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.353  1.323  0.030 2.00e-02 2.50e+03 2.31e+00
  ... (remaining 6787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 9035
        1.15 -     2.30: 187
        2.30 -     3.45: 39
        3.45 -     4.59: 4
        4.59 -     5.74: 11
  Bond angle restraints: 9276
  Sorted by residual:
  angle pdb=" N   GLY A 329 "
        pdb=" CA  GLY A 329 "
        pdb=" C   GLY A 329 "
      ideal   model   delta    sigma   weight residual
     113.18  107.44    5.74 2.37e+00 1.78e-01 5.87e+00
  angle pdb=" CA  GLU A  50 "
        pdb=" CB  GLU A  50 "
        pdb=" CG  GLU A  50 "
      ideal   model   delta    sigma   weight residual
     114.10  118.52   -4.42 2.00e+00 2.50e-01 4.88e+00
  angle pdb=" C   THR B  86 "
        pdb=" N   THR B  87 "
        pdb=" CA  THR B  87 "
      ideal   model   delta    sigma   weight residual
     122.46  125.55   -3.09 1.41e+00 5.03e-01 4.80e+00
  angle pdb=" C   VAL R  87 "
        pdb=" CA  VAL R  87 "
        pdb=" CB  VAL R  87 "
      ideal   model   delta    sigma   weight residual
     114.00  111.22    2.78 1.31e+00 5.83e-01 4.51e+00
  angle pdb=" C   TYR A 391 "
        pdb=" N   GLU A 392 "
        pdb=" CA  GLU A 392 "
      ideal   model   delta    sigma   weight residual
     122.21  119.08    3.13 1.48e+00 4.57e-01 4.47e+00
  ... (remaining 9271 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.94: 3585
       16.94 -    33.88: 301
       33.88 -    50.81: 42
       50.81 -    67.75: 5
       67.75 -    84.69: 2
  Dihedral angle restraints: 3935
    sinusoidal: 1308
      harmonic: 2627
  Sorted by residual:
  dihedral pdb=" CA  TRP B 332 "
           pdb=" C   TRP B 332 "
           pdb=" N   ASP B 333 "
           pdb=" CA  ASP B 333 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.69   18.31     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  ASP B  76 "
           pdb=" C   ASP B  76 "
           pdb=" N   GLY B  77 "
           pdb=" CA  GLY B  77 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.88  -17.12     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  ASP B 333 "
           pdb=" C   ASP B 333 "
           pdb=" N   SER B 334 "
           pdb=" CA  SER B 334 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.35  -15.65     0      5.00e+00 4.00e-02 9.79e+00
  ... (remaining 3932 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 731
       0.030 -    0.060: 242
       0.060 -    0.091: 88
       0.091 -    0.121: 40
       0.121 -    0.151: 3
  Chirality restraints: 1104
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.55   -0.15 2.00e-01 2.50e+01 5.71e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.08e-01
  chirality pdb=" CA  ILE A 288 "
            pdb=" N   ILE A 288 "
            pdb=" C   ILE A 288 "
            pdb=" CB  ILE A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  ... (remaining 1101 not shown)

  Planarity restraints: 1164
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  38 "    0.020 5.00e-02 4.00e+02   3.10e-02 1.54e+00
        pdb=" N   PRO B  39 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B  39 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B  39 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.009 2.00e-02 2.50e+03   8.45e-03 1.43e+00
        pdb=" CG  TYR B  59 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  50 "    0.006 2.00e-02 2.50e+03   1.17e-02 1.37e+00
        pdb=" C   GLU A  50 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   GLU A  50 "    0.008 2.00e-02 2.50e+03
        pdb=" N   SER A  51 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1161 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1426
        2.78 -     3.31: 6329
        3.31 -     3.84: 11129
        3.84 -     4.37: 12527
        4.37 -     4.90: 22886
  Nonbonded interactions: 54297
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 392 "
            pdb=" OG1 THR R 274 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" NE2 GLN B  75 "
            pdb=" O   VAL B 100 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OE1 GLN A  19 "
            pdb=" OG1 THR B  86 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" NE2 HIS B 311 "
            pdb=" OG1 THR B 329 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" OH  TYR R 185 "
            pdb=" O   PHE R 194 "
     model   vdw
     2.341 3.040
  ... (remaining 54292 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 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:             2.450
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     8.620
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
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      :  0.003   0.052   6793  Z= 0.140
  Angle     :  0.453   5.742   9278  Z= 0.242
  Chirality :  0.038   0.151   1104
  Planarity :  0.003   0.031   1164
  Dihedral  : 12.450  84.690   2226
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.29), residues: 885
  helix:  2.49 (0.26), residues: 404
  sheet:  0.01 (0.40), residues: 168
  loop : -0.12 (0.37), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 239 
 TYR   0.021   0.001   TYR B  59 
 PHE   0.016   0.001   PHE B 234 
 TRP   0.006   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6792)
  covalent geometry    : angle       0.45310 ( 9276)
  SS BOND              : bond        0.00212 (    1)
  SS BOND              : angle       0.71783 (    2)
  hydrogen bonds       : bond        0.15669 (  389)
  hydrogen bonds       : angle       6.50332 ( 1125)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8400 (t0) cc_final: 0.8032 (t0)
REVERT: A  339 TYR cc_start: 0.8312 (m-80) cc_final: 0.7722 (m-80)
REVERT: B  274 THR cc_start: 0.9326 (m) cc_final: 0.9033 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0995
  time to fit residues: 16.4525
Evaluate side-chains
  100 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
B 239 ASN
B 266 HIS
R 178 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.135384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.116995 restraints weight = 10125.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 2.09
r_work: 0.3354 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3248
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3248
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.0991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6793  Z= 0.129
  Angle     :  0.478   6.658   9278  Z= 0.258
  Chirality :  0.039   0.140   1104
  Planarity :  0.003   0.026   1164
  Dihedral  :  4.693  70.013    972
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  8.41 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.30), residues: 885
  helix:  2.41 (0.26), residues: 408
  sheet: -0.08 (0.39), residues: 170
  loop :  0.08 (0.39), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 239 
 TYR   0.019   0.001   TYR B  59 
 PHE   0.011   0.001   PHE B 241 
 TRP   0.019   0.001   TRP B 339 
 HIS   0.007   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6792)
  covalent geometry    : angle       0.47835 ( 9276)
  SS BOND              : bond        0.00229 (    1)
  SS BOND              : angle       0.32395 (    2)
  hydrogen bonds       : bond        0.03935 (  389)
  hydrogen bonds       : angle       4.53351 ( 1125)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8567 (t0) cc_final: 0.8172 (t0)
REVERT: A  339 TYR cc_start: 0.8674 (m-80) cc_final: 0.7974 (m-80)
REVERT: B  274 THR cc_start: 0.9337 (m) cc_final: 0.9043 (p)
REVERT: R  185 TYR cc_start: 0.6949 (m-10) cc_final: 0.6684 (m-10)
  outliers start: 10
  outliers final: 6
  residues processed: 122
  average time/residue: 0.0941
  time to fit residues: 15.1389
Evaluate side-chains
  109 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  192 ASP
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 71 optimal weight:    0.0770
   chunk 26 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 65 optimal weight:    0.3980
   chunk 46 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.6142

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.136240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.117479 restraints weight = 10160.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 2.13
r_work: 0.3349 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3244
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3244
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.1169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6793  Z= 0.117
  Angle     :  0.457   5.637   9278  Z= 0.246
  Chirality :  0.039   0.137   1104
  Planarity :  0.003   0.028   1164
  Dihedral  :  4.671  70.406    972
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.11 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.29), residues: 885
  helix:  2.51 (0.26), residues: 407
  sheet: -0.09 (0.39), residues: 172
  loop :  0.01 (0.38), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 239 
 TYR   0.017   0.001   TYR B  59 
 PHE   0.009   0.001   PHE A 212 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6792)
  covalent geometry    : angle       0.45723 ( 9276)
  SS BOND              : bond        0.00188 (    1)
  SS BOND              : angle       0.21627 (    2)
  hydrogen bonds       : bond        0.03716 (  389)
  hydrogen bonds       : angle       4.27534 ( 1125)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8582 (t0) cc_final: 0.8170 (t0)
REVERT: A  339 TYR cc_start: 0.8681 (m-80) cc_final: 0.7914 (m-80)
REVERT: B  274 THR cc_start: 0.9323 (m) cc_final: 0.9020 (p)
  outliers start: 9
  outliers final: 7
  residues processed: 118
  average time/residue: 0.0948
  time to fit residues: 14.6583
Evaluate side-chains
  110 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  192 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 23 optimal weight:   10.0000
   chunk 32 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0770
   chunk 3 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 57 optimal weight:    5.9990
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.132658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.114743 restraints weight = 9870.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.97
r_work: 0.3362 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3259
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6793  Z= 0.122
  Angle     :  0.453   5.470   9278  Z= 0.243
  Chirality :  0.039   0.135   1104
  Planarity :  0.003   0.027   1164
  Dihedral  :  4.672  71.204    972
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.06 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.72 (0.29), residues: 885
  helix:  2.52 (0.26), residues: 408
  sheet:  0.00 (0.39), residues: 173
  loop : -0.02 (0.38), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 239 
 TYR   0.016   0.001   TYR B  59 
 PHE   0.009   0.001   PHE A 212 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6792)
  covalent geometry    : angle       0.45267 ( 9276)
  SS BOND              : bond        0.00195 (    1)
  SS BOND              : angle       0.19205 (    2)
  hydrogen bonds       : bond        0.03610 (  389)
  hydrogen bonds       : angle       4.11922 ( 1125)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8616 (t0) cc_final: 0.8221 (t0)
REVERT: A  339 TYR cc_start: 0.8660 (m-80) cc_final: 0.7926 (m-80)
  outliers start: 12
  outliers final: 10
  residues processed: 111
  average time/residue: 0.0879
  time to fit residues: 13.1283
Evaluate side-chains
  107 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  192 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0870
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.6560

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
B 340 ASN
R 312 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.134743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.116525 restraints weight = 10117.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 2.07
r_work: 0.3347 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3245
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6793  Z= 0.119
  Angle     :  0.450   5.373   9278  Z= 0.241
  Chirality :  0.039   0.134   1104
  Planarity :  0.003   0.028   1164
  Dihedral  :  4.657  71.621    972
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.86 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.29), residues: 885
  helix:  2.54 (0.26), residues: 408
  sheet: -0.10 (0.38), residues: 179
  loop :  0.06 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 239 
 TYR   0.015   0.001   TYR B  59 
 PHE   0.008   0.001   PHE A 212 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6792)
  covalent geometry    : angle       0.45037 ( 9276)
  SS BOND              : bond        0.00186 (    1)
  SS BOND              : angle       0.14467 (    2)
  hydrogen bonds       : bond        0.03557 (  389)
  hydrogen bonds       : angle       4.05318 ( 1125)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8639 (t0) cc_final: 0.8251 (t0)
REVERT: A  339 TYR cc_start: 0.8675 (m-80) cc_final: 0.7947 (m-80)
REVERT: B   43 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8510 (mt)
  outliers start: 15
  outliers final: 12
  residues processed: 113
  average time/residue: 0.0913
  time to fit residues: 13.8436
Evaluate side-chains
  108 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  192 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0970
   chunk 5 optimal weight:    0.3980
   chunk 58 optimal weight:    0.8980
   chunk 43 optimal weight:    0.1980
   chunk 85 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 6 optimal weight:    0.4980
   chunk 51 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
B 239 ASN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.137080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.119519 restraints weight = 10113.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 2.00
r_work: 0.3374 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3275
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3275
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6793  Z= 0.096
  Angle     :  0.434   5.340   9278  Z= 0.233
  Chirality :  0.038   0.135   1104
  Planarity :  0.003   0.029   1164
  Dihedral  :  4.562  71.453    972
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 13.65 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.29), residues: 885
  helix:  2.67 (0.26), residues: 405
  sheet:  0.05 (0.39), residues: 169
  loop :  0.06 (0.37), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 228 
 TYR   0.014   0.001   TYR B  59 
 PHE   0.008   0.001   PHE A 212 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 6792)
  covalent geometry    : angle       0.43392 ( 9276)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.12117 (    2)
  hydrogen bonds       : bond        0.03379 (  389)
  hydrogen bonds       : angle       3.95873 ( 1125)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8633 (t0) cc_final: 0.8246 (t0)
REVERT: A  339 TYR cc_start: 0.8646 (m-80) cc_final: 0.7924 (m-80)
REVERT: B   43 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8480 (mt)
REVERT: B  301 LYS cc_start: 0.9141 (mtpp) cc_final: 0.8803 (mttp)
  outliers start: 16
  outliers final: 11
  residues processed: 112
  average time/residue: 0.0897
  time to fit residues: 13.3653
Evaluate side-chains
  106 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  192 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0030
   chunk 32 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 78 optimal weight:    0.5980
   chunk 69 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.136556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.119060 restraints weight = 9975.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.99
r_work: 0.3378 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6793  Z= 0.108
  Angle     :  0.440   5.380   9278  Z= 0.235
  Chirality :  0.039   0.134   1104
  Planarity :  0.003   0.029   1164
  Dihedral  :  4.590  71.657    972
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 13.97 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.29), residues: 885
  helix:  2.60 (0.26), residues: 411
  sheet: -0.08 (0.38), residues: 178
  loop :  0.02 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 228 
 TYR   0.015   0.001   TYR B  59 
 PHE   0.009   0.001   PHE A 315 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 6792)
  covalent geometry    : angle       0.44013 ( 9276)
  SS BOND              : bond        0.00135 (    1)
  SS BOND              : angle       0.11775 (    2)
  hydrogen bonds       : bond        0.03394 (  389)
  hydrogen bonds       : angle       3.93397 ( 1125)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8646 (t0) cc_final: 0.8252 (t0)
REVERT: A  339 TYR cc_start: 0.8665 (m-80) cc_final: 0.7941 (m-80)
REVERT: B   43 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8485 (mt)
REVERT: B  301 LYS cc_start: 0.9134 (mtpp) cc_final: 0.8786 (mttp)
  outliers start: 17
  outliers final: 15
  residues processed: 110
  average time/residue: 0.0859
  time to fit residues: 12.6854
Evaluate side-chains
  111 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  140 LYS
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  192 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.8784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.133740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.115478 restraints weight = 10193.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.08
r_work: 0.3340 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6793  Z= 0.142
  Angle     :  0.465   5.509   9278  Z= 0.248
  Chirality :  0.039   0.134   1104
  Planarity :  0.003   0.028   1164
  Dihedral  :  4.722  72.743    972
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 13.97 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.29), residues: 885
  helix:  2.55 (0.26), residues: 411
  sheet: -0.10 (0.38), residues: 178
  loop : -0.03 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 228 
 TYR   0.018   0.001   TYR B  59 
 PHE   0.010   0.001   PHE B 241 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6792)
  covalent geometry    : angle       0.46550 ( 9276)
  SS BOND              : bond        0.00240 (    1)
  SS BOND              : angle       0.12933 (    2)
  hydrogen bonds       : bond        0.03634 (  389)
  hydrogen bonds       : angle       4.01029 ( 1125)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  215 ASP cc_start: 0.8661 (t0) cc_final: 0.8307 (t0)
REVERT: A  339 TYR cc_start: 0.8737 (m-80) cc_final: 0.7944 (m-80)
REVERT: B   43 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8575 (mt)
REVERT: B  301 LYS cc_start: 0.9161 (mtpp) cc_final: 0.8806 (mttp)
REVERT: R  318 ASN cc_start: 0.8754 (t0) cc_final: 0.8529 (t0)
  outliers start: 17
  outliers final: 16
  residues processed: 113
  average time/residue: 0.0927
  time to fit residues: 14.0371
Evaluate side-chains
  116 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  140 LYS
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  192 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 15 optimal weight:    0.1980
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.134681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.116410 restraints weight = 10221.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.09
r_work: 0.3352 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.1627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6793  Z= 0.116
  Angle     :  0.453   5.321   9278  Z= 0.242
  Chirality :  0.039   0.134   1104
  Planarity :  0.003   0.028   1164
  Dihedral  :  4.682  72.543    972
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.29 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.29), residues: 885
  helix:  2.59 (0.26), residues: 408
  sheet: -0.11 (0.38), residues: 179
  loop :  0.01 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 228 
 TYR   0.015   0.001   TYR B  59 
 PHE   0.008   0.001   PHE B 241 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 6792)
  covalent geometry    : angle       0.45257 ( 9276)
  SS BOND              : bond        0.00204 (    1)
  SS BOND              : angle       0.13870 (    2)
  hydrogen bonds       : bond        0.03507 (  389)
  hydrogen bonds       : angle       3.96214 ( 1125)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  215 ASP cc_start: 0.8681 (t0) cc_final: 0.8326 (t0)
REVERT: A  339 TYR cc_start: 0.8713 (m-80) cc_final: 0.7917 (m-80)
REVERT: B   43 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8581 (mt)
REVERT: B  301 LYS cc_start: 0.9142 (mtpp) cc_final: 0.8833 (mttp)
  outliers start: 15
  outliers final: 11
  residues processed: 111
  average time/residue: 0.0900
  time to fit residues: 13.2783
Evaluate side-chains
  107 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  140 LYS
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  192 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 72 optimal weight:    0.1980
   chunk 45 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0050
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.4594

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

Flipped N/Q/H residues before XYZ refinement:
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.142824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.125549 restraints weight = 9865.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 1.90
r_work: 0.3448 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3350
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3350
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6793  Z= 0.104
  Angle     :  0.449   5.315   9278  Z= 0.239
  Chirality :  0.039   0.135   1104
  Planarity :  0.003   0.028   1164
  Dihedral  :  4.629  72.214    972
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.08 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.76 (0.29), residues: 885
  helix:  2.61 (0.26), residues: 405
  sheet: -0.05 (0.39), residues: 175
  loop : -0.00 (0.37), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 228 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.008   0.001   PHE B 241 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 6792)
  covalent geometry    : angle       0.44873 ( 9276)
  SS BOND              : bond        0.00167 (    1)
  SS BOND              : angle       0.25704 (    2)
  hydrogen bonds       : bond        0.03398 (  389)
  hydrogen bonds       : angle       3.93118 ( 1125)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  215 ASP cc_start: 0.8659 (t0) cc_final: 0.8265 (t0)
REVERT: A  339 TYR cc_start: 0.8665 (m-80) cc_final: 0.7972 (m-80)
REVERT: B   43 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8521 (mt)
REVERT: B   45 MET cc_start: 0.7613 (mtt) cc_final: 0.7231 (mtt)
REVERT: B  301 LYS cc_start: 0.9109 (mtpp) cc_final: 0.8794 (mttm)
  outliers start: 13
  outliers final: 10
  residues processed: 108
  average time/residue: 0.0948
  time to fit residues: 13.4619
Evaluate side-chains
  105 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  140 LYS
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  192 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 72 optimal weight:    0.4980
   chunk 40 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.141613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.124367 restraints weight = 9749.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 1.88
r_work: 0.3426 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3332
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3332 r_free = 0.3332    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3332 r_free = 0.3332    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3332
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6793  Z= 0.130
  Angle     :  0.466   5.399   9278  Z= 0.248
  Chirality :  0.039   0.134   1104
  Planarity :  0.003   0.028   1164
  Dihedral  :  4.706  72.701    972
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.24 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.29), residues: 885
  helix:  2.58 (0.26), residues: 404
  sheet: -0.30 (0.38), residues: 183
  loop :  0.02 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 175 
 TYR   0.017   0.001   TYR B  59 
 PHE   0.010   0.001   PHE B 241 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6792)
  covalent geometry    : angle       0.46588 ( 9276)
  SS BOND              : bond        0.00207 (    1)
  SS BOND              : angle       0.23912 (    2)
  hydrogen bonds       : bond        0.03539 (  389)
  hydrogen bonds       : angle       3.98319 ( 1125)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1918.67 seconds
wall clock time: 33 minutes 47.18 seconds (2027.18 seconds total)