Starting phenix.real_space_refine
on Thu Mar 13 02:16:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d2s_27148/03_2025/8d2s_27148_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d2s_27148/03_2025/8d2s_27148.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d2s_27148/03_2025/8d2s_27148.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d2s_27148/03_2025/8d2s_27148.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d2s_27148/03_2025/8d2s_27148_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d2s_27148/03_2025/8d2s_27148_neut.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.075
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1605 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      36      5.16       5
     Na      1      4.78       5
     C    4621      2.51       5
     N    1070      2.21       5
     O    1340      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7071
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3577
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 475, 3523
          Classifications: {'peptide': 475}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PTRANS': 22, 'TRANS': 452}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 185
          Unresolved non-hydrogen angles: 228
          Unresolved non-hydrogen dihedrals: 147
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 112
      Conformer: "B"
        Number of residues, atoms: 475, 3523
          Classifications: {'peptide': 475}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PTRANS': 22, 'TRANS': 452}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 185
          Unresolved non-hydrogen angles: 228
          Unresolved non-hydrogen dihedrals: 147
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 112
          bond proxies already assigned to first conformer: 3555
    Chain: "B"
      Number of atoms: 1423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1423
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 14, 'TRANS': 186}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "C"
      Number of atoms: 1443
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 203, 1432
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 12, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
      Conformer: "B"
        Number of residues, atoms: 203, 1432
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 12, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
          bond proxies already assigned to first conformer: 1460
    Chain: "A"
      Number of atoms: 623
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 43, 588
          Unusual residues: {' NA': 1, 'LMT': 17, 'ZGS': 3}
          Classifications: {'undetermined': 21, 'water': 22}
          Link IDs: {None: 42}
          Unresolved non-hydrogen bonds: 147
          Unresolved non-hydrogen angles: 219
          Unresolved non-hydrogen dihedrals: 311
          Unresolved non-hydrogen chiralities: 60
      Conformer: "B"
        Number of residues, atoms: 43, 588
          Unusual residues: {' NA': 1, 'LMT': 17, 'ZGS': 3}
          Classifications: {'undetermined': 21, 'water': 22}
          Link IDs: {None: 42}
          Unresolved non-hydrogen bonds: 147
          Unresolved non-hydrogen angles: 219
          Unresolved non-hydrogen dihedrals: 311
          Unresolved non-hydrogen chiralities: 60
          bond proxies already assigned to first conformer: 531
    Chain: "C"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N  AARG A 100 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 100 " occ=0.50
    residue:
      pdb=" N  AARG A 108 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 108 " occ=0.50
    residue:
      pdb=" N  AHIS A 420 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 420 " occ=0.50
    residue:
      pdb=" N  APHE A 427 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 427 " occ=0.50
    residue:
      pdb=" N  APHE A 449 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 449 " occ=0.50
    residue:
      pdb=" N  AARG C  13 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG C  13 " occ=0.50
    residue:
      pdb=" C1 ALMT A 616 " occ=0.50
      ... (68 atoms not shown)
      pdb=" O6BBLMT A 616 " occ=0.50
  Time building chain proxies: 7.94, per 1000 atoms: 1.12
  Number of scatterers: 7071
  At special positions: 0
  Unit cell: (73.428, 74.272, 142.636, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      36     16.00
     P       3     15.00
     Na      1     11.00
     O    1340      8.00
     N    1070      7.00
     C    4621      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  86 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 130 " - pdb=" SG  CYS B 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 139 " - pdb=" SG  CYS C 186 " 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: 5.20
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1604

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 11 sheets defined
      45.8% alpha, 17.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 47
      removed outlier: 3.659A  pdb=" N   GLY A  47 " --> pdb=" O   TYR A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 68
      removed outlier: 3.829A  pdb=" N   GLN A  51 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   GLN A  62 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      removed outlier: 5.676A  pdb=" N   ILE A  63 " --> pdb=" O   PHE A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 100
      Proline residue:  A  92  - end of helix
    Processing helix  chain 'A' and resid 109 through 128
      Proline residue:  A 118  - end of helix
      removed outlier: 3.745A  pdb=" N   TRP A 128 " --> pdb=" O   TYR A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 162
      Proline residue:  A 158  - end of helix
    Processing helix  chain 'A' and resid 162 through 167
      removed outlier: 4.476A  pdb=" N   SER A 167 " --> pdb=" O   THR A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 200
      removed outlier: 3.555A  pdb=" N   VAL A 185 " --> pdb=" O   MET A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 213
    Processing helix  chain 'A' and resid 232 through 262
    Processing helix  chain 'A' and resid 274 through 288
    Processing helix  chain 'A' and resid 288 through 311
    Processing helix  chain 'A' and resid 312 through 319
    Processing helix  chain 'A' and resid 325 through 351
      Proline residue:  A 342  - end of helix
    Processing helix  chain 'A' and resid 353 through 361
      removed outlier: 4.092A  pdb=" N   THR A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 372
      removed outlier: 4.304A  pdb=" N   PHE A 367 " --> pdb=" O   SER A 363 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   VAL A 372 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 414
      Proline residue:  A 399  - end of helix
      Proline residue:  A 404  - end of helix
      removed outlier: 3.536A  pdb=" N   ASP A 409 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 451
      removed outlier: 4.047A  pdb=" N   GLY A 437 " --> pdb=" O   LYS A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 473
    Processing helix  chain 'A' and resid 473 through 488
    Processing helix  chain 'A' and resid 493 through 507
      removed outlier: 3.703A  pdb=" N   GLN A 497 " --> pdb=" O   GLU A 493 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   ASN A 499 " --> pdb=" O   LYS A 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 123
    Processing helix  chain 'C' and resid 28 through 31
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5
      removed outlier: 3.777A  pdb=" N   ALA B  18 " --> pdb=" O   SER B  73 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.138A  pdb=" N   LYS B  11 " --> pdb=" O   ASN B 102 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   VAL B  32 " --> pdb=" O   TYR B  48 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   TYR B  48 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   TRP B  34 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 114
      removed outlier: 4.747A  pdb=" N   ALA B 127 " --> pdb=" O   ILE B 174 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   ILE B 174 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
      removed outlier: 5.648A  pdb=" N   VAL B 129 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   LEU B 172 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
      removed outlier: 5.513A  pdb=" N   PHE B 131 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   ALA B 170 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
      removed outlier: 5.395A  pdb=" N   MET B 168 " --> pdb=" O   PRO B 133 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149
      removed outlier: 4.617A  pdb=" N   TRP B 143 " --> pdb=" O   GLN B 149 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'C' and resid 56 through 58
      removed outlier: 7.031A  pdb=" N   TRP C  36 " --> pdb=" O   PRO C  47 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   ALA C  49 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   VAL C  34 " --> pdb=" O   ALA C  49 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 91
    Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 123
      removed outlier: 5.945A  pdb=" N   TRP C 170 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA C 175 " --> pdb=" O   LEU C 159 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 123
      removed outlier: 5.945A  pdb=" N   TRP C 170 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU C 169 " --> pdb=" O   ASN C 166 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 135 through 136
    Processing sheet with id=AB2, first strand: chain 'C' and resid 149 through 151
      removed outlier: 4.743A  pdb=" N   ALA C 184 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)

    392 hydrogen bonds defined for protein.
    1106 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.22

  Time building geometry restraints manager: 2.58 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1024
        1.30 -     1.43: 1895
        1.43 -     1.56: 4137
        1.56 -     1.68: 119
        1.68 -     1.81: 51
  Bond restraints: 7226
  Sorted by residual:
  bond pdb=" C1B LMT A 611 "
       pdb=" O5B LMT A 611 "
    ideal  model  delta    sigma   weight residual
    1.393  1.516 -0.123 2.00e-02 2.50e+03 3.76e+01
  bond pdb=" C1BBLMT A 616 "
       pdb=" O5BBLMT A 616 "
    ideal  model  delta    sigma   weight residual
    1.393  1.514 -0.121 2.00e-02 2.50e+03 3.63e+01
  bond pdb=" C1B LMT A 609 "
       pdb=" O5B LMT A 609 "
    ideal  model  delta    sigma   weight residual
    1.393  1.513 -0.120 2.00e-02 2.50e+03 3.62e+01
  bond pdb=" C1B LMT A 612 "
       pdb=" O5B LMT A 612 "
    ideal  model  delta    sigma   weight residual
    1.393  1.513 -0.120 2.00e-02 2.50e+03 3.57e+01
  bond pdb=" C1BALMT A 616 "
       pdb=" O5BALMT A 616 "
    ideal  model  delta    sigma   weight residual
    1.393  1.512 -0.119 2.00e-02 2.50e+03 3.54e+01
  ... (remaining 7221 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.09: 9650
        6.09 -    12.18: 133
       12.18 -    18.27: 12
       18.27 -    24.36: 8
       24.36 -    30.45: 7
  Bond angle restraints: 9810
  Sorted by residual:
  angle pdb=" C06 ZGS A 601 "
        pdb=" C07 ZGS A 601 "
        pdb=" C08 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.52  157.97  -30.45 3.00e+00 1.11e-01 1.03e+02
  angle pdb=" C09 ZGS A 601 "
        pdb=" C10 ZGS A 601 "
        pdb=" C11 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.16  154.21  -27.05 3.00e+00 1.11e-01 8.13e+01
  angle pdb=" C04 ZGS A 601 "
        pdb=" C05 ZGS A 601 "
        pdb=" C06 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     110.70  137.41  -26.71 3.00e+00 1.11e-01 7.93e+01
  angle pdb=" C06 ZGS A 603 "
        pdb=" C07 ZGS A 603 "
        pdb=" C08 ZGS A 603 "
      ideal   model   delta    sigma   weight residual
     127.52  152.93  -25.41 3.00e+00 1.11e-01 7.17e+01
  angle pdb=" C03 ZGS A 603 "
        pdb=" C04 ZGS A 603 "
        pdb=" C05 ZGS A 603 "
      ideal   model   delta    sigma   weight residual
     127.34  152.52  -25.18 3.00e+00 1.11e-01 7.04e+01
  ... (remaining 9805 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.93: 4343
       35.93 -    71.86: 230
       71.86 -   107.78: 93
      107.78 -   143.71: 33
      143.71 -   179.64: 4
  Dihedral angle restraints: 4703
    sinusoidal: 2183
      harmonic: 2520
  Sorted by residual:
  dihedral pdb=" C23 ZGS A 602 "
           pdb=" O24 ZGS A 602 "
           pdb=" P25 ZGS A 602 "
           pdb=" O26 ZGS A 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.58   -2.06  179.64     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C23 ZGS A 603 "
           pdb=" O24 ZGS A 603 "
           pdb=" P25 ZGS A 603 "
           pdb=" O28 ZGS A 603 "
      ideal   model   delta sinusoidal    sigma   weight residual
      66.18 -107.87  174.05     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C23 ZGS A 602 "
           pdb=" O24 ZGS A 602 "
           pdb=" P25 ZGS A 602 "
           pdb=" O28 ZGS A 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
      66.18 -125.94 -167.88     1      3.00e+01 1.11e-03 2.11e+01
  ... (remaining 4700 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 903
       0.054 -    0.109: 194
       0.109 -    0.163: 43
       0.163 -    0.217: 8
       0.217 -    0.271: 1
  Chirality restraints: 1149
  Sorted by residual:
  chirality pdb=" C1B LMT A 608 "
            pdb=" C2B LMT A 608 "
            pdb=" O1B LMT A 608 "
            pdb=" O5B LMT A 608 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.47    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" C4' LMT A 608 "
            pdb=" C3' LMT A 608 "
            pdb=" C5' LMT A 608 "
            pdb=" O1B LMT A 608 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.34   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" C1B LMT A 613 "
            pdb=" C2B LMT A 613 "
            pdb=" O1B LMT A 613 "
            pdb=" O5B LMT A 613 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.41    0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 1146 not shown)

  Planarity restraints: 1173
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C  46 "   -0.046 5.00e-02 4.00e+02   6.99e-02 7.82e+00
        pdb=" N   PRO C  47 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO C  47 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO C  47 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 431 "    0.012 2.00e-02 2.50e+03   2.50e-02 6.25e+00
        pdb=" C   PHE A 431 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   PHE A 431 "    0.016 2.00e-02 2.50e+03
        pdb=" N   THR A 432 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A  85 "    0.009 2.00e-02 2.50e+03   1.89e-02 3.58e+00
        pdb=" C   ALA A  85 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   ALA A  85 "    0.012 2.00e-02 2.50e+03
        pdb=" N   TRP A  86 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1170 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1998
        2.82 -     3.34: 6356
        3.34 -     3.86: 12101
        3.86 -     4.38: 13833
        4.38 -     4.90: 24264
  Nonbonded interactions: 58552
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 209 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OG1 THR A  53 "
            pdb=" NE2 GLN A 152 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" OD1 ASP A  67 "
            pdb=" OH  TYR A 452 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" NZ  LYS A 353 "
            pdb=" OD2 ASP A 405 "
     model   vdw
     2.347 3.120
  nonbonded pdb=" O   TYR A 452 "
            pdb=" ND2 ASN C  99 "
     model   vdw
     2.353 3.120
  ... (remaining 58547 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=0.50 max=1.00 mean=0.99
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:             3.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     25.490
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.050
  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:13.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
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      :  0.012   0.123   7226  Z= 0.703
  Angle     :  1.683  30.451   9810  Z= 0.619
  Chirality :  0.049   0.271   1149
  Planarity :  0.006   0.070   1173
  Dihedral  : 27.127 179.641   3087
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  5.91 %
    Favored  : 93.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.27), residues: 891
  helix:  0.58 (0.25), residues: 385
  sheet: -0.50 (0.38), residues: 189
  loop : -2.46 (0.31), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 140 
 HIS   0.005   0.001   HIS A 156 
 PHE   0.016   0.002   PHE B  89 
 TYR   0.013   0.001   TYR A 251 
 ARG   0.002   0.000   ARG C  92 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 140
  time to evaluate  : 0.662 
Fit side-chains
REVERT: A  106 PHE cc_start: 0.8869 (m-80) cc_final: 0.8656 (m-80)
REVERT: A  132 SER cc_start: 0.8705 (p) cc_final: 0.8156 (m)
REVERT: A  134 ASP cc_start: 0.6688 (p0) cc_final: 0.6453 (p0)
REVERT: A  180 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7670 (ttp-170)
REVERT: A  345 GLN cc_start: 0.8644 (mt0) cc_final: 0.8371 (mt0)
REVERT: B   91 LYS cc_start: 0.7936 (mttt) cc_final: 0.7563 (mmtm)
REVERT: B  168 MET cc_start: 0.8467 (ttt) cc_final: 0.8262 (ttp)
REVERT: C   37 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7449 (mt)
  outliers start: 5
  outliers final: 1
  residues processed: 143
  average time/residue: 1.0762
  time to fit residues: 164.0653
Evaluate side-chains
  106 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain C residue   37 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 195 GLN
A 420 HIS    B
B 187 ASN
C  19 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.177094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.146903 restraints weight = 38561.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 4.37
r_work: 0.3186 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3133
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3133 r_free = 0.3133    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3132
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   7226  Z= 0.304
  Angle     :  0.836   9.807   9810  Z= 0.375
  Chirality :  0.048   0.292   1149
  Planarity :  0.006   0.066   1173
  Dihedral  : 19.602 176.681   1827
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 12.30 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.28), residues: 891
  helix:  1.25 (0.26), residues: 384
  sheet: -0.29 (0.39), residues: 184
  loop : -2.39 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  95 
 HIS   0.003   0.001   HIS A 156 
 PHE   0.027   0.003   PHE C  38 
 TYR   0.012   0.002   TYR A 251 
 ARG   0.005   0.001   ARG C  31 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A  106 PHE cc_start: 0.9054 (m-80) cc_final: 0.8679 (m-80)
REVERT: A  132 SER cc_start: 0.9113 (p) cc_final: 0.8638 (m)
REVERT: A  180 ARG cc_start: 0.8286 (ttp80) cc_final: 0.8050 (ttp80)
REVERT: A  345 GLN cc_start: 0.8525 (mt0) cc_final: 0.8095 (mt0)
REVERT: B   91 LYS cc_start: 0.8484 (mttt) cc_final: 0.8028 (mmtm)
REVERT: C   19 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8974 (tp40)
REVERT: C   95 TRP cc_start: 0.7349 (p-90) cc_final: 0.7109 (p-90)
REVERT: C  188 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7895 (t)
  outliers start: 18
  outliers final: 7
  residues processed: 114
  average time/residue: 0.9708
  time to fit residues: 118.8519
Evaluate side-chains
  114 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain C residue   19 GLN
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 58 optimal weight:    6.9990
   chunk 44 optimal weight:    0.0870
   chunk 11 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
A 197 GLN
B  27 GLN
B 187 ASN
C  19 GLN
** C  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 112 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.178155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.150258 restraints weight = 29955.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 3.59
r_work: 0.3214 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7226  Z= 0.251
  Angle     :  0.691   8.368   9810  Z= 0.325
  Chirality :  0.043   0.161   1149
  Planarity :  0.005   0.069   1173
  Dihedral  : 15.414 174.731   1825
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 13.42 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.28), residues: 891
  helix:  1.54 (0.25), residues: 384
  sheet: -0.41 (0.38), residues: 197
  loop : -2.37 (0.32), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  95 
 HIS   0.004   0.001   HIS A 156 
 PHE   0.021   0.002   PHE C  38 
 TYR   0.012   0.002   TYR B 136 
 ARG   0.003   0.001   ARG A 455 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.666 
Fit side-chains
REVERT: A  106 PHE cc_start: 0.9070 (m-80) cc_final: 0.8733 (m-80)
REVERT: A  132 SER cc_start: 0.9075 (p) cc_final: 0.8604 (m)
REVERT: A  134 ASP cc_start: 0.7488 (p0) cc_final: 0.7241 (p0)
REVERT: A  180 ARG cc_start: 0.8320 (ttp80) cc_final: 0.8101 (ttp80)
REVERT: B   91 LYS cc_start: 0.8366 (mttt) cc_final: 0.7986 (mmtm)
REVERT: C   37 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7717 (mp)
REVERT: C  188 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.8162 (t)
  outliers start: 18
  outliers final: 11
  residues processed: 119
  average time/residue: 0.9720
  time to fit residues: 123.8725
Evaluate side-chains
  117 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0030
   chunk 5 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0040
   chunk 50 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.4002

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
C  19 GLN
C  74 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.179273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.150986 restraints weight = 34700.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 4.04
r_work: 0.3238 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3146
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3146
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7226  Z= 0.211
  Angle     :  0.633   8.188   9810  Z= 0.302
  Chirality :  0.041   0.142   1149
  Planarity :  0.005   0.070   1173
  Dihedral  : 13.713 168.556   1825
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 13.74 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.28), residues: 891
  helix:  1.78 (0.26), residues: 382
  sheet: -0.40 (0.38), residues: 197
  loop : -2.38 (0.32), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C  95 
 HIS   0.003   0.001   HIS A 156 
 PHE   0.017   0.002   PHE B  89 
 TYR   0.011   0.001   TYR A 251 
 ARG   0.008   0.001   ARG B  38 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.756 
Fit side-chains
REVERT: A  106 PHE cc_start: 0.9022 (m-80) cc_final: 0.8676 (m-80)
REVERT: A  132 SER cc_start: 0.9073 (p) cc_final: 0.8603 (m)
REVERT: A  134 ASP cc_start: 0.7513 (p0) cc_final: 0.7274 (p0)
REVERT: A  431 PHE cc_start: 0.8664 (m-80) cc_final: 0.8213 (m-80)
REVERT: B   91 LYS cc_start: 0.8344 (mttt) cc_final: 0.7946 (mmtm)
REVERT: C   37 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7757 (mp)
REVERT: C  118 LYS cc_start: 0.7875 (mtpp) cc_final: 0.7448 (mttt)
REVERT: C  188 VAL cc_start: 0.8382 (OUTLIER) cc_final: 0.8157 (t)
  outliers start: 18
  outliers final: 9
  residues processed: 114
  average time/residue: 0.9752
  time to fit residues: 118.9372
Evaluate side-chains
  110 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 58 optimal weight:    4.9990
   chunk 77 optimal weight:    0.4980
   chunk 50 optimal weight:    0.1980
   chunk 75 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 25 optimal weight:    6.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
C  19 GLN
C  74 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.176229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.150565 restraints weight = 31075.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.96
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3633
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3633 r_free = 0.3633    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3632 r_free = 0.3632    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3632
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7226  Z= 0.274
  Angle     :  0.666   8.728   9810  Z= 0.322
  Chirality :  0.042   0.144   1149
  Planarity :  0.005   0.070   1173
  Dihedral  : 13.549 165.511   1825
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 13.90 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.28), residues: 891
  helix:  1.77 (0.25), residues: 384
  sheet: -0.38 (0.40), residues: 182
  loop : -2.33 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP C  95 
 HIS   0.004   0.001   HIS A 156 
 PHE   0.021   0.002   PHE C  35 
 TYR   0.014   0.002   TYR B 136 
 ARG   0.007   0.001   ARG A 180 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 1.127 
Fit side-chains
REVERT: A  106 PHE cc_start: 0.8917 (m-80) cc_final: 0.8673 (m-80)
REVERT: A  132 SER cc_start: 0.8702 (p) cc_final: 0.8107 (m)
REVERT: A  431 PHE cc_start: 0.8375 (m-80) cc_final: 0.8077 (m-80)
REVERT: B   91 LYS cc_start: 0.7970 (mttt) cc_final: 0.7727 (mmtm)
REVERT: B  105 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.6992 (tt0)
REVERT: C   37 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7427 (mt)
  outliers start: 22
  outliers final: 14
  residues processed: 111
  average time/residue: 1.0718
  time to fit residues: 128.0324
Evaluate side-chains
  114 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 33 optimal weight:    0.1980
   chunk 49 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0770
   chunk 28 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
C  19 GLN
C  74 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.178189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.153223 restraints weight = 30203.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 2.86
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3646
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3646 r_free = 0.3646    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3646 r_free = 0.3646    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3646
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7226  Z= 0.220
  Angle     :  0.624   8.348   9810  Z= 0.301
  Chirality :  0.041   0.139   1149
  Planarity :  0.005   0.070   1173
  Dihedral  : 12.936 164.523   1825
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.02 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.28), residues: 891
  helix:  1.94 (0.26), residues: 383
  sheet: -0.46 (0.39), residues: 182
  loop : -2.27 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C  95 
 HIS   0.003   0.001   HIS A 156 
 PHE   0.017   0.002   PHE B  89 
 TYR   0.013   0.001   TYR B 136 
 ARG   0.007   0.001   ARG B  38 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.664 
Fit side-chains
REVERT: A  106 PHE cc_start: 0.8892 (m-80) cc_final: 0.8615 (m-80)
REVERT: A  132 SER cc_start: 0.8678 (p) cc_final: 0.8102 (m)
REVERT: A  180 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7983 (ttp80)
REVERT: B   91 LYS cc_start: 0.7877 (mttt) cc_final: 0.7646 (mmtm)
REVERT: C   37 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7419 (mp)
  outliers start: 17
  outliers final: 11
  residues processed: 109
  average time/residue: 1.0387
  time to fit residues: 120.8037
Evaluate side-chains
  112 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 16 optimal weight:    0.1980
   chunk 69 optimal weight:    0.3980
   chunk 25 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 81 optimal weight:    0.0870
   chunk 45 optimal weight:    0.7980
   chunk 78 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.3758

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

Flipped N/Q/H residues before XYZ refinement:
B  63 GLN
B 142 GLN
C  19 GLN
C  74 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.178973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.149085 restraints weight = 37232.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 4.11
r_work: 0.3264 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7226  Z= 0.206
  Angle     :  0.608   7.576   9810  Z= 0.295
  Chirality :  0.041   0.143   1149
  Planarity :  0.005   0.069   1173
  Dihedral  : 12.446 164.731   1825
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 16.29 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.28), residues: 891
  helix:  2.04 (0.26), residues: 383
  sheet: -0.40 (0.39), residues: 182
  loop : -2.23 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  95 
 HIS   0.003   0.001   HIS A 156 
 PHE   0.025   0.002   PHE A 431 
 TYR   0.012   0.001   TYR B 136 
 ARG   0.010   0.001   ARG B  38 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.832 
Fit side-chains
REVERT: A  106 PHE cc_start: 0.9050 (m-80) cc_final: 0.8706 (m-80)
REVERT: A  132 SER cc_start: 0.9083 (p) cc_final: 0.8629 (m)
REVERT: A  180 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8173 (tmm-80)
REVERT: A  184 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8153 (mt-10)
REVERT: A  431 PHE cc_start: 0.8683 (m-80) cc_final: 0.8274 (m-80)
REVERT: B   91 LYS cc_start: 0.8252 (mttt) cc_final: 0.7911 (mmtm)
REVERT: C   37 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7712 (mp)
  outliers start: 15
  outliers final: 11
  residues processed: 107
  average time/residue: 1.0332
  time to fit residues: 118.1861
Evaluate side-chains
  110 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0870
   chunk 7 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0980
   chunk 53 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 81 optimal weight:    0.4980
   chunk 32 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.3958

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

Flipped N/Q/H residues before XYZ refinement:
B 142 GLN
C  19 GLN
C  74 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.179054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.153286 restraints weight = 31614.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 3.01
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3664
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3664 r_free = 0.3664    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3664 r_free = 0.3664    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3664
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7226  Z= 0.212
  Angle     :  0.612   8.512   9810  Z= 0.296
  Chirality :  0.041   0.143   1149
  Planarity :  0.005   0.070   1173
  Dihedral  : 12.286 165.117   1825
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.97 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.29), residues: 891
  helix:  2.07 (0.26), residues: 383
  sheet: -0.41 (0.38), residues: 197
  loop : -2.21 (0.32), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  95 
 HIS   0.003   0.001   HIS A 156 
 PHE   0.024   0.002   PHE A 431 
 TYR   0.014   0.001   TYR B 136 
 ARG   0.009   0.001   ARG B  38 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.666 
Fit side-chains
REVERT: A  106 PHE cc_start: 0.8902 (m-80) cc_final: 0.8623 (m-80)
REVERT: A  132 SER cc_start: 0.8714 (p) cc_final: 0.8091 (m)
REVERT: A  180 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7921 (tmm-80)
REVERT: A  184 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7992 (mt-10)
REVERT: A  431 PHE cc_start: 0.8504 (m-80) cc_final: 0.8141 (m-80)
REVERT: B   91 LYS cc_start: 0.7847 (mttt) cc_final: 0.7642 (mmtm)
REVERT: C   37 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7429 (mp)
  outliers start: 16
  outliers final: 10
  residues processed: 106
  average time/residue: 1.0088
  time to fit residues: 114.3461
Evaluate side-chains
  108 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 67 optimal weight:    0.0570
   chunk 79 optimal weight:    0.0030
   chunk 6 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0070
   chunk 74 optimal weight:    0.0970
   chunk 13 optimal weight:    0.9990
   chunk 76 optimal weight:    0.6980
   chunk 77 optimal weight:    0.1980
   chunk 10 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.0724

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

Flipped N/Q/H residues before XYZ refinement:
B 142 GLN
C  19 GLN
C  74 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.186106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.160493 restraints weight = 33000.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 3.14
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3728
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3728 r_free = 0.3728    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3728 r_free = 0.3728    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3728
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7226  Z= 0.140
  Angle     :  0.555   8.806   9810  Z= 0.267
  Chirality :  0.039   0.135   1149
  Planarity :  0.005   0.070   1173
  Dihedral  : 11.441 167.708   1825
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.61 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.29), residues: 891
  helix:  2.31 (0.26), residues: 384
  sheet: -0.26 (0.38), residues: 199
  loop : -2.11 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 400 
 HIS   0.001   0.000   HIS A 156 
 PHE   0.021   0.001   PHE A 431 
 TYR   0.010   0.001   TYR A 251 
 ARG   0.010   0.001   ARG B  38 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.651 
Fit side-chains
REVERT: A  106 PHE cc_start: 0.8868 (m-80) cc_final: 0.8632 (m-80)
REVERT: A  132 SER cc_start: 0.8703 (p) cc_final: 0.8122 (m)
REVERT: A  180 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7985 (ttp80)
REVERT: A  184 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7712 (mt-10)
REVERT: A  431 PHE cc_start: 0.8379 (m-80) cc_final: 0.8053 (m-80)
REVERT: C   19 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7336 (tp40)
REVERT: C   78 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.6583 (mm-30)
REVERT: C  188 VAL cc_start: 0.7957 (m) cc_final: 0.7707 (t)
  outliers start: 12
  outliers final: 9
  residues processed: 110
  average time/residue: 0.9366
  time to fit residues: 110.6367
Evaluate side-chains
  102 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain C residue   19 GLN
Chi-restraints excluded: chain C residue   78 GLU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 45 optimal weight:    0.0470
   chunk 35 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0020
   chunk 79 optimal weight:    0.0970
   chunk 73 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.3084

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

Flipped N/Q/H residues before XYZ refinement:
B  37 GLN
B 187 ASN
C  74 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.185520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.159339 restraints weight = 33745.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 3.29
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3722
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3722 r_free = 0.3722    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3722 r_free = 0.3722    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3722
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.165   7226  Z= 0.321
  Angle     :  1.015  59.120   9810  Z= 0.577
  Chirality :  0.046   0.808   1149
  Planarity :  0.005   0.070   1173
  Dihedral  : 11.442 167.719   1825
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 17.89 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.29), residues: 891
  helix:  2.32 (0.26), residues: 384
  sheet: -0.24 (0.38), residues: 199
  loop : -2.11 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP C  95 
 HIS   0.001   0.000   HIS A 156 
 PHE   0.048   0.002   PHE C  32 
 TYR   0.010   0.001   TYR A 251 
 ARG   0.008   0.001   ARG B  38 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.652 
Fit side-chains
REVERT: A  106 PHE cc_start: 0.8878 (m-80) cc_final: 0.8643 (m-80)
REVERT: A  132 SER cc_start: 0.8692 (p) cc_final: 0.8142 (m)
REVERT: A  180 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7955 (ttp80)
REVERT: A  184 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7717 (mt-10)
REVERT: A  431 PHE cc_start: 0.8381 (m-80) cc_final: 0.8078 (m-80)
REVERT: C   78 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.6663 (mm-30)
REVERT: C  188 VAL cc_start: 0.7966 (m) cc_final: 0.7710 (t)
  outliers start: 10
  outliers final: 7
  residues processed: 100
  average time/residue: 0.9360
  time to fit residues: 100.2273
Evaluate side-chains
  101 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain C residue   78 GLU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0770
   chunk 8 optimal weight:    0.5980
   chunk 25 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 77 optimal weight:    0.1980
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
B  37 GLN
C  74 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.185475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.158632 restraints weight = 35392.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3711 rms_B_bonded: 3.47
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3711
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3711 r_free = 0.3711    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3711 r_free = 0.3711    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3711
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.165   7226  Z= 0.321
  Angle     :  1.015  59.120   9810  Z= 0.577
  Chirality :  0.046   0.808   1149
  Planarity :  0.005   0.070   1173
  Dihedral  : 11.442 167.719   1825
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 17.89 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.29), residues: 891
  helix:  2.32 (0.26), residues: 384
  sheet: -0.24 (0.38), residues: 199
  loop : -2.11 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP C  95 
 HIS   0.001   0.000   HIS A 156 
 PHE   0.048   0.002   PHE C  32 
 TYR   0.010   0.001   TYR A 251 
 ARG   0.008   0.001   ARG B  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4543.22 seconds
wall clock time: 80 minutes 41.65 seconds (4841.65 seconds total)