Starting phenix.real_space_refine
on Sat May 10 06:08:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8aw3_15690/05_2025/8aw3_15690.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8aw3_15690/05_2025/8aw3_15690.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8aw3_15690/05_2025/8aw3_15690.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8aw3_15690/05_2025/8aw3_15690.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8aw3_15690/05_2025/8aw3_15690.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8aw3_15690/05_2025/8aw3_15690.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      73      5.49       5
     S      26      5.16       5
     C    2899      2.51       5
     N     903      2.21       5
     O    1156      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5059
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "1"
      Number of atoms: 1557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1557
          Classifications: {'RNA': 73}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 30, 'rna3p_pyr': 30}
          Link IDs: {'rna2p': 13, 'rna3p': 59}
    Chain: "2"
      Number of atoms: 1341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 177, 1341
          Classifications: {'peptide': 177}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 172}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "3"
      Number of atoms: 2159
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2159
          Classifications: {'peptide': 279}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 18, 'TRANS': 260}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "2"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "3"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2293  SG  CYS 2 136      45.404  41.101  78.006  1.00 52.15           S
  ATOM   2315  SG  CYS 2 139      46.023  40.789  81.160  1.00 49.74           S
  ATOM   4670  SG  CYS 3 291      40.792  29.700  77.854  1.00 52.47           S
  ATOM   4691  SG  CYS 3 294      44.534  28.750  76.195  1.00 55.91           S

  Time building chain proxies: 3.92, per 1000 atoms: 0.77
  Number of scatterers: 5059
  At special positions: 0
  Unit cell: (76.14, 76.95, 115.83, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      26     16.00
     P      73     15.00
     O    1156      8.00
     N     903      7.00
     C    2899      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.30
  Conformation dependent library (CDL) restraints added in 566.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN 2 501 "
        pdb="ZN    ZN 2 501 " - pdb=" ND1 HIS 2  90 "
        pdb="ZN    ZN 2 501 " - pdb=" SG  CYS 2 136 "
        pdb="ZN    ZN 2 501 " - pdb=" SG  CYS 2 139 "
      pdb="  ZN 3 501 "
        pdb="ZN    ZN 3 501 " - pdb=" SG  CYS 3 294 "
        pdb="ZN    ZN 3 501 " - pdb=" ND1 HIS 3 252 "
        pdb="ZN    ZN 3 501 " - pdb=" SG  CYS 3 291 "


  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  856

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 3 sheets defined
      37.1% alpha, 12.1% beta
      20 base pairs and 35 stacking pairs defined.
    Time for finding SS restraints: 1.82
  Creating SS restraints...
    Processing helix  chain '2' and resid 24 through 42
      removed outlier: 3.525A  pdb=" N   ALA 2  35 " --> pdb=" O   ALA 2  31 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   THR 2  36 " --> pdb=" O   LEU 2  32 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   CYS 2  37 " --> pdb=" O   LYS 2  33 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ALA 2  38 " --> pdb=" O   GLU 2  34 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 53 through 56
      removed outlier: 4.032A  pdb=" N   SER 2  56 " --> pdb=" O   ALA 2  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain '2' and resid 53 through 56'
    Processing helix  chain '2' and resid 57 through 61
    Processing helix  chain '2' and resid 65 through 72
    Processing helix  chain '2' and resid 91 through 103
      removed outlier: 3.620A  pdb=" N   VAL 2  96 " --> pdb=" O   GLU 2  92 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   GLU 2  97 " --> pdb=" O   PHE 2  93 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ALA 2 103 " --> pdb=" O   LEU 2  99 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 136 through 146
    Processing helix  chain '2' and resid 193 through 207
      removed outlier: 3.712A  pdb=" N   LEU 2 201 " --> pdb=" O   ALA 2 197 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE 2 204 " --> pdb=" O   LEU 2 200 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   TYR 2 205 " --> pdb=" O   LEU 2 201 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ARG 2 207 " --> pdb=" O   GLN 2 203 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 23 through 38
      removed outlier: 3.592A  pdb=" N   CYS 3  27 " --> pdb=" O   GLN 3  23 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   SER 3  32 " --> pdb=" O   THR 3  28 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 41 through 45
      removed outlier: 3.670A  pdb=" N   CYS 3  45 " --> pdb=" O   PRO 3  42 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 117 through 129
    Processing helix  chain '3' and resid 147 through 154
      removed outlier: 3.775A  pdb=" N   TRP 3 154 " --> pdb=" O   GLU 3 150 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 172 through 186
      removed outlier: 3.551A  pdb=" N   VAL 3 176 " --> pdb=" O   SER 3 172 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLY 3 177 " --> pdb=" O   GLU 3 173 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 186 through 195
      removed outlier: 3.838A  pdb=" N   ARG 3 195 " --> pdb=" O   ALA 3 191 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 220 through 224
    Processing helix  chain '3' and resid 254 through 259
      removed outlier: 3.669A  pdb=" N   LEU 3 258 " --> pdb=" O   VAL 3 254 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 291 through 301
      removed outlier: 3.506A  pdb=" N   MET 3 296 " --> pdb=" O   VAL 3 292 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 323 through 327
    Processing sheet with id=AA1, first strand: chain '2' and resid 73 through 78
      removed outlier: 7.200A  pdb=" N   GLY 2  47 " --> pdb=" O   VAL 2 132 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   LEU 2 129 " --> pdb=" O   TYR 2 152 " (cutoff:3.500A)
      removed outlier: 8.177A  pdb=" N   GLY 2 154 " --> pdb=" O   LEU 2 129 " (cutoff:3.500A)
      removed outlier: 9.061A  pdb=" N   VAL 2 131 " --> pdb=" O   GLY 2 154 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain '3' and resid 1 through 4
      removed outlier: 4.868A  pdb=" N   VAL 3 336 " --> pdb=" O   VAL 3   4 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   VAL 3 306 " --> pdb=" O   PHE 3 337 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   CYS 3 339 " --> pdb=" O   VAL 3 306 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   TYR 3 308 " --> pdb=" O   CYS 3 339 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   LEU 3 206 " --> pdb=" O   LEU 3 216 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ARG 3 214 " --> pdb=" O   ASP 3 208 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain '3' and resid 106 through 111
      removed outlier: 3.915A  pdb=" N   LEU 3 106 " --> pdb=" O   VAL 3  21 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   LEU 3  17 " --> pdb=" O   LEU 3 110 " (cutoff:3.500A)

    115 hydrogen bonds defined for protein.
    312 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      50 hydrogen bonds
      88 hydrogen bond angles
      0 basepair planarities
      20 basepair parallelities
      35 stacking parallelities
  Total time for adding SS restraints: 1.41

  Time building geometry restraints manager: 1.51 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 701
        1.32 -     1.44: 1769
        1.44 -     1.56: 2652
        1.56 -     1.69: 145
        1.69 -     1.81: 36
  Bond restraints: 5303
  Sorted by residual:
  bond pdb=" C1'   G 1  70 "
       pdb=" N9    G 1  70 "
    ideal  model  delta    sigma   weight residual
    1.475  1.383  0.092 1.50e-02 4.44e+03 3.72e+01
  bond pdb=" C1'   U 1  73 "
       pdb=" N1    U 1  73 "
    ideal  model  delta    sigma   weight residual
    1.480  1.561 -0.081 1.50e-02 4.44e+03 2.89e+01
  bond pdb=" C1'   C 1  20 "
       pdb=" N1    C 1  20 "
    ideal  model  delta    sigma   weight residual
    1.480  1.558 -0.078 1.50e-02 4.44e+03 2.73e+01
  bond pdb=" C1'   A 1  52 "
       pdb=" N9    A 1  52 "
    ideal  model  delta    sigma   weight residual
    1.475  1.397  0.078 1.50e-02 4.44e+03 2.70e+01
  bond pdb=" C1'   C 1  65 "
       pdb=" N1    C 1  65 "
    ideal  model  delta    sigma   weight residual
    1.480  1.556 -0.076 1.50e-02 4.44e+03 2.57e+01
  ... (remaining 5298 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.44: 7177
        2.44 -     4.88: 312
        4.88 -     7.33: 41
        7.33 -     9.77: 6
        9.77 -    12.21: 5
  Bond angle restraints: 7541
  Sorted by residual:
  angle pdb=" C   LEU 3 194 "
        pdb=" N   ARG 3 195 "
        pdb=" CA  ARG 3 195 "
      ideal   model   delta    sigma   weight residual
     123.05  110.84   12.21 1.40e+00 5.10e-01 7.61e+01
  angle pdb=" N   THR 3 196 "
        pdb=" CA  THR 3 196 "
        pdb=" C   THR 3 196 "
      ideal   model   delta    sigma   weight residual
     109.86   98.09   11.77 1.55e+00 4.16e-01 5.77e+01
  angle pdb=" N   ARG 3 195 "
        pdb=" CA  ARG 3 195 "
        pdb=" C   ARG 3 195 "
      ideal   model   delta    sigma   weight residual
     108.52  120.41  -11.89 1.63e+00 3.76e-01 5.32e+01
  angle pdb=" C   THR 3 199 "
        pdb=" CA  THR 3 199 "
        pdb=" CB  THR 3 199 "
      ideal   model   delta    sigma   weight residual
     109.80  121.45  -11.65 1.65e+00 3.67e-01 4.98e+01
  angle pdb=" N   GLU 3 198 "
        pdb=" CA  GLU 3 198 "
        pdb=" C   GLU 3 198 "
      ideal   model   delta    sigma   weight residual
     111.28  117.87   -6.59 1.09e+00 8.42e-01 3.66e+01
  ... (remaining 7536 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.21: 3061
       34.21 -    68.42: 239
       68.42 -   102.62: 26
      102.62 -   136.83: 1
      136.83 -   171.04: 1
  Dihedral angle restraints: 3328
    sinusoidal: 2008
      harmonic: 1320
  Sorted by residual:
  dihedral pdb=" O4'   U 1  36 "
           pdb=" C1'   U 1  36 "
           pdb=" N1    U 1  36 "
           pdb=" C2    U 1  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   43.04 -171.04     1      1.70e+01 3.46e-03 6.60e+01
  dihedral pdb=" C   THR 3 199 "
           pdb=" N   THR 3 199 "
           pdb=" CA  THR 3 199 "
           pdb=" CB  THR 3 199 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.09   13.09     0      2.50e+00 1.60e-01 2.74e+01
  dihedral pdb=" C   PHE 2 204 "
           pdb=" N   PHE 2 204 "
           pdb=" CA  PHE 2 204 "
           pdb=" CB  PHE 2 204 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.32  -11.28     0      2.50e+00 1.60e-01 2.04e+01
  ... (remaining 3325 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 801
       0.111 -    0.222: 105
       0.222 -    0.332: 10
       0.332 -    0.443: 6
       0.443 -    0.554: 1
  Chirality restraints: 923
  Sorted by residual:
  chirality pdb=" P     G 1   1 "
            pdb=" OP1   G 1   1 "
            pdb=" OP2   G 1   1 "
            pdb=" O5'   G 1   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.96   -0.55 2.00e-01 2.50e+01 7.66e+00
  chirality pdb=" P     C 1  71 "
            pdb=" OP1   C 1  71 "
            pdb=" OP2   C 1  71 "
            pdb=" O5'   C 1  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.80   -0.39 2.00e-01 2.50e+01 3.73e+00
  chirality pdb=" P     G 1  69 "
            pdb=" OP1   G 1  69 "
            pdb=" OP2   G 1  69 "
            pdb=" O5'   G 1  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.78   -0.37 2.00e-01 2.50e+01 3.49e+00
  ... (remaining 920 not shown)

  Planarity restraints: 695
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN 2 203 "   -0.019 2.00e-02 2.50e+03   3.87e-02 1.50e+01
        pdb=" C   GLN 2 203 "    0.067 2.00e-02 2.50e+03
        pdb=" O   GLN 2 203 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   PHE 2 204 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR 2 130 "   -0.005 2.00e-02 2.50e+03   2.15e-02 9.23e+00
        pdb=" CG  TYR 2 130 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR 2 130 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR 2 130 "    0.045 2.00e-02 2.50e+03
        pdb=" CE1 TYR 2 130 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 TYR 2 130 "   -0.030 2.00e-02 2.50e+03
        pdb=" CZ  TYR 2 130 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR 2 130 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA 3 191 "    0.013 2.00e-02 2.50e+03   2.59e-02 6.71e+00
        pdb=" C   ALA 3 191 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ALA 3 191 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LYS 3 192 "    0.015 2.00e-02 2.50e+03
  ... (remaining 692 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.48: 15
        2.48 -     3.08: 3272
        3.08 -     3.69: 8450
        3.69 -     4.29: 12081
        4.29 -     4.90: 17548
  Nonbonded interactions: 41366
  Sorted by model distance:
  nonbonded pdb=" OH  TYR 3 236 "
            pdb="ZN    ZN 3 501 "
     model   vdw
     1.874 2.230
  nonbonded pdb=" O   ARG 3 181 "
            pdb=" OG1 THR 3 185 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   ALA 3 143 "
            pdb=" NH1 ARG 3 145 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" O   GLU 3 289 "
            pdb=" ND2 ASN 3 312 "
     model   vdw
     2.349 3.120
  nonbonded pdb=" O   ILE 3 327 "
            pdb=" NE2 HIS 3 333 "
     model   vdw
     2.350 3.120
  ... (remaining 41361 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.43 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:             1.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.010
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6542
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      :  0.008   0.092   5309  Z= 0.519
  Angle     :  1.102  12.209   7541  Z= 0.715
  Chirality :  0.079   0.554    923
  Planarity :  0.005   0.039    695
  Dihedral  : 20.772 171.040   2472
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  3.44 %
    Favored  : 94.44 %
  Cbeta Deviations :  0.70 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.38), residues: 444
  helix: -0.66 (0.47), residues: 137
  sheet: -2.56 (0.81), residues: 44
  loop : -1.41 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP 3 158 
 HIS   0.007   0.001   HIS 3 300 
 PHE   0.013   0.002   PHE 3 256 
 TYR   0.045   0.004   TYR 2 130 
 ARG   0.007   0.001   ARG 3 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22117 (  165)
  hydrogen bonds       : angle       9.67033 (  400)
  metal coordination   : bond        0.00737 (    6)
  covalent geometry    : bond        0.00789 ( 5303)
  covalent geometry    : angle       1.10164 ( 7541)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   28 MET cc_start: 0.7808 (mmt) cc_final: 0.7552 (tpp)
  outliers start: 8
  outliers final: 2
  residues processed: 75
  average time/residue: 0.2618
  time to fit residues: 23.3491
Evaluate side-chains
  35 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   21 VAL
Chi-restraints excluded: chain 2 residue   44 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 24 optimal weight:   20.0000
   chunk 29 optimal weight:   20.0000
   chunk 46 optimal weight:    0.8980
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
2 211 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.078956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.054179 restraints weight = 29741.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.055160 restraints weight = 16735.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.055823 restraints weight = 12308.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3438
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3438 r_free = 0.3438    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3437
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5309  Z= 0.168
  Angle     :  0.620   7.619   7541  Z= 0.321
  Chirality :  0.039   0.170    923
  Planarity :  0.004   0.035    695
  Dihedral  : 21.958 177.382   1662
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 12.17 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.39), residues: 444
  helix: -0.20 (0.45), residues: 148
  sheet: -2.92 (0.74), residues: 44
  loop : -1.12 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP 3 158 
 HIS   0.004   0.001   HIS 3 300 
 PHE   0.016   0.002   PHE 3 256 
 TYR   0.016   0.002   TYR 2  23 
 ARG   0.005   0.001   ARG 3 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04967 (  165)
  hydrogen bonds       : angle       4.67682 (  400)
  metal coordination   : bond        0.00939 (    6)
  covalent geometry    : bond        0.00365 ( 5303)
  covalent geometry    : angle       0.62045 ( 7541)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   23 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.7079 (t80)
REVERT: 2   28 MET cc_start: 0.8863 (mmt) cc_final: 0.8414 (tpp)
REVERT: 2  134 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6951 (pt0)
  outliers start: 13
  outliers final: 7
  residues processed: 47
  average time/residue: 0.1881
  time to fit residues: 11.4420
Evaluate side-chains
  37 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   21 VAL
Chi-restraints excluded: chain 2 residue   23 TYR
Chi-restraints excluded: chain 2 residue   44 VAL
Chi-restraints excluded: chain 2 residue   86 HIS
Chi-restraints excluded: chain 2 residue   99 LEU
Chi-restraints excluded: chain 2 residue  134 GLU
Chi-restraints excluded: chain 3 residue    6 VAL
Chi-restraints excluded: chain 3 residue  169 THR
Chi-restraints excluded: chain 3 residue  278 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:   40.0000
   chunk 34 optimal weight:    2.9990
   chunk 29 optimal weight:   20.0000
   chunk 26 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 49 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    0.2980
   overall best weight:    3.2588

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

Flipped N/Q/H residues before XYZ refinement:
3 246 ASN
** 3 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.073319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.049942 restraints weight = 29768.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.051142 restraints weight = 17265.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.051999 restraints weight = 12504.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3348
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3348
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5309  Z= 0.239
  Angle     :  0.671  10.700   7541  Z= 0.344
  Chirality :  0.040   0.192    923
  Planarity :  0.005   0.035    695
  Dihedral  : 22.000 175.966   1662
  Min Nonbonded Distance : 1.791

Molprobity Statistics.
  All-atom Clashscore : 15.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 10.85 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.84 (0.39), residues: 444
  helix: -0.81 (0.41), residues: 165
  sheet: -3.18 (0.62), residues: 48
  loop : -0.96 (0.40), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP 3 138 
 HIS   0.004   0.001   HIS 3 223 
 PHE   0.018   0.002   PHE 3 256 
 TYR   0.017   0.003   TYR 2 205 
 ARG   0.007   0.001   ARG 2 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06190 (  165)
  hydrogen bonds       : angle       4.40853 (  400)
  metal coordination   : bond        0.01341 (    6)
  covalent geometry    : bond        0.00511 ( 5303)
  covalent geometry    : angle       0.67146 ( 7541)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 29
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
REVERT: 2   23 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7589 (t80)
REVERT: 2   28 MET cc_start: 0.8695 (mmt) cc_final: 0.8245 (tpp)
REVERT: 2  134 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6969 (pt0)
REVERT: 3  188 MET cc_start: 0.7914 (tmm) cc_final: 0.7405 (ttm)
  outliers start: 22
  outliers final: 14
  residues processed: 49
  average time/residue: 0.1606
  time to fit residues: 10.8029
Evaluate side-chains
  39 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 23
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   21 VAL
Chi-restraints excluded: chain 2 residue   23 TYR
Chi-restraints excluded: chain 2 residue   44 VAL
Chi-restraints excluded: chain 2 residue   86 HIS
Chi-restraints excluded: chain 2 residue   99 LEU
Chi-restraints excluded: chain 2 residue  134 GLU
Chi-restraints excluded: chain 2 residue  173 TYR
Chi-restraints excluded: chain 2 residue  188 SER
Chi-restraints excluded: chain 3 residue    1 MET
Chi-restraints excluded: chain 3 residue    6 VAL
Chi-restraints excluded: chain 3 residue   15 SER
Chi-restraints excluded: chain 3 residue  169 THR
Chi-restraints excluded: chain 3 residue  202 ILE
Chi-restraints excluded: chain 3 residue  278 LEU
Chi-restraints excluded: chain 3 residue  286 VAL
Chi-restraints excluded: chain 3 residue  324 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 24 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0970
   chunk 36 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** 2  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.074812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.051689 restraints weight = 31188.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.052814 restraints weight = 16973.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.053427 restraints weight = 12041.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3399
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3399
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.3940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5309  Z= 0.113
  Angle     :  0.554   9.390   7541  Z= 0.283
  Chirality :  0.037   0.158    923
  Planarity :  0.004   0.029    695
  Dihedral  : 21.690 171.559   1662
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.14 %
    Favored  : 80.42 %
  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: -1.44 (0.39), residues: 444
  helix: -0.36 (0.43), residues: 159
  sheet: -2.84 (0.61), residues: 50
  loop : -0.84 (0.40), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP 3 151 
 HIS   0.002   0.001   HIS 3 300 
 PHE   0.012   0.002   PHE 3 307 
 TYR   0.016   0.001   TYR 2  23 
 ARG   0.004   0.000   ARG 2 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04671 (  165)
  hydrogen bonds       : angle       3.80623 (  400)
  metal coordination   : bond        0.00598 (    6)
  covalent geometry    : bond        0.00242 ( 5303)
  covalent geometry    : angle       0.55358 ( 7541)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 27
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
REVERT: 2   23 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.7314 (t80)
REVERT: 2   28 MET cc_start: 0.8756 (mmt) cc_final: 0.7884 (tpp)
REVERT: 3  188 MET cc_start: 0.7813 (tmm) cc_final: 0.7342 (ttm)
  outliers start: 13
  outliers final: 9
  residues processed: 37
  average time/residue: 0.1574
  time to fit residues: 7.9793
Evaluate side-chains
  34 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 24
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   21 VAL
Chi-restraints excluded: chain 2 residue   23 TYR
Chi-restraints excluded: chain 2 residue   49 VAL
Chi-restraints excluded: chain 2 residue   86 HIS
Chi-restraints excluded: chain 3 residue    1 MET
Chi-restraints excluded: chain 3 residue    6 VAL
Chi-restraints excluded: chain 3 residue  169 THR
Chi-restraints excluded: chain 3 residue  278 LEU
Chi-restraints excluded: chain 3 residue  286 VAL
Chi-restraints excluded: chain 3 residue  321 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0970
   chunk 2 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    3.2186

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

Flipped N/Q/H residues before XYZ refinement:
2  70 GLN
** 3 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.074306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.050625 restraints weight = 31767.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.051494 restraints weight = 17653.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.051984 restraints weight = 12790.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3353
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3353 r_free = 0.3353    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.4687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   5309  Z= 0.244
  Angle     :  0.667  11.337   7541  Z= 0.336
  Chirality :  0.039   0.168    923
  Planarity :  0.005   0.031    695
  Dihedral  : 21.961 174.112   1661
  Min Nonbonded Distance : 1.820

Molprobity Statistics.
  All-atom Clashscore : 16.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 15.34 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.39), residues: 444
  helix: -0.51 (0.43), residues: 160
  sheet: -2.69 (0.60), residues: 48
  loop : -0.97 (0.40), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP 3 138 
 HIS   0.004   0.001   HIS 3 223 
 PHE   0.010   0.002   PHE 3 285 
 TYR   0.015   0.003   TYR 2 205 
 ARG   0.004   0.001   ARG 2 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06555 (  165)
  hydrogen bonds       : angle       4.06076 (  400)
  metal coordination   : bond        0.01076 (    6)
  covalent geometry    : bond        0.00520 ( 5303)
  covalent geometry    : angle       0.66717 ( 7541)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 20
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
REVERT: 2   23 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.7658 (t80)
REVERT: 2   28 MET cc_start: 0.8709 (mmt) cc_final: 0.8310 (tpp)
REVERT: 3  188 MET cc_start: 0.7902 (tmm) cc_final: 0.7637 (tmm)
  outliers start: 19
  outliers final: 13
  residues processed: 37
  average time/residue: 0.1223
  time to fit residues: 6.6473
Evaluate side-chains
  32 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 18
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   21 VAL
Chi-restraints excluded: chain 2 residue   23 TYR
Chi-restraints excluded: chain 2 residue   49 VAL
Chi-restraints excluded: chain 2 residue   70 GLN
Chi-restraints excluded: chain 2 residue   86 HIS
Chi-restraints excluded: chain 2 residue   99 LEU
Chi-restraints excluded: chain 2 residue  188 SER
Chi-restraints excluded: chain 3 residue    1 MET
Chi-restraints excluded: chain 3 residue    6 VAL
Chi-restraints excluded: chain 3 residue  169 THR
Chi-restraints excluded: chain 3 residue  278 LEU
Chi-restraints excluded: chain 3 residue  286 VAL
Chi-restraints excluded: chain 3 residue  321 THR
Chi-restraints excluded: chain 3 residue  324 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 20 optimal weight:    0.2980
   chunk 30 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 5 optimal weight:   10.9990
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    1.8588

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

Flipped N/Q/H residues before XYZ refinement:
2  70 GLN
** 3 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.072707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.049696 restraints weight = 30782.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.050705 restraints weight = 17172.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.051578 restraints weight = 12297.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3357
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3357
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.4861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5309  Z= 0.151
  Angle     :  0.572  10.092   7541  Z= 0.292
  Chirality :  0.037   0.167    923
  Planarity :  0.004   0.029    695
  Dihedral  : 21.856 172.233   1661
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 17.99 %
    Favored  : 78.31 %
  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: -1.30 (0.40), residues: 444
  helix: -0.26 (0.44), residues: 160
  sheet: -2.51 (0.63), residues: 50
  loop : -0.80 (0.40), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP 3 151 
 HIS   0.008   0.001   HIS 3 223 
 PHE   0.009   0.002   PHE 3 256 
 TYR   0.014   0.002   TYR 2  23 
 ARG   0.003   0.000   ARG 3 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05115 (  165)
  hydrogen bonds       : angle       3.76605 (  400)
  metal coordination   : bond        0.00705 (    6)
  covalent geometry    : bond        0.00324 ( 5303)
  covalent geometry    : angle       0.57159 ( 7541)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 21
  time to evaluate  : 0.480 
Fit side-chains
REVERT: 2   23 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.7584 (t80)
REVERT: 2   28 MET cc_start: 0.8725 (mmt) cc_final: 0.7999 (tpp)
REVERT: 3  188 MET cc_start: 0.7857 (tmm) cc_final: 0.7564 (tmm)
REVERT: 3  256 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7676 (t80)
  outliers start: 14
  outliers final: 11
  residues processed: 33
  average time/residue: 0.1256
  time to fit residues: 6.3636
Evaluate side-chains
  33 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 20
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   21 VAL
Chi-restraints excluded: chain 2 residue   23 TYR
Chi-restraints excluded: chain 2 residue   49 VAL
Chi-restraints excluded: chain 2 residue   86 HIS
Chi-restraints excluded: chain 2 residue   99 LEU
Chi-restraints excluded: chain 3 residue    1 MET
Chi-restraints excluded: chain 3 residue    6 VAL
Chi-restraints excluded: chain 3 residue  169 THR
Chi-restraints excluded: chain 3 residue  202 ILE
Chi-restraints excluded: chain 3 residue  256 PHE
Chi-restraints excluded: chain 3 residue  278 LEU
Chi-restraints excluded: chain 3 residue  286 VAL
Chi-restraints excluded: chain 3 residue  321 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 11 optimal weight:    0.4980
   chunk 23 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 15 optimal weight:   10.0000
   chunk 29 optimal weight:    0.6980
   chunk 4 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** 3 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.073691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.051043 restraints weight = 31406.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.051679 restraints weight = 17282.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.052693 restraints weight = 13048.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3397
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3397 r_free = 0.3397    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3397 r_free = 0.3397    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3397
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.4999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5309  Z= 0.110
  Angle     :  0.557  11.117   7541  Z= 0.283
  Chirality :  0.037   0.159    923
  Planarity :  0.003   0.028    695
  Dihedral  : 21.703 171.137   1661
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 18.25 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.40), residues: 444
  helix: -0.04 (0.44), residues: 159
  sheet: -2.17 (0.67), residues: 50
  loop : -0.79 (0.40), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP 3 158 
 HIS   0.005   0.001   HIS 3 223 
 PHE   0.008   0.002   PHE 3 307 
 TYR   0.015   0.001   TYR 2  23 
 ARG   0.002   0.000   ARG 3 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04453 (  165)
  hydrogen bonds       : angle       3.81780 (  400)
  metal coordination   : bond        0.00497 (    6)
  covalent geometry    : bond        0.00238 ( 5303)
  covalent geometry    : angle       0.55733 ( 7541)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 21
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
REVERT: 2   23 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.7373 (t80)
REVERT: 2   28 MET cc_start: 0.8672 (mmt) cc_final: 0.7745 (tpp)
REVERT: 3  188 MET cc_start: 0.7790 (tmm) cc_final: 0.7335 (ttm)
  outliers start: 14
  outliers final: 10
  residues processed: 33
  average time/residue: 0.1268
  time to fit residues: 6.2048
Evaluate side-chains
  30 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 19
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   21 VAL
Chi-restraints excluded: chain 2 residue   23 TYR
Chi-restraints excluded: chain 2 residue   49 VAL
Chi-restraints excluded: chain 2 residue   86 HIS
Chi-restraints excluded: chain 2 residue   99 LEU
Chi-restraints excluded: chain 3 residue    1 MET
Chi-restraints excluded: chain 3 residue    6 VAL
Chi-restraints excluded: chain 3 residue  169 THR
Chi-restraints excluded: chain 3 residue  202 ILE
Chi-restraints excluded: chain 3 residue  278 LEU
Chi-restraints excluded: chain 3 residue  286 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 23 optimal weight:    0.1980
   chunk 13 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    2.2388

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

Flipped N/Q/H residues before XYZ refinement:
** 3 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.072869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.050529 restraints weight = 31823.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.051449 restraints weight = 17602.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.051709 restraints weight = 12358.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3363
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3363
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.5127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5309  Z= 0.168
  Angle     :  0.586   9.147   7541  Z= 0.296
  Chirality :  0.037   0.161    923
  Planarity :  0.004   0.030    695
  Dihedral  : 21.752 173.721   1661
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 18.78 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.40), residues: 444
  helix: -0.04 (0.44), residues: 159
  sheet: -2.07 (0.71), residues: 50
  loop : -0.78 (0.40), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP 3 158 
 HIS   0.005   0.001   HIS 3 223 
 PHE   0.008   0.001   PHE 3 256 
 TYR   0.014   0.002   TYR 2  23 
 ARG   0.003   0.000   ARG 2 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05219 (  165)
  hydrogen bonds       : angle       3.79072 (  400)
  metal coordination   : bond        0.00910 (    6)
  covalent geometry    : bond        0.00357 ( 5303)
  covalent geometry    : angle       0.58571 ( 7541)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 19
  time to evaluate  : 0.438 
Fit side-chains
REVERT: 2   23 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7498 (t80)
REVERT: 2   28 MET cc_start: 0.8700 (mmt) cc_final: 0.7837 (tpp)
REVERT: 3  188 MET cc_start: 0.7837 (tmm) cc_final: 0.7380 (ttm)
  outliers start: 13
  outliers final: 10
  residues processed: 30
  average time/residue: 0.1350
  time to fit residues: 5.9416
Evaluate side-chains
  29 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 18
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   21 VAL
Chi-restraints excluded: chain 2 residue   23 TYR
Chi-restraints excluded: chain 2 residue   49 VAL
Chi-restraints excluded: chain 2 residue   86 HIS
Chi-restraints excluded: chain 2 residue   99 LEU
Chi-restraints excluded: chain 3 residue    1 MET
Chi-restraints excluded: chain 3 residue    6 VAL
Chi-restraints excluded: chain 3 residue  169 THR
Chi-restraints excluded: chain 3 residue  202 ILE
Chi-restraints excluded: chain 3 residue  278 LEU
Chi-restraints excluded: chain 3 residue  286 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 48 optimal weight:    0.6980
   chunk 3 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9990
   chunk 23 optimal weight:    0.4980
   chunk 29 optimal weight:   30.0000
   chunk 1 optimal weight:   10.0000
   chunk 30 optimal weight:   30.0000
   chunk 0 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** 3 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
3 332 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.075989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.051837 restraints weight = 30890.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.052853 restraints weight = 17282.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.053595 restraints weight = 12587.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3417
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3417 r_free = 0.3417    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3417 r_free = 0.3417    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3417
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.5282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5309  Z= 0.101
  Angle     :  0.577  11.701   7541  Z= 0.287
  Chirality :  0.036   0.150    923
  Planarity :  0.003   0.028    695
  Dihedral  : 21.618 171.187   1661
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 20.37 %
    Favored  : 76.98 %
  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: -0.98 (0.40), residues: 444
  helix:  0.03 (0.43), residues: 160
  sheet: -2.00 (0.70), residues: 50
  loop : -0.72 (0.40), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP 3 158 
 HIS   0.004   0.001   HIS 3 223 
 PHE   0.008   0.001   PHE 3 307 
 TYR   0.015   0.001   TYR 2  23 
 ARG   0.002   0.000   ARG 2 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04028 (  165)
  hydrogen bonds       : angle       3.76390 (  400)
  metal coordination   : bond        0.00441 (    6)
  covalent geometry    : bond        0.00215 ( 5303)
  covalent geometry    : angle       0.57737 ( 7541)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 20
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
REVERT: 2   28 MET cc_start: 0.8632 (mmt) cc_final: 0.8056 (tpp)
REVERT: 3  188 MET cc_start: 0.7822 (tmm) cc_final: 0.7366 (ttm)
  outliers start: 10
  outliers final: 9
  residues processed: 29
  average time/residue: 0.1452
  time to fit residues: 6.3719
Evaluate side-chains
  29 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 20
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   49 VAL
Chi-restraints excluded: chain 2 residue   86 HIS
Chi-restraints excluded: chain 3 residue    1 MET
Chi-restraints excluded: chain 3 residue    6 VAL
Chi-restraints excluded: chain 3 residue  169 THR
Chi-restraints excluded: chain 3 residue  202 ILE
Chi-restraints excluded: chain 3 residue  278 LEU
Chi-restraints excluded: chain 3 residue  286 VAL
Chi-restraints excluded: chain 3 residue  321 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 26 optimal weight:    0.3980
   chunk 16 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 42 optimal weight:    0.2980
   chunk 43 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** 3 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.073424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.051286 restraints weight = 30749.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 17)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.051944 restraints weight = 16380.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.052898 restraints weight = 12159.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3455
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3455 r_free = 0.3455    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3453 r_free = 0.3453    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3453
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.5345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5309  Z= 0.102
  Angle     :  0.572  11.937   7541  Z= 0.284
  Chirality :  0.035   0.152    923
  Planarity :  0.003   0.030    695
  Dihedral  : 21.597 171.595   1660
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 20.37 %
    Favored  : 76.98 %
  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: -0.90 (0.40), residues: 444
  helix:  0.07 (0.43), residues: 160
  sheet: -1.89 (0.70), residues: 50
  loop : -0.69 (0.40), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP 3 158 
 HIS   0.003   0.001   HIS 3 332 
 PHE   0.007   0.001   PHE 3 307 
 TYR   0.017   0.001   TYR 2 127 
 ARG   0.003   0.000   ARG 3 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04051 (  165)
  hydrogen bonds       : angle       3.72746 (  400)
  metal coordination   : bond        0.00467 (    6)
  covalent geometry    : bond        0.00222 ( 5303)
  covalent geometry    : angle       0.57186 ( 7541)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 21
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: 2   23 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.7353 (t80)
REVERT: 2   28 MET cc_start: 0.8659 (mmt) cc_final: 0.7732 (tpp)
REVERT: 3  188 MET cc_start: 0.7822 (tmm) cc_final: 0.7367 (ttm)
  outliers start: 10
  outliers final: 9
  residues processed: 30
  average time/residue: 0.1271
  time to fit residues: 5.7486
Evaluate side-chains
  31 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 21
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   23 TYR
Chi-restraints excluded: chain 2 residue   49 VAL
Chi-restraints excluded: chain 2 residue   86 HIS
Chi-restraints excluded: chain 3 residue    1 MET
Chi-restraints excluded: chain 3 residue    6 VAL
Chi-restraints excluded: chain 3 residue  169 THR
Chi-restraints excluded: chain 3 residue  202 ILE
Chi-restraints excluded: chain 3 residue  278 LEU
Chi-restraints excluded: chain 3 residue  286 VAL
Chi-restraints excluded: chain 3 residue  321 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 24 optimal weight:    0.5980
   chunk 3 optimal weight:    8.9990
   chunk 50 optimal weight:    5.9990
   chunk 38 optimal weight:    0.2980
   chunk 8 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0980
   chunk 15 optimal weight:    8.9990
   overall best weight:    0.5182

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

Flipped N/Q/H residues before XYZ refinement:
3 223 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.075099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.052821 restraints weight = 31896.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.053496 restraints weight = 16966.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 73)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.054686 restraints weight = 12615.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3503
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3503
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.5730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5309  Z= 0.089
  Angle     :  0.555  11.882   7541  Z= 0.272
  Chirality :  0.034   0.145    923
  Planarity :  0.003   0.027    695
  Dihedral  : 21.406 172.291   1660
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 20.90 %
    Favored  : 76.72 %
  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: -0.71 (0.40), residues: 444
  helix:  0.29 (0.44), residues: 160
  sheet: -1.57 (0.73), residues: 49
  loop : -0.69 (0.40), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP 3 158 
 HIS   0.005   0.001   HIS 3 252 
 PHE   0.011   0.001   PHE 3 160 
 TYR   0.016   0.001   TYR 2  23 
 ARG   0.003   0.000   ARG 3 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03465 (  165)
  hydrogen bonds       : angle       3.56267 (  400)
  metal coordination   : bond        0.00168 (    6)
  covalent geometry    : bond        0.00195 ( 5303)
  covalent geometry    : angle       0.55507 ( 7541)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2280.11 seconds
wall clock time: 40 minutes 27.30 seconds (2427.30 seconds total)