Starting phenix.real_space_refine
on Tue Feb  3 18:22:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yq4_73323/02_2026/9yq4_73323.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yq4_73323/02_2026/9yq4_73323.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yq4_73323/02_2026/9yq4_73323.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yq4_73323/02_2026/9yq4_73323.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yq4_73323/02_2026/9yq4_73323.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yq4_73323/02_2026/9yq4_73323.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.053
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: 6
    Type Number    sf(0)   Gaussians
     Mn      1      7.51       5
     P       2      5.49       5
     S      35      5.16       5
     C    3866      2.51       5
     N     983      2.21       5
     O    1106      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5993
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 494, 4024
          Classifications: {'peptide': 494}
          Link IDs: {'PTRANS': 13, 'TRANS': 480}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 950
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "C"
      Number of atoms: 946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 946
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
    Chain: "A"
      Number of atoms: 73
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 73
          Unusual residues: {' MN': 1, 'UGA': 1, 'Y01': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.51, per 1000 atoms: 0.25
  Number of scatterers: 5993
  At special positions: 0
  Unit cell: (70.2, 95.04, 141.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      1     24.99
     S      35     16.00
     P       2     15.00
     O    1106      8.00
     N     983      7.00
     C    3866      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.52
  Conformation dependent library (CDL) restraints added in 345.4 milliseconds
  

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1370

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 8 sheets defined
      43.6% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 74
      removed outlier: 6.330A  pdb=" N   VAL A  45 " --> pdb=" O   TRP A  41 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   TYR A  46 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   PHE A  53 " --> pdb=" O   PHE A  49 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   TYR A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASP A  70 " --> pdb=" O   MET A  66 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   TRP A  71 " --> pdb=" O   ARG A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 108
    Processing helix  chain 'A' and resid 127 through 136
      removed outlier: 5.548A  pdb=" N   ILE A 133 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   TYR A 134 " --> pdb=" O   MET A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 188
      removed outlier: 4.013A  pdb=" N   GLY A 184 " --> pdb=" O   SER A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 221
      removed outlier: 3.638A  pdb=" N   TYR A 216 " --> pdb=" O   LEU A 212 " (cutoff:3.500A)
      Proline residue:  A 217  - end of helix
      removed outlier: 3.514A  pdb=" N   ASP A 221 " --> pdb=" O   PRO A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 253
      removed outlier: 3.632A  pdb=" N   LEU A 243 " --> pdb=" O   ILE A 239 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   SER A 245 " --> pdb=" O   SER A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 262
      removed outlier: 3.583A  pdb=" N   GLN A 259 " --> pdb=" O   GLU A 255 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   SER A 260 " --> pdb=" O   ARG A 256 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A 261 " --> pdb=" O   GLY A 257 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   TRP A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 288
      removed outlier: 4.603A  pdb=" N   GLU A 282 " --> pdb=" O   ASP A 278 " (cutoff:3.500A)
      removed outlier: 5.397A  pdb=" N   ASP A 285 " --> pdb=" O   ASN A 281 " (cutoff:3.500A)
      Proline residue:  A 286  - end of helix
    Processing helix  chain 'A' and resid 300 through 311
    Processing helix  chain 'A' and resid 331 through 356
      removed outlier: 3.714A  pdb=" N   ARG A 348 " --> pdb=" O   LYS A 344 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLU A 349 " --> pdb=" O   SER A 345 " (cutoff:3.500A)
      removed outlier: 5.360A  pdb=" N   TRP A 351 " --> pdb=" O   CYS A 347 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   TYR A 352 " --> pdb=" O   ARG A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 359
      No H-bonds generated for 'chain 'A' and resid 357 through 359'
    Processing helix  chain 'A' and resid 364 through 391
      removed outlier: 3.502A  pdb=" N   ALA A 368 " --> pdb=" O   GLY A 364 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   CYS A 371 " --> pdb=" O   LEU A 367 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   PHE A 378 " --> pdb=" O   GLN A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 420
      removed outlier: 3.758A  pdb=" N   ALA A 399 " --> pdb=" O   ARG A 395 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   THR A 400 " --> pdb=" O   ALA A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 428
      removed outlier: 3.507A  pdb=" N   TYR A 426 " --> pdb=" O   LYS A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 449
      removed outlier: 3.766A  pdb=" N   VAL A 433 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   ILE A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
      Proline residue:  A 440  - end of helix
    Processing helix  chain 'A' and resid 476 through 497
    Processing helix  chain 'A' and resid 504 through 534
    Processing helix  chain 'A' and resid 541 through 549
      removed outlier: 4.119A  pdb=" N   GLU A 547 " --> pdb=" O   LYS A 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 3.628A  pdb=" N   THR B  31 " --> pdb=" O   ALA B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 90
      removed outlier: 3.683A  pdb=" N   THR B  90 " --> pdb=" O   PRO B  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 113
      removed outlier: 3.741A  pdb=" N   TYR C 113 " --> pdb=" O   PRO C 110 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143
      removed outlier: 3.529A  pdb=" N   GLN A 172 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   VAL A  84 " --> pdb=" O   ARG A 115 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   ILE A 117 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   VAL A  86 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   VAL A 119 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   ILE A  88 " --> pdb=" O   VAL A 119 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   ASP A 121 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   GLY A  90 " --> pdb=" O   ASP A 121 " (cutoff:3.500A)
      removed outlier: 5.958A  pdb=" N   ALA A  85 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   ILE A 200 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   ILE A  87 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 7.365A  pdb=" N   LYS A 225 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   ILE A 224 " --> pdb=" O   ILE A 316 " (cutoff:3.500A)
      removed outlier: 10.596A  pdb=" N   TYR A 318 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
      removed outlier: 11.024A  pdb=" N   ALA A 226 " --> pdb=" O   TYR A 318 " (cutoff:3.500A)
      removed outlier: 10.590A  pdb=" N   ALA A 228 " --> pdb=" O   PRO A 320 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ALA A 322 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLU A 230 " --> pdb=" O   ALA A 322 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   TRP A 325 " --> pdb=" O   VAL A 205 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501
      removed outlier: 6.204A  pdb=" N   PHE A 500 " --> pdb=" O   GLY B 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7
    Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12
      removed outlier: 5.691A  pdb=" N   ARG B  38 " --> pdb=" O   PHE B  47 " (cutoff:3.500A)
      removed outlier: 5.913A  pdb=" N   PHE B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12
      removed outlier: 3.533A  pdb=" N   TYR B 113 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 67 through 68
    Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 56 through 57
      removed outlier: 3.615A  pdb=" N   GLY C  56 " --> pdb=" O   ARG C  52 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ARG C  52 " --> pdb=" O   GLY C  56 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   ALA C  50 " --> pdb=" O   LEU C  34 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   LEU C  34 " --> pdb=" O   ALA C  50 " (cutoff:3.500A)

    273 hydrogen bonds defined for protein.
    762 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: 0.93

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        0.49 -     0.79: 1
        0.79 -     1.08: 0
        1.08 -     1.38: 2279
        1.38 -     1.67: 3810
        1.67 -     1.97: 56
  Warning: very small bond lengths.
  Bond restraints: 6146
  Sorted by residual:
  bond pdb=" CG  PRO A 286 "
       pdb=" CD  PRO A 286 "
    ideal  model  delta    sigma   weight residual
    1.503  0.495  1.008 3.40e-02 8.65e+02 8.79e+02
  bond pdb=" CB  PRO A 286 "
       pdb=" CG  PRO A 286 "
    ideal  model  delta    sigma   weight residual
    1.492  1.966 -0.474 5.00e-02 4.00e+02 8.98e+01
  bond pdb=" CA  PRO A 286 "
       pdb=" CB  PRO A 286 "
    ideal  model  delta    sigma   weight residual
    1.534  1.445  0.089 1.79e-02 3.12e+03 2.49e+01
  bond pdb=" O5D UGA A 601 "
       pdb=" PA  UGA A 601 "
    ideal  model  delta    sigma   weight residual
    1.645  1.741 -0.096 2.00e-02 2.50e+03 2.28e+01
  bond pdb=" CAI Y01 A 603 "
       pdb=" CAK Y01 A 603 "
    ideal  model  delta    sigma   weight residual
    1.492  1.406  0.086 2.00e-02 2.50e+03 1.85e+01
  ... (remaining 6141 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    12.25: 8348
       12.25 -    24.50: 3
       24.50 -    36.75: 1
       36.75 -    49.00: 0
       49.00 -    61.26: 1
  Bond angle restraints: 8353
  Sorted by residual:
  angle pdb=" N   PRO A 286 "
        pdb=" CD  PRO A 286 "
        pdb=" CG  PRO A 286 "
      ideal   model   delta    sigma   weight residual
     103.20   41.94   61.26 1.50e+00 4.44e-01 1.67e+03
  angle pdb=" CA  PRO A 286 "
        pdb=" CB  PRO A 286 "
        pdb=" CG  PRO A 286 "
      ideal   model   delta    sigma   weight residual
     104.50   74.45   30.05 1.90e+00 2.77e-01 2.50e+02
  angle pdb=" N   PRO A 286 "
        pdb=" CA  PRO A 286 "
        pdb=" CB  PRO A 286 "
      ideal   model   delta    sigma   weight residual
     103.20   94.01    9.19 9.50e-01 1.11e+00 9.35e+01
  angle pdb=" PA  UGA A 601 "
        pdb=" O3A UGA A 601 "
        pdb=" PB  UGA A 601 "
      ideal   model   delta    sigma   weight residual
     123.32  146.56  -23.24 3.00e+00 1.11e-01 6.00e+01
  angle pdb=" CB  PRO A 286 "
        pdb=" CG  PRO A 286 "
        pdb=" CD  PRO A 286 "
      ideal   model   delta    sigma   weight residual
     106.10   84.49   21.61 3.20e+00 9.77e-02 4.56e+01
  ... (remaining 8348 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.39: 3230
       21.39 -    42.78: 336
       42.78 -    64.16: 61
       64.16 -    85.55: 17
       85.55 -   106.94: 6
  Dihedral angle restraints: 3650
    sinusoidal: 1496
      harmonic: 2154
  Sorted by residual:
  dihedral pdb=" CA  PRO A 286 "
           pdb=" CB  PRO A 286 "
           pdb=" CG  PRO A 286 "
           pdb=" CD  PRO A 286 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -38.00 -144.94  106.94     1      2.00e+01 2.50e-03 3.10e+01
  dihedral pdb=" CA  LYS A 129 "
           pdb=" C   LYS A 129 "
           pdb=" N   MET A 130 "
           pdb=" CA  MET A 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.15   24.85     0      5.00e+00 4.00e-02 2.47e+01
  dihedral pdb=" CA  THR A 289 "
           pdb=" C   THR A 289 "
           pdb=" N   GLN A 290 "
           pdb=" CA  GLN A 290 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.91  -23.09     0      5.00e+00 4.00e-02 2.13e+01
  ... (remaining 3647 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 838
       0.082 -    0.164: 68
       0.164 -    0.246: 3
       0.246 -    0.328: 3
       0.328 -    0.410: 1
  Chirality restraints: 913
  Sorted by residual:
  chirality pdb=" C2' UGA A 601 "
            pdb=" C1' UGA A 601 "
            pdb=" C3' UGA A 601 "
            pdb=" O2' UGA A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.23   -2.64    0.41 2.00e-01 2.50e+01 4.21e+00
  chirality pdb=" C1D UGA A 601 "
            pdb=" C2D UGA A 601 "
            pdb=" N1  UGA A 601 "
            pdb=" O4D UGA A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.21    2.49   -0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" C5' UGA A 601 "
            pdb=" C4' UGA A 601 "
            pdb=" C6' UGA A 601 "
            pdb=" O5' UGA A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.74    0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 910 not shown)

  Planarity restraints: 1031
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 104 "   -0.018 2.00e-02 2.50e+03   3.51e-02 1.23e+01
        pdb=" CG  ASP B 104 "    0.061 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 104 "   -0.023 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 104 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 252 "    0.013 2.00e-02 2.50e+03   2.69e-02 7.22e+00
        pdb=" C   PHE A 252 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   PHE A 252 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ASN A 253 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 118 "    0.012 2.00e-02 2.50e+03   2.38e-02 5.65e+00
        pdb=" C   THR B 118 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   THR B 118 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLN B 119 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1028 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 114
        2.67 -     3.23: 5575
        3.23 -     3.79: 9011
        3.79 -     4.34: 12196
        4.34 -     4.90: 20701
  Nonbonded interactions: 47597
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A  93 "
            pdb="MN    MN A 602 "
     model   vdw
     2.113 2.320
  nonbonded pdb=" OH  TYR A 432 "
            pdb=" OH  TYR A 517 "
     model   vdw
     2.123 3.040
  nonbonded pdb=" OD1 ASN A 235 "
            pdb=" OG  SER A 241 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" ND2 ASN A 167 "
            pdb=" O   ARG C 101 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   SER A 165 "
            pdb=" OG  SER C 103 "
     model   vdw
     2.229 3.040
  ... (remaining 47592 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  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:             0.020
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.520
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
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      :  0.015   1.008   6148  Z= 0.468
  Angle     :  1.097  61.256   8357  Z= 0.617
  Chirality :  0.050   0.410    913
  Planarity :  0.004   0.038   1031
  Dihedral  : 17.928 106.940   2274
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.34 %
    Favored  : 91.66 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  : 20.63 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.31), residues: 731
  helix:  0.52 (0.31), residues: 294
  sheet: -0.19 (0.45), residues: 151
  loop : -1.75 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  75 
 TYR   0.016   0.001   TYR A 528 
 PHE   0.024   0.001   PHE A  49 
 TRP   0.033   0.001   TRP A 346 
 HIS   0.004   0.002   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.01514 ( 6146)
  covalent geometry    : angle       1.09713 ( 8353)
  SS BOND              : bond        0.00375 (    2)
  SS BOND              : angle       0.99741 (    4)
  hydrogen bonds       : bond        0.13837 (  270)
  hydrogen bonds       : angle       5.39506 (  762)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 ASN cc_start: 0.6136 (m-40) cc_final: 0.5926 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0884
  time to fit residues: 11.8950
Evaluate side-chains
  101 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 174 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.171184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.148366 restraints weight = 7888.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 1.52
r_work: 0.3416 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.0655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6148  Z= 0.136
  Angle     :  0.546  10.739   8357  Z= 0.294
  Chirality :  0.041   0.169    913
  Planarity :  0.004   0.036   1031
  Dihedral  : 10.308  84.890    953
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 21.43 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.32), residues: 731
  helix:  0.77 (0.31), residues: 289
  sheet: -0.21 (0.44), residues: 161
  loop : -1.75 (0.35), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  99 
 TYR   0.015   0.001   TYR A 414 
 PHE   0.011   0.001   PHE C  47 
 TRP   0.017   0.001   TRP A 346 
 HIS   0.002   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6146)
  covalent geometry    : angle       0.54628 ( 8353)
  SS BOND              : bond        0.00285 (    2)
  SS BOND              : angle       0.69214 (    4)
  hydrogen bonds       : bond        0.04081 (  270)
  hydrogen bonds       : angle       4.37137 (  762)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 ASN cc_start: 0.8772 (t0) cc_final: 0.8355 (p0)
REVERT: A  495 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8861 (p)
REVERT: C   81 GLU cc_start: 0.6933 (mp0) cc_final: 0.6684 (pm20)
  outliers start: 13
  outliers final: 7
  residues processed: 113
  average time/residue: 0.0864
  time to fit residues: 13.1603
Evaluate side-chains
  107 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  544 GLU
Chi-restraints excluded: chain A residue  546 ILE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain C residue   92 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 72 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 17 optimal weight:    0.2980
   chunk 3 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A  80 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.171997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.149258 restraints weight = 7791.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 1.46
r_work: 0.3417 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.0875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6148  Z= 0.118
  Angle     :  0.500   7.404   8357  Z= 0.269
  Chirality :  0.040   0.144    913
  Planarity :  0.004   0.037   1031
  Dihedral  :  9.042  76.810    953
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 20.48 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.32), residues: 731
  helix:  0.89 (0.32), residues: 283
  sheet: -0.09 (0.44), residues: 159
  loop : -1.57 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  99 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.011   0.001   PHE C  47 
 TRP   0.020   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6146)
  covalent geometry    : angle       0.49992 ( 8353)
  SS BOND              : bond        0.00275 (    2)
  SS BOND              : angle       0.70742 (    4)
  hydrogen bonds       : bond        0.03765 (  270)
  hydrogen bonds       : angle       4.22483 (  762)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 ASN cc_start: 0.8695 (t0) cc_final: 0.8030 (p0)
REVERT: A  370 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6633 (tm-30)
REVERT: A  495 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8804 (p)
REVERT: B  104 ASP cc_start: 0.7768 (p0) cc_final: 0.7504 (p0)
REVERT: C   81 GLU cc_start: 0.6853 (mp0) cc_final: 0.6493 (pm20)
  outliers start: 18
  outliers final: 8
  residues processed: 117
  average time/residue: 0.0789
  time to fit residues: 12.4083
Evaluate side-chains
  108 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  544 GLU
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain C residue   12 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3848 r_free = 0.3848 target = 0.170978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.147093 restraints weight = 7803.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 1.66
r_work: 0.3382 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.0983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6148  Z= 0.127
  Angle     :  0.495   6.174   8357  Z= 0.269
  Chirality :  0.040   0.142    913
  Planarity :  0.004   0.039   1031
  Dihedral  :  8.054  75.225    953
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 20.48 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.32), residues: 731
  helix:  0.91 (0.32), residues: 283
  sheet: -0.12 (0.44), residues: 159
  loop : -1.51 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  99 
 TYR   0.015   0.001   TYR A 414 
 PHE   0.042   0.001   PHE C  47 
 TRP   0.021   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6146)
  covalent geometry    : angle       0.49458 ( 8353)
  SS BOND              : bond        0.00357 (    2)
  SS BOND              : angle       0.75314 (    4)
  hydrogen bonds       : bond        0.03723 (  270)
  hydrogen bonds       : angle       4.18576 (  762)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 ASN cc_start: 0.8708 (t0) cc_final: 0.8014 (p0)
REVERT: A  370 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6735 (tm-30)
REVERT: A  495 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8843 (p)
REVERT: B  104 ASP cc_start: 0.7675 (p0) cc_final: 0.7408 (p0)
REVERT: C   81 GLU cc_start: 0.6819 (mp0) cc_final: 0.6521 (pm20)
  outliers start: 23
  outliers final: 14
  residues processed: 121
  average time/residue: 0.0813
  time to fit residues: 13.3639
Evaluate side-chains
  113 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  544 GLU
Chi-restraints excluded: chain A residue  546 ILE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue   79 CYS
Chi-restraints excluded: chain C residue   92 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3858 r_free = 0.3858 target = 0.171962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.148960 restraints weight = 7919.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 1.51
r_work: 0.3418 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6148  Z= 0.119
  Angle     :  0.487   5.846   8357  Z= 0.265
  Chirality :  0.040   0.146    913
  Planarity :  0.004   0.039   1031
  Dihedral  :  7.330  76.847    953
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 21.43 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.32), residues: 731
  helix:  0.98 (0.32), residues: 283
  sheet:  0.04 (0.45), residues: 148
  loop : -1.47 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  99 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.029   0.001   PHE C  47 
 TRP   0.023   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6146)
  covalent geometry    : angle       0.48680 ( 8353)
  SS BOND              : bond        0.00322 (    2)
  SS BOND              : angle       0.56714 (    4)
  hydrogen bonds       : bond        0.03678 (  270)
  hydrogen bonds       : angle       4.11078 (  762)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 ASN cc_start: 0.8657 (t0) cc_final: 0.7915 (p0)
REVERT: A  237 ASP cc_start: 0.7933 (p0) cc_final: 0.7699 (p0)
REVERT: A  370 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6697 (tm-30)
REVERT: A  495 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8853 (p)
REVERT: B  104 ASP cc_start: 0.7574 (p0) cc_final: 0.7295 (p0)
  outliers start: 22
  outliers final: 16
  residues processed: 119
  average time/residue: 0.0797
  time to fit residues: 12.7959
Evaluate side-chains
  114 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  544 GLU
Chi-restraints excluded: chain A residue  546 ILE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue   79 CYS
Chi-restraints excluded: chain C residue   92 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 49 optimal weight:    7.9990
   chunk 50 optimal weight:    0.1980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
A 141 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.169215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.145365 restraints weight = 7807.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.61
r_work: 0.3362 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.1142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6148  Z= 0.164
  Angle     :  0.531   5.754   8357  Z= 0.287
  Chirality :  0.042   0.176    913
  Planarity :  0.004   0.039   1031
  Dihedral  :  7.192  80.611    953
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 21.75 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.32), residues: 731
  helix:  0.69 (0.31), residues: 289
  sheet:  0.02 (0.45), residues: 148
  loop : -1.54 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  99 
 TYR   0.015   0.001   TYR A 528 
 PHE   0.026   0.001   PHE C  47 
 TRP   0.024   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 6146)
  covalent geometry    : angle       0.53052 ( 8353)
  SS BOND              : bond        0.00351 (    2)
  SS BOND              : angle       0.66891 (    4)
  hydrogen bonds       : bond        0.04059 (  270)
  hydrogen bonds       : angle       4.17969 (  762)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A  370 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6806 (tm-30)
REVERT: A  495 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8875 (p)
REVERT: B  104 ASP cc_start: 0.7589 (p0) cc_final: 0.7272 (p0)
REVERT: C   89 ASP cc_start: 0.7915 (t0) cc_final: 0.7480 (t0)
  outliers start: 24
  outliers final: 17
  residues processed: 118
  average time/residue: 0.0654
  time to fit residues: 10.2713
Evaluate side-chains
  115 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 SER
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  544 GLU
Chi-restraints excluded: chain A residue  546 ILE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue   92 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 49 optimal weight:   10.0000
   chunk 34 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 50 optimal weight:   30.0000
   chunk 31 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3856 r_free = 0.3856 target = 0.171692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.148594 restraints weight = 7790.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.51
r_work: 0.3408 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6148  Z= 0.115
  Angle     :  0.489   5.568   8357  Z= 0.266
  Chirality :  0.040   0.149    913
  Planarity :  0.004   0.040   1031
  Dihedral  :  6.893  79.134    953
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 21.90 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.32), residues: 731
  helix:  0.96 (0.32), residues: 283
  sheet: -0.01 (0.45), residues: 148
  loop : -1.45 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  99 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.038   0.001   PHE C  47 
 TRP   0.024   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6146)
  covalent geometry    : angle       0.48915 ( 8353)
  SS BOND              : bond        0.00302 (    2)
  SS BOND              : angle       0.64667 (    4)
  hydrogen bonds       : bond        0.03685 (  270)
  hydrogen bonds       : angle       4.07521 (  762)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 ASN cc_start: 0.8739 (t0) cc_final: 0.8345 (p0)
REVERT: A  237 ASP cc_start: 0.7892 (p0) cc_final: 0.7655 (p0)
REVERT: A  370 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6768 (tm-30)
REVERT: A  495 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8881 (p)
REVERT: B  104 ASP cc_start: 0.7500 (p0) cc_final: 0.7218 (p0)
REVERT: C   89 ASP cc_start: 0.7958 (t0) cc_final: 0.7626 (t0)
  outliers start: 23
  outliers final: 17
  residues processed: 118
  average time/residue: 0.0681
  time to fit residues: 10.9287
Evaluate side-chains
  115 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  394 ILE
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  544 GLU
Chi-restraints excluded: chain A residue  546 ILE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue   79 CYS
Chi-restraints excluded: chain C residue   92 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 54 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0050
   chunk 43 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0570
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.4512

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

Flipped N/Q/H residues before XYZ refinement:
B  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.167957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.143998 restraints weight = 7884.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 1.54
r_work: 0.3448 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3356 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6148  Z= 0.096
  Angle     :  0.463   5.478   8357  Z= 0.252
  Chirality :  0.039   0.147    913
  Planarity :  0.003   0.040   1031
  Dihedral  :  6.494  77.036    953
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 22.38 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.32), residues: 731
  helix:  0.93 (0.32), residues: 292
  sheet:  0.02 (0.44), residues: 148
  loop : -1.44 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  99 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.037   0.001   PHE C  47 
 TRP   0.027   0.001   TRP A 346 
 HIS   0.002   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 6146)
  covalent geometry    : angle       0.46271 ( 8353)
  SS BOND              : bond        0.00266 (    2)
  SS BOND              : angle       0.60343 (    4)
  hydrogen bonds       : bond        0.03370 (  270)
  hydrogen bonds       : angle       3.94473 (  762)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 ASN cc_start: 0.8657 (t0) cc_final: 0.8327 (p0)
REVERT: A  237 ASP cc_start: 0.7800 (p0) cc_final: 0.7550 (p0)
REVERT: A  370 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6636 (tm-30)
REVERT: C   89 ASP cc_start: 0.7958 (t0) cc_final: 0.7603 (t0)
REVERT: C  106 TYR cc_start: 0.8449 (t80) cc_final: 0.7976 (t80)
  outliers start: 20
  outliers final: 15
  residues processed: 116
  average time/residue: 0.0689
  time to fit residues: 10.8200
Evaluate side-chains
  111 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  544 GLU
Chi-restraints excluded: chain A residue  546 ILE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue   79 CYS
Chi-restraints excluded: chain C residue   92 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0570
   chunk 32 optimal weight:    0.7980
   chunk 61 optimal weight:    6.9990
   chunk 56 optimal weight:    0.3980
   chunk 26 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 68 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.167612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.142385 restraints weight = 7924.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 1.58
r_work: 0.3421 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6148  Z= 0.108
  Angle     :  0.482   5.445   8357  Z= 0.264
  Chirality :  0.040   0.226    913
  Planarity :  0.003   0.039   1031
  Dihedral  :  6.435  76.616    953
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 21.90 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.32), residues: 731
  helix:  0.94 (0.32), residues: 292
  sheet:  0.04 (0.44), residues: 148
  loop : -1.42 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  99 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.038   0.001   PHE C  47 
 TRP   0.029   0.001   TRP A 346 
 HIS   0.002   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6146)
  covalent geometry    : angle       0.48166 ( 8353)
  SS BOND              : bond        0.00269 (    2)
  SS BOND              : angle       0.59997 (    4)
  hydrogen bonds       : bond        0.03430 (  270)
  hydrogen bonds       : angle       3.95579 (  762)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 ASN cc_start: 0.8704 (t0) cc_final: 0.8296 (p0)
REVERT: A  237 ASP cc_start: 0.7854 (p0) cc_final: 0.7613 (p0)
REVERT: A  370 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6662 (tm-30)
REVERT: A  495 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8864 (p)
REVERT: C   89 ASP cc_start: 0.7944 (t0) cc_final: 0.7587 (t0)
REVERT: C  106 TYR cc_start: 0.8486 (t80) cc_final: 0.8004 (t80)
  outliers start: 21
  outliers final: 17
  residues processed: 112
  average time/residue: 0.0639
  time to fit residues: 9.8751
Evaluate side-chains
  112 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 SER
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  394 ILE
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  544 GLU
Chi-restraints excluded: chain A residue  546 ILE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue   79 CYS
Chi-restraints excluded: chain C residue   92 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 38 optimal weight:    0.3980
   chunk 4 optimal weight:    0.2980
   chunk 46 optimal weight:    0.7980
   chunk 67 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0270
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.168987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.144984 restraints weight = 7886.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 1.48
r_work: 0.3515 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3425 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6148  Z= 0.098
  Angle     :  0.466   5.426   8357  Z= 0.255
  Chirality :  0.040   0.153    913
  Planarity :  0.004   0.040   1031
  Dihedral  :  6.304  75.422    953
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 22.86 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.32), residues: 731
  helix:  1.01 (0.32), residues: 292
  sheet:  0.04 (0.44), residues: 148
  loop : -1.41 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  99 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.040   0.001   PHE C  47 
 TRP   0.030   0.001   TRP A 346 
 HIS   0.002   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 6146)
  covalent geometry    : angle       0.46544 ( 8353)
  SS BOND              : bond        0.00278 (    2)
  SS BOND              : angle       0.67311 (    4)
  hydrogen bonds       : bond        0.03298 (  270)
  hydrogen bonds       : angle       3.92326 (  762)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 ASN cc_start: 0.8593 (t0) cc_final: 0.8288 (p0)
REVERT: A  237 ASP cc_start: 0.7740 (p0) cc_final: 0.7479 (p0)
REVERT: A  370 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6662 (tm-30)
REVERT: A  495 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8856 (p)
REVERT: C   89 ASP cc_start: 0.7897 (t0) cc_final: 0.7625 (t0)
REVERT: C  106 TYR cc_start: 0.8429 (t80) cc_final: 0.7977 (t80)
  outliers start: 19
  outliers final: 16
  residues processed: 110
  average time/residue: 0.0589
  time to fit residues: 8.9695
Evaluate side-chains
  110 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  394 ILE
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  544 GLU
Chi-restraints excluded: chain A residue  546 ILE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   69 PHE
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue   79 CYS
Chi-restraints excluded: chain C residue   92 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 52 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.169483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.145578 restraints weight = 7896.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 1.59
r_work: 0.3363 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6148  Z= 0.177
  Angle     :  0.543   5.327   8357  Z= 0.296
  Chirality :  0.042   0.159    913
  Planarity :  0.004   0.039   1031
  Dihedral  :  6.721  78.439    953
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 22.22 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.32), residues: 731
  helix:  0.70 (0.31), residues: 289
  sheet: -0.07 (0.43), residues: 151
  loop : -1.44 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  99 
 TYR   0.016   0.002   TYR C 104 
 PHE   0.030   0.002   PHE C  47 
 TRP   0.031   0.002   TRP A 346 
 HIS   0.004   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 6146)
  covalent geometry    : angle       0.54256 ( 8353)
  SS BOND              : bond        0.00351 (    2)
  SS BOND              : angle       0.70736 (    4)
  hydrogen bonds       : bond        0.04122 (  270)
  hydrogen bonds       : angle       4.17529 (  762)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1525.17 seconds
wall clock time: 26 minutes 52.66 seconds (1612.66 seconds total)