Starting phenix.real_space_refine
on Tue Mar  3 18:15:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6sni_10258/03_2026/6sni_10258.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6sni_10258/03_2026/6sni_10258.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6sni_10258/03_2026/6sni_10258.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6sni_10258/03_2026/6sni_10258.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6sni_10258/03_2026/6sni_10258.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6sni_10258/03_2026/6sni_10258.map"
  }
  resolution = 3.0
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      31      5.16       5
     C    4967      2.51       5
     N    1156      2.21       5
     O    1355      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7510
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "X"
      Number of atoms: 3924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 479, 3924
          Classifications: {'peptide': 479}
          Link IDs: {'PTRANS': 25, 'TRANS': 453}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1687
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 225, 1684
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213}
      Conformer: "B"
        Number of residues, atoms: 225, 1684
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213}
          bond proxies already assigned to first conformer: 1725
    Chain: "L"
      Number of atoms: 1659
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 214, 1641
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202}
      Conformer: "B"
        Number of residues, atoms: 214, 1641
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202}
          bond proxies already assigned to first conformer: 1654
    Chain: "X"
      Number of atoms: 163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 163
          Unusual residues: {'PTY': 5, 'Y01': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 122
          Unresolved non-hydrogen angles: 138
          Unresolved non-hydrogen dihedrals: 106
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PTY:plan-2': 3}
          Unresolved non-hydrogen planarities: 8
    Chain: "H"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 70
          Unusual residues: {'Y01': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "X"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "H"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 2.62, per 1000 atoms: 0.35
  Number of scatterers: 7510
  At special positions: 0
  Unit cell: (115.92, 86.52, 113.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      31     16.00
     P       1     15.00
     O    1355      8.00
     N    1156      7.00
     C    4967      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS X 314 " - pdb=" SG  CYS X 515 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 149 " - pdb=" SG  CYS H 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 494.1 milliseconds
  

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1734

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 11 sheets defined
      42.7% alpha, 19.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'X' and resid 41 through 53
      removed outlier: 3.886A  pdb=" N   VAL X  47 " --> pdb=" O   PHE X  43 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 54 through 56
      No H-bonds generated for 'chain 'X' and resid 54 through 56'
    Processing helix  chain 'X' and resid 68 through 81
      removed outlier: 3.749A  pdb=" N   ALA X  72 " --> pdb=" O   GLY X  68 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN X  73 " --> pdb=" O   ASP X  69 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   GLN X  81 " --> pdb=" O   MET X  77 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 101 through 119
      removed outlier: 3.674A  pdb=" N   ALA X 105 " --> pdb=" O   PRO X 101 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   PHE X 118 " --> pdb=" O   ILE X 114 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 140 through 154
      removed outlier: 3.541A  pdb=" N   ILE X 147 " --> pdb=" O   ARG X 143 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 154 through 170
    Processing helix  chain 'X' and resid 172 through 185
      removed outlier: 3.593A  pdb=" N   ALA X 179 " --> pdb=" O   GLY X 175 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ILE X 183 " --> pdb=" O   ALA X 179 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 186 through 194
    Processing helix  chain 'X' and resid 199 through 217
      removed outlier: 4.425A  pdb=" N   MET X 203 " --> pdb=" O   TYR X 199 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   THR X 207 " --> pdb=" O   MET X 203 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 218 through 231
      removed outlier: 3.921A  pdb=" N   VAL X 224 " --> pdb=" O   ALA X 220 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 232 through 237
      removed outlier: 6.959A  pdb=" N   MET X 235 " --> pdb=" O   PHE X 232 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 239 through 253
      removed outlier: 4.127A  pdb=" N   ALA X 245 " --> pdb=" O   PRO X 241 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 258 through 282
      removed outlier: 3.904A  pdb=" N   LEU X 262 " --> pdb=" O   ASN X 258 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU X 270 " --> pdb=" O   ALA X 266 " (cutoff:3.500A)
      Proline residue:  X 279  - end of helix
    Processing helix  chain 'X' and resid 286 through 298
      removed outlier: 3.596A  pdb=" N   ILE X 290 " --> pdb=" O   GLY X 286 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 312 through 317
      removed outlier: 3.729A  pdb=" N   THR X 316 " --> pdb=" O   PHE X 312 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 321 through 325
    Processing helix  chain 'X' and resid 327 through 352
      removed outlier: 3.647A  pdb=" N   LEU X 336 " --> pdb=" O   GLN X 332 " (cutoff:3.500A)
      Proline residue:  X 345  - end of helix
    Processing helix  chain 'X' and resid 358 through 374
      removed outlier: 3.666A  pdb=" N   SER X 369 " --> pdb=" O   ALA X 365 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 382 through 392
      Proline residue:  X 388  - end of helix
    Processing helix  chain 'X' and resid 393 through 395
      No H-bonds generated for 'chain 'X' and resid 393 through 395'
    Processing helix  chain 'X' and resid 398 through 414
    Processing helix  chain 'X' and resid 415 through 421
      removed outlier: 3.846A  pdb=" N   LYS X 421 " --> pdb=" O   PRO X 417 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 424 through 440
      removed outlier: 3.508A  pdb=" N   ALA X 429 " --> pdb=" O   HIS X 425 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ASN X 436 " --> pdb=" O   PHE X 432 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLY X 440 " --> pdb=" O   ASN X 436 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 476 through 491
      removed outlier: 3.845A  pdb=" N   LYS X 480 " --> pdb=" O   ASN X 476 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   SER X 481 " --> pdb=" O   VAL X 477 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   PHE X 482 " --> pdb=" O   VAL X 478 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 492 through 497
      removed outlier: 3.623A  pdb=" N   LEU X 496 " --> pdb=" O   PHE X 492 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 509 through 536
      removed outlier: 3.554A  pdb=" N   GLY X 518 " --> pdb=" O   ASN X 514 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   PHE X 519 " --> pdb=" O   CYS X 515 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ILE X 520 " --> pdb=" O   ALA X 516 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   CYS X 521 " --> pdb=" O   VAL X 517 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU X 527 " --> pdb=" O   SER X 523 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   PHE X 534 " --> pdb=" O   TYR X 530 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.674A  pdb=" N   SER H  31 " --> pdb=" O   ASN H  28 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   SER H  32 " --> pdb=" O   VAL H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing helix  chain 'H' and resid 61 through 64
    Processing helix  chain 'H' and resid 101 through 105
      removed outlier: 3.624A  pdb=" N   SER H 104 " --> pdb=" O   SER H 101 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TYR H 105 " --> pdb=" O   TRP H 102 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 101 through 105'
    Processing helix  chain 'H' and resid 194 through 198
      removed outlier: 4.024A  pdb=" N   LEU H 198 " --> pdb=" O   SER H 195 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 4.299A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 123 through 128
      removed outlier: 3.584A  pdb=" N   LYS L 128 " --> pdb=" O   ASP L 124 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 185 through 191
    Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.985A  pdb=" N   ILE H  34 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   SER H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   SER H  58 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.912A  pdb=" N   TYR H 111 " --> pdb=" O   ARG H  97 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 129 through 133
      removed outlier: 6.186A  pdb=" N   TYR H 185 " --> pdb=" O   ASP H 153 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 160 through 162
      removed outlier: 4.386A  pdb=" N   TYR H 203 " --> pdb=" O   VAL H 220 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.800A  pdb=" N   LEU L  11 " --> pdb=" O   LYS L 105 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   GLU L 107 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54
      removed outlier: 6.514A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 89 through 91
    Processing sheet with id=AB1, first strand: chain 'L' and resid 116 through 120
      removed outlier: 5.898A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 147 through 152

    341 hydrogen bonds defined for protein.
    947 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: 1.21

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.16 -     1.30: 1122
        1.30 -     1.44: 2314
        1.44 -     1.58: 4221
        1.58 -     1.72: 33
        1.72 -     1.86: 47
  Bond restraints: 7737
  Sorted by residual:
  bond pdb=" CAK Y01 H2202 "
       pdb=" CBD Y01 H2202 "
    ideal  model  delta    sigma   weight residual
    1.525  1.160  0.365 2.00e-02 2.50e+03 3.33e+02
  bond pdb=" CAU Y01 H2202 "
       pdb=" CBI Y01 H2202 "
    ideal  model  delta    sigma   weight residual
    1.530  1.166  0.364 2.00e-02 2.50e+03 3.31e+02
  bond pdb=" CAK Y01 X1606 "
       pdb=" CBD Y01 X1606 "
    ideal  model  delta    sigma   weight residual
    1.525  1.162  0.363 2.00e-02 2.50e+03 3.30e+02
  bond pdb=" CAU Y01 X1606 "
       pdb=" CBI Y01 X1606 "
    ideal  model  delta    sigma   weight residual
    1.530  1.172  0.358 2.00e-02 2.50e+03 3.20e+02
  bond pdb=" CAK Y01 H2201 "
       pdb=" CBD Y01 H2201 "
    ideal  model  delta    sigma   weight residual
    1.525  1.168  0.357 2.00e-02 2.50e+03 3.18e+02
  ... (remaining 7732 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.27: 10323
        3.27 -     6.55: 175
        6.55 -     9.82: 26
        9.82 -    13.09: 5
       13.09 -    16.37: 5
  Bond angle restraints: 10534
  Sorted by residual:
  angle pdb=" CA  PRO H 156 "
        pdb=" N   PRO H 156 "
        pdb=" CD  PRO H 156 "
      ideal   model   delta    sigma   weight residual
     111.50   98.22   13.28 1.40e+00 5.10e-01 9.00e+01
  angle pdb=" O   SER L  10 "
        pdb=" C   SER L  10 "
        pdb=" CA ASER L  10 "
      ideal   model   delta    sigma   weight residual
     119.98  130.90  -10.92 1.22e+00 6.72e-01 8.00e+01
  angle pdb=" O   SER L  10 "
        pdb=" C   SER L  10 "
        pdb=" CA BSER L  10 "
      ideal   model   delta    sigma   weight residual
     119.98  130.90  -10.92 1.22e+00 6.72e-01 8.00e+01
  angle pdb=" N   SER L  10 "
        pdb=" CA ASER L  10 "
        pdb=" C   SER L  10 "
      ideal   model   delta    sigma   weight residual
     107.93  121.33  -13.40 1.65e+00 3.67e-01 6.59e+01
  angle pdb=" N   SER L  10 "
        pdb=" CA BSER L  10 "
        pdb=" C   SER L  10 "
      ideal   model   delta    sigma   weight residual
     107.93  121.33  -13.40 1.65e+00 3.67e-01 6.59e+01
  ... (remaining 10529 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 4250
       17.99 -    35.98: 313
       35.98 -    53.97: 98
       53.97 -    71.96: 22
       71.96 -    89.94: 2
  Dihedral angle restraints: 4685
    sinusoidal: 1966
      harmonic: 2719
  Sorted by residual:
  dihedral pdb=" CA  MET X 541 "
           pdb=" C   MET X 541 "
           pdb=" N   LYS X 542 "
           pdb=" CA  LYS X 542 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.98  -26.02     0      5.00e+00 4.00e-02 2.71e+01
  dihedral pdb=" CB  CYS X 314 "
           pdb=" SG  CYS X 314 "
           pdb=" SG  CYS X 515 "
           pdb=" CB  CYS X 515 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.33   40.33     1      1.00e+01 1.00e-02 2.28e+01
  dihedral pdb=" CA  TRP X  90 "
           pdb=" C   TRP X  90 "
           pdb=" N   TYR X  91 "
           pdb=" CA  TYR X  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.27  -19.73     0      5.00e+00 4.00e-02 1.56e+01
  ... (remaining 4682 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.315: 1144
       0.315 -    0.631: 12
       0.631 -    0.946: 3
       0.946 -    1.262: 0
       1.262 -    1.577: 3
  Chirality restraints: 1162
  Sorted by residual:
  chirality pdb=" CBD Y01 H2201 "
            pdb=" CAK Y01 H2201 "
            pdb=" CBF Y01 H2201 "
            pdb=" CBG Y01 H2201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.70    1.12    1.58 2.00e-01 2.50e+01 6.22e+01
  chirality pdb=" CBD Y01 X1606 "
            pdb=" CAK Y01 X1606 "
            pdb=" CBF Y01 X1606 "
            pdb=" CBG Y01 X1606 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.70    1.12    1.57 2.00e-01 2.50e+01 6.19e+01
  chirality pdb=" CBD Y01 H2202 "
            pdb=" CAK Y01 H2202 "
            pdb=" CBF Y01 H2202 "
            pdb=" CBG Y01 H2202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.70    1.13    1.56 2.00e-01 2.50e+01 6.11e+01
  ... (remaining 1159 not shown)

  Planarity restraints: 1275
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA X 278 "    0.026 5.00e-02 4.00e+02   3.86e-02 2.39e+00
        pdb=" N   PRO X 279 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO X 279 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO X 279 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL H 193 "   -0.024 5.00e-02 4.00e+02   3.70e-02 2.20e+00
        pdb=" N   PRO H 194 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO H 194 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO H 194 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE X 384 "    0.024 5.00e-02 4.00e+02   3.56e-02 2.03e+00
        pdb=" N   PRO X 385 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO X 385 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO X 385 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1272 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.62: 102
        2.62 -     3.19: 6680
        3.19 -     3.76: 10613
        3.76 -     4.33: 16211
        4.33 -     4.90: 27373
  Nonbonded interactions: 60979
  Sorted by model distance:
  nonbonded pdb=" O   LYS X 380 "
            pdb=" OG1 THR X 381 "
     model   vdw
     2.044 3.040
  nonbonded pdb=" CE1 TYR H 154 "
            pdb=" OE2 GLU H 157 "
     model   vdw
     2.057 3.340
  nonbonded pdb=" O   THR H 140 "
            pdb=" OG  SER H 195 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   GLN L 126 "
            pdb=" OG  SER L 129 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" N   GLU H   6 "
            pdb=" OE1 GLU H   6 "
     model   vdw
     2.206 3.120
  ... (remaining 60974 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.30 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:             1.770
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.200
  Find NCS groups from input model:        0.030
  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:             0.000
  Load rotamer database and sin/cos tables:6.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
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      :  0.020   0.365   7742  Z= 1.016
  Angle     :  1.039  16.368  10544  Z= 0.550
  Chirality :  0.106   1.577   1162
  Planarity :  0.004   0.039   1275
  Dihedral  : 14.298  89.944   2936
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 24.53
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  9.23 %
    Favored  : 90.55 %
  Rotamer:
    Outliers :  8.07 %
    Allowed  :  8.20 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -4.21 (0.23), residues: 917
  helix: -2.35 (0.22), residues: 343
  sheet: -1.68 (0.35), residues: 193
  loop : -3.79 (0.25), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L 213 
 TYR   0.016   0.002   TYR L 175 
 PHE   0.019   0.001   PHE X 197 
 TRP   0.012   0.001   TRP X  90 
 HIS   0.008   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.02007 ( 7737)
  covalent geometry    : angle       1.03816 (10534)
  SS BOND              : bond        0.00777 (    5)
  SS BOND              : angle       1.81194 (   10)
  hydrogen bonds       : bond        0.15630 (  336)
  hydrogen bonds       : angle       7.22983 (  947)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 111
  time to evaluate  : 0.197 
Fit side-chains
REVERT: X   98 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8136 (tt)
REVERT: X  142 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7852 (mmt)
REVERT: X  167 ARG cc_start: 0.7684 (tmm160) cc_final: 0.6745 (mtm110)
REVERT: X  473 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8018 (mt)
REVERT: H   46 GLU cc_start: 0.7778 (tt0) cc_final: 0.7541 (tt0)
REVERT: H  157 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5519 (mp0)
  outliers start: 65
  outliers final: 33
  residues processed: 167
  average time/residue: 0.3900
  time to fit residues: 70.3750
Evaluate side-chains
  118 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 81
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   41 ILE
Chi-restraints excluded: chain X residue   78 GLU
Chi-restraints excluded: chain X residue   79 ILE
Chi-restraints excluded: chain X residue   98 LEU
Chi-restraints excluded: chain X residue  142 MET
Chi-restraints excluded: chain X residue  150 ASP
Chi-restraints excluded: chain X residue  264 VAL
Chi-restraints excluded: chain X residue  273 PHE
Chi-restraints excluded: chain X residue  289 ASN
Chi-restraints excluded: chain X residue  343 PHE
Chi-restraints excluded: chain X residue  367 SER
Chi-restraints excluded: chain X residue  387 LEU
Chi-restraints excluded: chain X residue  397 ASP
Chi-restraints excluded: chain X residue  430 VAL
Chi-restraints excluded: chain X residue  473 LEU
Chi-restraints excluded: chain X residue  477 VAL
Chi-restraints excluded: chain X residue  500 VAL
Chi-restraints excluded: chain X residue  515 CYS
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  157 GLU
Chi-restraints excluded: chain H residue  162 SER
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  203 TYR
Chi-restraints excluded: chain H residue  205 CYS
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   88 CYS
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue   94 VAL
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain L residue  199 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.2980
   chunk 61 optimal weight:   40.0000
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
X 171 GLN
X 317 ASN
H  13 GLN
H  76 ASN
** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 191 HIS
L 201 GLN
L 212 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.171345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.129761 restraints weight = 27648.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 5.53
r_work: 0.3235 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3235
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7742  Z= 0.137
  Angle     :  0.648   9.748  10544  Z= 0.326
  Chirality :  0.044   0.155   1162
  Planarity :  0.006   0.082   1275
  Dihedral  : 11.780  59.352   1382
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 12.80 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -2.17 (0.27), residues: 917
  helix: -0.21 (0.28), residues: 343
  sheet: -0.78 (0.36), residues: 201
  loop : -3.02 (0.28), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  18 
 TYR   0.010   0.001   TYR X 141 
 PHE   0.025   0.001   PHE X 343 
 TRP   0.008   0.001   TRP H 112 
 HIS   0.004   0.001   HIS X  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7737)
  covalent geometry    : angle       0.64673 (10534)
  SS BOND              : bond        0.00559 (    5)
  SS BOND              : angle       1.59467 (   10)
  hydrogen bonds       : bond        0.03959 (  336)
  hydrogen bonds       : angle       5.38571 (  947)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 86
  time to evaluate  : 0.305 
Fit side-chains
REVERT: X   98 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.7963 (tt)
REVERT: X  167 ARG cc_start: 0.7678 (tmm160) cc_final: 0.6828 (ttp-110)
REVERT: X  473 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7994 (mt)
REVERT: X  530 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.8561 (m-80)
REVERT: H   46 GLU cc_start: 0.8690 (tt0) cc_final: 0.8456 (tt0)
REVERT: H  205 CYS cc_start: 0.2982 (OUTLIER) cc_final: 0.2623 (t)
REVERT: L   59 PRO cc_start: 0.8178 (Cg_exo) cc_final: 0.7863 (Cg_endo)
  outliers start: 40
  outliers final: 17
  residues processed: 121
  average time/residue: 0.4809
  time to fit residues: 62.1414
Evaluate side-chains
  101 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   41 ILE
Chi-restraints excluded: chain X residue   85 LEU
Chi-restraints excluded: chain X residue   98 LEU
Chi-restraints excluded: chain X residue  150 ASP
Chi-restraints excluded: chain X residue  264 VAL
Chi-restraints excluded: chain X residue  273 PHE
Chi-restraints excluded: chain X residue  289 ASN
Chi-restraints excluded: chain X residue  393 TYR
Chi-restraints excluded: chain X residue  473 LEU
Chi-restraints excluded: chain X residue  477 VAL
Chi-restraints excluded: chain X residue  500 VAL
Chi-restraints excluded: chain X residue  515 CYS
Chi-restraints excluded: chain X residue  517 VAL
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  193 VAL
Chi-restraints excluded: chain H residue  203 TYR
Chi-restraints excluded: chain H residue  205 CYS
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   94 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 60 optimal weight:    7.9990
   chunk 78 optimal weight:    0.7980
   chunk 75 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 67 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0670
   chunk 68 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 87 optimal weight:    0.1980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
H  76 ASN
** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.172984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.130436 restraints weight = 24121.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 4.87
r_work: 0.3268 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   7742  Z= 0.116
  Angle     :  0.581   9.368  10544  Z= 0.293
  Chirality :  0.042   0.151   1162
  Planarity :  0.005   0.076   1275
  Dihedral  : 10.278  59.626   1350
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 15.16 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -1.37 (0.28), residues: 917
  helix:  0.46 (0.29), residues: 342
  sheet: -0.26 (0.37), residues: 200
  loop : -2.64 (0.29), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  18 
 TYR   0.019   0.001   TYR H 154 
 PHE   0.023   0.001   PHE X 343 
 TRP   0.008   0.001   TRP X  90 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 7737)
  covalent geometry    : angle       0.58001 (10534)
  SS BOND              : bond        0.00582 (    5)
  SS BOND              : angle       1.29241 (   10)
  hydrogen bonds       : bond        0.03468 (  336)
  hydrogen bonds       : angle       4.95850 (  947)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 81
  time to evaluate  : 0.307 
Fit side-chains
REVERT: X   98 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.7909 (tt)
REVERT: X  117 PHE cc_start: 0.8137 (t80) cc_final: 0.7905 (t80)
REVERT: X  132 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7061 (mm-30)
REVERT: H   46 GLU cc_start: 0.8577 (tt0) cc_final: 0.8362 (tt0)
REVERT: H  205 CYS cc_start: 0.2951 (OUTLIER) cc_final: 0.2581 (t)
REVERT: L   59 PRO cc_start: 0.8159 (Cg_exo) cc_final: 0.7862 (Cg_endo)
  outliers start: 25
  outliers final: 16
  residues processed: 104
  average time/residue: 0.5120
  time to fit residues: 57.0009
Evaluate side-chains
  98 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   41 ILE
Chi-restraints excluded: chain X residue   85 LEU
Chi-restraints excluded: chain X residue   98 LEU
Chi-restraints excluded: chain X residue  132 GLU
Chi-restraints excluded: chain X residue  150 ASP
Chi-restraints excluded: chain X residue  264 VAL
Chi-restraints excluded: chain X residue  273 PHE
Chi-restraints excluded: chain X residue  289 ASN
Chi-restraints excluded: chain X residue  393 TYR
Chi-restraints excluded: chain X residue  500 VAL
Chi-restraints excluded: chain X residue  515 CYS
Chi-restraints excluded: chain X residue  524 ILE
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  193 VAL
Chi-restraints excluded: chain H residue  203 TYR
Chi-restraints excluded: chain H residue  205 CYS
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   67 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 26 optimal weight:    0.0270
   chunk 71 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 82 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  76 ASN
L 102 GLN
** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.173207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.130073 restraints weight = 22365.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 4.31
r_work: 0.3295 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3300
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3300 r_free = 0.3300    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3300 r_free = 0.3300    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3300
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   7742  Z= 0.118
  Angle     :  0.564   8.417  10544  Z= 0.286
  Chirality :  0.041   0.144   1162
  Planarity :  0.005   0.075   1275
  Dihedral  :  9.400  56.815   1345
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 16.27 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.89 (0.28), residues: 917
  helix:  0.77 (0.29), residues: 344
  sheet:  0.11 (0.38), residues: 200
  loop : -2.36 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  24 
 TYR   0.010   0.001   TYR H  94 
 PHE   0.023   0.001   PHE X 343 
 TRP   0.008   0.001   TRP X  90 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7737)
  covalent geometry    : angle       0.56286 (10534)
  SS BOND              : bond        0.00573 (    5)
  SS BOND              : angle       1.38262 (   10)
  hydrogen bonds       : bond        0.03381 (  336)
  hydrogen bonds       : angle       4.71494 (  947)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 77
  time to evaluate  : 0.277 
Fit side-chains
REVERT: X   98 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.7840 (tt)
REVERT: X  117 PHE cc_start: 0.8066 (t80) cc_final: 0.7799 (t80)
REVERT: X  132 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7010 (mm-30)
REVERT: X  167 ARG cc_start: 0.7772 (tmm160) cc_final: 0.6995 (ttp-110)
REVERT: H   46 GLU cc_start: 0.8513 (tt0) cc_final: 0.8251 (tt0)
REVERT: H  205 CYS cc_start: 0.2941 (OUTLIER) cc_final: 0.2558 (t)
REVERT: L   24 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.7337 (ttm110)
  outliers start: 27
  outliers final: 16
  residues processed: 101
  average time/residue: 0.4768
  time to fit residues: 51.7095
Evaluate side-chains
  91 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   41 ILE
Chi-restraints excluded: chain X residue   85 LEU
Chi-restraints excluded: chain X residue   98 LEU
Chi-restraints excluded: chain X residue  132 GLU
Chi-restraints excluded: chain X residue  150 ASP
Chi-restraints excluded: chain X residue  273 PHE
Chi-restraints excluded: chain X residue  289 ASN
Chi-restraints excluded: chain X residue  309 VAL
Chi-restraints excluded: chain X residue  393 TYR
Chi-restraints excluded: chain X residue  500 VAL
Chi-restraints excluded: chain X residue  515 CYS
Chi-restraints excluded: chain X residue  524 ILE
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  193 VAL
Chi-restraints excluded: chain H residue  203 TYR
Chi-restraints excluded: chain H residue  205 CYS
Chi-restraints excluded: chain L residue    2 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0060
   chunk 78 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 73 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0050
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0470
   overall best weight:    0.3708

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

Flipped N/Q/H residues before XYZ refinement:
X 291 HIS
** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  76 ASN
** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.177197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.134809 restraints weight = 27654.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 5.36
r_work: 0.3281 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   7742  Z= 0.098
  Angle     :  0.526   7.566  10544  Z= 0.266
  Chirality :  0.040   0.141   1162
  Planarity :  0.005   0.077   1275
  Dihedral  :  8.883  57.404   1344
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 17.64 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.53 (0.29), residues: 917
  helix:  1.11 (0.29), residues: 343
  sheet:  0.24 (0.38), residues: 200
  loop : -2.15 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  18 
 TYR   0.019   0.001   TYR H 154 
 PHE   0.021   0.001   PHE X 343 
 TRP   0.008   0.001   TRP X  90 
 HIS   0.004   0.001   HIS X 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 7737)
  covalent geometry    : angle       0.52506 (10534)
  SS BOND              : bond        0.00446 (    5)
  SS BOND              : angle       1.10684 (   10)
  hydrogen bonds       : bond        0.03016 (  336)
  hydrogen bonds       : angle       4.47234 (  947)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 83
  time to evaluate  : 0.308 
Fit side-chains
REVERT: X  117 PHE cc_start: 0.7896 (t80) cc_final: 0.7665 (t80)
REVERT: X  132 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7108 (mm-30)
REVERT: X  167 ARG cc_start: 0.7847 (tmm160) cc_final: 0.6899 (ttp-110)
REVERT: X  368 MET cc_start: 0.8645 (tpp) cc_final: 0.8408 (mmt)
REVERT: H   46 GLU cc_start: 0.8467 (tt0) cc_final: 0.8244 (tt0)
REVERT: H  114 GLN cc_start: 0.7492 (mm-40) cc_final: 0.7241 (mm110)
REVERT: L   29 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8522 (t)
  outliers start: 27
  outliers final: 17
  residues processed: 106
  average time/residue: 0.4957
  time to fit residues: 56.0656
Evaluate side-chains
  92 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   41 ILE
Chi-restraints excluded: chain X residue   85 LEU
Chi-restraints excluded: chain X residue  132 GLU
Chi-restraints excluded: chain X residue  150 ASP
Chi-restraints excluded: chain X residue  211 ILE
Chi-restraints excluded: chain X residue  289 ASN
Chi-restraints excluded: chain X residue  309 VAL
Chi-restraints excluded: chain X residue  393 TYR
Chi-restraints excluded: chain X residue  500 VAL
Chi-restraints excluded: chain X residue  515 CYS
Chi-restraints excluded: chain X residue  524 ILE
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue  110 ASP
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  193 VAL
Chi-restraints excluded: chain H residue  203 TYR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   67 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 61 optimal weight:   40.0000
   chunk 76 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0980
   chunk 56 optimal weight:    4.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
X 186 GLN
H  76 ASN
H  81 GLN
** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.173325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.130750 restraints weight = 29097.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 5.66
r_work: 0.3238 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3237
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3237
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   7742  Z= 0.121
  Angle     :  0.551   7.518  10544  Z= 0.279
  Chirality :  0.041   0.139   1162
  Planarity :  0.005   0.079   1275
  Dihedral  :  8.625  58.194   1339
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.01 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.37 (0.29), residues: 917
  helix:  1.17 (0.29), residues: 344
  sheet:  0.33 (0.38), residues: 200
  loop : -1.98 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L 110 
 TYR   0.011   0.001   TYR H  94 
 PHE   0.023   0.001   PHE X 343 
 TRP   0.010   0.001   TRP X 437 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7737)
  covalent geometry    : angle       0.54946 (10534)
  SS BOND              : bond        0.00577 (    5)
  SS BOND              : angle       1.38637 (   10)
  hydrogen bonds       : bond        0.03343 (  336)
  hydrogen bonds       : angle       4.50842 (  947)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 0.293 
Fit side-chains
REVERT: X  117 PHE cc_start: 0.7961 (t80) cc_final: 0.7713 (t80)
REVERT: X  132 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7079 (mm-30)
REVERT: X  167 ARG cc_start: 0.7857 (tmm160) cc_final: 0.6904 (ttp-110)
REVERT: H  114 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7254 (pt0)
REVERT: L   29 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8526 (t)
  outliers start: 23
  outliers final: 16
  residues processed: 93
  average time/residue: 0.4618
  time to fit residues: 46.1612
Evaluate side-chains
  87 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   85 LEU
Chi-restraints excluded: chain X residue  132 GLU
Chi-restraints excluded: chain X residue  150 ASP
Chi-restraints excluded: chain X residue  211 ILE
Chi-restraints excluded: chain X residue  289 ASN
Chi-restraints excluded: chain X residue  309 VAL
Chi-restraints excluded: chain X residue  368 MET
Chi-restraints excluded: chain X residue  500 VAL
Chi-restraints excluded: chain X residue  515 CYS
Chi-restraints excluded: chain X residue  524 ILE
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue  193 VAL
Chi-restraints excluded: chain H residue  203 TYR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue  119 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0030
   chunk 67 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 80 optimal weight:    9.9990
   chunk 12 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
X 289 ASN
H  76 ASN
** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.173564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.131248 restraints weight = 28523.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 5.58
r_work: 0.3252 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3250
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3250
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.3125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7742  Z= 0.117
  Angle     :  0.543   7.022  10544  Z= 0.275
  Chirality :  0.041   0.136   1162
  Planarity :  0.005   0.079   1275
  Dihedral  :  8.548  58.596   1337
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 18.76 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.25 (0.29), residues: 917
  helix:  1.24 (0.29), residues: 345
  sheet:  0.43 (0.38), residues: 200
  loop : -1.92 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L 110 
 TYR   0.018   0.001   TYR H 154 
 PHE   0.022   0.001   PHE X 343 
 TRP   0.011   0.001   TRP X 437 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7737)
  covalent geometry    : angle       0.54192 (10534)
  SS BOND              : bond        0.00564 (    5)
  SS BOND              : angle       1.34645 (   10)
  hydrogen bonds       : bond        0.03320 (  336)
  hydrogen bonds       : angle       4.50823 (  947)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 73
  time to evaluate  : 0.283 
Fit side-chains
REVERT: X  117 PHE cc_start: 0.7897 (t80) cc_final: 0.7671 (t80)
REVERT: X  132 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7040 (mm-30)
REVERT: X  167 ARG cc_start: 0.7851 (tmm160) cc_final: 0.6863 (ttp-110)
REVERT: H  114 GLN cc_start: 0.7421 (mm-40) cc_final: 0.7068 (pt0)
REVERT: L   29 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8509 (t)
  outliers start: 24
  outliers final: 15
  residues processed: 96
  average time/residue: 0.4922
  time to fit residues: 50.7086
Evaluate side-chains
  88 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   85 LEU
Chi-restraints excluded: chain X residue  132 GLU
Chi-restraints excluded: chain X residue  150 ASP
Chi-restraints excluded: chain X residue  289 ASN
Chi-restraints excluded: chain X residue  309 VAL
Chi-restraints excluded: chain X residue  500 VAL
Chi-restraints excluded: chain X residue  515 CYS
Chi-restraints excluded: chain X residue  524 ILE
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue  193 VAL
Chi-restraints excluded: chain H residue  203 TYR
Chi-restraints excluded: chain H residue  205 CYS
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue  119 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0980
   chunk 1 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 24 optimal weight:    0.1980
   chunk 58 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
H  76 ASN
** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.174533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.131907 restraints weight = 25195.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 5.05
r_work: 0.3288 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3285
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3285
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.073   7742  Z= 0.108
  Angle     :  0.539   9.114  10544  Z= 0.273
  Chirality :  0.041   0.151   1162
  Planarity :  0.005   0.078   1275
  Dihedral  :  8.384  58.018   1337
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.88 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.05 (0.29), residues: 917
  helix:  1.44 (0.29), residues: 343
  sheet:  0.61 (0.38), residues: 189
  loop : -1.81 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  18 
 TYR   0.018   0.001   TYR H 154 
 PHE   0.020   0.001   PHE X 343 
 TRP   0.012   0.001   TRP X 437 
 HIS   0.004   0.001   HIS X 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 7737)
  covalent geometry    : angle       0.53803 (10534)
  SS BOND              : bond        0.00518 (    5)
  SS BOND              : angle       1.25074 (   10)
  hydrogen bonds       : bond        0.03136 (  336)
  hydrogen bonds       : angle       4.41130 (  947)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: X   41 ILE cc_start: 0.7911 (pt) cc_final: 0.7496 (mm)
REVERT: X  117 PHE cc_start: 0.7864 (t80) cc_final: 0.7640 (t80)
REVERT: X  132 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7020 (mm-30)
REVERT: X  167 ARG cc_start: 0.7819 (tmm160) cc_final: 0.6889 (ttp-110)
REVERT: H  114 GLN cc_start: 0.7417 (mm-40) cc_final: 0.7174 (mm110)
REVERT: L   29 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8467 (t)
  outliers start: 23
  outliers final: 17
  residues processed: 93
  average time/residue: 0.4725
  time to fit residues: 47.1497
Evaluate side-chains
  89 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   85 LEU
Chi-restraints excluded: chain X residue  132 GLU
Chi-restraints excluded: chain X residue  150 ASP
Chi-restraints excluded: chain X residue  211 ILE
Chi-restraints excluded: chain X residue  289 ASN
Chi-restraints excluded: chain X residue  309 VAL
Chi-restraints excluded: chain X residue  500 VAL
Chi-restraints excluded: chain X residue  515 CYS
Chi-restraints excluded: chain X residue  524 ILE
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue  110 ASP
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  193 VAL
Chi-restraints excluded: chain H residue  203 TYR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue  119 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0060
   chunk 59 optimal weight:    9.9990
   chunk 85 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.9198

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

Flipped N/Q/H residues before XYZ refinement:
H  76 ASN
** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.172298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.130651 restraints weight = 28097.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 5.54
r_work: 0.3238 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.3218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   7742  Z= 0.130
  Angle     :  0.559   8.641  10544  Z= 0.283
  Chirality :  0.042   0.135   1162
  Planarity :  0.005   0.078   1275
  Dihedral  :  8.521  58.155   1337
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 18.39 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.06 (0.29), residues: 917
  helix:  1.31 (0.28), residues: 351
  sheet:  0.58 (0.38), residues: 200
  loop : -1.80 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  18 
 TYR   0.016   0.001   TYR H 154 
 PHE   0.022   0.001   PHE X 343 
 TRP   0.011   0.001   TRP X 437 
 HIS   0.004   0.001   HIS X 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7737)
  covalent geometry    : angle       0.55771 (10534)
  SS BOND              : bond        0.00656 (    5)
  SS BOND              : angle       1.49366 (   10)
  hydrogen bonds       : bond        0.03498 (  336)
  hydrogen bonds       : angle       4.50498 (  947)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.272 
Fit side-chains
REVERT: X   41 ILE cc_start: 0.7908 (pt) cc_final: 0.7502 (mm)
REVERT: X  117 PHE cc_start: 0.7930 (t80) cc_final: 0.7679 (t80)
REVERT: X  132 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7098 (mm-30)
REVERT: X  167 ARG cc_start: 0.7815 (tmm160) cc_final: 0.6889 (ttp-110)
REVERT: H  114 GLN cc_start: 0.7469 (mm-40) cc_final: 0.7213 (mm110)
REVERT: L   24 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7251 (ttm110)
REVERT: L   29 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8502 (t)
REVERT: L  109 LYS cc_start: 0.7294 (ttpt) cc_final: 0.6273 (tptt)
  outliers start: 22
  outliers final: 16
  residues processed: 97
  average time/residue: 0.4790
  time to fit residues: 49.7143
Evaluate side-chains
  91 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   85 LEU
Chi-restraints excluded: chain X residue  132 GLU
Chi-restraints excluded: chain X residue  150 ASP
Chi-restraints excluded: chain X residue  289 ASN
Chi-restraints excluded: chain X residue  309 VAL
Chi-restraints excluded: chain X residue  500 VAL
Chi-restraints excluded: chain X residue  515 CYS
Chi-restraints excluded: chain X residue  524 ILE
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue   76 ASN
Chi-restraints excluded: chain H residue  110 ASP
Chi-restraints excluded: chain H residue  193 VAL
Chi-restraints excluded: chain H residue  203 TYR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue  119 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 41 optimal weight:    0.3980
   chunk 6 optimal weight:    0.1980
   chunk 44 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
H  76 ASN
** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.173441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.131772 restraints weight = 26268.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 5.29
r_work: 0.3261 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   7742  Z= 0.112
  Angle     :  0.550   8.574  10544  Z= 0.278
  Chirality :  0.041   0.146   1162
  Planarity :  0.005   0.079   1275
  Dihedral  :  8.440  57.514   1337
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 18.88 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  0.00 (0.29), residues: 917
  helix:  1.41 (0.28), residues: 351
  sheet:  0.67 (0.39), residues: 189
  loop : -1.78 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  24 
 TYR   0.010   0.001   TYR H  94 
 PHE   0.021   0.001   PHE X 343 
 TRP   0.011   0.001   TRP X 437 
 HIS   0.005   0.001   HIS X 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7737)
  covalent geometry    : angle       0.54883 (10534)
  SS BOND              : bond        0.00576 (    5)
  SS BOND              : angle       1.30044 (   10)
  hydrogen bonds       : bond        0.03325 (  336)
  hydrogen bonds       : angle       4.46268 (  947)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.264 
Fit side-chains
REVERT: X   41 ILE cc_start: 0.7885 (pt) cc_final: 0.7505 (mm)
REVERT: X  117 PHE cc_start: 0.7889 (t80) cc_final: 0.7652 (t80)
REVERT: X  167 ARG cc_start: 0.7798 (tmm160) cc_final: 0.6873 (ttp-110)
REVERT: H  114 GLN cc_start: 0.7422 (mm-40) cc_final: 0.7151 (mm110)
REVERT: L   29 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8478 (t)
REVERT: L  109 LYS cc_start: 0.7239 (ttpt) cc_final: 0.6207 (tptt)
  outliers start: 19
  outliers final: 14
  residues processed: 89
  average time/residue: 0.4678
  time to fit residues: 44.4849
Evaluate side-chains
  87 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   85 LEU
Chi-restraints excluded: chain X residue  150 ASP
Chi-restraints excluded: chain X residue  289 ASN
Chi-restraints excluded: chain X residue  309 VAL
Chi-restraints excluded: chain X residue  500 VAL
Chi-restraints excluded: chain X residue  524 ILE
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue   76 ASN
Chi-restraints excluded: chain H residue  193 VAL
Chi-restraints excluded: chain H residue  203 TYR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue  119 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   chunk 15 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0010
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 68 optimal weight:    4.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
H  76 ASN
** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.174391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.131810 restraints weight = 28781.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 5.59
r_work: 0.3257 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3259
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   7742  Z= 0.109
  Angle     :  0.550   8.827  10544  Z= 0.279
  Chirality :  0.040   0.147   1162
  Planarity :  0.005   0.078   1275
  Dihedral  :  8.219  57.658   1336
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 19.25 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  0.16 (0.29), residues: 917
  helix:  1.61 (0.29), residues: 339
  sheet:  0.77 (0.39), residues: 189
  loop : -1.68 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  18 
 TYR   0.010   0.001   TYR H  94 
 PHE   0.023   0.001   PHE X 343 
 TRP   0.010   0.001   TRP X 437 
 HIS   0.005   0.001   HIS X 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7737)
  covalent geometry    : angle       0.54565 (10534)
  SS BOND              : bond        0.00765 (    5)
  SS BOND              : angle       2.21007 (   10)
  hydrogen bonds       : bond        0.03208 (  336)
  hydrogen bonds       : angle       4.41570 (  947)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2958.58 seconds
wall clock time: 51 minutes 3.03 seconds (3063.03 seconds total)