Starting phenix.real_space_refine
on Thu Jul 18 22:52:22 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/07_2024/8wxe_37904.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/07_2024/8wxe_37904.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/07_2024/8wxe_37904.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/07_2024/8wxe_37904.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/07_2024/8wxe_37904.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/07_2024/8wxe_37904.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    2865      2.51       5
     N     692      2.21       5
     O     794      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "a PHE   40": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "a TYR   42": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "d TYR   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "d PHE  123": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "e GLU  124": "OE1" <-> "OE2"
    Residue "f GLU   86": "OE1" <-> "OE2"
    Residue "f GLU   89": "OE1" <-> "OE2"
    Residue "g GLU  109": "OE1" <-> "OE2"
    Residue "g PHE  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "m GLU  257": "OE1" <-> "OE2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib"
  Total number of atoms: 4388
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "a"
      Number of atoms: 226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 226
          Classifications: {'peptide': 28}
          Link IDs: {'PTRANS': 1, 'TRANS': 26}
    Chain: "b"
      Number of atoms: 226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 226
          Classifications: {'peptide': 28}
          Link IDs: {'PTRANS': 1, 'TRANS': 26}
    Chain: "d"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 817
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 3, 'TRANS': 101}
    Chain: "e"
      Number of atoms: 853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 853
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 4, 'TRANS': 101}
          Chain breaks: 2
    Chain: "f"
      Number of atoms: 847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 847
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 3, 'TRANS': 102}
          Chain breaks: 2
    Chain: "g"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 821
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 2, 'TRANS': 101}
          Chain breaks: 2
    Chain: "m"
      Number of atoms: 268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 268
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
    Chain: "n"
      Number of atoms: 302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 302
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "g"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.13, per 1000 atoms: 0.71
  Number of scatterers: 4388
  At special positions: 0
  Unit cell: (94.569, 82.612, 98.917, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O     794      8.00
     N     692      7.00
     C    2865      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS a  32 " - pdb=" SG  CYS b  32 " distance=2.03
    Simple disulfide: pdb=" SG  CYS d  37 " - pdb=" SG  CYS d  73 " distance=2.03
    Simple disulfide: pdb=" SG  CYS d  93 " - pdb=" SG  CYS d  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS e  49 " - pdb=" SG  CYS e  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS e 119 " - pdb=" SG  CYS e 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS f  49 " - pdb=" SG  CYS f  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS f 119 " - pdb=" SG  CYS f 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS g  46 " - pdb=" SG  CYS g  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS g 104 " - pdb=" SG  CYS g 107 " distance=2.04

  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=0, symmetry=0
  Time building additional restraints: 1.62
  Conformation dependent library (CDL) restraints added in 778.5 milliseconds
  

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1028

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 9 sheets defined
      42.2% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'a' and resid 27 through 54
      removed outlier: 4.323A  pdb=" N   LEU a  35 " --> pdb=" O   LEU a  31 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ASP a  36 " --> pdb=" O   CYS a  32 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ILE a  38 " --> pdb=" O   LEU a  34 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 28 through 54
    Processing helix  chain 'd' and resid 100 through 125
      removed outlier: 3.787A  pdb=" N   VAL d 104 " --> pdb=" O   ASP d 100 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR d 110 " --> pdb=" O   GLY d 106 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 126 through 152
      removed outlier: 3.706A  pdb=" N   VAL e 130 " --> pdb=" O   ASP e 126 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   ILE e 133 " --> pdb=" O   SER e 129 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   VAL e 134 " --> pdb=" O   VAL e 130 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE e 135 " --> pdb=" O   ALA e 131 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 128 through 153
    Processing helix  chain 'g' and resid 111 through 140
      removed outlier: 4.749A  pdb=" N   GLY g 117 " --> pdb=" O   ALA g 113 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 258 through 288
      removed outlier: 3.667A  pdb=" N   PHE m 288 " --> pdb=" O   THR m 284 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 253 through 288
      removed outlier: 3.891A  pdb=" N   TYR n 264 " --> pdb=" O   THR n 260 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   MET n 265 " --> pdb=" O   SER n 261 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   VAL n 275 " --> pdb=" O   LEU n 271 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   TYR n 276 " --> pdb=" O   LYS n 272 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   CYS n 283 " --> pdb=" O   ILE n 279 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'd' and resid 33 through 36
      removed outlier: 7.108A  pdb=" N   VAL d  33 " --> pdb=" O   LEU d  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'd' and resid 41 through 46
      removed outlier: 3.668A  pdb=" N   VAL d  44 " --> pdb=" O   ILE d  70 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ILE d  70 " --> pdb=" O   VAL d  44 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   GLY d  46 " --> pdb=" O   ARG d  68 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   ARG d  68 " --> pdb=" O   GLY d  46 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY d  69 " --> pdb=" O   VAL d  88 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL d  88 " --> pdb=" O   GLY d  69 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   TYR d  71 " --> pdb=" O   VAL d  86 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL d  86 " --> pdb=" O   TYR d  71 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   THR d  85 " --> pdb=" O   TYR e 111 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   TYR e 113 " --> pdb=" O   THR d  85 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   GLN d  87 " --> pdb=" O   TYR e 113 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   ARG e 115 " --> pdb=" O   GLN d  87 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   HIS d  89 " --> pdb=" O   ARG e 115 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   PHE e 110 " --> pdb=" O   CYS e  98 " (cutoff:3.500A)
      removed outlier: 5.287A  pdb=" N   CYS e  98 " --> pdb=" O   PHE e 110 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   VAL e  97 " --> pdb=" O   GLN e  60 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   TYR e  99 " --> pdb=" O   LEU e  58 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 40
      removed outlier: 4.132A  pdb=" N   LYS e  37 " --> pdb=" O   THR e  48 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   SER e  83 " --> pdb=" O   GLY e  76 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLY e  76 " --> pdb=" O   SER e  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'f' and resid 45 through 47
      removed outlier: 3.536A  pdb=" N   LEU f  82 " --> pdb=" O   LEU f  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'f' and resid 122 through 123
      removed outlier: 3.588A  pdb=" N   MET f 123 " --> pdb=" O   ILE g 108 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'g' and resid 31 through 34
      removed outlier: 4.439A  pdb=" N   LEU g  43 " --> pdb=" O   TYR g  34 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLY g  75 " --> pdb=" O   VAL g  42 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   LEU g  44 " --> pdb=" O   ASN g  73 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   ASN g  73 " --> pdb=" O   LEU g  44 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'g' and resid 55 through 57
      removed outlier: 7.219A  pdb=" N   TRP g  55 " --> pdb=" O   ILE g  62 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   ILE g  62 " --> pdb=" O   TRP g  55 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'g' and resid 84 through 85
      removed outlier: 4.063A  pdb=" N   TYR g  85 " --> pdb=" O   LEU g  97 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   LEU g  97 " --> pdb=" O   TYR g  85 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    215 hydrogen bonds defined for protein.
    624 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: 1.01

  Time building geometry restraints manager: 1.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1333
        1.34 -     1.47: 1083
        1.47 -     1.59: 2000
        1.59 -     1.71: 1
        1.71 -     1.83: 51
  Bond restraints: 4468
  Sorted by residual:
  bond pdb=" CB  PRO g  96 "
       pdb=" CG  PRO g  96 "
    ideal  model  delta    sigma   weight residual
    1.492  1.622 -0.130 5.00e-02 4.00e+02 6.72e+00
  bond pdb=" C   ASP a  28 "
       pdb=" N   PRO a  29 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.019 1.28e-02 6.10e+03 2.10e+00
  bond pdb=" N   PRO g  96 "
       pdb=" CA  PRO g  96 "
    ideal  model  delta    sigma   weight residual
    1.469  1.450  0.018 1.28e-02 6.10e+03 2.05e+00
  bond pdb=" CB  CYS a  32 "
       pdb=" SG  CYS a  32 "
    ideal  model  delta    sigma   weight residual
    1.808  1.772  0.036 3.30e-02 9.18e+02 1.17e+00
  bond pdb=" C3  CLR g 201 "
       pdb=" O1  CLR g 201 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.13e+00
  ... (remaining 4463 not shown)

  Histogram of bond angle deviations from ideal:
       97.67 -   104.94: 57
      104.94 -   112.21: 2286
      112.21 -   119.47: 1402
      119.47 -   126.74: 2266
      126.74 -   134.00: 40
  Bond angle restraints: 6051
  Sorted by residual:
  angle pdb=" CA  PRO g  96 "
        pdb=" N   PRO g  96 "
        pdb=" CD  PRO g  96 "
      ideal   model   delta    sigma   weight residual
     112.00   98.30   13.70 1.40e+00 5.10e-01 9.58e+01
  angle pdb=" CA  GLU f 106 "
        pdb=" CB  GLU f 106 "
        pdb=" CG  GLU f 106 "
      ideal   model   delta    sigma   weight residual
     114.10  123.42   -9.32 2.00e+00 2.50e-01 2.17e+01
  angle pdb=" CB  MET f 123 "
        pdb=" CG  MET f 123 "
        pdb=" SD  MET f 123 "
      ideal   model   delta    sigma   weight residual
     112.70  124.29  -11.59 3.00e+00 1.11e-01 1.49e+01
  angle pdb=" N   PRO g  96 "
        pdb=" CD  PRO g  96 "
        pdb=" CG  PRO g  96 "
      ideal   model   delta    sigma   weight residual
     103.20   97.67    5.53 1.50e+00 4.44e-01 1.36e+01
  angle pdb=" N   PRO g  96 "
        pdb=" CA  PRO g  96 "
        pdb=" CB  PRO g  96 "
      ideal   model   delta    sigma   weight residual
     103.25   99.87    3.38 1.05e+00 9.07e-01 1.04e+01
  ... (remaining 6046 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 2228
       17.86 -    35.72: 372
       35.72 -    53.58: 94
       53.58 -    71.44: 20
       71.44 -    89.30: 4
  Dihedral angle restraints: 2718
    sinusoidal: 1122
      harmonic: 1596
  Sorted by residual:
  dihedral pdb=" CB  CYS a  32 "
           pdb=" SG  CYS a  32 "
           pdb=" SG  CYS b  32 "
           pdb=" CB  CYS b  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -158.21   72.21     1      1.00e+01 1.00e-02 6.67e+01
  dihedral pdb=" CB  CYS g 104 "
           pdb=" SG  CYS g 104 "
           pdb=" SG  CYS g 107 "
           pdb=" CB  CYS g 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -147.58   61.58     1      1.00e+01 1.00e-02 5.03e+01
  dihedral pdb=" CB  CYS d  37 "
           pdb=" SG  CYS d  37 "
           pdb=" SG  CYS d  73 "
           pdb=" CB  CYS d  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -132.94   46.94     1      1.00e+01 1.00e-02 3.05e+01
  ... (remaining 2715 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 472
       0.034 -    0.068: 170
       0.068 -    0.102: 53
       0.102 -    0.136: 21
       0.136 -    0.170: 5
  Chirality restraints: 721
  Sorted by residual:
  chirality pdb=" CA  PRO f 105 "
            pdb=" N   PRO f 105 "
            pdb=" C   PRO f 105 "
            pdb=" CB  PRO f 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.25e-01
  chirality pdb=" C20 CLR g 201 "
            pdb=" C17 CLR g 201 "
            pdb=" C21 CLR g 201 "
            pdb=" C22 CLR g 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.43    0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" CA  ASN g  28 "
            pdb=" N   ASN g  28 "
            pdb=" C   ASN g  28 "
            pdb=" CB  ASN g  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.44e-01
  ... (remaining 718 not shown)

  Planarity restraints: 728
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS g  95 "    0.119 5.00e-02 4.00e+02   1.68e-01 4.53e+01
        pdb=" N   PRO g  96 "   -0.290 5.00e-02 4.00e+02
        pdb=" CA  PRO g  96 "    0.090 5.00e-02 4.00e+02
        pdb=" CD  PRO g  96 "    0.081 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE d  24 "    0.037 5.00e-02 4.00e+02   5.62e-02 5.05e+00
        pdb=" N   PRO d  25 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO d  25 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO d  25 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU f  86 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.66e+00
        pdb=" CD  GLU f  86 "    0.037 2.00e-02 2.50e+03
        pdb=" OE1 GLU f  86 "   -0.014 2.00e-02 2.50e+03
        pdb=" OE2 GLU f  86 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 725 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 223
        2.72 -     3.27: 4463
        3.27 -     3.81: 7031
        3.81 -     4.36: 7314
        4.36 -     4.90: 12724
  Nonbonded interactions: 31755
  Sorted by model distance:
  nonbonded pdb=" O   SER f  41 "
            pdb=" OG1 THR f  44 "
     model   vdw
     2.178 2.440
  nonbonded pdb=" NZ  LYS f 104 "
            pdb=" OE1 GLU f 106 "
     model   vdw
     2.199 2.520
  nonbonded pdb=" O   GLN e  92 "
            pdb=" OH  TYR e  96 "
     model   vdw
     2.216 2.440
  nonbonded pdb=" N   GLU e 124 "
            pdb=" OE1 GLU e 124 "
     model   vdw
     2.272 2.520
  nonbonded pdb=" OG  SER g 125 "
            pdb=" NZ  LYS n 272 "
     model   vdw
     2.321 2.520
  ... (remaining 31750 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'
}
ncs_group {
  reference = (chain 'e' and (resid 33 through 49 or resid 58 through 65 or resid 75 through 1 \ 
53))
  selection = (chain 'f' and (resid 33 through 65 or resid 75 through 101 or resid 109 through \ 
 153))
}

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:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     16.220
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
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      :  0.004   0.130   4468  Z= 0.244
  Angle     :  0.862  13.704   6051  Z= 0.451
  Chirality :  0.043   0.170    721
  Planarity :  0.008   0.168    728
  Dihedral  : 18.180  89.302   1663
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 19.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 40.73 %
    Favored  : 57.23 %
  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: -0.75 (0.35), residues: 520
  helix:  1.55 (0.33), residues: 217
  sheet: -1.07 (0.61), residues: 71
  loop : -2.43 (0.35), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP e  59 
 HIS   0.005   0.001   HIS g  29 
 PHE   0.009   0.001   PHE f 110 
 TYR   0.023   0.001   TYR f  36 
 ARG   0.007   0.001   ARG e 115 

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 214
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   52 ARG cc_start: 0.6571 (ttt180) cc_final: 0.6177 (ttt180)
REVERT: d   63 ARG cc_start: 0.8723 (ttm170) cc_final: 0.8450 (mtp85)
REVERT: d   92 MET cc_start: 0.8431 (mtp) cc_final: 0.7769 (mmt)
REVERT: d   97 VAL cc_start: 0.8955 (t) cc_final: 0.8619 (p)
REVERT: d  109 VAL cc_start: 0.8934 (m) cc_final: 0.8674 (p)
REVERT: e   92 GLN cc_start: 0.8518 (tt0) cc_final: 0.8028 (tt0)
REVERT: e   95 TYR cc_start: 0.6958 (m-80) cc_final: 0.6366 (m-10)
REVERT: e  145 LEU cc_start: 0.8539 (mm) cc_final: 0.8173 (tt)
REVERT: e  147 LEU cc_start: 0.8127 (tt) cc_final: 0.7907 (mm)
REVERT: f   97 VAL cc_start: 0.8610 (m) cc_final: 0.8233 (p)
REVERT: f  101 ARG cc_start: 0.7297 (mmt90) cc_final: 0.7068 (mpt180)
REVERT: f  121 ASN cc_start: 0.9297 (t0) cc_final: 0.8889 (t0)
REVERT: f  125 MET cc_start: 0.7019 (pmm) cc_final: 0.6524 (pmm)
REVERT: g   34 TYR cc_start: 0.8520 (t80) cc_final: 0.8285 (t80)
REVERT: g   39 ASP cc_start: 0.7355 (m-30) cc_final: 0.6303 (m-30)
REVERT: g   73 ASN cc_start: 0.9503 (t0) cc_final: 0.9215 (t0)
REVERT: g  103 MET cc_start: 0.7179 (mmp) cc_final: 0.6798 (mmp)
REVERT: g  119 LEU cc_start: 0.9204 (tp) cc_final: 0.8856 (tp)
REVERT: n  259 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7496 (t0)
  outliers start: 10
  outliers final: 5
  residues processed: 221
  average time/residue: 0.1514
  time to fit residues: 41.6318
Evaluate side-chains
  164 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 158
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   41 ILE
Chi-restraints excluded: chain a residue   42 TYR
Chi-restraints excluded: chain d residue  120 LEU
Chi-restraints excluded: chain d residue  124 CYS
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain n residue  259 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 37 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 20 optimal weight:    7.9990
   chunk 39 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0030
   chunk 45 optimal weight:    0.6980
   overall best weight:    1.4994

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

Flipped N/Q/H residues before XYZ refinement:
d  89 HIS
e  92 GLN
** f  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** g  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4468  Z= 0.250
  Angle     :  0.755   8.703   6051  Z= 0.377
  Chirality :  0.043   0.147    721
  Planarity :  0.005   0.087    728
  Dihedral  :  7.610  57.496    662
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 16.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  8.55 %
    Allowed  : 35.03 %
    Favored  : 56.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.35), residues: 520
  helix:  2.18 (0.32), residues: 221
  sheet: -0.92 (0.63), residues: 68
  loop : -2.38 (0.34), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP e  59 
 HIS   0.003   0.001   HIS g  29 
 PHE   0.020   0.002   PHE g 127 
 TYR   0.017   0.001   TYR f 149 
 ARG   0.005   0.001   ARG n 287 

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 172
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   46 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7214 (tt)
REVERT: a   52 ARG cc_start: 0.6678 (ttt180) cc_final: 0.6229 (ttt180)
REVERT: b   34 LEU cc_start: 0.7972 (tt) cc_final: 0.7253 (mm)
REVERT: d   63 ARG cc_start: 0.8852 (ttm170) cc_final: 0.8132 (mtp-110)
REVERT: d   72 ARG cc_start: 0.7707 (tpt-90) cc_final: 0.7318 (tpt-90)
REVERT: d   92 MET cc_start: 0.8499 (mtp) cc_final: 0.7944 (mmt)
REVERT: d   97 VAL cc_start: 0.8931 (t) cc_final: 0.8575 (p)
REVERT: d   98 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7727 (tm-30)
REVERT: d  120 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8205 (tp)
REVERT: e   92 GLN cc_start: 0.8737 (tt0) cc_final: 0.8284 (tt0)
REVERT: e  145 LEU cc_start: 0.8626 (mm) cc_final: 0.8070 (tt)
REVERT: e  147 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7962 (mm)
REVERT: f  101 ARG cc_start: 0.7343 (mmt90) cc_final: 0.7107 (mpt180)
REVERT: f  121 ASN cc_start: 0.9220 (t0) cc_final: 0.8810 (t0)
REVERT: f  125 MET cc_start: 0.7032 (pmm) cc_final: 0.6815 (pmm)
REVERT: g   34 TYR cc_start: 0.8624 (t80) cc_final: 0.8165 (t80)
REVERT: g   38 GLU cc_start: 0.8065 (pm20) cc_final: 0.7297 (pm20)
REVERT: g   44 LEU cc_start: 0.8665 (tt) cc_final: 0.8229 (tp)
REVERT: g   73 ASN cc_start: 0.9481 (t0) cc_final: 0.9275 (t0)
REVERT: g   82 ARG cc_start: 0.8747 (mmt90) cc_final: 0.8176 (mmt-90)
REVERT: g  119 LEU cc_start: 0.9071 (tp) cc_final: 0.8787 (tp)
REVERT: m  262 MET cc_start: 0.8051 (tpp) cc_final: 0.7524 (tpp)
REVERT: m  272 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8433 (mp)
REVERT: n  259 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.7313 (t0)
  outliers start: 42
  outliers final: 24
  residues processed: 194
  average time/residue: 0.1513
  time to fit residues: 36.8199
Evaluate side-chains
  186 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 157
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   34 LEU
Chi-restraints excluded: chain a residue   46 LEU
Chi-restraints excluded: chain b residue   39 LEU
Chi-restraints excluded: chain b residue   41 ILE
Chi-restraints excluded: chain b residue   53 VAL
Chi-restraints excluded: chain d residue   60 LEU
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain d residue  120 LEU
Chi-restraints excluded: chain d residue  124 CYS
Chi-restraints excluded: chain e residue   34 THR
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   65 ASN
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  129 SER
Chi-restraints excluded: chain e residue  147 LEU
Chi-restraints excluded: chain f residue   75 ILE
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain m residue  266 VAL
Chi-restraints excluded: chain m residue  272 LEU
Chi-restraints excluded: chain m residue  276 THR
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain m residue  279 VAL
Chi-restraints excluded: chain m residue  283 LEU
Chi-restraints excluded: chain m residue  284 THR
Chi-restraints excluded: chain n residue  259 ASN
Chi-restraints excluded: chain n residue  274 VAL
Chi-restraints excluded: chain n residue  280 ILE
Chi-restraints excluded: chain n residue  281 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:    0.0980
   chunk 14 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** f  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
g  86 GLN
m 280 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.3312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4468  Z= 0.183
  Angle     :  0.699   7.816   6051  Z= 0.347
  Chirality :  0.041   0.198    721
  Planarity :  0.004   0.061    728
  Dihedral  :  7.212  56.016    658
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  8.76 %
    Allowed  : 35.85 %
    Favored  : 55.40 %
  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 (0.35), residues: 520
  helix:  2.43 (0.32), residues: 221
  sheet: -0.63 (0.68), residues: 62
  loop : -2.46 (0.32), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP e  59 
 HIS   0.002   0.001   HIS g  29 
 PHE   0.024   0.002   PHE e 110 
 TYR   0.015   0.001   TYR e  36 
 ARG   0.003   0.000   ARG n 287 

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 165
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   30 LYS cc_start: 0.8287 (tmmt) cc_final: 0.8044 (mmtm)
REVERT: a   46 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7164 (tt)
REVERT: a   52 ARG cc_start: 0.6744 (ttt180) cc_final: 0.6264 (ttt180)
REVERT: b   34 LEU cc_start: 0.7793 (tt) cc_final: 0.7203 (mm)
REVERT: d   63 ARG cc_start: 0.8887 (ttm170) cc_final: 0.8178 (mtp-110)
REVERT: d   72 ARG cc_start: 0.7681 (tpt-90) cc_final: 0.7228 (tpt-90)
REVERT: d   92 MET cc_start: 0.8506 (mtp) cc_final: 0.7906 (mmt)
REVERT: d   97 VAL cc_start: 0.8985 (t) cc_final: 0.8646 (p)
REVERT: d   98 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7825 (tm-30)
REVERT: d  120 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8124 (tp)
REVERT: e   87 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.8090 (t80)
REVERT: e   92 GLN cc_start: 0.8753 (tt0) cc_final: 0.8304 (tt0)
REVERT: e  145 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8235 (tt)
REVERT: e  147 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7880 (mm)
REVERT: f   97 VAL cc_start: 0.9019 (m) cc_final: 0.8694 (p)
REVERT: f  101 ARG cc_start: 0.7291 (mmt90) cc_final: 0.7044 (mpt180)
REVERT: f  104 LYS cc_start: 0.9239 (tmmt) cc_final: 0.8689 (ttpp)
REVERT: f  106 GLU cc_start: 0.8242 (mp0) cc_final: 0.7955 (mp0)
REVERT: f  120 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8725 (tm-30)
REVERT: f  121 ASN cc_start: 0.9221 (t0) cc_final: 0.8772 (t0)
REVERT: f  125 MET cc_start: 0.7101 (pmm) cc_final: 0.6826 (pmm)
REVERT: g   34 TYR cc_start: 0.8570 (t80) cc_final: 0.8314 (t80)
REVERT: g   38 GLU cc_start: 0.8348 (pm20) cc_final: 0.8067 (pm20)
REVERT: g   61 MET cc_start: 0.6847 (mmm) cc_final: 0.6643 (tpt)
REVERT: g   74 LEU cc_start: 0.8795 (tt) cc_final: 0.8308 (mt)
REVERT: g   82 ARG cc_start: 0.8593 (mmt90) cc_final: 0.8193 (mmt-90)
REVERT: g  119 LEU cc_start: 0.9082 (tp) cc_final: 0.8790 (tp)
REVERT: m  262 MET cc_start: 0.8075 (tpp) cc_final: 0.7604 (tpp)
  outliers start: 43
  outliers final: 23
  residues processed: 192
  average time/residue: 0.1395
  time to fit residues: 34.0421
Evaluate side-chains
  184 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 156
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   46 LEU
Chi-restraints excluded: chain d residue   60 LEU
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue   96 CYS
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain d residue  116 LEU
Chi-restraints excluded: chain d residue  120 LEU
Chi-restraints excluded: chain d residue  124 CYS
Chi-restraints excluded: chain e residue   34 THR
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   65 ASN
Chi-restraints excluded: chain e residue   87 PHE
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  145 LEU
Chi-restraints excluded: chain e residue  147 LEU
Chi-restraints excluded: chain e residue  152 SER
Chi-restraints excluded: chain f residue   88 SER
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  126 ILE
Chi-restraints excluded: chain g residue  136 ILE
Chi-restraints excluded: chain m residue  266 VAL
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain m residue  279 VAL
Chi-restraints excluded: chain m residue  283 LEU
Chi-restraints excluded: chain n residue  274 VAL
Chi-restraints excluded: chain n residue  280 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 45 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
e  60 GLN
** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4468  Z= 0.190
  Angle     :  0.693   8.441   6051  Z= 0.342
  Chirality :  0.041   0.188    721
  Planarity :  0.004   0.047    728
  Dihedral  :  6.958  54.605    656
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  9.37 %
    Allowed  : 34.83 %
    Favored  : 55.80 %
  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 (0.36), residues: 520
  helix:  2.32 (0.33), residues: 223
  sheet: -0.40 (0.70), residues: 62
  loop : -2.49 (0.32), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP e  59 
 HIS   0.002   0.001   HIS g  29 
 PHE   0.037   0.002   PHE e 110 
 TYR   0.017   0.001   TYR g 100 
 ARG   0.003   0.000   ARG g  82 

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 166
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   30 LYS cc_start: 0.8326 (tmmt) cc_final: 0.8099 (mmtm)
REVERT: a   46 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7089 (tt)
REVERT: a   52 ARG cc_start: 0.6776 (ttt180) cc_final: 0.6272 (ttt180)
REVERT: b   34 LEU cc_start: 0.7703 (tt) cc_final: 0.7119 (mm)
REVERT: d   22 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.8018 (m-80)
REVERT: d   63 ARG cc_start: 0.8911 (ttm170) cc_final: 0.8194 (mtp-110)
REVERT: d   72 ARG cc_start: 0.7752 (tpt-90) cc_final: 0.7444 (tpt-90)
REVERT: d   92 MET cc_start: 0.8543 (mtp) cc_final: 0.7986 (mmt)
REVERT: d   98 GLU cc_start: 0.8371 (tm-30) cc_final: 0.6984 (tm-30)
REVERT: d  120 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8150 (tp)
REVERT: e   87 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8149 (t80)
REVERT: e   92 GLN cc_start: 0.8763 (tt0) cc_final: 0.8304 (tt0)
REVERT: e  145 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8065 (tt)
REVERT: e  147 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7939 (mm)
REVERT: f   97 VAL cc_start: 0.9077 (m) cc_final: 0.8765 (p)
REVERT: f  104 LYS cc_start: 0.9267 (ttmt) cc_final: 0.8742 (tmmt)
REVERT: f  106 GLU cc_start: 0.8282 (mp0) cc_final: 0.7967 (mp0)
REVERT: f  121 ASN cc_start: 0.9219 (t0) cc_final: 0.8736 (t0)
REVERT: f  125 MET cc_start: 0.7114 (pmm) cc_final: 0.6834 (pmm)
REVERT: g   34 TYR cc_start: 0.8579 (t80) cc_final: 0.8309 (t80)
REVERT: g   61 MET cc_start: 0.6651 (mmm) cc_final: 0.6358 (tpt)
REVERT: g  119 LEU cc_start: 0.9066 (tp) cc_final: 0.8765 (tp)
REVERT: n  259 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7652 (t0)
  outliers start: 46
  outliers final: 29
  residues processed: 193
  average time/residue: 0.1425
  time to fit residues: 34.8944
Evaluate side-chains
  192 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 156
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   46 LEU
Chi-restraints excluded: chain b residue   41 ILE
Chi-restraints excluded: chain d residue   22 PHE
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue   96 CYS
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain d residue  116 LEU
Chi-restraints excluded: chain d residue  120 LEU
Chi-restraints excluded: chain e residue   34 THR
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   65 ASN
Chi-restraints excluded: chain e residue   87 PHE
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  129 SER
Chi-restraints excluded: chain e residue  145 LEU
Chi-restraints excluded: chain e residue  147 LEU
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   46 ILE
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue   88 SER
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  126 ILE
Chi-restraints excluded: chain g residue  136 ILE
Chi-restraints excluded: chain m residue  266 VAL
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain m residue  279 VAL
Chi-restraints excluded: chain m residue  283 LEU
Chi-restraints excluded: chain m residue  284 THR
Chi-restraints excluded: chain m residue  286 LYS
Chi-restraints excluded: chain n residue  259 ASN
Chi-restraints excluded: chain n residue  274 VAL
Chi-restraints excluded: chain n residue  280 ILE
Chi-restraints excluded: chain n residue  281 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 35 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9980
   chunk 12 optimal weight:    0.3980
   chunk 16 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   overall best weight:    2.6786

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

Flipped N/Q/H residues before XYZ refinement:
n 259 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.4361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4468  Z= 0.319
  Angle     :  0.812   7.180   6051  Z= 0.405
  Chirality :  0.045   0.175    721
  Planarity :  0.004   0.034    728
  Dihedral  :  7.008  53.709    655
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers : 12.83 %
    Allowed  : 32.18 %
    Favored  : 54.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.34), residues: 520
  helix:  1.88 (0.31), residues: 223
  sheet: -1.18 (0.58), residues: 85
  loop : -2.63 (0.32), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP e  59 
 HIS   0.004   0.001   HIS d  89 
 PHE   0.022   0.002   PHE g 120 
 TYR   0.024   0.002   TYR f 149 
 ARG   0.006   0.001   ARG g  82 

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 63
    poor density    : 160
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   42 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.6168 (t80)
REVERT: a   46 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7130 (tt)
REVERT: a   52 ARG cc_start: 0.6900 (ttt180) cc_final: 0.6307 (ttt180)
REVERT: b   34 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7416 (mm)
REVERT: b   40 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8035 (t80)
REVERT: d   22 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7355 (m-10)
REVERT: d   63 ARG cc_start: 0.9001 (ttm170) cc_final: 0.8259 (mtp-110)
REVERT: d   92 MET cc_start: 0.8476 (mtp) cc_final: 0.8006 (mmt)
REVERT: d   98 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8032 (tm-30)
REVERT: e   79 GLU cc_start: 0.8057 (tp30) cc_final: 0.7854 (tp30)
REVERT: e   87 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8209 (t80)
REVERT: e  145 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8202 (tt)
REVERT: e  147 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7863 (mm)
REVERT: f  104 LYS cc_start: 0.9376 (ttmt) cc_final: 0.8434 (ttpp)
REVERT: f  106 GLU cc_start: 0.8379 (mp0) cc_final: 0.8068 (mp0)
REVERT: f  120 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8817 (tm-30)
REVERT: f  121 ASN cc_start: 0.9198 (t0) cc_final: 0.8513 (t0)
REVERT: f  125 MET cc_start: 0.7509 (pmm) cc_final: 0.7085 (pmm)
REVERT: g   34 TYR cc_start: 0.8546 (t80) cc_final: 0.8196 (t80)
REVERT: g   38 GLU cc_start: 0.8536 (pm20) cc_final: 0.8313 (pm20)
REVERT: g   61 MET cc_start: 0.6935 (mmm) cc_final: 0.6430 (tpt)
REVERT: m  272 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8480 (mp)
REVERT: n  259 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.7866 (t0)
  outliers start: 63
  outliers final: 40
  residues processed: 198
  average time/residue: 0.1421
  time to fit residues: 36.3408
Evaluate side-chains
  202 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 152
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   34 LEU
Chi-restraints excluded: chain a residue   42 TYR
Chi-restraints excluded: chain a residue   46 LEU
Chi-restraints excluded: chain a residue   53 VAL
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain b residue   40 PHE
Chi-restraints excluded: chain b residue   41 ILE
Chi-restraints excluded: chain b residue   53 VAL
Chi-restraints excluded: chain d residue   22 PHE
Chi-restraints excluded: chain d residue   35 VAL
Chi-restraints excluded: chain d residue   42 THR
Chi-restraints excluded: chain d residue   60 LEU
Chi-restraints excluded: chain d residue   66 ASP
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain e residue   34 THR
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   65 ASN
Chi-restraints excluded: chain e residue   66 ILE
Chi-restraints excluded: chain e residue   87 PHE
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  129 SER
Chi-restraints excluded: chain e residue  145 LEU
Chi-restraints excluded: chain e residue  147 LEU
Chi-restraints excluded: chain e residue  152 SER
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   46 ILE
Chi-restraints excluded: chain f residue   77 SER
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  137 ASP
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  147 LEU
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  126 ILE
Chi-restraints excluded: chain m residue  256 THR
Chi-restraints excluded: chain m residue  266 VAL
Chi-restraints excluded: chain m residue  269 LEU
Chi-restraints excluded: chain m residue  272 LEU
Chi-restraints excluded: chain m residue  276 THR
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain m residue  279 VAL
Chi-restraints excluded: chain m residue  283 LEU
Chi-restraints excluded: chain m residue  284 THR
Chi-restraints excluded: chain m residue  286 LYS
Chi-restraints excluded: chain n residue  259 ASN
Chi-restraints excluded: chain n residue  274 VAL
Chi-restraints excluded: chain n residue  281 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 4 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
e 109 ASN
n 259 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.4522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4468  Z= 0.203
  Angle     :  0.734  10.294   6051  Z= 0.358
  Chirality :  0.042   0.149    721
  Planarity :  0.003   0.029    728
  Dihedral  :  6.749  54.522    653
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  9.57 %
    Allowed  : 37.88 %
    Favored  : 52.55 %
  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 (0.35), residues: 520
  helix:  2.10 (0.32), residues: 223
  sheet: -1.19 (0.57), residues: 85
  loop : -2.64 (0.33), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP e  59 
 HIS   0.002   0.001   HIS e  61 
 PHE   0.032   0.002   PHE a  40 
 TYR   0.021   0.001   TYR g  85 
 ARG   0.003   0.000   ARG g  82 

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 157
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   42 TYR cc_start: 0.6964 (OUTLIER) cc_final: 0.5203 (t80)
REVERT: a   46 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7119 (tt)
REVERT: a   52 ARG cc_start: 0.6854 (ttt180) cc_final: 0.6186 (ttt180)
REVERT: b   34 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7349 (mm)
REVERT: d   22 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7366 (m-10)
REVERT: d   63 ARG cc_start: 0.8965 (ttm170) cc_final: 0.8248 (mtp-110)
REVERT: d   92 MET cc_start: 0.8491 (mtp) cc_final: 0.7986 (mmt)
REVERT: d   98 GLU cc_start: 0.8550 (tm-30) cc_final: 0.7340 (tm-30)
REVERT: e   79 GLU cc_start: 0.8010 (tp30) cc_final: 0.7807 (tp30)
REVERT: e   87 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8170 (t80)
REVERT: e  110 PHE cc_start: 0.7517 (t80) cc_final: 0.7086 (t80)
REVERT: e  145 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8205 (tt)
REVERT: e  147 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7928 (mm)
REVERT: f   59 TRP cc_start: 0.7654 (m100) cc_final: 0.7177 (m100)
REVERT: f  115 ARG cc_start: 0.7338 (ttm-80) cc_final: 0.7050 (ttm-80)
REVERT: f  120 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8729 (tm-30)
REVERT: f  121 ASN cc_start: 0.9192 (t0) cc_final: 0.8479 (t0)
REVERT: f  125 MET cc_start: 0.7302 (pmm) cc_final: 0.6906 (pmm)
REVERT: g   34 TYR cc_start: 0.8609 (t80) cc_final: 0.8294 (t80)
REVERT: g   61 MET cc_start: 0.6823 (mmm) cc_final: 0.6573 (tpt)
REVERT: g  111 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8510 (p0)
REVERT: g  119 LEU cc_start: 0.9070 (tp) cc_final: 0.8868 (tp)
REVERT: n  256 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7736 (tm-30)
  outliers start: 47
  outliers final: 34
  residues processed: 183
  average time/residue: 0.1517
  time to fit residues: 35.4587
Evaluate side-chains
  194 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 152
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   42 TYR
Chi-restraints excluded: chain a residue   46 LEU
Chi-restraints excluded: chain b residue   32 CYS
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain b residue   40 PHE
Chi-restraints excluded: chain b residue   41 ILE
Chi-restraints excluded: chain d residue   22 PHE
Chi-restraints excluded: chain d residue   35 VAL
Chi-restraints excluded: chain d residue   42 THR
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain e residue   34 THR
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   65 ASN
Chi-restraints excluded: chain e residue   66 ILE
Chi-restraints excluded: chain e residue   87 PHE
Chi-restraints excluded: chain e residue  109 ASN
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  129 SER
Chi-restraints excluded: chain e residue  145 LEU
Chi-restraints excluded: chain e residue  147 LEU
Chi-restraints excluded: chain e residue  152 SER
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   46 ILE
Chi-restraints excluded: chain f residue   77 SER
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  137 ASP
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  111 ASN
Chi-restraints excluded: chain g residue  126 ILE
Chi-restraints excluded: chain m residue  266 VAL
Chi-restraints excluded: chain m residue  269 LEU
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain m residue  279 VAL
Chi-restraints excluded: chain m residue  283 LEU
Chi-restraints excluded: chain m residue  284 THR
Chi-restraints excluded: chain n residue  274 VAL
Chi-restraints excluded: chain n residue  280 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 29 optimal weight:    8.9990
   chunk 22 optimal weight:    0.0060
   chunk 19 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 32 optimal weight:    7.9990
   overall best weight:    1.1202

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

Flipped N/Q/H residues before XYZ refinement:
e 109 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.4646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4468  Z= 0.209
  Angle     :  0.758  10.299   6051  Z= 0.369
  Chirality :  0.042   0.146    721
  Planarity :  0.003   0.028    728
  Dihedral  :  6.697  53.635    653
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers : 10.39 %
    Allowed  : 38.70 %
    Favored  : 50.92 %
  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: -0.39 (0.35), residues: 520
  helix:  2.09 (0.32), residues: 224
  sheet: -1.14 (0.57), residues: 85
  loop : -2.62 (0.33), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP e  59 
 HIS   0.002   0.001   HIS e  61 
 PHE   0.025   0.002   PHE g 120 
 TYR   0.015   0.001   TYR g 100 
 ARG   0.003   0.000   ARG g  82 

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 154
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   42 TYR cc_start: 0.6967 (OUTLIER) cc_final: 0.5540 (t80)
REVERT: a   46 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7115 (tt)
REVERT: a   52 ARG cc_start: 0.6793 (ttt180) cc_final: 0.6065 (ttt180)
REVERT: b   34 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7285 (mm)
REVERT: d   22 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7368 (m-10)
REVERT: d   63 ARG cc_start: 0.8965 (ttm170) cc_final: 0.8248 (mtp-110)
REVERT: d   72 ARG cc_start: 0.7555 (tpp80) cc_final: 0.7329 (tpp80)
REVERT: d   92 MET cc_start: 0.8500 (mtp) cc_final: 0.7995 (mmt)
REVERT: d   98 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7496 (tm-30)
REVERT: e   79 GLU cc_start: 0.8137 (tp30) cc_final: 0.7902 (tp30)
REVERT: e   87 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.8246 (t80)
REVERT: e  110 PHE cc_start: 0.7497 (t80) cc_final: 0.7096 (t80)
REVERT: e  115 ARG cc_start: 0.8146 (ttm110) cc_final: 0.7890 (ttm110)
REVERT: e  119 CYS cc_start: 0.5159 (OUTLIER) cc_final: 0.4642 (t)
REVERT: e  145 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8150 (tt)
REVERT: e  147 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7888 (mm)
REVERT: f   59 TRP cc_start: 0.7618 (m100) cc_final: 0.7156 (m100)
REVERT: f  104 LYS cc_start: 0.9239 (ttmt) cc_final: 0.8853 (ttpp)
REVERT: f  110 PHE cc_start: 0.7120 (p90) cc_final: 0.6743 (p90)
REVERT: f  115 ARG cc_start: 0.7340 (ttm-80) cc_final: 0.7024 (ttm-80)
REVERT: f  120 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8717 (tm-30)
REVERT: f  121 ASN cc_start: 0.9214 (t0) cc_final: 0.8506 (t0)
REVERT: f  125 MET cc_start: 0.7278 (pmm) cc_final: 0.6886 (pmm)
REVERT: g   34 TYR cc_start: 0.8622 (t80) cc_final: 0.8302 (t80)
REVERT: g   61 MET cc_start: 0.6685 (mmm) cc_final: 0.6439 (tpt)
REVERT: g   82 ARG cc_start: 0.8652 (mmt90) cc_final: 0.8281 (mmt-90)
REVERT: g  111 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8523 (p0)
REVERT: g  119 LEU cc_start: 0.9072 (tp) cc_final: 0.8870 (tp)
REVERT: n  256 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7757 (tm-30)
  outliers start: 51
  outliers final: 36
  residues processed: 185
  average time/residue: 0.1443
  time to fit residues: 33.6490
Evaluate side-chains
  194 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 149
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   42 TYR
Chi-restraints excluded: chain a residue   46 LEU
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain b residue   41 ILE
Chi-restraints excluded: chain b residue   53 VAL
Chi-restraints excluded: chain d residue   22 PHE
Chi-restraints excluded: chain d residue   35 VAL
Chi-restraints excluded: chain d residue   42 THR
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain d residue  116 LEU
Chi-restraints excluded: chain e residue   34 THR
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   65 ASN
Chi-restraints excluded: chain e residue   66 ILE
Chi-restraints excluded: chain e residue   87 PHE
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain e residue  129 SER
Chi-restraints excluded: chain e residue  145 LEU
Chi-restraints excluded: chain e residue  147 LEU
Chi-restraints excluded: chain e residue  152 SER
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   46 ILE
Chi-restraints excluded: chain f residue   77 SER
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  137 ASP
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  144 LEU
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  111 ASN
Chi-restraints excluded: chain g residue  126 ILE
Chi-restraints excluded: chain m residue  256 THR
Chi-restraints excluded: chain m residue  266 VAL
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain m residue  279 VAL
Chi-restraints excluded: chain m residue  283 LEU
Chi-restraints excluded: chain m residue  284 THR
Chi-restraints excluded: chain n residue  257 LEU
Chi-restraints excluded: chain n residue  274 VAL
Chi-restraints excluded: chain n residue  280 ILE
Chi-restraints excluded: chain n residue  281 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0470
   chunk 27 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 35 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    1.5682

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

Flipped N/Q/H residues before XYZ refinement:
g  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.4935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4468  Z= 0.233
  Angle     :  0.754  11.164   6051  Z= 0.370
  Chirality :  0.042   0.147    721
  Planarity :  0.004   0.027    728
  Dihedral  :  6.656  53.081    653
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers : 10.39 %
    Allowed  : 38.29 %
    Favored  : 51.32 %
  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 (0.34), residues: 520
  helix:  2.11 (0.32), residues: 223
  sheet: -1.00 (0.62), residues: 71
  loop : -2.64 (0.31), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP e  59 
 HIS   0.001   0.001   HIS d  89 
 PHE   0.028   0.002   PHE a  40 
 TYR   0.026   0.002   TYR n 276 
 ARG   0.002   0.000   ARG g  82 

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 153
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   42 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6400 (t80)
REVERT: a   46 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7109 (tt)
REVERT: a   52 ARG cc_start: 0.6817 (ttt180) cc_final: 0.6084 (ttt180)
REVERT: b   34 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7404 (mm)
REVERT: d   22 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7368 (m-10)
REVERT: d   63 ARG cc_start: 0.8980 (ttm170) cc_final: 0.8205 (mtp-110)
REVERT: d   72 ARG cc_start: 0.7511 (tpp80) cc_final: 0.7270 (tpp80)
REVERT: d   92 MET cc_start: 0.8514 (mtp) cc_final: 0.8072 (mmt)
REVERT: d   98 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7613 (tm-30)
REVERT: e   79 GLU cc_start: 0.8248 (tp30) cc_final: 0.7972 (tp30)
REVERT: e   87 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8176 (t80)
REVERT: e  110 PHE cc_start: 0.7574 (t80) cc_final: 0.7205 (t80)
REVERT: e  115 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7869 (ttm110)
REVERT: e  119 CYS cc_start: 0.5468 (OUTLIER) cc_final: 0.4901 (t)
REVERT: e  145 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8172 (tt)
REVERT: e  147 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7793 (mm)
REVERT: f   59 TRP cc_start: 0.7501 (m100) cc_final: 0.6608 (m100)
REVERT: f  104 LYS cc_start: 0.9215 (ttmt) cc_final: 0.8865 (ttpp)
REVERT: f  110 PHE cc_start: 0.7206 (p90) cc_final: 0.6816 (p90)
REVERT: f  115 ARG cc_start: 0.7384 (ttm-80) cc_final: 0.7076 (ttm-80)
REVERT: f  120 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8723 (tm-30)
REVERT: f  121 ASN cc_start: 0.9222 (t0) cc_final: 0.8462 (t0)
REVERT: f  125 MET cc_start: 0.7285 (pmm) cc_final: 0.6912 (pmm)
REVERT: g   34 TYR cc_start: 0.8621 (t80) cc_final: 0.8256 (t80)
REVERT: g   61 MET cc_start: 0.6712 (mmm) cc_final: 0.6489 (tpt)
REVERT: g  111 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8513 (p0)
  outliers start: 51
  outliers final: 37
  residues processed: 185
  average time/residue: 0.1534
  time to fit residues: 35.7465
Evaluate side-chains
  194 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 148
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   42 TYR
Chi-restraints excluded: chain a residue   46 LEU
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain b residue   41 ILE
Chi-restraints excluded: chain b residue   49 LEU
Chi-restraints excluded: chain b residue   53 VAL
Chi-restraints excluded: chain d residue   22 PHE
Chi-restraints excluded: chain d residue   35 VAL
Chi-restraints excluded: chain d residue   42 THR
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain d residue  116 LEU
Chi-restraints excluded: chain d residue  124 CYS
Chi-restraints excluded: chain e residue   34 THR
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   65 ASN
Chi-restraints excluded: chain e residue   66 ILE
Chi-restraints excluded: chain e residue   87 PHE
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain e residue  129 SER
Chi-restraints excluded: chain e residue  145 LEU
Chi-restraints excluded: chain e residue  147 LEU
Chi-restraints excluded: chain e residue  152 SER
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   46 ILE
Chi-restraints excluded: chain f residue   77 SER
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  137 ASP
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  144 LEU
Chi-restraints excluded: chain g residue   42 VAL
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  111 ASN
Chi-restraints excluded: chain m residue  266 VAL
Chi-restraints excluded: chain m residue  269 LEU
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain m residue  279 VAL
Chi-restraints excluded: chain m residue  283 LEU
Chi-restraints excluded: chain m residue  284 THR
Chi-restraints excluded: chain n residue  257 LEU
Chi-restraints excluded: chain n residue  274 VAL
Chi-restraints excluded: chain n residue  280 ILE
Chi-restraints excluded: chain n residue  281 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0270
   chunk 29 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0870
   chunk 28 optimal weight:    0.0670
   chunk 22 optimal weight:    0.1980
   chunk 33 optimal weight:    7.9990
   chunk 49 optimal weight:    0.2980
   chunk 45 optimal weight:    0.8980
   chunk 39 optimal weight:   10.0000
   overall best weight:    0.1354

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

Flipped N/Q/H residues before XYZ refinement:
** f  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
m 280 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.5033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4468  Z= 0.203
  Angle     :  0.809  11.454   6051  Z= 0.388
  Chirality :  0.043   0.150    721
  Planarity :  0.003   0.028    728
  Dihedral  :  6.710  55.043    653
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  : 42.57 %
    Favored  : 50.92 %
  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: -0.41 (0.34), residues: 520
  helix:  2.11 (0.32), residues: 225
  sheet: -1.42 (0.64), residues: 61
  loop : -2.51 (0.31), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP e  59 
 HIS   0.004   0.001   HIS e  61 
 PHE   0.025   0.002   PHE g 120 
 TYR   0.012   0.001   TYR g 100 
 ARG   0.003   0.000   ARG n 287 

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 157
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
REVERT: a   42 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.4564 (t80)
REVERT: a   46 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7169 (tt)
REVERT: a   52 ARG cc_start: 0.6786 (ttt180) cc_final: 0.6029 (ttt180)
REVERT: b   34 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7241 (mm)
REVERT: b   40 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.7870 (t80)
REVERT: d   22 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7292 (m-10)
REVERT: d   63 ARG cc_start: 0.8910 (ttm170) cc_final: 0.8145 (mtp-110)
REVERT: d   72 ARG cc_start: 0.7516 (tpp80) cc_final: 0.7211 (tpp80)
REVERT: d   92 MET cc_start: 0.8513 (mtp) cc_final: 0.8036 (mmt)
REVERT: d   98 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7764 (tm-30)
REVERT: e   87 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8225 (t80)
REVERT: e  110 PHE cc_start: 0.7561 (t80) cc_final: 0.7254 (t80)
REVERT: e  115 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7660 (ttp-110)
REVERT: e  119 CYS cc_start: 0.5013 (OUTLIER) cc_final: 0.4435 (t)
REVERT: e  145 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8281 (tt)
REVERT: f  104 LYS cc_start: 0.9170 (ttmt) cc_final: 0.8946 (ttpt)
REVERT: f  110 PHE cc_start: 0.7266 (p90) cc_final: 0.6866 (p90)
REVERT: f  121 ASN cc_start: 0.9237 (t0) cc_final: 0.8584 (t0)
REVERT: f  125 MET cc_start: 0.7072 (pmm) cc_final: 0.6709 (pmm)
REVERT: g   34 TYR cc_start: 0.8714 (t80) cc_final: 0.8450 (t80)
REVERT: g   61 MET cc_start: 0.6455 (mmm) cc_final: 0.6156 (tpt)
REVERT: g   82 ARG cc_start: 0.8573 (mmt90) cc_final: 0.8318 (mmt-90)
REVERT: g  111 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8459 (p0)
  outliers start: 32
  outliers final: 19
  residues processed: 172
  average time/residue: 0.1561
  time to fit residues: 33.4734
Evaluate side-chains
  177 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 149
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   42 TYR
Chi-restraints excluded: chain a residue   46 LEU
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain b residue   40 PHE
Chi-restraints excluded: chain b residue   49 LEU
Chi-restraints excluded: chain d residue   22 PHE
Chi-restraints excluded: chain d residue   35 VAL
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain d residue  116 LEU
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   87 PHE
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain e residue  145 LEU
Chi-restraints excluded: chain f residue   36 TYR
Chi-restraints excluded: chain f residue   77 SER
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  137 ASP
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  147 LEU
Chi-restraints excluded: chain g residue  111 ASN
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain n residue  257 LEU
Chi-restraints excluded: chain n residue  280 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 12 optimal weight:    0.1980
   chunk 36 optimal weight:    0.0870
   chunk 5 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 16 optimal weight:    0.3980
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
** f  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
g  86 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.5260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4468  Z= 0.214
  Angle     :  0.804   8.427   6051  Z= 0.390
  Chirality :  0.043   0.221    721
  Planarity :  0.004   0.027    728
  Dihedral  :  6.509  51.442    653
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 43.99 %
    Favored  : 50.31 %
  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: -0.27 (0.35), residues: 520
  helix:  2.32 (0.32), residues: 224
  sheet: -1.40 (0.63), residues: 61
  loop : -2.50 (0.31), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP e  59 
 HIS   0.002   0.001   HIS e  61 
 PHE   0.029   0.002   PHE a  40 
 TYR   0.012   0.001   TYR g 100 
 ARG   0.002   0.000   ARG g  82 

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 147
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   42 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.4449 (t80)
REVERT: a   46 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7140 (tt)
REVERT: a   52 ARG cc_start: 0.6699 (ttt180) cc_final: 0.6079 (ttt180)
REVERT: b   34 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7194 (mm)
REVERT: b   40 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7948 (t80)
REVERT: d   22 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7351 (m-10)
REVERT: d   63 ARG cc_start: 0.8938 (ttm170) cc_final: 0.8129 (mtp-110)
REVERT: d   72 ARG cc_start: 0.7521 (tpp80) cc_final: 0.7191 (tpp80)
REVERT: d   92 MET cc_start: 0.8444 (mtp) cc_final: 0.8004 (mmt)
REVERT: d   98 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7805 (tm-30)
REVERT: e   87 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.8220 (t80)
REVERT: e  115 ARG cc_start: 0.8067 (ttm110) cc_final: 0.7643 (ttp-110)
REVERT: e  119 CYS cc_start: 0.5270 (OUTLIER) cc_final: 0.4723 (t)
REVERT: e  145 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8071 (tt)
REVERT: f  104 LYS cc_start: 0.9164 (ttmt) cc_final: 0.8843 (ttpp)
REVERT: f  110 PHE cc_start: 0.7265 (p90) cc_final: 0.6852 (p90)
REVERT: f  121 ASN cc_start: 0.9246 (t0) cc_final: 0.8292 (t0)
REVERT: f  125 MET cc_start: 0.7137 (pmm) cc_final: 0.6806 (pmm)
REVERT: g   34 TYR cc_start: 0.8716 (t80) cc_final: 0.8438 (t80)
REVERT: g  111 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8433 (p0)
  outliers start: 28
  outliers final: 18
  residues processed: 161
  average time/residue: 0.1527
  time to fit residues: 31.0904
Evaluate side-chains
  172 residues out of total 491 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   42 TYR
Chi-restraints excluded: chain a residue   46 LEU
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain b residue   40 PHE
Chi-restraints excluded: chain b residue   49 LEU
Chi-restraints excluded: chain d residue   22 PHE
Chi-restraints excluded: chain d residue   35 VAL
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain d residue  116 LEU
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   87 PHE
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain e residue  145 LEU
Chi-restraints excluded: chain e residue  152 SER
Chi-restraints excluded: chain f residue   77 SER
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  147 LEU
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  111 ASN
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain n residue  257 LEU
Chi-restraints excluded: chain n residue  280 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    0.0770
   chunk 5 optimal weight:    8.9990
   chunk 7 optimal weight:    7.9990
   chunk 34 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 31 optimal weight:   20.0000
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** f  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
m 280 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.139205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.108651 restraints weight = 9981.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.110700 restraints weight = 7471.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.111567 restraints weight = 5065.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.5402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4468  Z= 0.208
  Angle     :  0.824  11.469   6051  Z= 0.394
  Chirality :  0.042   0.148    721
  Planarity :  0.003   0.027    728
  Dihedral  :  6.558  51.697    653
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  : 43.38 %
    Favored  : 50.10 %
  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: -0.20 (0.35), residues: 520
  helix:  2.38 (0.32), residues: 224
  sheet: -0.94 (0.62), residues: 71
  loop : -2.66 (0.30), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP e  59 
 HIS   0.003   0.001   HIS e  61 
 PHE   0.025   0.002   PHE g 120 
 TYR   0.012   0.001   TYR e  36 
 ARG   0.002   0.000   ARG n 287 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1404.68 seconds
wall clock time: 25 minutes 27.25 seconds (1527.25 seconds total)