Starting phenix.real_space_refine
on Mon Apr 28 00:09:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pvv_17973/04_2025/8pvv_17973.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pvv_17973/04_2025/8pvv_17973.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pvv_17973/04_2025/8pvv_17973.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pvv_17973/04_2025/8pvv_17973.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pvv_17973/04_2025/8pvv_17973.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pvv_17973/04_2025/8pvv_17973.cif"
  }
  resolution = 2.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      50      5.49       5
     Mg      1      5.21       5
     S      13      5.16       5
     C    3979      2.51       5
     N    1079      2.21       5
     O    1355      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 6477
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 3478
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3478
          Classifications: {'peptide': 427}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 403}
    Chain: "C"
      Number of atoms: 1913
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 229, 1894
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 8, 'TRANS': 220}
      Conformer: "B"
        Number of residues, atoms: 229, 1894
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 8, 'TRANS': 220}
          bond proxies already assigned to first conformer: 1916
    Chain: "R"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 549
          Classifications: {'RNA': 25}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 18, 'rna3p_pyr': 6}
          Link IDs: {'rna2p': 1, 'rna3p': 23}
    Chain: "S"
      Number of atoms: 500
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 500
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
    Chain: "R"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "C"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "R"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 14
          Classifications: {'water': 14}
          Link IDs: {None: 13}
    Chain: "S"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 9
          Classifications: {'water': 9}
          Link IDs: {None: 8}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  ALYS C  52 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS C  52 " occ=0.50
    residue:
      pdb=" N  AHIS C 137 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS C 137 " occ=0.50
  Time building chain proxies: 5.76, per 1000 atoms: 0.89
  Number of scatterers: 6477
  At special positions: 0
  Unit cell: (75.9, 83.6, 99, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      13     16.00
     P      50     15.00
     Mg      1     11.99
     O    1355      8.00
     N    1079      7.00
     C    3979      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: 2.04
  Conformation dependent library (CDL) restraints added in 887.1 milliseconds
  

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1240

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 7 sheets defined
      36.0% alpha, 30.8% beta
      22 base pairs and 37 stacking pairs defined.
    Time for finding SS restraints: 2.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 37
    Processing helix  chain 'A' and resid 58 through 74
    Processing helix  chain 'A' and resid 92 through 107
    Processing helix  chain 'A' and resid 119 through 132
      removed outlier: 3.961A  pdb=" N   TYR A 129 " --> pdb=" O   LYS A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 147
    Processing helix  chain 'A' and resid 148 through 164
    Processing helix  chain 'A' and resid 221 through 241
    Processing helix  chain 'A' and resid 263 through 278
    Processing helix  chain 'A' and resid 303 through 307
    Processing helix  chain 'A' and resid 359 through 376
      removed outlier: 3.705A  pdb=" N   LYS A 376 " --> pdb=" O   TYR A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 407
      Proline residue:  A 394  - end of helix
    Processing helix  chain 'A' and resid 417 through 423
      removed outlier: 3.674A  pdb=" N   GLN A 421 " --> pdb=" O   ASN A 417 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 66
      removed outlier: 3.601A  pdb=" N   ILE C  66 " --> pdb=" O   GLY C  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 63 through 66'
    Processing helix  chain 'C' and resid 77 through 93
      removed outlier: 4.174A  pdb=" N   GLY C  81 " --> pdb=" O   ASN C  77 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LYS C  82 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 163 through 172
    Processing helix  chain 'C' and resid 172 through 187
    Processing helix  chain 'C' and resid 199 through 216
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213
      removed outlier: 5.566A  pdb=" N   TRP A 210 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   PHE A 202 " --> pdb=" O   TRP A 210 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 213
      removed outlier: 5.566A  pdb=" N   TRP A 210 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   PHE A 202 " --> pdb=" O   TRP A 210 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   ILE A 181 " --> pdb=" O   THR A 250 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   HIS A 252 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   ILE A 183 " --> pdb=" O   HIS A 252 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   GLU A 247 " --> pdb=" O   LYS A 286 " (cutoff:3.500A)
      removed outlier: 8.385A  pdb=" N   ALA A 288 " --> pdb=" O   GLU A 247 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   LEU A 249 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
      removed outlier: 8.002A  pdb=" N   LEU A 290 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   LEU A 251 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   LEU A 292 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   VAL A 253 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   TYR A 287 " --> pdb=" O   ASP A 353 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   ASP A 353 " --> pdb=" O   TYR A 287 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ILE A 289 " --> pdb=" O   VAL A 351 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   GLU A   3 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   MET A   2 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 22
      removed outlier: 3.769A  pdb=" N   ILE A 170 " --> pdb=" O   ARG A  14 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 87
      removed outlier: 7.040A  pdb=" N   ILE A  49 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
      removed outlier: 8.053A  pdb=" N   PHE A  86 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   LEU A  51 " --> pdb=" O   PHE A  86 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ALA A  50 " --> pdb=" O   MET A 112 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   VAL A 114 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   ILE A  52 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 105
      removed outlier: 6.707A  pdb=" N   ARG C 110 " --> pdb=" O   LYS C 103 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 105
      removed outlier: 6.707A  pdb=" N   ARG C 110 " --> pdb=" O   LYS C 103 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   PHE C 143 " --> pdb=" O   ILE C  28 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ASN C  30 " --> pdb=" O   LYS C 233 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 52 through 55
      removed outlier: 3.551A  pdb=" N   ILE C  73 " --> pdb=" O   ILE C  35 " (cutoff:3.500A)

    271 hydrogen bonds defined for protein.
    762 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      54 hydrogen bonds
      104 hydrogen bond angles
      0 basepair planarities
      22 basepair parallelities
      37 stacking parallelities
  Total time for adding SS restraints: 2.55

  Time building geometry restraints manager: 2.35 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1563
        1.33 -     1.45: 1532
        1.45 -     1.57: 3480
        1.57 -     1.69: 98
        1.69 -     1.80: 25
  Bond restraints: 6698
  Sorted by residual:
  bond pdb=" O3'   C R  14 "
       pdb=" P     U R  15 "
    ideal  model  delta    sigma   weight residual
    1.607  1.652 -0.045 1.50e-02 4.44e+03 9.12e+00
  bond pdb=" O3'   G R  10 "
       pdb=" P     A R  11 "
    ideal  model  delta    sigma   weight residual
    1.607  1.642 -0.035 1.50e-02 4.44e+03 5.49e+00
  bond pdb=" O3'   A R  22 "
       pdb=" P     A R  23 "
    ideal  model  delta    sigma   weight residual
    1.607  1.642 -0.035 1.50e-02 4.44e+03 5.33e+00
  bond pdb=" O3'   A R   1 "
       pdb=" P     G R   2 "
    ideal  model  delta    sigma   weight residual
    1.607  1.581  0.026 1.50e-02 4.44e+03 3.12e+00
  bond pdb=" O3'   A R   4 "
       pdb=" P     G R   5 "
    ideal  model  delta    sigma   weight residual
    1.607  1.629 -0.022 1.50e-02 4.44e+03 2.22e+00
  ... (remaining 6693 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 9099
        1.83 -     3.67: 183
        3.67 -     5.50: 18
        5.50 -     7.34: 7
        7.34 -     9.17: 1
  Bond angle restraints: 9308
  Sorted by residual:
  angle pdb=" C4'   G R  12 "
        pdb=" C3'   G R  12 "
        pdb=" O3'   G R  12 "
      ideal   model   delta    sigma   weight residual
     113.00  107.26    5.74 1.50e+00 4.44e-01 1.46e+01
  angle pdb=" C   GLU C  67 "
        pdb=" N   ASN C  68 "
        pdb=" CA  ASN C  68 "
      ideal   model   delta    sigma   weight residual
     124.31  130.52   -6.21 1.67e+00 3.59e-01 1.38e+01
  angle pdb=" O3'   A R   1 "
        pdb=" C3'   A R   1 "
        pdb=" C2'   A R   1 "
      ideal   model   delta    sigma   weight residual
     109.50  114.31   -4.81 1.50e+00 4.44e-01 1.03e+01
  angle pdb=" C4'   A R   1 "
        pdb=" C3'   A R   1 "
        pdb=" O3'   A R   1 "
      ideal   model   delta    sigma   weight residual
     109.40  104.73    4.67 1.50e+00 4.44e-01 9.67e+00
  angle pdb=" C   LYS A 256 "
        pdb=" N   ARG A 257 "
        pdb=" CA  ARG A 257 "
      ideal   model   delta    sigma   weight residual
     120.69  111.52    9.17 2.95e+00 1.15e-01 9.66e+00
  ... (remaining 9303 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.05: 3375
       17.05 -    34.09: 356
       34.09 -    51.14: 138
       51.14 -    68.18: 72
       68.18 -    85.23: 9
  Dihedral angle restraints: 3950
    sinusoidal: 2012
      harmonic: 1938
  Sorted by residual:
  dihedral pdb=" CA  ASP C 155 "
           pdb=" C   ASP C 155 "
           pdb=" N   ARG C 156 "
           pdb=" CA  ARG C 156 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.87  -19.13     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  TYR C  22 "
           pdb=" C   TYR C  22 "
           pdb=" N   ILE C  23 "
           pdb=" CA  ILE C  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.36  -16.64     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CB  MET C 201 "
           pdb=" CG  MET C 201 "
           pdb=" SD  MET C 201 "
           pdb=" CE  MET C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.17   57.17     3      1.50e+01 4.44e-03 9.43e+00
  ... (remaining 3947 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 801
       0.050 -    0.100: 179
       0.100 -    0.149: 56
       0.149 -    0.199: 9
       0.199 -    0.249: 2
  Chirality restraints: 1047
  Sorted by residual:
  chirality pdb=" C2'   G R  12 "
            pdb=" C3'   G R  12 "
            pdb=" O2'   G R  12 "
            pdb=" C1'   G R  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.50   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" C3'   G R  12 "
            pdb=" C4'   G R  12 "
            pdb=" O3'   G R  12 "
            pdb=" C2'   G R  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.70    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  ASN C  68 "
            pdb=" N   ASN C  68 "
            pdb=" C   ASN C  68 "
            pdb=" CB  ASN C  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.83e-01
  ... (remaining 1044 not shown)

  Planarity restraints: 995
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 423 "    0.051 5.00e-02 4.00e+02   7.84e-02 9.84e+00
        pdb=" N   PRO A 424 "   -0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO A 424 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 424 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 341 "    0.035 5.00e-02 4.00e+02   5.33e-02 4.55e+00
        pdb=" N   PRO A 342 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 342 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 342 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 134 "    0.032 5.00e-02 4.00e+02   4.85e-02 3.77e+00
        pdb=" N   PRO A 135 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 135 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 135 "    0.027 5.00e-02 4.00e+02
  ... (remaining 992 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.35: 12
        2.35 -     2.98: 3172
        2.98 -     3.62: 10221
        3.62 -     4.26: 17559
        4.26 -     4.90: 27536
  Nonbonded interactions: 58500
  Sorted by model distance:
  nonbonded pdb=" OP1   A R   1 "
            pdb="MG    MG R 101 "
     model   vdw
     1.707 2.170
  nonbonded pdb=" NE2 GLN A 159 "
            pdb="MG    MG R 101 "
     model   vdw
     2.033 2.250
  nonbonded pdb=" O   THR C 191 "
            pdb=" O   HOH C 301 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   LEU A 427 "
            pdb="MG    MG R 101 "
     model   vdw
     2.264 2.170
  nonbonded pdb=" OD1 ASP C  57 "
            pdb=" O2'   G R  18 "
     model   vdw
     2.268 3.040
  ... (remaining 58495 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.490
  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:          0.590
  Check model and map are aligned:         0.090
  Set scattering table:                    0.090
  Process input model:                     26.280
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6698  Z= 0.181
  Angle     :  0.631   9.169   9308  Z= 0.358
  Chirality :  0.049   0.249   1047
  Planarity :  0.005   0.078    995
  Dihedral  : 18.006  85.227   2710
  Min Nonbonded Distance : 1.707

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  0.00 %
    Favored  : 99.67 %
  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:  0.55 (0.32), residues: 658
  helix:  1.38 (0.35), residues: 216
  sheet:  0.36 (0.44), residues: 157
  loop : -0.33 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 180 
 HIS   0.005   0.001   HIS C 187 
 PHE   0.027   0.002   PHE C 205 
 TYR   0.019   0.002   TYR C 197 
 ARG   0.004   0.001   ARG A 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18685 (  300)
  hydrogen bonds       : angle       7.52433 (  866)
  covalent geometry    : bond        0.00363 ( 6698)
  covalent geometry    : angle       0.63064 ( 9308)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.709 
Fit side-chains
REVERT: C  229 ASP cc_start: 0.7901 (m-30) cc_final: 0.7633 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 1.1223
  time to fit residues: 97.3356
Evaluate side-chains
  59 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 28 optimal weight:    0.4980
   chunk 17 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 27 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 102 ASN
C 136 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.135794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.113309 restraints weight = 29728.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 3.57
r_work: 0.3394 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3364
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6698  Z= 0.168
  Angle     :  0.604   6.970   9308  Z= 0.327
  Chirality :  0.046   0.192   1047
  Planarity :  0.005   0.051    995
  Dihedral  : 19.134  91.545   1357
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  9.26 %
    Favored  : 89.75 %
  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:  0.73 (0.32), residues: 658
  helix:  1.61 (0.35), residues: 218
  sheet:  0.45 (0.43), residues: 157
  loop : -0.30 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 180 
 HIS   0.004   0.001   HIS C 187 
 PHE   0.013   0.001   PHE C 205 
 TYR   0.015   0.002   TYR C 197 
 ARG   0.002   0.000   ARG A 189 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05568 (  300)
  hydrogen bonds       : angle       4.98537 (  866)
  covalent geometry    : bond        0.00374 ( 6698)
  covalent geometry    : angle       0.60386 ( 9308)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.642 
Fit side-chains
  outliers start: 4
  outliers final: 1
  residues processed: 68
  average time/residue: 1.0875
  time to fit residues: 78.3902
Evaluate side-chains
  61 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A  17 ASN
A  99 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.133303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.110329 restraints weight = 26988.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 3.19
r_work: 0.3363 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3333
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3333
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6698  Z= 0.219
  Angle     :  0.606   6.236   9308  Z= 0.330
  Chirality :  0.046   0.194   1047
  Planarity :  0.005   0.049    995
  Dihedral  : 18.979  89.245   1357
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.07 %
    Favored  : 86.12 %
  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:  0.61 (0.32), residues: 658
  helix:  1.53 (0.34), residues: 218
  sheet:  0.29 (0.43), residues: 159
  loop : -0.34 (0.34), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 180 
 HIS   0.004   0.001   HIS C 187 
 PHE   0.015   0.002   PHE C 205 
 TYR   0.016   0.002   TYR C 197 
 ARG   0.004   0.000   ARG C 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05753 (  300)
  hydrogen bonds       : angle       4.83904 (  866)
  covalent geometry    : bond        0.00497 ( 6698)
  covalent geometry    : angle       0.60646 ( 9308)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.744 
Fit side-chains
REVERT: A  421 GLN cc_start: 0.7907 (mp10) cc_final: 0.7678 (mp10)
  outliers start: 9
  outliers final: 7
  residues processed: 66
  average time/residue: 1.1650
  time to fit residues: 81.6692
Evaluate side-chains
  63 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 MET
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  365 HIS
Chi-restraints excluded: chain C residue   57 ASP
Chi-restraints excluded: chain C residue   74 ASP
Chi-restraints excluded: chain C residue  107 SER
Chi-restraints excluded: chain C residue  161 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 61 optimal weight:    0.2980
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  17 ASN
A  99 GLN
A 211 ASN
C 137 HIS    B

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.136600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.113925 restraints weight = 21614.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 2.49
r_work: 0.3445 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3339 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3321
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3321
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6698  Z= 0.139
  Angle     :  0.535   6.108   9308  Z= 0.295
  Chirality :  0.044   0.189   1047
  Planarity :  0.005   0.049    995
  Dihedral  : 18.931  92.892   1357
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.21 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.32), residues: 658
  helix:  1.63 (0.35), residues: 218
  sheet:  0.59 (0.43), residues: 157
  loop : -0.30 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 180 
 HIS   0.004   0.001   HIS C 187 
 PHE   0.010   0.001   PHE A 426 
 TYR   0.019   0.001   TYR A 124 
 ARG   0.002   0.000   ARG A 383 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05035 (  300)
  hydrogen bonds       : angle       4.55165 (  866)
  covalent geometry    : bond        0.00303 ( 6698)
  covalent geometry    : angle       0.53513 ( 9308)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7226 (ppp)
REVERT: A  421 GLN cc_start: 0.7915 (mp10) cc_final: 0.7657 (mp10)
REVERT: C   36 LYS cc_start: 0.8050 (mppt) cc_final: 0.7800 (mppt)
  outliers start: 10
  outliers final: 2
  residues processed: 74
  average time/residue: 1.1309
  time to fit residues: 88.5903
Evaluate side-chains
  64 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 MET
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain C residue   57 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 50 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0980
   chunk 29 optimal weight:    0.0870
   chunk 52 optimal weight:    2.9990
   chunk 44 optimal weight:    0.2980
   chunk 64 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.3758

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
A 306 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.142096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.120222 restraints weight = 25834.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.59
r_work: 0.3515 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3502
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3502 r_free = 0.3502    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3502 r_free = 0.3502    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3502
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6698  Z= 0.118
  Angle     :  0.510   6.040   9308  Z= 0.282
  Chirality :  0.043   0.186   1047
  Planarity :  0.004   0.047    995
  Dihedral  : 18.825  94.403   1357
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.21 %
    Favored  : 82.48 %
  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:  1.02 (0.32), residues: 658
  helix:  1.86 (0.35), residues: 218
  sheet:  0.73 (0.42), residues: 162
  loop : -0.25 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 100 
 HIS   0.003   0.001   HIS C 187 
 PHE   0.010   0.001   PHE A 426 
 TYR   0.016   0.001   TYR C  62 
 ARG   0.001   0.000   ARG A 383 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04739 (  300)
  hydrogen bonds       : angle       4.29034 (  866)
  covalent geometry    : bond        0.00250 ( 6698)
  covalent geometry    : angle       0.50989 ( 9308)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.713 
Fit side-chains
REVERT: A  421 GLN cc_start: 0.7822 (mp10) cc_final: 0.7600 (mp10)
  outliers start: 12
  outliers final: 4
  residues processed: 82
  average time/residue: 1.0290
  time to fit residues: 89.7557
Evaluate side-chains
  71 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  365 HIS
Chi-restraints excluded: chain C residue  107 SER
Chi-restraints excluded: chain C residue  201 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 53 optimal weight:    0.3980
   chunk 26 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 6 optimal weight:    8.9990
   chunk 60 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A  17 ASN
A  99 GLN
A 102 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.136841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.114847 restraints weight = 21617.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 2.75
r_work: 0.3427 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3404
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3404 r_free = 0.3404    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3404 r_free = 0.3404    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3404
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6698  Z= 0.182
  Angle     :  0.555   6.063   9308  Z= 0.304
  Chirality :  0.044   0.185   1047
  Planarity :  0.005   0.047    995
  Dihedral  : 18.648  89.714   1357
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.69 %
    Favored  : 81.16 %
  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 (0.32), residues: 658
  helix:  1.68 (0.34), residues: 218
  sheet:  0.78 (0.44), residues: 157
  loop : -0.32 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 180 
 HIS   0.004   0.001   HIS C 187 
 PHE   0.011   0.001   PHE C 205 
 TYR   0.022   0.002   TYR A 124 
 ARG   0.003   0.000   ARG A 383 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05319 (  300)
  hydrogen bonds       : angle       4.45474 (  866)
  covalent geometry    : bond        0.00409 ( 6698)
  covalent geometry    : angle       0.55516 ( 9308)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.695 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7012 (ppp)
  outliers start: 11
  outliers final: 6
  residues processed: 72
  average time/residue: 1.0742
  time to fit residues: 82.1257
Evaluate side-chains
  68 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  260 MET
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  365 HIS
Chi-restraints excluded: chain C residue  107 SER
Chi-restraints excluded: chain C residue  201 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  17 ASN
A  99 GLN
A 194 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.138651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.116410 restraints weight = 27144.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 3.06
r_work: 0.3449 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3427
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3427 r_free = 0.3427    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3427 r_free = 0.3427    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3427
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6698  Z= 0.138
  Angle     :  0.522   5.989   9308  Z= 0.288
  Chirality :  0.043   0.185   1047
  Planarity :  0.004   0.046    995
  Dihedral  : 18.588  91.021   1357
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 16.36 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.32), residues: 658
  helix:  1.78 (0.34), residues: 218
  sheet:  0.67 (0.44), residues: 144
  loop : -0.22 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 180 
 HIS   0.003   0.001   HIS C 187 
 PHE   0.010   0.001   PHE A 426 
 TYR   0.013   0.001   TYR A 225 
 ARG   0.002   0.000   ARG A 383 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05026 (  300)
  hydrogen bonds       : angle       4.37226 (  866)
  covalent geometry    : bond        0.00307 ( 6698)
  covalent geometry    : angle       0.52196 ( 9308)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7054 (ppp)
  outliers start: 15
  outliers final: 6
  residues processed: 74
  average time/residue: 1.0808
  time to fit residues: 84.7722
Evaluate side-chains
  73 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 MET
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  365 HIS
Chi-restraints excluded: chain C residue  107 SER
Chi-restraints excluded: chain C residue  201 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 20 optimal weight:    0.3980
   chunk 26 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 41 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 8 optimal weight:    7.9990
   chunk 16 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A  17 ASN
A  25 ASN
A  99 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.139566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.117822 restraints weight = 23905.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 3.01
r_work: 0.3469 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3445
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3445 r_free = 0.3445    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3445 r_free = 0.3445    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3445
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6698  Z= 0.134
  Angle     :  0.524   5.959   9308  Z= 0.287
  Chirality :  0.044   0.233   1047
  Planarity :  0.004   0.047    995
  Dihedral  : 18.391  87.700   1357
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.36 %
    Favored  : 80.33 %
  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:  1.12 (0.32), residues: 658
  helix:  1.95 (0.35), residues: 217
  sheet:  0.84 (0.43), residues: 162
  loop : -0.24 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 138 
 HIS   0.003   0.001   HIS C 187 
 PHE   0.010   0.001   PHE A 426 
 TYR   0.013   0.001   TYR A 225 
 ARG   0.002   0.000   ARG A 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05000 (  300)
  hydrogen bonds       : angle       4.33016 (  866)
  covalent geometry    : bond        0.00298 ( 6698)
  covalent geometry    : angle       0.52398 ( 9308)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.645 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7029 (ppp)
  outliers start: 12
  outliers final: 6
  residues processed: 79
  average time/residue: 1.0774
  time to fit residues: 90.2011
Evaluate side-chains
  72 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 MET
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  365 HIS
Chi-restraints excluded: chain C residue  107 SER
Chi-restraints excluded: chain C residue  201 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0070
   chunk 62 optimal weight:    7.9990
   chunk 39 optimal weight:    0.4980
   chunk 48 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.0802

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.137021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.115199 restraints weight = 19940.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 2.63
r_work: 0.3424 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3411
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3411 r_free = 0.3411    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3411 r_free = 0.3411    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3411
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6698  Z= 0.159
  Angle     :  0.546   5.964   9308  Z= 0.297
  Chirality :  0.044   0.185   1047
  Planarity :  0.005   0.047    995
  Dihedral  : 18.359  83.046   1357
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.85 %
    Favored  : 80.00 %
  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:  1.02 (0.32), residues: 658
  helix:  1.82 (0.34), residues: 218
  sheet:  0.82 (0.42), residues: 162
  loop : -0.29 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 138 
 HIS   0.003   0.001   HIS C 187 
 PHE   0.010   0.001   PHE A 426 
 TYR   0.020   0.002   TYR A 124 
 ARG   0.003   0.000   ARG A 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05142 (  300)
  hydrogen bonds       : angle       4.38773 (  866)
  covalent geometry    : bond        0.00359 ( 6698)
  covalent geometry    : angle       0.54584 ( 9308)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.708 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.6945 (ppp)
  outliers start: 11
  outliers final: 7
  residues processed: 72
  average time/residue: 1.0378
  time to fit residues: 79.4617
Evaluate side-chains
  74 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  260 MET
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  365 HIS
Chi-restraints excluded: chain C residue  107 SER
Chi-restraints excluded: chain C residue  201 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.137721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.114513 restraints weight = 26464.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 2.74
r_work: 0.3429 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3414
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3414 r_free = 0.3414    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3414 r_free = 0.3414    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3414
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6698  Z= 0.146
  Angle     :  0.536   5.951   9308  Z= 0.293
  Chirality :  0.043   0.185   1047
  Planarity :  0.004   0.047    995
  Dihedral  : 18.353  83.563   1357
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 17.85 %
    Favored  : 79.67 %
  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:  1.05 (0.32), residues: 658
  helix:  1.85 (0.34), residues: 217
  sheet:  0.86 (0.42), residues: 162
  loop : -0.28 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 138 
 HIS   0.003   0.001   HIS C 187 
 PHE   0.010   0.001   PHE A 426 
 TYR   0.014   0.001   TYR A 225 
 ARG   0.002   0.000   ARG A 383 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05041 (  300)
  hydrogen bonds       : angle       4.35835 (  866)
  covalent geometry    : bond        0.00325 ( 6698)
  covalent geometry    : angle       0.53637 ( 9308)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.660 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.6950 (ppp)
  outliers start: 13
  outliers final: 7
  residues processed: 73
  average time/residue: 1.0547
  time to fit residues: 81.9707
Evaluate side-chains
  73 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  260 MET
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  365 HIS
Chi-restraints excluded: chain C residue  107 SER
Chi-restraints excluded: chain C residue  201 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.134067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.112551 restraints weight = 18121.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.47
r_work: 0.3393 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6698  Z= 0.235
  Angle     :  0.604   6.033   9308  Z= 0.327
  Chirality :  0.046   0.186   1047
  Planarity :  0.005   0.047    995
  Dihedral  : 18.406  81.766   1357
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.02 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.32), residues: 658
  helix:  1.55 (0.34), residues: 217
  sheet:  0.70 (0.42), residues: 162
  loop : -0.37 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C 180 
 HIS   0.004   0.001   HIS C 136 
 PHE   0.011   0.002   PHE C 216 
 TYR   0.018   0.002   TYR A 225 
 ARG   0.004   0.001   ARG A 383 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05633 (  300)
  hydrogen bonds       : angle       4.58799 (  866)
  covalent geometry    : bond        0.00536 ( 6698)
  covalent geometry    : angle       0.60449 ( 9308)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4438.56 seconds
wall clock time: 76 minutes 33.38 seconds (4593.38 seconds total)