Starting phenix.real_space_refine
on Sat May 10 17:02:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9chv_45603/05_2025/9chv_45603.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9chv_45603/05_2025/9chv_45603.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9chv_45603/05_2025/9chv_45603.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9chv_45603/05_2025/9chv_45603.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9chv_45603/05_2025/9chv_45603.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9chv_45603/05_2025/9chv_45603.cif"
  }
  resolution = 3.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.049
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      40      5.16       5
     C    4277      2.51       5
     N    1115      2.21       5
     O    1212      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6644
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 414, 2969
          Classifications: {'peptide': 414}
          Incomplete info: {'truncation_to_alanine': 95}
          Link IDs: {'PTRANS': 9, 'TRANS': 404}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 383
          Unresolved non-hydrogen angles: 496
          Unresolved non-hydrogen dihedrals: 336
          Unresolved non-hydrogen chiralities: 36
          Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 11, 'GLU:plan': 4, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 204
    Chain: "B"
      Number of atoms: 2810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2810
          Classifications: {'peptide': 352}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 20, 'TRANS': 331}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 41
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 44
    Chain: "C"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 808
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'GLU%COO:oxt': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "C"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 57
          Unusual residues: {'FK5': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.13, per 1000 atoms: 0.77
  Number of scatterers: 6644
  At special positions: 0
  Unit cell: (65.45, 85.85, 154.7, 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      40     16.00
     O    1212      8.00
     N    1115      7.00
     C    4277      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 106 " - pdb=" SG  CYS A 191 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.67
  Conformation dependent library (CDL) restraints added in 954.8 milliseconds
  

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1636

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 6 sheets defined
      53.4% alpha, 4.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 61
      removed outlier: 3.533A  pdb=" N   VAL A  54 " --> pdb=" O   GLY A  50 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ILE A  55 " --> pdb=" O   ASN A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 78
    Processing helix  chain 'A' and resid 80 through 85
    Processing helix  chain 'A' and resid 85 through 97
      removed outlier: 3.637A  pdb=" N   PHE A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLY A  90 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ILE A  94 " --> pdb=" O   GLY A  90 " (cutoff:3.500A)
      removed outlier: 5.048A  pdb=" N   LEU A  95 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   MET A  96 " --> pdb=" O   ALA A  92 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LYS A  97 " --> pdb=" O   HIS A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 115
      removed outlier: 4.384A  pdb=" N   GLU A 107 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 104 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   THR A 110 " --> pdb=" O   CYS A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 137
      removed outlier: 3.811A  pdb=" N   GLU A 122 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   SER A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 145
      removed outlier: 3.953A  pdb=" N   TYR A 141 " --> pdb=" O   SER A 137 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   LEU A 145 " --> pdb=" O   TYR A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 172
      removed outlier: 3.691A  pdb=" N   ALA A 150 " --> pdb=" O   THR A 146 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ARG A 151 " --> pdb=" O   LYS A 147 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   VAL A 152 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE A 159 " --> pdb=" O   LEU A 155 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   VAL A 160 " --> pdb=" O   MET A 156 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   SER A 161 " --> pdb=" O   VAL A 157 " (cutoff:3.500A)
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 197 through 207
      removed outlier: 3.532A  pdb=" N   SER A 207 " --> pdb=" O   SER A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 215
      removed outlier: 3.845A  pdb=" N   ILE A 214 " --> pdb=" O   VAL A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 225
    Processing helix  chain 'A' and resid 226 through 231
      removed outlier: 3.940A  pdb=" N   LEU A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ASP A 231 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 226 through 231'
    Processing helix  chain 'A' and resid 236 through 246
    Processing helix  chain 'A' and resid 255 through 259
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 286 through 296
      removed outlier: 3.825A  pdb=" N   ILE A 291 " --> pdb=" O   PHE A 287 " (cutoff:3.500A)
      removed outlier: 5.215A  pdb=" N   GLU A 292 " --> pdb=" O   LYS A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 315
      removed outlier: 3.932A  pdb=" N   LYS A 306 " --> pdb=" O   ASP A 302 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   TYR A 314 " --> pdb=" O   ALA A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 336
      removed outlier: 4.501A  pdb=" N   LEU A 331 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   MET A 334 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 356
      removed outlier: 3.858A  pdb=" N   LEU A 344 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 373
    Processing helix  chain 'A' and resid 377 through 381
      removed outlier: 3.888A  pdb=" N   MET A 381 " --> pdb=" O   HIS A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 394
      removed outlier: 3.858A  pdb=" N   ALA A 394 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 408
      removed outlier: 4.477A  pdb=" N   THR A 406 " --> pdb=" O   MET A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 421
      removed outlier: 3.984A  pdb=" N   PHE A 413 " --> pdb=" O   TRP A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 435
    Processing helix  chain 'A' and resid 436 through 445
      removed outlier: 3.930A  pdb=" N   VAL A 440 " --> pdb=" O   TRP A 436 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ASN A 441 " --> pdb=" O   ILE A 437 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   SER A 442 " --> pdb=" O   GLY A 438 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLY A 443 " --> pdb=" O   TYR A 439 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASN A 445 " --> pdb=" O   ASN A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 451
      removed outlier: 3.812A  pdb=" N   CYS A 450 " --> pdb=" O   LEU A 447 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ARG A 451 " --> pdb=" O   ILE A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 461
      removed outlier: 3.659A  pdb=" N   ALA A 458 " --> pdb=" O   ASP A 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 50
    Processing helix  chain 'B' and resid 56 through 73
      removed outlier: 4.315A  pdb=" N   GLN B  73 " --> pdb=" O   SER B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 104
      removed outlier: 3.905A  pdb=" N   LYS B  99 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 139
    Processing helix  chain 'B' and resid 153 through 159
    Processing helix  chain 'B' and resid 161 through 169
    Processing helix  chain 'B' and resid 170 through 182
      removed outlier: 3.729A  pdb=" N   TYR B 174 " --> pdb=" O   SER B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 213
      removed outlier: 4.025A  pdb=" N   LYS B 213 " --> pdb=" O   ASP B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 230
      removed outlier: 3.898A  pdb=" N   LEU B 230 " --> pdb=" O   MET B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 271
    Processing helix  chain 'B' and resid 309 through 313
    Processing helix  chain 'B' and resid 347 through 369
      Proline residue:  B 354  - end of helix
      removed outlier: 4.360A  pdb=" N   GLU B 358 " --> pdb=" O   PRO B 354 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ASN B 369 " --> pdb=" O   VAL B 365 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 63
      removed outlier: 3.512A  pdb=" N   GLU C  60 " --> pdb=" O   ILE C  56 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 66
      No H-bonds generated for 'chain 'C' and resid 64 through 66'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 253 through 254
    Processing sheet with id=AA2, first strand: chain 'B' and resid 85 through 86
      removed outlier: 6.528A  pdb=" N   THR B  85 " --> pdb=" O   LEU B 113 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 189 through 190
      removed outlier: 4.030A  pdb=" N   MET B 190 " --> pdb=" O   PHE B 194 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   LEU B 195 " --> pdb=" O   LEU B 277 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ILE B 276 " --> pdb=" O   ILE B 302 " (cutoff:3.500A)
      removed outlier: 8.130A  pdb=" N   ILE B 304 " --> pdb=" O   ILE B 276 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   ARG B 278 " --> pdb=" O   ILE B 304 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   THR B 303 " --> pdb=" O   ARG B 288 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ARG B 288 " --> pdb=" O   THR B 303 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 319 through 324
      removed outlier: 3.687A  pdb=" N   ASN B 329 " --> pdb=" O   LYS B 322 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 3
      removed outlier: 3.630A  pdb=" N   THR C  75 " --> pdb=" O   GLN C   3 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 46 through 49
      removed outlier: 3.827A  pdb=" N   PHE C  48 " --> pdb=" O   CYS C  22 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   CYS C  22 " --> pdb=" O   PHE C  48 " (cutoff:3.500A)
      removed outlier: 7.688A  pdb=" N   THR C  21 " --> pdb=" O   LEU C 106 " (cutoff:3.500A)
      removed outlier: 5.719A  pdb=" N   LEU C 106 " --> pdb=" O   THR C  21 " (cutoff:3.500A)
      removed outlier: 7.326A  pdb=" N   VAL C  23 " --> pdb=" O   LEU C 104 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   HIS C  25 " --> pdb=" O   GLU C 102 " (cutoff:3.500A)

    259 hydrogen bonds defined for protein.
    738 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: 1.53

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1093
        1.30 -     1.43: 1763
        1.43 -     1.56: 3871
        1.56 -     1.69: 2
        1.69 -     1.81: 60
  Bond restraints: 6789
  Sorted by residual:
  bond pdb=" C9  FK5 C 201 "
       pdb=" O4  FK5 C 201 "
    ideal  model  delta    sigma   weight residual
    1.206  1.408 -0.202 2.00e-02 2.50e+03 1.02e+02
  bond pdb=" C1  FK5 C 201 "
       pdb=" O2  FK5 C 201 "
    ideal  model  delta    sigma   weight residual
    1.211  1.408 -0.197 2.00e-02 2.50e+03 9.74e+01
  bond pdb=" C22 FK5 C 201 "
       pdb=" O9  FK5 C 201 "
    ideal  model  delta    sigma   weight residual
    1.215  1.409 -0.194 2.00e-02 2.50e+03 9.40e+01
  bond pdb=" C   THR A 164 "
       pdb=" O   THR A 164 "
    ideal  model  delta    sigma   weight residual
    1.236  1.338 -0.102 1.15e-02 7.56e+03 7.81e+01
  bond pdb=" C   TYR A 209 "
       pdb=" O   TYR A 209 "
    ideal  model  delta    sigma   weight residual
    1.236  1.338 -0.102 1.15e-02 7.56e+03 7.81e+01
  ... (remaining 6784 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.46: 8991
        4.46 -     8.92: 201
        8.92 -    13.38: 28
       13.38 -    17.85: 4
       17.85 -    22.31: 1
  Bond angle restraints: 9225
  Sorted by residual:
  angle pdb=" N   VAL A 206 "
        pdb=" CA  VAL A 206 "
        pdb=" C   VAL A 206 "
      ideal   model   delta    sigma   weight residual
     111.45  133.76  -22.31 9.30e-01 1.16e+00 5.75e+02
  angle pdb=" C   VAL A 206 "
        pdb=" CA  VAL A 206 "
        pdb=" CB  VAL A 206 "
      ideal   model   delta    sigma   weight residual
     111.92   96.50   15.42 1.31e+00 5.83e-01 1.39e+02
  angle pdb=" N   PHE A 208 "
        pdb=" CA  PHE A 208 "
        pdb=" C   PHE A 208 "
      ideal   model   delta    sigma   weight residual
     112.68   97.55   15.13 1.33e+00 5.65e-01 1.29e+02
  angle pdb=" C   VAL A 213 "
        pdb=" N   ILE A 214 "
        pdb=" CA  ILE A 214 "
      ideal   model   delta    sigma   weight residual
     120.56  133.54  -12.98 1.26e+00 6.30e-01 1.06e+02
  angle pdb=" N   LYS A  60 "
        pdb=" CA  LYS A  60 "
        pdb=" C   LYS A  60 "
      ideal   model   delta    sigma   weight residual
     111.28  121.88  -10.60 1.09e+00 8.42e-01 9.45e+01
  ... (remaining 9220 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.82: 3972
       35.82 -    71.65: 108
       71.65 -   107.47: 10
      107.47 -   143.30: 4
      143.30 -   179.12: 4
  Dihedral angle restraints: 4098
    sinusoidal: 1566
      harmonic: 2532
  Sorted by residual:
  dihedral pdb=" CB  CYS A 106 "
           pdb=" SG  CYS A 106 "
           pdb=" SG  CYS A 191 "
           pdb=" CB  CYS A 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  169.43  -76.43     1      1.00e+01 1.00e-02 7.35e+01
  dihedral pdb=" C   VAL A 114 "
           pdb=" N   VAL A 114 "
           pdb=" CA  VAL A 114 "
           pdb=" CB  VAL A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -142.76   20.76     0      2.50e+00 1.60e-01 6.89e+01
  dihedral pdb=" N   VAL A 114 "
           pdb=" C   VAL A 114 "
           pdb=" CA  VAL A 114 "
           pdb=" CB  VAL A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  141.76  -18.36     0      2.50e+00 1.60e-01 5.39e+01
  ... (remaining 4095 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.155: 957
       0.155 -    0.311: 69
       0.311 -    0.466: 21
       0.466 -    0.622: 7
       0.622 -    0.777: 4
  Chirality restraints: 1058
  Sorted by residual:
  chirality pdb=" CA  PRO A 211 "
            pdb=" N   PRO A 211 "
            pdb=" C   PRO A 211 "
            pdb=" CB  PRO A 211 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    1.94    0.78 2.00e-01 2.50e+01 1.51e+01
  chirality pdb=" CA  VAL A 114 "
            pdb=" N   VAL A 114 "
            pdb=" C   VAL A 114 "
            pdb=" CB  VAL A 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.71    0.73 2.00e-01 2.50e+01 1.34e+01
  chirality pdb=" CA  ALA A 128 "
            pdb=" N   ALA A 128 "
            pdb=" C   ALA A 128 "
            pdb=" CB  ALA A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.76    0.72 2.00e-01 2.50e+01 1.30e+01
  ... (remaining 1055 not shown)

  Planarity restraints: 1183
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C26 FK5 C 201 "    0.127 2.00e-02 2.50e+03   1.39e-01 2.41e+02
        pdb=" C27 FK5 C 201 "   -0.049 2.00e-02 2.50e+03
        pdb=" C28 FK5 C 201 "   -0.218 2.00e-02 2.50e+03
        pdb=" C29 FK5 C 201 "    0.171 2.00e-02 2.50e+03
        pdb=" C42 FK5 C 201 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C18 FK5 C 201 "    0.063 2.00e-02 2.50e+03   6.84e-02 5.85e+01
        pdb=" C19 FK5 C 201 "   -0.022 2.00e-02 2.50e+03
        pdb=" C20 FK5 C 201 "   -0.108 2.00e-02 2.50e+03
        pdb=" C21 FK5 C 201 "    0.084 2.00e-02 2.50e+03
        pdb=" C37 FK5 C 201 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 148 "    0.038 2.00e-02 2.50e+03   7.14e-02 5.10e+01
        pdb=" C   ASN A 148 "   -0.124 2.00e-02 2.50e+03
        pdb=" O   ASN A 148 "    0.044 2.00e-02 2.50e+03
        pdb=" N   LYS A 149 "    0.042 2.00e-02 2.50e+03
  ... (remaining 1180 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.66: 194
        2.66 -     3.22: 6325
        3.22 -     3.78: 9254
        3.78 -     4.34: 12079
        4.34 -     4.90: 18996
  Nonbonded interactions: 46848
  Sorted by model distance:
  nonbonded pdb=" O10 FK5 C 201 "
            pdb=" O9  FK5 C 201 "
     model   vdw
     2.106 3.040
  nonbonded pdb=" OH  TYR C  82 "
            pdb=" O3  FK5 C 201 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OD1 ASP C  37 "
            pdb=" N   SER C  38 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" O   ASP C  11 "
            pdb=" NE2 GLN C  70 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" NH2 ARG A 272 "
            pdb=" O   ARG A 312 "
     model   vdw
     2.315 3.120
  ... (remaining 46843 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.840
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6366
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      :  0.011   0.202   6790  Z= 0.702
  Angle     :  1.544  22.306   9227  Z= 1.098
  Chirality :  0.112   0.777   1058
  Planarity :  0.010   0.142   1183
  Dihedral  : 18.200 179.122   2459
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  :  3.95 %
    Favored  : 91.20 %
  Cbeta Deviations :  4.03 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.29), residues: 861
  helix: -0.41 (0.27), residues: 374
  sheet: -3.30 (0.66), residues: 42
  loop : -1.63 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.005   TRP A 109 
 HIS   0.011   0.001   HIS B 280 
 PHE   0.029   0.002   PHE B 181 
 TYR   0.033   0.002   TYR A 132 
 ARG   0.002   0.000   ARG B 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19809 (  259)
  hydrogen bonds       : angle       8.19128 (  738)
  SS BOND              : bond        0.00635 (    1)
  SS BOND              : angle       0.94528 (    2)
  covalent geometry    : bond        0.01059 ( 6789)
  covalent geometry    : angle       1.54406 ( 9225)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 148
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 SER cc_start: 0.6572 (OUTLIER) cc_final: 0.6331 (t)
REVERT: A  360 ASP cc_start: 0.6098 (p0) cc_final: 0.5089 (t0)
REVERT: A  402 MET cc_start: 0.6873 (mtt) cc_final: 0.6662 (mtm)
  outliers start: 32
  outliers final: 12
  residues processed: 175
  average time/residue: 0.1664
  time to fit residues: 39.3278
Evaluate side-chains
  106 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   74 SER
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  211 PRO
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  448 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0010
   chunk 34 optimal weight:    0.4980
   chunk 67 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 249 ASN
A 337 ASN
A 392 HIS
** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 271 ASN
B 309 ASN
B 326 ASN
C  25 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.209059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.196634 restraints weight = 8538.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.195545 restraints weight = 14402.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.195181 restraints weight = 14011.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.4412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6787
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6790  Z= 0.147
  Angle     :  0.664  10.241   9227  Z= 0.339
  Chirality :  0.044   0.159   1058
  Planarity :  0.004   0.033   1183
  Dihedral  : 14.926 179.789   1054
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.69 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.28), residues: 861
  helix: -0.15 (0.26), residues: 405
  sheet: -3.30 (0.58), residues: 61
  loop : -1.59 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 133 
 HIS   0.006   0.001   HIS B 280 
 PHE   0.020   0.001   PHE B 181 
 TYR   0.012   0.001   TYR B 340 
 ARG   0.004   0.000   ARG B 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03895 (  259)
  hydrogen bonds       : angle       4.75042 (  738)
  SS BOND              : bond        0.00214 (    1)
  SS BOND              : angle       2.56695 (    2)
  covalent geometry    : bond        0.00326 ( 6789)
  covalent geometry    : angle       0.66269 ( 9225)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
REVERT: B  289 MET cc_start: 0.6748 (mtt) cc_final: 0.6440 (mtt)
REVERT: B  346 MET cc_start: 0.7982 (mmt) cc_final: 0.7320 (mtt)
REVERT: C   29 MET cc_start: 0.7685 (ttm) cc_final: 0.7420 (ttm)
  outliers start: 19
  outliers final: 13
  residues processed: 115
  average time/residue: 0.1475
  time to fit residues: 24.0697
Evaluate side-chains
  98 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue   25 HIS
Chi-restraints excluded: chain C residue   85 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0980
   chunk 70 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0870
   chunk 82 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 3 optimal weight:    5.9990
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
A 445 ASN
C  20 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.208282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.196192 restraints weight = 8584.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.188417 restraints weight = 14526.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.184776 restraints weight = 18624.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.4295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.4145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6790  Z= 0.132
  Angle     :  0.606   7.164   9227  Z= 0.310
  Chirality :  0.042   0.145   1058
  Planarity :  0.004   0.033   1183
  Dihedral  : 13.638 178.725   1040
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.73 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.29), residues: 861
  helix:  0.30 (0.27), residues: 407
  sheet: -3.15 (0.60), residues: 61
  loop : -1.53 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 133 
 HIS   0.035   0.002   HIS C  25 
 PHE   0.016   0.001   PHE B 181 
 TYR   0.017   0.001   TYR B 323 
 ARG   0.002   0.000   ARG B 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03867 (  259)
  hydrogen bonds       : angle       4.23174 (  738)
  SS BOND              : bond        0.00121 (    1)
  SS BOND              : angle       1.42045 (    2)
  covalent geometry    : bond        0.00298 ( 6789)
  covalent geometry    : angle       0.60560 ( 9225)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.690 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 MET cc_start: 0.8060 (tmm) cc_final: 0.7659 (tmm)
REVERT: A  360 ASP cc_start: 0.6975 (p0) cc_final: 0.6081 (t0)
REVERT: B  178 MET cc_start: 0.7968 (mmt) cc_final: 0.7160 (mmm)
REVERT: B  346 MET cc_start: 0.8225 (mmt) cc_final: 0.7781 (mtt)
REVERT: C   29 MET cc_start: 0.7579 (ttm) cc_final: 0.7302 (ttm)
  outliers start: 15
  outliers final: 11
  residues processed: 109
  average time/residue: 0.1448
  time to fit residues: 22.6157
Evaluate side-chains
  101 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  367 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0870
   chunk 62 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.214771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.205296 restraints weight = 8876.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.204338 restraints weight = 16050.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.204223 restraints weight = 14941.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.4390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.5545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6790  Z= 0.141
  Angle     :  0.638  13.240   9227  Z= 0.319
  Chirality :  0.042   0.143   1058
  Planarity :  0.004   0.048   1183
  Dihedral  : 13.598 179.349   1037
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 18.06 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.29), residues: 861
  helix:  0.45 (0.27), residues: 405
  sheet: -3.28 (0.60), residues: 63
  loop : -1.42 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 133 
 HIS   0.003   0.001   HIS C  25 
 PHE   0.023   0.001   PHE A 193 
 TYR   0.013   0.001   TYR B 323 
 ARG   0.003   0.000   ARG A 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03966 (  259)
  hydrogen bonds       : angle       4.05299 (  738)
  SS BOND              : bond        0.00146 (    1)
  SS BOND              : angle       0.78892 (    2)
  covalent geometry    : bond        0.00325 ( 6789)
  covalent geometry    : angle       0.63840 ( 9225)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 86
  time to evaluate  : 0.676 
Fit side-chains
REVERT: A  215 MET cc_start: 0.8224 (tmm) cc_final: 0.7703 (tmm)
REVERT: A  360 ASP cc_start: 0.6825 (p0) cc_final: 0.5947 (t0)
  outliers start: 31
  outliers final: 15
  residues processed: 110
  average time/residue: 0.1645
  time to fit residues: 25.2631
Evaluate side-chains
  93 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  367 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 57 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 3 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 31 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0000
   chunk 71 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.6384

-------------------------------------------------------------------------------
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 = 0.4506 r_free = 0.4506 target = 0.213499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.204797 restraints weight = 8818.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.193718 restraints weight = 15047.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.188457 restraints weight = 14361.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.6096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6790  Z= 0.132
  Angle     :  0.583   9.833   9227  Z= 0.294
  Chirality :  0.041   0.131   1058
  Planarity :  0.004   0.042   1183
  Dihedral  : 13.466 179.941   1037
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 21.24 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.29), residues: 861
  helix:  0.56 (0.27), residues: 407
  sheet: -2.64 (0.75), residues: 40
  loop : -1.51 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 133 
 HIS   0.002   0.001   HIS A  93 
 PHE   0.015   0.001   PHE A 242 
 TYR   0.020   0.001   TYR B 323 
 ARG   0.002   0.000   ARG B 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03754 (  259)
  hydrogen bonds       : angle       4.01558 (  738)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       0.27612 (    2)
  covalent geometry    : bond        0.00309 ( 6789)
  covalent geometry    : angle       0.58273 ( 9225)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A  215 MET cc_start: 0.8377 (tmm) cc_final: 0.7759 (tmm)
REVERT: A  360 ASP cc_start: 0.7150 (p0) cc_final: 0.6229 (t0)
REVERT: B   98 MET cc_start: 0.7940 (mmp) cc_final: 0.7412 (mmm)
  outliers start: 21
  outliers final: 13
  residues processed: 103
  average time/residue: 0.1605
  time to fit residues: 23.3358
Evaluate side-chains
  94 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue  101 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 20 optimal weight:    0.0670
   chunk 68 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 84 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.7120

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

Flipped N/Q/H residues before XYZ refinement:
B 366 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.212478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.203410 restraints weight = 8720.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.195805 restraints weight = 14887.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.191481 restraints weight = 17292.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.4255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.6558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6790  Z= 0.143
  Angle     :  0.604   9.768   9227  Z= 0.304
  Chirality :  0.041   0.134   1058
  Planarity :  0.004   0.036   1183
  Dihedral  : 13.535 179.960   1037
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 21.24 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.30), residues: 861
  helix:  0.60 (0.27), residues: 402
  sheet: -2.75 (0.76), residues: 40
  loop : -1.44 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 133 
 HIS   0.002   0.001   HIS A  93 
 PHE   0.012   0.001   PHE A 193 
 TYR   0.014   0.001   TYR B 323 
 ARG   0.002   0.000   ARG A 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03956 (  259)
  hydrogen bonds       : angle       4.06054 (  738)
  SS BOND              : bond        0.00064 (    1)
  SS BOND              : angle       0.28804 (    2)
  covalent geometry    : bond        0.00339 ( 6789)
  covalent geometry    : angle       0.60423 ( 9225)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 77
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A  215 MET cc_start: 0.8476 (tmm) cc_final: 0.8050 (tmm)
REVERT: A  360 ASP cc_start: 0.7029 (p0) cc_final: 0.6276 (t0)
REVERT: B  246 HIS cc_start: 0.6002 (OUTLIER) cc_final: 0.5048 (t-90)
  outliers start: 24
  outliers final: 17
  residues processed: 95
  average time/residue: 0.1626
  time to fit residues: 21.8499
Evaluate side-chains
  91 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain B residue   13 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue  101 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 68 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 30 optimal weight:    0.4980
   chunk 7 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 315 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.202507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.189819 restraints weight = 8594.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.187969 restraints weight = 13830.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.186787 restraints weight = 15824.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.4308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.6850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6790  Z= 0.147
  Angle     :  0.602   9.435   9227  Z= 0.301
  Chirality :  0.041   0.135   1058
  Planarity :  0.004   0.036   1183
  Dihedral  : 13.572 179.804   1037
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 21.55 %
    Favored  : 74.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.30), residues: 861
  helix:  0.62 (0.28), residues: 403
  sheet: -2.76 (0.76), residues: 40
  loop : -1.44 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 133 
 HIS   0.002   0.001   HIS A  93 
 PHE   0.019   0.001   PHE A 287 
 TYR   0.013   0.001   TYR B 323 
 ARG   0.004   0.000   ARG A 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04019 (  259)
  hydrogen bonds       : angle       4.07326 (  738)
  SS BOND              : bond        0.00062 (    1)
  SS BOND              : angle       0.26091 (    2)
  covalent geometry    : bond        0.00355 ( 6789)
  covalent geometry    : angle       0.60157 ( 9225)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 74
  time to evaluate  : 0.705 
Fit side-chains
REVERT: A  215 MET cc_start: 0.8494 (tmm) cc_final: 0.8073 (tmm)
REVERT: A  360 ASP cc_start: 0.6968 (p0) cc_final: 0.6109 (t0)
REVERT: B   98 MET cc_start: 0.7881 (mmp) cc_final: 0.7621 (mmm)
REVERT: B  246 HIS cc_start: 0.6129 (OUTLIER) cc_final: 0.5298 (t-90)
  outliers start: 29
  outliers final: 21
  residues processed: 99
  average time/residue: 0.1554
  time to fit residues: 22.2826
Evaluate side-chains
  93 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain B residue   13 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  101 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 21 optimal weight:    0.3980
   chunk 76 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 58 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 48 optimal weight:    0.4980
   chunk 57 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 445 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.213257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.204423 restraints weight = 8812.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.202574 restraints weight = 13385.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.200993 restraints weight = 16305.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.4387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.7057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6790  Z= 0.122
  Angle     :  0.580   9.471   9227  Z= 0.290
  Chirality :  0.040   0.133   1058
  Planarity :  0.003   0.033   1183
  Dihedral  : 13.404 179.459   1037
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 21.40 %
    Favored  : 73.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.30), residues: 861
  helix:  0.66 (0.28), residues: 407
  sheet: -2.67 (0.78), residues: 40
  loop : -1.41 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 133 
 HIS   0.003   0.001   HIS B 280 
 PHE   0.013   0.001   PHE A 287 
 TYR   0.010   0.001   TYR B 323 
 ARG   0.002   0.000   ARG A 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03548 (  259)
  hydrogen bonds       : angle       3.93758 (  738)
  SS BOND              : bond        0.00019 (    1)
  SS BOND              : angle       0.10003 (    2)
  covalent geometry    : bond        0.00287 ( 6789)
  covalent geometry    : angle       0.57958 ( 9225)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 68
  time to evaluate  : 0.799 
Fit side-chains
REVERT: A  215 MET cc_start: 0.8534 (tmm) cc_final: 0.8142 (tmm)
REVERT: A  360 ASP cc_start: 0.6968 (p0) cc_final: 0.6156 (t0)
REVERT: B   98 MET cc_start: 0.7909 (mmp) cc_final: 0.7655 (mmm)
REVERT: B  246 HIS cc_start: 0.6158 (OUTLIER) cc_final: 0.5242 (t-90)
  outliers start: 31
  outliers final: 22
  residues processed: 95
  average time/residue: 0.1431
  time to fit residues: 19.9039
Evaluate side-chains
  88 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 65
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  419 HIS
Chi-restraints excluded: chain B residue   13 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  101 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0170
   chunk 79 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 1 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0270
   chunk 74 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   overall best weight:    0.4476

-------------------------------------------------------------------------------
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 = 0.4514 r_free = 0.4514 target = 0.214309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.205401 restraints weight = 8873.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.202924 restraints weight = 15013.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.201255 restraints weight = 17784.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.4367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.7189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6790  Z= 0.113
  Angle     :  0.578   9.647   9227  Z= 0.287
  Chirality :  0.040   0.146   1058
  Planarity :  0.003   0.036   1183
  Dihedral  : 13.288 179.315   1037
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 22.91 %
    Favored  : 73.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.30), residues: 861
  helix:  0.76 (0.28), residues: 407
  sheet: -2.53 (0.79), residues: 40
  loop : -1.40 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 133 
 HIS   0.003   0.000   HIS B 280 
 PHE   0.009   0.001   PHE A 287 
 TYR   0.010   0.001   TYR B 174 
 ARG   0.001   0.000   ARG A 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03301 (  259)
  hydrogen bonds       : angle       3.83313 (  738)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       0.05811 (    2)
  covalent geometry    : bond        0.00263 ( 6789)
  covalent geometry    : angle       0.57768 ( 9225)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
REVERT: A  360 ASP cc_start: 0.6891 (p0) cc_final: 0.6097 (t0)
REVERT: B   98 MET cc_start: 0.7872 (mmp) cc_final: 0.7623 (mmm)
REVERT: B  246 HIS cc_start: 0.6110 (OUTLIER) cc_final: 0.5231 (t-90)
REVERT: B  259 TYR cc_start: 0.8027 (p90) cc_final: 0.7767 (p90)
  outliers start: 24
  outliers final: 22
  residues processed: 91
  average time/residue: 0.1568
  time to fit residues: 20.3724
Evaluate side-chains
  90 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 67
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  419 HIS
Chi-restraints excluded: chain B residue   13 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  101 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 40 optimal weight:    0.0670
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0470
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0040
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   overall best weight:    0.2828

-------------------------------------------------------------------------------
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 = 0.4540 r_free = 0.4540 target = 0.217696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.208924 restraints weight = 8889.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.197228 restraints weight = 14319.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.191585 restraints weight = 12522.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.7332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6790  Z= 0.104
  Angle     :  0.595   9.876   9227  Z= 0.291
  Chirality :  0.040   0.145   1058
  Planarity :  0.003   0.035   1183
  Dihedral  : 13.177 179.241   1037
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 23.98 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.30), residues: 861
  helix:  0.90 (0.28), residues: 405
  sheet: -2.51 (0.80), residues: 40
  loop : -1.40 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 133 
 HIS   0.003   0.000   HIS B 280 
 PHE   0.008   0.001   PHE A 387 
 TYR   0.014   0.001   TYR B 323 
 ARG   0.001   0.000   ARG A 272 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02900 (  259)
  hydrogen bonds       : angle       3.77192 (  738)
  SS BOND              : bond        0.00016 (    1)
  SS BOND              : angle       0.10531 (    2)
  covalent geometry    : bond        0.00236 ( 6789)
  covalent geometry    : angle       0.59530 ( 9225)

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.687 
Fit side-chains
REVERT: A  263 GLU cc_start: 0.6488 (mp0) cc_final: 0.6099 (mt-10)
REVERT: A  360 ASP cc_start: 0.7259 (p0) cc_final: 0.6392 (t0)
REVERT: B   98 MET cc_start: 0.7892 (mmp) cc_final: 0.7329 (mmm)
REVERT: B  246 HIS cc_start: 0.5931 (OUTLIER) cc_final: 0.5217 (t-90)
REVERT: B  259 TYR cc_start: 0.8061 (p90) cc_final: 0.7832 (p90)
REVERT: C  100 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8539 (t70)
REVERT: C  106 LEU cc_start: 0.8134 (tt) cc_final: 0.7878 (tt)
  outliers start: 20
  outliers final: 17
  residues processed: 89
  average time/residue: 0.1481
  time to fit residues: 18.8733
Evaluate side-chains
  91 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  419 HIS
Chi-restraints excluded: chain B residue   13 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  101 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0970
   chunk 41 optimal weight:    0.0570
   chunk 3 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 81 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.4096

-------------------------------------------------------------------------------
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 = 0.4518 r_free = 0.4518 target = 0.215555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.206963 restraints weight = 8831.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.204240 restraints weight = 12978.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.200736 restraints weight = 14768.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.4378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.7388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6790  Z= 0.110
  Angle     :  0.583   9.434   9227  Z= 0.289
  Chirality :  0.041   0.285   1058
  Planarity :  0.003   0.034   1183
  Dihedral  : 13.189 179.190   1037
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 23.37 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.30), residues: 861
  helix:  0.93 (0.28), residues: 404
  sheet: -2.51 (0.81), residues: 40
  loop : -1.32 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 133 
 HIS   0.003   0.000   HIS B 280 
 PHE   0.008   0.001   PHE A 387 
 TYR   0.014   0.001   TYR B 323 
 ARG   0.003   0.000   ARG B  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03202 (  259)
  hydrogen bonds       : angle       3.77544 (  738)
  SS BOND              : bond        0.00016 (    1)
  SS BOND              : angle       0.12571 (    2)
  covalent geometry    : bond        0.00254 ( 6789)
  covalent geometry    : angle       0.58319 ( 9225)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2243.85 seconds
wall clock time: 40 minutes 11.01 seconds (2411.01 seconds total)