Starting phenix.real_space_refine
on Thu Mar  6 07:17:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8aw3_15690/03_2025/8aw3_15690.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8aw3_15690/03_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_15690/03_2025/8aw3_15690.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8aw3_15690/03_2025/8aw3_15690.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8aw3_15690/03_2025/8aw3_15690.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8aw3_15690/03_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-5624/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: 4.35, per 1000 atoms: 0.86
  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: 1.38
  Conformation dependent library (CDL) restraints added in 633.8 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: 1.87
  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: 1.40

  Time building geometry restraints manager: 1.64 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:             1.700
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.030
  Find NCS groups from input model:        0.040
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.880
-------------------------------------------------------------------------------
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   5303  Z= 0.496
  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 

*********************** 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  : 0.433 
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: 0.2864
  time to fit residues: 25.4190
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  : 0.476 
-------------------------------------------------------------------------------
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 = 0.078957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.054141 restraints weight = 29741.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.055232 restraints weight = 16700.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.055755 restraints weight = 12208.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3435
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3435 r_free = 0.3435    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 = 0.3434 r_free = 0.3434    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3434
-------------------------------------------------------------------------------
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   5303  Z= 0.235
  Angle     :  0.620   7.618   7541  Z= 0.320
  Chirality :  0.039   0.170    923
  Planarity :  0.004   0.035    695
  Dihedral  : 21.958 177.381   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 

*********************** 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  : 0.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   23 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.7079 (t80)
REVERT: 2   28 MET cc_start: 0.8861 (mmt) cc_final: 0.8412 (tpp)
REVERT: 2  134 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6942 (pt0)
  outliers start: 13
  outliers final: 7
  residues processed: 47
  average time/residue: 0.1862
  time to fit residues: 11.4337
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  : 0.436 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 32 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 29 optimal weight:   20.0000
   chunk 26 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   chunk 49 optimal weight:    8.9990
   chunk 4 optimal weight:    9.9990
   chunk 45 optimal weight:    7.9990
   chunk 0 optimal weight:    9.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    4.9188

-------------------------------------------------------------------------------
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 = 0.3869 r_free = 0.3869 target = 0.073914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.049993 restraints weight = 31098.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.050821 restraints weight = 17536.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.051309 restraints weight = 12833.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3327
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    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 = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3327
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.4147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053   5303  Z= 0.470
  Angle     :  0.771   6.907   7541  Z= 0.397
  Chirality :  0.043   0.198    923
  Planarity :  0.006   0.038    695
  Dihedral  : 22.343 176.090   1662
  Min Nonbonded Distance : 1.743

Molprobity Statistics.
  All-atom Clashscore : 19.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 11.38 %
    Favored  : 82.80 %
  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: -2.10 (0.38), residues: 444
  helix: -1.10 (0.40), residues: 165
  sheet: -3.45 (0.60), residues: 48
  loop : -1.02 (0.40), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP 3 138 
 HIS   0.006   0.001   HIS 3 223 
 PHE   0.018   0.003   PHE 3 285 
 TYR   0.022   0.003   TYR 2 205 
 ARG   0.006   0.001   ARG 2 206 

*********************** 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
  49 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 27
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   28 MET cc_start: 0.8717 (mmt) cc_final: 0.8402 (tpp)
REVERT: 2   70 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8966 (mp10)
REVERT: 2  134 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7082 (pt0)
REVERT: 3  188 MET cc_start: 0.7939 (tmm) cc_final: 0.7435 (ttm)
  outliers start: 22
  outliers final: 14
  residues processed: 47
  average time/residue: 0.1522
  time to fit residues: 9.7499
Evaluate side-chains
  36 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 20
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   21 VAL
Chi-restraints excluded: chain 2 residue   44 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  134 GLU
Chi-restraints excluded: chain 2 residue  173 TYR
Chi-restraints excluded: chain 2 residue  188 SER
Chi-restraints excluded: chain 3 residue    3 GLU
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:    1.9990
   chunk 24 optimal weight:   20.0000
   chunk 14 optimal weight:    0.8980
   chunk 1 optimal weight:   10.0000
   chunk 15 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 23 optimal weight:    4.9990
   chunk 40 optimal weight:    0.1980
   chunk 36 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.073641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.050443 restraints weight = 30168.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.051659 restraints weight = 16835.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.051979 restraints weight = 12071.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    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: 0.8100
moved from start:          0.4218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5303  Z= 0.168
  Angle     :  0.571   9.988   7541  Z= 0.292
  Chirality :  0.038   0.170    923
  Planarity :  0.004   0.029    695
  Dihedral  : 21.959 170.850   1662
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 15.34 %
    Favored  : 80.95 %
  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: -1.65 (0.39), residues: 444
  helix: -0.51 (0.43), residues: 160
  sheet: -3.23 (0.57), residues: 50
  loop : -0.91 (0.40), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP 3 158 
 HIS   0.003   0.001   HIS 3 300 
 PHE   0.014   0.002   PHE 3 256 
 TYR   0.018   0.002   TYR 2  23 
 ARG   0.004   0.000   ARG 2 206 

*********************** 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
  42 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 28
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
REVERT: 2   28 MET cc_start: 0.8685 (mmt) cc_final: 0.7981 (tpp)
REVERT: 3  188 MET cc_start: 0.7846 (tmm) cc_final: 0.7390 (ttm)
  outliers start: 14
  outliers final: 9
  residues processed: 39
  average time/residue: 0.1673
  time to fit residues: 8.7190
Evaluate side-chains
  31 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 22
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   21 VAL
Chi-restraints excluded: chain 2 residue   49 VAL
Chi-restraints excluded: chain 2 residue   86 HIS
Chi-restraints excluded: chain 2 residue  173 TYR
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:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 11 optimal weight:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 49 optimal weight:    0.3980
   chunk 8 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    3.8788

-------------------------------------------------------------------------------
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**
** 3 332 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 = 0.3862 r_free = 0.3862 target = 0.073437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.049962 restraints weight = 31901.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.050453 restraints weight = 17699.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.051299 restraints weight = 13561.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3332
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3332 r_free = 0.3332    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 = 0.3332 r_free = 0.3332    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3332
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.4916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   5303  Z= 0.375
  Angle     :  0.704  10.323   7541  Z= 0.356
  Chirality :  0.041   0.182    923
  Planarity :  0.005   0.032    695
  Dihedral  : 22.183 174.859   1661
  Min Nonbonded Distance : 1.821

Molprobity Statistics.
  All-atom Clashscore : 17.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 14.55 %
    Favored  : 79.89 %
  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: -1.83 (0.39), residues: 444
  helix: -0.77 (0.42), residues: 160
  sheet: -3.04 (0.59), residues: 48
  loop : -1.02 (0.40), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP 3 158 
 HIS   0.005   0.001   HIS 3 223 
 PHE   0.010   0.002   PHE 3 256 
 TYR   0.016   0.003   TYR 2 205 
 ARG   0.004   0.001   ARG 2 193 

*********************** 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
  42 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 21
  time to evaluate  : 0.443 
Fit side-chains
REVERT: 2   28 MET cc_start: 0.8639 (mmt) cc_final: 0.8370 (tpp)
REVERT: 3  188 MET cc_start: 0.7924 (tmm) cc_final: 0.7419 (ttm)
  outliers start: 21
  outliers final: 15
  residues processed: 40
  average time/residue: 0.1486
  time to fit residues: 8.3965
Evaluate side-chains
  33 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 18
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   21 VAL
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 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    3 GLU
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
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:    0.1980
   chunk 30 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 28 optimal weight:    9.9990
   chunk 36 optimal weight:    0.0870
   chunk 5 optimal weight:   10.9990
   chunk 29 optimal weight:    0.2980
   chunk 23 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.3958

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.076134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.052566 restraints weight = 31441.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.053405 restraints weight = 16874.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.053871 restraints weight = 12286.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3412
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3412 r_free = 0.3412    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 = 0.3412 r_free = 0.3412    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3412
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.4966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5303  Z= 0.135
  Angle     :  0.549   9.624   7541  Z= 0.279
  Chirality :  0.037   0.165    923
  Planarity :  0.004   0.028    695
  Dihedral  : 21.785 168.945   1661
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.93 %
    Favored  : 79.89 %
  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: -1.31 (0.39), residues: 444
  helix: -0.30 (0.43), residues: 160
  sheet: -2.50 (0.61), residues: 52
  loop : -0.77 (0.40), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP 3 154 
 HIS   0.006   0.001   HIS 3 223 
 PHE   0.009   0.001   PHE 3 256 
 TYR   0.020   0.001   TYR 2  23 
 ARG   0.003   0.000   ARG 3 263 

*********************** 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
  38 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 26
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
REVERT: 2   28 MET cc_start: 0.8623 (mmt) cc_final: 0.8019 (tpp)
REVERT: 3  188 MET cc_start: 0.7762 (tmm) cc_final: 0.7312 (ttm)
  outliers start: 12
  outliers final: 6
  residues processed: 37
  average time/residue: 0.1271
  time to fit residues: 6.9659
Evaluate side-chains
  30 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
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    3 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 34 optimal weight:    0.0000
   chunk 22 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0870
   chunk 15 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 41 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.1566

-------------------------------------------------------------------------------
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 = 0.3914 r_free = 0.3914 target = 0.073153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.051228 restraints weight = 31578.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.051845 restraints weight = 16844.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.052831 restraints weight = 12519.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3447
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3447 r_free = 0.3447    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3446 r_free = 0.3446    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3446
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.5084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5303  Z= 0.153
  Angle     :  0.561  11.127   7541  Z= 0.285
  Chirality :  0.036   0.157    923
  Planarity :  0.003   0.028    695
  Dihedral  : 21.742 171.587   1660
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 18.78 %
    Favored  : 78.57 %
  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: -1.08 (0.40), residues: 444
  helix: -0.17 (0.43), residues: 160
  sheet: -2.11 (0.66), residues: 52
  loop : -0.65 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP 3 138 
 HIS   0.006   0.001   HIS 3 223 
 PHE   0.009   0.002   PHE 3  30 
 TYR   0.016   0.002   TYR 2  23 
 ARG   0.003   0.000   ARG 2 206 

*********************** 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
  33 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 23
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: 2   28 MET cc_start: 0.8638 (mmt) cc_final: 0.8010 (tpp)
REVERT: 3  188 MET cc_start: 0.7808 (tmm) cc_final: 0.7360 (ttm)
REVERT: 3  256 PHE cc_start: 0.7548 (t80) cc_final: 0.7305 (t80)
  outliers start: 10
  outliers final: 7
  residues processed: 32
  average time/residue: 0.1466
  time to fit residues: 6.6810
Evaluate side-chains
  29 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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    3 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=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:    0.0970
   chunk 48 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.3382

-------------------------------------------------------------------------------
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 = 0.3910 r_free = 0.3910 target = 0.073081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.050562 restraints weight = 30780.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.051623 restraints weight = 16338.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.052239 restraints weight = 11603.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3436
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3436 r_free = 0.3436    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3436 r_free = 0.3436    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3436
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.5178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5303  Z= 0.164
  Angle     :  0.573  11.928   7541  Z= 0.288
  Chirality :  0.036   0.158    923
  Planarity :  0.003   0.028    695
  Dihedral  : 21.737 172.183   1660
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 19.58 %
    Favored  : 77.51 %
  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: -0.97 (0.40), residues: 444
  helix: -0.02 (0.43), residues: 159
  sheet: -1.91 (0.69), residues: 52
  loop : -0.68 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP 3 138 
 HIS   0.004   0.001   HIS 3 252 
 PHE   0.009   0.001   PHE 3  30 
 TYR   0.015   0.002   TYR 2 127 
 ARG   0.002   0.000   ARG 2 206 

*********************** 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
  34 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 23
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
REVERT: 2   28 MET cc_start: 0.8618 (mmt) cc_final: 0.8018 (tpp)
REVERT: 3  188 MET cc_start: 0.7803 (tmm) cc_final: 0.7358 (ttm)
REVERT: 3  256 PHE cc_start: 0.7676 (t80) cc_final: 0.7387 (t80)
  outliers start: 11
  outliers final: 7
  residues processed: 33
  average time/residue: 0.1296
  time to fit residues: 6.2563
Evaluate side-chains
  30 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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    3 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 3 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9990
   chunk 23 optimal weight:    0.1980
   chunk 29 optimal weight:   30.0000
   chunk 1 optimal weight:   10.0000
   chunk 30 optimal weight:   30.0000
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.3904 r_free = 0.3904 target = 0.072973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.050445 restraints weight = 30824.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.051116 restraints weight = 16732.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.051955 restraints weight = 12514.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3431
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3431 r_free = 0.3431    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3431 r_free = 0.3431    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3431
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.5224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5303  Z= 0.168
  Angle     :  0.572   9.844   7541  Z= 0.288
  Chirality :  0.036   0.169    923
  Planarity :  0.003   0.028    695
  Dihedral  : 21.738 172.212   1660
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 20.63 %
    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: -0.92 (0.40), residues: 444
  helix:  0.00 (0.43), residues: 159
  sheet: -1.80 (0.71), residues: 52
  loop : -0.66 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP 3 138 
 HIS   0.004   0.001   HIS 3 223 
 PHE   0.006   0.001   PHE 3  30 
 TYR   0.015   0.002   TYR 2  23 
 ARG   0.003   0.000   ARG 2 206 

*********************** 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
  32 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 22
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
REVERT: 2   28 MET cc_start: 0.8602 (mmt) cc_final: 0.8015 (tpp)
REVERT: 3  188 MET cc_start: 0.7803 (tmm) cc_final: 0.7358 (ttm)
REVERT: 3  256 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7473 (t80)
  outliers start: 10
  outliers final: 9
  residues processed: 30
  average time/residue: 0.1427
  time to fit residues: 6.3791
Evaluate side-chains
  32 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 22
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 3 residue    3 GLU
Chi-restraints excluded: chain 3 residue    6 VAL
Chi-restraints excluded: chain 3 residue  110 LEU
Chi-restraints excluded: chain 3 residue  169 THR
Chi-restraints excluded: chain 3 residue  256 PHE
Chi-restraints excluded: chain 3 residue  278 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 42 optimal weight:    0.3980
   chunk 43 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0270
   overall best weight:    1.4842

-------------------------------------------------------------------------------
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 = 0.3908 r_free = 0.3908 target = 0.072944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.051109 restraints weight = 31550.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.052139 restraints weight = 16826.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.052858 restraints weight = 11807.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3448
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3448 r_free = 0.3448    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3448 r_free = 0.3448    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3448
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.5248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5303  Z= 0.175
  Angle     :  0.573   9.644   7541  Z= 0.289
  Chirality :  0.036   0.156    923
  Planarity :  0.003   0.028    695
  Dihedral  : 21.739 172.345   1660
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  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: -0.90 (0.40), residues: 444
  helix:  0.03 (0.43), residues: 159
  sheet: -1.76 (0.72), residues: 52
  loop : -0.66 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP 3 138 
 HIS   0.004   0.001   HIS 3 223 
 PHE   0.007   0.001   PHE 3 160 
 TYR   0.015   0.002   TYR 2 127 
 ARG   0.003   0.000   ARG 2 206 

********************** 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: 9
    poor density    : 22
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
REVERT: 2   28 MET cc_start: 0.8629 (mmt) cc_final: 0.8024 (tpp)
REVERT: 3  188 MET cc_start: 0.7800 (tmm) cc_final: 0.7351 (ttm)
REVERT: 3  256 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7500 (t80)
  outliers start: 9
  outliers final: 7
  residues processed: 29
  average time/residue: 0.1412
  time to fit residues: 6.0300
Evaluate side-chains
  30 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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    3 GLU
Chi-restraints excluded: chain 3 residue    6 VAL
Chi-restraints excluded: chain 3 residue  169 THR
Chi-restraints excluded: chain 3 residue  256 PHE
Chi-restraints excluded: chain 3 residue  278 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0970
   chunk 22 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 38 optimal weight:    0.3980
   chunk 8 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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**
3 332 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.088197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.058826 restraints weight = 36175.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.059435 restraints weight = 19970.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.060223 restraints weight = 15148.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3443
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    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 = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3443
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.5444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5303  Z= 0.146
  Angle     :  0.559  10.141   7541  Z= 0.280
  Chirality :  0.036   0.165    923
  Planarity :  0.003   0.031    695
  Dihedral  : 21.673 171.156   1660
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  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: -0.82 (0.40), residues: 444
  helix:  0.12 (0.43), residues: 159
  sheet: -1.70 (0.70), residues: 52
  loop : -0.64 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP 3 138 
 HIS   0.005   0.001   HIS 3 223 
 PHE   0.007   0.001   PHE 3 307 
 TYR   0.018   0.002   TYR 2 127 
 ARG   0.003   0.000   ARG 3 184 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2280.90 seconds
wall clock time: 40 minutes 10.37 seconds (2410.37 seconds total)