Starting phenix.real_space_refine
on Sun Mar 10 22:03:28 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrd_33414/03_2024/7xrd_33414_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrd_33414/03_2024/7xrd_33414.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrd_33414/03_2024/7xrd_33414.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrd_33414/03_2024/7xrd_33414.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrd_33414/03_2024/7xrd_33414_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xrd_33414/03_2024/7xrd_33414_updated.pdb"
  }
  resolution = 3.9
  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=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     Mg      4      5.21       5
     S      24      5.16       5
     C    3420      2.51       5
     N     964      2.21       5
     O    1036      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR   31": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR   78": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  163": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   31": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   78": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  163": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   31": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   78": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  163": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   31": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   78": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  163": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 5460
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1332
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 5, 'TRANS': 158}
    Chain: "B"
      Number of atoms: 1332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1332
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 5, 'TRANS': 158}
    Chain: "C"
      Number of atoms: 1332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1332
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 5, 'TRANS': 158}
    Chain: "D"
      Number of atoms: 1332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1332
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 5, 'TRANS': 158}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.54, per 1000 atoms: 0.65
  Number of scatterers: 5460
  At special positions: 0
  Unit cell: (91.3, 104.5, 86.9, 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      24     16.00
     P      12     15.00
     Mg      4     11.99
     O    1036      8.00
     N     964      7.00
     C    3420      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.09
  Conformation dependent library (CDL) restraints added in 977.6 milliseconds
  

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1216

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      28 helices and 4 sheets defined
      35.7% alpha, 22.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 35
    Processing helix  chain 'A' and resid 68 through 77
      Proline residue:  A  72  - end of helix
    Processing helix  chain 'A' and resid 93 through 107
      removed outlier: 3.633A  pdb=" N   ILE A  96 " --> pdb=" O   ARG A  93 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   ASP A  97 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ILE A 107 " --> pdb=" O   HIS A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 114
      removed outlier: 4.328A  pdb=" N   ASP A 114 " --> pdb=" O   GLU A 111 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 111 through 114'
    Processing helix  chain 'A' and resid 132 through 139
    Processing helix  chain 'A' and resid 141 through 143
      No H-bonds generated for 'chain 'A' and resid 141 through 143'
    Processing helix  chain 'A' and resid 162 through 171
    Processing helix  chain 'B' and resid 26 through 34
    Processing helix  chain 'B' and resid 68 through 77
      Proline residue:  B  72  - end of helix
    Processing helix  chain 'B' and resid 93 through 107
      removed outlier: 5.191A  pdb=" N   ASP B  97 " --> pdb=" O   ASP B  94 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ILE B 107 " --> pdb=" O   HIS B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 114
      removed outlier: 4.287A  pdb=" N   ASP B 114 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 111 through 114'
    Processing helix  chain 'B' and resid 132 through 139
    Processing helix  chain 'B' and resid 141 through 143
      No H-bonds generated for 'chain 'B' and resid 141 through 143'
    Processing helix  chain 'B' and resid 162 through 171
    Processing helix  chain 'C' and resid 26 through 34
    Processing helix  chain 'C' and resid 68 through 77
      removed outlier: 3.542A  pdb=" N   ARG C  71 " --> pdb=" O   ASP C  68 " (cutoff:3.500A)
      Proline residue:  C  72  - end of helix
    Processing helix  chain 'C' and resid 93 through 107
      removed outlier: 3.634A  pdb=" N   ILE C  96 " --> pdb=" O   ARG C  93 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   ASP C  97 " --> pdb=" O   ASP C  94 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ILE C 107 " --> pdb=" O   HIS C 104 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 114
      removed outlier: 4.285A  pdb=" N   ASP C 114 " --> pdb=" O   GLU C 111 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 111 through 114'
    Processing helix  chain 'C' and resid 132 through 138
    Processing helix  chain 'C' and resid 141 through 143
      No H-bonds generated for 'chain 'C' and resid 141 through 143'
    Processing helix  chain 'C' and resid 162 through 171
    Processing helix  chain 'D' and resid 26 through 35
    Processing helix  chain 'D' and resid 68 through 77
      Proline residue:  D  72  - end of helix
    Processing helix  chain 'D' and resid 96 through 107
    Processing helix  chain 'D' and resid 111 through 114
      removed outlier: 4.286A  pdb=" N   ASP D 114 " --> pdb=" O   GLU D 111 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 111 through 114'
    Processing helix  chain 'D' and resid 132 through 139
    Processing helix  chain 'D' and resid 141 through 143
      No H-bonds generated for 'chain 'D' and resid 141 through 143'
    Processing helix  chain 'D' and resid 162 through 171
    Processing sheet with id=  A, first strand: chain 'A' and resid 149 through 153
      removed outlier: 6.860A  pdb=" N   ILE A 117 " --> pdb=" O   TYR A 150 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   GLN A 152 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ILE A 119 " --> pdb=" O   GLN A 152 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   VAL A  64 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
      removed outlier: 5.814A  pdb=" N   GLY A  20 " --> pdb=" O   VAL A  64 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 149 through 153
      removed outlier: 6.922A  pdb=" N   ILE B 117 " --> pdb=" O   TYR B 150 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   GLN B 152 " --> pdb=" O   ILE B 117 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ILE B 119 " --> pdb=" O   GLN B 152 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL B  64 " --> pdb=" O   MET B  18 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'C' and resid 149 through 153
      removed outlier: 6.925A  pdb=" N   ILE C 117 " --> pdb=" O   TYR C 150 " (cutoff:3.500A)
      removed outlier: 8.084A  pdb=" N   GLN C 152 " --> pdb=" O   ILE C 117 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ILE C 119 " --> pdb=" O   GLN C 152 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   VAL C  64 " --> pdb=" O   MET C  18 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'D' and resid 149 through 153
      removed outlier: 7.039A  pdb=" N   ILE D 117 " --> pdb=" O   TYR D 150 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   GLN D 152 " --> pdb=" O   ILE D 117 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ILE D 119 " --> pdb=" O   GLN D 152 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   VAL D  64 " --> pdb=" O   MET D  18 " (cutoff:3.500A)
      removed outlier: 5.605A  pdb=" N   GLY D  20 " --> pdb=" O   VAL D  64 " (cutoff:3.500A)

    204 hydrogen bonds defined for protein.
    471 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: 1.32

  Time building geometry restraints manager: 2.26 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1771
        1.34 -     1.46: 1205
        1.46 -     1.58: 2532
        1.58 -     1.69: 20
        1.69 -     1.81: 40
  Bond restraints: 5568
  Sorted by residual:
  bond pdb=" N   LYS B  55 "
       pdb=" CA  LYS B  55 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 9.86e-01
  bond pdb=" C   ARG A  71 "
       pdb=" N   PRO A  72 "
    ideal  model  delta    sigma   weight residual
    1.335  1.341 -0.006 1.19e-02 7.06e+03 2.62e-01
  bond pdb=" CA  GLY A  20 "
       pdb=" C   GLY A  20 "
    ideal  model  delta    sigma   weight residual
    1.509  1.515 -0.005 1.04e-02 9.25e+03 2.61e-01
  bond pdb=" O3A GTP D 202 "
       pdb=" PB  GTP D 202 "
    ideal  model  delta    sigma   weight residual
    1.610  1.620 -0.010 2.00e-02 2.50e+03 2.48e-01
  bond pdb=" C   ILE B  42 "
       pdb=" N   PRO B  43 "
    ideal  model  delta    sigma   weight residual
    1.334  1.345 -0.012 2.34e-02 1.83e+03 2.45e-01
  ... (remaining 5563 not shown)

  Histogram of bond angle deviations from ideal:
      100.73 -   107.37: 192
      107.37 -   114.02: 3186
      114.02 -   120.67: 2254
      120.67 -   127.32: 1861
      127.32 -   133.96: 71
  Bond angle restraints: 7564
  Sorted by residual:
  angle pdb=" O3A GTP D 202 "
        pdb=" PB  GTP D 202 "
        pdb=" O3B GTP D 202 "
      ideal   model   delta    sigma   weight residual
     102.60  109.71   -7.11 3.00e+00 1.11e-01 5.61e+00
  angle pdb=" C1' GTP B 202 "
        pdb=" C2' GTP B 202 "
        pdb=" C3' GTP B 202 "
      ideal   model   delta    sigma   weight residual
     111.00  104.06    6.94 3.00e+00 1.11e-01 5.36e+00
  angle pdb=" C1' GTP C 202 "
        pdb=" C2' GTP C 202 "
        pdb=" C3' GTP C 202 "
      ideal   model   delta    sigma   weight residual
     111.00  104.11    6.89 3.00e+00 1.11e-01 5.28e+00
  angle pdb=" C1' GTP D 202 "
        pdb=" C2' GTP D 202 "
        pdb=" C3' GTP D 202 "
      ideal   model   delta    sigma   weight residual
     111.00  104.18    6.82 3.00e+00 1.11e-01 5.17e+00
  angle pdb=" C1' GTP A 202 "
        pdb=" C2' GTP A 202 "
        pdb=" C3' GTP A 202 "
      ideal   model   delta    sigma   weight residual
     111.00  104.24    6.76 3.00e+00 1.11e-01 5.07e+00
  ... (remaining 7559 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.18: 3220
       24.18 -    48.37: 65
       48.37 -    72.55: 13
       72.55 -    96.74: 6
       96.74 -   120.92: 12
  Dihedral angle restraints: 3316
    sinusoidal: 1420
      harmonic: 1896
  Sorted by residual:
  dihedral pdb=" C8  GTP C 202 "
           pdb=" C1' GTP C 202 "
           pdb=" N9  GTP C 202 "
           pdb=" O4' GTP C 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -16.33  120.92     1      2.00e+01 2.50e-03 3.63e+01
  dihedral pdb=" C8  GTP A 202 "
           pdb=" C1' GTP A 202 "
           pdb=" N9  GTP A 202 "
           pdb=" O4' GTP A 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -15.29  119.88     1      2.00e+01 2.50e-03 3.60e+01
  dihedral pdb=" C8  GTP B 202 "
           pdb=" C1' GTP B 202 "
           pdb=" N9  GTP B 202 "
           pdb=" O4' GTP B 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -14.75  119.34     1      2.00e+01 2.50e-03 3.58e+01
  ... (remaining 3313 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 522
       0.031 -    0.062: 185
       0.062 -    0.093: 53
       0.093 -    0.124: 62
       0.124 -    0.155: 10
  Chirality restraints: 832
  Sorted by residual:
  chirality pdb=" CA  ILE C  42 "
            pdb=" N   ILE C  42 "
            pdb=" C   ILE C  42 "
            pdb=" CB  ILE C  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.01e-01
  chirality pdb=" CA  ILE D  42 "
            pdb=" N   ILE D  42 "
            pdb=" C   ILE D  42 "
            pdb=" CB  ILE D  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.75e-01
  chirality pdb=" CA  ILE A  42 "
            pdb=" N   ILE A  42 "
            pdb=" C   ILE A  42 "
            pdb=" CB  ILE A  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.65e-01
  ... (remaining 829 not shown)

  Planarity restraints: 940
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 131 "   -0.021 5.00e-02 4.00e+02   3.13e-02 1.57e+00
        pdb=" N   PRO C 132 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO C 132 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 132 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D 131 "   -0.019 5.00e-02 4.00e+02   2.86e-02 1.31e+00
        pdb=" N   PRO D 132 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO D 132 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO D 132 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B  71 "   -0.019 5.00e-02 4.00e+02   2.86e-02 1.30e+00
        pdb=" N   PRO B  72 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO B  72 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B  72 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 937 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 30
        2.59 -     3.17: 4334
        3.17 -     3.74: 7838
        3.74 -     4.32: 11770
        4.32 -     4.90: 18800
  Nonbonded interactions: 42772
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D  63 "
            pdb="MG    MG D 201 "
     model   vdw
     2.012 2.170
  nonbonded pdb=" OG1 THR A  27 "
            pdb="MG    MG A 201 "
     model   vdw
     2.017 2.170
  nonbonded pdb=" OG1 THR D  27 "
            pdb="MG    MG D 201 "
     model   vdw
     2.024 2.170
  nonbonded pdb=" OD2 ASP A  63 "
            pdb="MG    MG A 201 "
     model   vdw
     2.041 2.170
  nonbonded pdb=" OD1 ASP B  22 "
            pdb="MG    MG B 201 "
     model   vdw
     2.074 2.170
  ... (remaining 42767 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          12.150
  Check model and map are aligned:         0.090
  Set scattering table:                    0.050
  Process input model:                     19.600
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
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      :  0.002   0.013   5568  Z= 0.114
  Angle     :  0.575   7.107   7564  Z= 0.298
  Chirality :  0.045   0.155    832
  Planarity :  0.003   0.031    940
  Dihedral  : 14.120 120.919   2100
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 1.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  0.69 %
    Favored  : 98.78 %
  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: -0.70 (0.32), residues: 648
  helix: -1.41 (0.31), residues: 216
  sheet:  0.16 (0.38), residues: 164
  loop :  0.24 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 168 
 HIS   0.002   0.001   HIS D  76 
 PHE   0.005   0.001   PHE D 120 
 TYR   0.010   0.001   TYR A  77 
 ARG   0.002   0.000   ARG C 105 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 213
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 THR cc_start: 0.7924 (m) cc_final: 0.7711 (m)
REVERT: B  130 MET cc_start: 0.7631 (mtm) cc_final: 0.7138 (mtm)
REVERT: C  169 LEU cc_start: 0.8897 (mt) cc_final: 0.8614 (tt)
REVERT: D  125 ASP cc_start: 0.8467 (p0) cc_final: 0.8013 (m-30)
REVERT: D  131 LYS cc_start: 0.7896 (mppt) cc_final: 0.7643 (mmmt)
  outliers start: 3
  outliers final: 0
  residues processed: 216
  average time/residue: 0.2894
  time to fit residues: 72.7301
Evaluate side-chains
  183 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0010
   chunk 30 optimal weight:    3.9990
   chunk 37 optimal weight:    8.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    3.1792

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

Flipped N/Q/H residues before XYZ refinement:
B 148 ASN
C 136 GLN
C 148 ASN
C 172 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   5568  Z= 0.295
  Angle     :  0.697   7.607   7564  Z= 0.344
  Chirality :  0.050   0.168    832
  Planarity :  0.005   0.035    940
  Dihedral  : 15.985 118.413    784
  Min Nonbonded Distance : 1.798

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 11.11 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.32), residues: 648
  helix: -1.07 (0.33), residues: 240
  sheet:  0.24 (0.35), residues: 172
  loop : -0.25 (0.40), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 168 
 HIS   0.004   0.001   HIS D  76 
 PHE   0.013   0.002   PHE B  59 
 TYR   0.016   0.002   TYR B 163 
 ARG   0.007   0.001   ARG A  75 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 191
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 THR cc_start: 0.7981 (m) cc_final: 0.7746 (m)
REVERT: A   32 LYS cc_start: 0.9120 (tptt) cc_final: 0.8837 (tptt)
REVERT: A   37 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8185 (mp10)
REVERT: A   69 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8680 (mmmm)
REVERT: A   95 ARG cc_start: 0.8053 (ptm160) cc_final: 0.7852 (ptm160)
REVERT: A  100 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7898 (tmm-80)
REVERT: B   73 LEU cc_start: 0.7982 (tp) cc_final: 0.7750 (tp)
REVERT: B   93 ARG cc_start: 0.6006 (mtt-85) cc_final: 0.5626 (mmt180)
REVERT: B  122 ASN cc_start: 0.9274 (t0) cc_final: 0.9055 (t0)
REVERT: B  130 MET cc_start: 0.7726 (mtm) cc_final: 0.6963 (mtm)
REVERT: C   37 GLN cc_start: 0.8759 (mt0) cc_final: 0.8538 (mt0)
REVERT: C   73 LEU cc_start: 0.8185 (tp) cc_final: 0.7884 (tp)
REVERT: C  133 HIS cc_start: 0.6493 (p-80) cc_final: 0.6278 (p-80)
REVERT: D   32 LYS cc_start: 0.9076 (tppt) cc_final: 0.8147 (tppt)
REVERT: D   97 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7237 (p0)
  outliers start: 16
  outliers final: 9
  residues processed: 198
  average time/residue: 0.2647
  time to fit residues: 62.0594
Evaluate side-chains
  196 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 186
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  114 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  133 HIS
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue  136 GLN
Chi-restraints excluded: chain D residue   42 ILE
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   97 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 32 optimal weight:   10.0000
   chunk 18 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    8.9990
   chunk 57 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 GLN
C  56 ASN
C 136 GLN
C 172 ASN
D 172 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.4414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   5568  Z= 0.304
  Angle     :  0.679   7.090   7564  Z= 0.335
  Chirality :  0.050   0.166    832
  Planarity :  0.005   0.030    940
  Dihedral  : 15.781 125.382    784
  Min Nonbonded Distance : 1.848

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 13.72 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.83 (0.32), residues: 648
  helix: -1.00 (0.34), residues: 236
  sheet:  0.35 (0.36), residues: 172
  loop : -0.52 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 168 
 HIS   0.003   0.001   HIS B 104 
 PHE   0.015   0.002   PHE B  59 
 TYR   0.019   0.002   TYR A 150 
 ARG   0.004   0.001   ARG A  75 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 184
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8231 (mp10)
REVERT: B   73 LEU cc_start: 0.8097 (tp) cc_final: 0.7876 (tp)
REVERT: B  125 ASP cc_start: 0.9008 (p0) cc_final: 0.8803 (p0)
REVERT: C   73 LEU cc_start: 0.8205 (tp) cc_final: 0.7891 (tp)
REVERT: C  133 HIS cc_start: 0.6751 (p-80) cc_final: 0.6511 (p-80)
REVERT: D   32 LYS cc_start: 0.9214 (tppt) cc_final: 0.8889 (tppt)
REVERT: D   54 TYR cc_start: 0.7698 (t80) cc_final: 0.7249 (t80)
REVERT: D  125 ASP cc_start: 0.8465 (p0) cc_final: 0.7688 (m-30)
  outliers start: 27
  outliers final: 17
  residues processed: 199
  average time/residue: 0.2576
  time to fit residues: 60.7713
Evaluate side-chains
  195 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 178
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   94 ASP
Chi-restraints excluded: chain A residue  114 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  133 HIS
Chi-restraints excluded: chain B residue  136 GLN
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   79 THR
Chi-restraints excluded: chain C residue  136 GLN
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue  120 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 57 optimal weight:    9.9990
   chunk 43 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 16 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  56 ASN
C 136 GLN
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.4802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5568  Z= 0.258
  Angle     :  0.649   6.739   7564  Z= 0.318
  Chirality :  0.050   0.167    832
  Planarity :  0.004   0.033    940
  Dihedral  : 15.372 126.041    784
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 15.97 %
    Favored  : 79.17 %
  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: -0.42 (0.32), residues: 648
  helix: -0.32 (0.38), residues: 208
  sheet:  0.29 (0.37), residues: 176
  loop : -0.45 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 168 
 HIS   0.003   0.001   HIS B 104 
 PHE   0.013   0.002   PHE B  59 
 TYR   0.016   0.002   TYR A 150 
 ARG   0.003   0.000   ARG A 143 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 180
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8115 (mp10)
REVERT: A   69 LYS cc_start: 0.9015 (mmmt) cc_final: 0.8725 (mmmt)
REVERT: A  101 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7959 (tp40)
REVERT: B   73 LEU cc_start: 0.8204 (tp) cc_final: 0.7977 (tp)
REVERT: B  122 ASN cc_start: 0.9321 (t0) cc_final: 0.9109 (t0)
REVERT: C   73 LEU cc_start: 0.8180 (tp) cc_final: 0.7875 (tp)
REVERT: D   32 LYS cc_start: 0.9230 (tppt) cc_final: 0.8938 (tppt)
REVERT: D   54 TYR cc_start: 0.7544 (t80) cc_final: 0.6840 (t80)
REVERT: D   97 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7267 (p0)
REVERT: D  125 ASP cc_start: 0.8508 (p0) cc_final: 0.7777 (m-30)
REVERT: D  138 LYS cc_start: 0.8311 (mmmm) cc_final: 0.8071 (mtpp)
  outliers start: 28
  outliers final: 17
  residues processed: 194
  average time/residue: 0.2623
  time to fit residues: 60.3701
Evaluate side-chains
  197 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 178
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  101 GLN
Chi-restraints excluded: chain A residue  114 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  133 HIS
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   79 THR
Chi-restraints excluded: chain C residue  136 GLN
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  120 PHE
Chi-restraints excluded: chain D residue  122 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0570
   chunk 42 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   overall best weight:    2.4106

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 136 GLN
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.5044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5568  Z= 0.231
  Angle     :  0.637   6.613   7564  Z= 0.311
  Chirality :  0.049   0.169    832
  Planarity :  0.004   0.033    940
  Dihedral  : 14.939 123.678    784
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 18.23 %
    Favored  : 76.39 %
  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: -0.31 (0.32), residues: 648
  helix: -0.06 (0.39), residues: 204
  sheet:  0.29 (0.37), residues: 176
  loop : -0.50 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 168 
 HIS   0.003   0.001   HIS A 104 
 PHE   0.012   0.001   PHE B  59 
 TYR   0.016   0.002   TYR A  54 
 ARG   0.005   0.000   ARG B  93 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 179
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLN cc_start: 0.8361 (mm-40) cc_final: 0.8106 (mp10)
REVERT: B   73 LEU cc_start: 0.8227 (tp) cc_final: 0.7968 (tp)
REVERT: B   82 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7501 (mt0)
REVERT: B  122 ASN cc_start: 0.9303 (t0) cc_final: 0.9082 (t0)
REVERT: C   14 MET cc_start: 0.7118 (ttm) cc_final: 0.6890 (ttm)
REVERT: C   15 ARG cc_start: 0.7239 (mtp85) cc_final: 0.6683 (mtp85)
REVERT: C   73 LEU cc_start: 0.8174 (tp) cc_final: 0.7849 (tp)
REVERT: C   82 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7136 (mt0)
REVERT: C  141 LEU cc_start: 0.8508 (mt) cc_final: 0.8304 (mt)
REVERT: C  174 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6731 (pttt)
REVERT: D   32 LYS cc_start: 0.9224 (tppt) cc_final: 0.8904 (tppt)
REVERT: D   54 TYR cc_start: 0.7588 (t80) cc_final: 0.6764 (t80)
REVERT: D   97 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7144 (p0)
REVERT: D  125 ASP cc_start: 0.8455 (p0) cc_final: 0.7818 (m-30)
REVERT: D  138 LYS cc_start: 0.8351 (mmmm) cc_final: 0.8103 (mtpp)
  outliers start: 31
  outliers final: 19
  residues processed: 194
  average time/residue: 0.2559
  time to fit residues: 59.0084
Evaluate side-chains
  197 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 174
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  114 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  172 ASN
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  133 HIS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   82 GLN
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  120 PHE
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  120 PHE
Chi-restraints excluded: chain D residue  122 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0670
   chunk 51 optimal weight:    9.9990
   chunk 28 optimal weight:    0.0980
   chunk 5 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 59 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 35 optimal weight:   10.0000
   overall best weight:    1.2324

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

Flipped N/Q/H residues before XYZ refinement:
** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  56 ASN
B 124 GLN
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.5213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5568  Z= 0.168
  Angle     :  0.615   6.472   7564  Z= 0.298
  Chirality :  0.049   0.176    832
  Planarity :  0.004   0.036    940
  Dihedral  : 13.978 113.343    784
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 19.10 %
    Favored  : 75.52 %
  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: -0.23 (0.32), residues: 648
  helix:  0.02 (0.38), residues: 204
  sheet:  0.38 (0.37), residues: 176
  loop : -0.50 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP C 168 
 HIS   0.003   0.001   HIS B 104 
 PHE   0.010   0.001   PHE B  59 
 TYR   0.012   0.001   TYR D 163 
 ARG   0.004   0.000   ARG D 143 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 170
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.9102 (tptt) cc_final: 0.8853 (tptt)
REVERT: A   69 LYS cc_start: 0.9039 (mmmt) cc_final: 0.8773 (mmmt)
REVERT: A  112 MET cc_start: 0.7654 (mmm) cc_final: 0.7155 (mmt)
REVERT: A  125 ASP cc_start: 0.8578 (p0) cc_final: 0.8062 (m-30)
REVERT: B   73 LEU cc_start: 0.8162 (tp) cc_final: 0.7925 (tp)
REVERT: B   82 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7647 (mt0)
REVERT: C   73 LEU cc_start: 0.8085 (tp) cc_final: 0.7774 (tp)
REVERT: C  141 LEU cc_start: 0.8441 (mt) cc_final: 0.8218 (mt)
REVERT: C  174 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6793 (pttt)
REVERT: D   32 LYS cc_start: 0.9185 (tppt) cc_final: 0.8928 (tppt)
REVERT: D   37 GLN cc_start: 0.8324 (mp10) cc_final: 0.8069 (mp10)
REVERT: D   54 TYR cc_start: 0.7279 (t80) cc_final: 0.6556 (t80)
REVERT: D   97 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7159 (p0)
REVERT: D  125 ASP cc_start: 0.8420 (p0) cc_final: 0.7777 (m-30)
  outliers start: 31
  outliers final: 19
  residues processed: 185
  average time/residue: 0.2658
  time to fit residues: 58.5638
Evaluate side-chains
  188 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 166
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  114 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue   94 ASP
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  133 HIS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  120 PHE
Chi-restraints excluded: chain D residue  154 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 52 optimal weight:   10.0000
   chunk 34 optimal weight:    0.8980
   chunk 61 optimal weight:    0.4980
   chunk 38 optimal weight:    8.9990
   chunk 37 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
** B  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.5417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5568  Z= 0.199
  Angle     :  0.627   6.440   7564  Z= 0.304
  Chirality :  0.049   0.180    832
  Planarity :  0.004   0.038    940
  Dihedral  : 13.510 112.759    784
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 17.88 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.33), residues: 648
  helix:  0.03 (0.38), residues: 204
  sheet:  0.29 (0.36), residues: 188
  loop : -0.33 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C 168 
 HIS   0.003   0.001   HIS B 104 
 PHE   0.010   0.001   PHE B  59 
 TYR   0.016   0.001   TYR A  54 
 ARG   0.003   0.000   ARG A 143 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 174
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8722 (mmmt)
REVERT: A  112 MET cc_start: 0.7624 (mmm) cc_final: 0.7012 (mmt)
REVERT: A  125 ASP cc_start: 0.8556 (p0) cc_final: 0.8090 (m-30)
REVERT: B   73 LEU cc_start: 0.8177 (tp) cc_final: 0.7930 (tp)
REVERT: B   82 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7674 (mt0)
REVERT: B  103 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7343 (tt)
REVERT: C   73 LEU cc_start: 0.8139 (tp) cc_final: 0.7804 (tp)
REVERT: C  141 LEU cc_start: 0.8477 (mt) cc_final: 0.8267 (mt)
REVERT: C  174 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6672 (pttt)
REVERT: D   32 LYS cc_start: 0.9220 (tppt) cc_final: 0.8956 (tppt)
REVERT: D   37 GLN cc_start: 0.8317 (mp10) cc_final: 0.8082 (mp10)
REVERT: D   54 TYR cc_start: 0.7226 (t80) cc_final: 0.6806 (t80)
REVERT: D   97 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7202 (p0)
REVERT: D  125 ASP cc_start: 0.8407 (p0) cc_final: 0.7745 (m-30)
REVERT: D  163 TYR cc_start: 0.7742 (m-80) cc_final: 0.7404 (m-80)
  outliers start: 34
  outliers final: 21
  residues processed: 192
  average time/residue: 0.2677
  time to fit residues: 60.9733
Evaluate side-chains
  195 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 170
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  114 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue   94 ASP
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  113 ARG
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  133 HIS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  120 PHE
Chi-restraints excluded: chain D residue  154 SER
Chi-restraints excluded: chain D residue  172 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 11 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0870
   chunk 42 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    1.9362

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

Flipped N/Q/H residues before XYZ refinement:
** B  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 124 GLN
C 152 GLN
** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.5621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5568  Z= 0.205
  Angle     :  0.639   6.434   7564  Z= 0.310
  Chirality :  0.049   0.192    832
  Planarity :  0.004   0.039    940
  Dihedral  : 13.058 113.807    784
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 18.58 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.22 (0.33), residues: 648
  helix: -0.09 (0.37), residues: 208
  sheet:  0.10 (0.37), residues: 196
  loop : -0.17 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 168 
 HIS   0.003   0.001   HIS B 104 
 PHE   0.010   0.001   PHE B  59 
 TYR   0.015   0.001   TYR A  54 
 ARG   0.004   0.000   ARG A 143 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 167
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8637 (mmmt)
REVERT: A  125 ASP cc_start: 0.8425 (p0) cc_final: 0.7925 (m-30)
REVERT: B   73 LEU cc_start: 0.8243 (tp) cc_final: 0.7968 (tp)
REVERT: B   82 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7697 (mt0)
REVERT: B  103 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7386 (tt)
REVERT: C   73 LEU cc_start: 0.8171 (tp) cc_final: 0.7841 (tp)
REVERT: C  122 ASN cc_start: 0.9099 (t0) cc_final: 0.8785 (t0)
REVERT: C  141 LEU cc_start: 0.8505 (mt) cc_final: 0.8285 (mt)
REVERT: C  174 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6652 (pttt)
REVERT: D   32 LYS cc_start: 0.9213 (tppt) cc_final: 0.8957 (tppt)
REVERT: D   37 GLN cc_start: 0.8248 (mp10) cc_final: 0.8033 (mp10)
REVERT: D   97 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7214 (p0)
REVERT: D  125 ASP cc_start: 0.8367 (p0) cc_final: 0.7683 (m-30)
  outliers start: 32
  outliers final: 22
  residues processed: 185
  average time/residue: 0.2597
  time to fit residues: 57.1503
Evaluate side-chains
  190 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 164
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  114 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue   94 ASP
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  133 HIS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  124 GLN
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  120 PHE
Chi-restraints excluded: chain D residue  154 SER
Chi-restraints excluded: chain D residue  172 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 34 optimal weight:    0.5980
   chunk 25 optimal weight:    7.9990
   chunk 45 optimal weight:    0.0170
   chunk 17 optimal weight:   10.0000
   chunk 51 optimal weight:    0.0970
   chunk 54 optimal weight:    0.9990
   chunk 57 optimal weight:    9.9990
   chunk 37 optimal weight:    9.9990
   chunk 60 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7420

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
** B  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 124 GLN
** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.5745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5568  Z= 0.155
  Angle     :  0.630   8.356   7564  Z= 0.303
  Chirality :  0.049   0.197    832
  Planarity :  0.004   0.043    940
  Dihedral  : 12.512 106.123    784
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 21.53 %
    Favored  : 74.65 %
  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 (0.33), residues: 648
  helix: -0.07 (0.37), residues: 212
  sheet:  0.20 (0.37), residues: 196
  loop : -0.16 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  62 
 HIS   0.003   0.001   HIS B 104 
 PHE   0.009   0.001   PHE B  59 
 TYR   0.012   0.001   TYR A  54 
 ARG   0.005   0.000   ARG B  15 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 164
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 LYS cc_start: 0.8915 (mmmt) cc_final: 0.8652 (mmmt)
REVERT: A  125 ASP cc_start: 0.8370 (p0) cc_final: 0.7930 (m-30)
REVERT: B   15 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6899 (mtp180)
REVERT: B   73 LEU cc_start: 0.8144 (tp) cc_final: 0.7904 (tp)
REVERT: B  103 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7283 (tt)
REVERT: C   62 TRP cc_start: 0.8037 (m100) cc_final: 0.7674 (m100)
REVERT: C   73 LEU cc_start: 0.8095 (tp) cc_final: 0.7788 (tp)
REVERT: C  122 ASN cc_start: 0.9087 (t0) cc_final: 0.8777 (t0)
REVERT: C  141 LEU cc_start: 0.8466 (mt) cc_final: 0.8240 (mt)
REVERT: C  174 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6666 (pttt)
REVERT: D   32 LYS cc_start: 0.9188 (tppt) cc_final: 0.8928 (tppt)
REVERT: D   37 GLN cc_start: 0.8254 (mp10) cc_final: 0.8037 (mp10)
REVERT: D  125 ASP cc_start: 0.8514 (p0) cc_final: 0.7793 (m-30)
  outliers start: 22
  outliers final: 15
  residues processed: 175
  average time/residue: 0.2725
  time to fit residues: 56.6742
Evaluate side-chains
  175 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 158
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain B residue   94 ASP
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  133 HIS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue  154 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 63 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0010
   overall best weight:    0.6786

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

Flipped N/Q/H residues before XYZ refinement:
** B  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.5833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5568  Z= 0.154
  Angle     :  0.636   7.890   7564  Z= 0.307
  Chirality :  0.049   0.205    832
  Planarity :  0.004   0.047    940
  Dihedral  : 12.147 104.940    784
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 22.22 %
    Favored  : 74.83 %
  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: -0.05 (0.33), residues: 648
  helix:  0.03 (0.38), residues: 208
  sheet:  0.22 (0.37), residues: 196
  loop : -0.06 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP C 168 
 HIS   0.003   0.001   HIS B 104 
 PHE   0.009   0.001   PHE B  59 
 TYR   0.012   0.001   TYR A  54 
 ARG   0.005   0.000   ARG B  15 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 160
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 LYS cc_start: 0.8903 (mmmt) cc_final: 0.8647 (mmmt)
REVERT: B   73 LEU cc_start: 0.8155 (tp) cc_final: 0.7916 (tp)
REVERT: B  103 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7236 (tt)
REVERT: C   73 LEU cc_start: 0.8092 (tp) cc_final: 0.7780 (tp)
REVERT: C  122 ASN cc_start: 0.9088 (t0) cc_final: 0.8855 (t0)
REVERT: C  141 LEU cc_start: 0.8433 (mt) cc_final: 0.8195 (mt)
REVERT: C  174 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6598 (pttt)
REVERT: D   32 LYS cc_start: 0.9143 (tppt) cc_final: 0.8897 (tppt)
REVERT: D   37 GLN cc_start: 0.8359 (mp10) cc_final: 0.8155 (mp10)
REVERT: D  125 ASP cc_start: 0.8479 (p0) cc_final: 0.7787 (m-30)
  outliers start: 17
  outliers final: 13
  residues processed: 168
  average time/residue: 0.2776
  time to fit residues: 55.0717
Evaluate side-chains
  174 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 159
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain B residue   94 ASP
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue  120 PHE
Chi-restraints excluded: chain D residue  154 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 7 optimal weight:    0.0980
   chunk 14 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 9 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 124 GLN
** B  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 124 GLN
** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 152 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 = 0.3280 r_free = 0.3280 target = 0.121824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.098388 restraints weight = 7162.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.101697 restraints weight = 4688.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.104170 restraints weight = 3485.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.5906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5568  Z= 0.213
  Angle     :  0.660   7.766   7564  Z= 0.324
  Chirality :  0.050   0.202    832
  Planarity :  0.004   0.041    940
  Dihedral  : 12.485 108.238    784
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 22.40 %
    Favored  : 73.96 %
  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: -0.07 (0.33), residues: 648
  helix:  0.02 (0.37), residues: 208
  sheet:  0.22 (0.37), residues: 196
  loop : -0.09 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C 168 
 HIS   0.003   0.001   HIS B 104 
 PHE   0.010   0.001   PHE B  59 
 TYR   0.021   0.001   TYR D  54 
 ARG   0.004   0.000   ARG A 143 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1968.63 seconds
wall clock time: 35 minutes 41.80 seconds (2141.80 seconds total)