Starting phenix.real_space_refine
on Tue Feb 11 21:55:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pvv_17973/02_2025/8pvv_17973.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pvv_17973/02_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_17973/02_2025/8pvv_17973.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pvv_17973/02_2025/8pvv_17973.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pvv_17973/02_2025/8pvv_17973.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pvv_17973/02_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-5592/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: 5.11, per 1000 atoms: 0.79
  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: 2.22
  Conformation dependent library (CDL) restraints added in 903.1 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: 2.47
  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: 2.60

  Time building geometry restraints manager: 2.31 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:             0.510
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     22.640
  Find NCS groups from input model:        0.060
  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:14.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.980
-------------------------------------------------------------------------------
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= 0.231
  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 

*********************** 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  : 0.643 
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: 1.2082
  time to fit residues: 104.7462
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  : 0.735 
-------------------------------------------------------------------------------
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 = 0.135808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.113252 restraints weight = 29700.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 3.56
r_work: 0.3393 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
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: 0.8069
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= 0.239
  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 

*********************** 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  : 0.657 
Fit side-chains
  outliers start: 4
  outliers final: 1
  residues processed: 68
  average time/residue: 1.1441
  time to fit residues: 82.4862
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  : 0.705 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
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 = 0.3772 r_free = 0.3772 target = 0.130249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.107598 restraints weight = 26610.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 3.03
r_work: 0.3335 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3303
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3303
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.073   6698  Z= 0.469
  Angle     :  0.692   6.373   9308  Z= 0.371
  Chirality :  0.050   0.198   1047
  Planarity :  0.006   0.054    995
  Dihedral  : 19.099  87.049   1357
  Min Nonbonded Distance : 1.838

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.73 %
    Favored  : 85.29 %
  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:  0.33 (0.31), residues: 658
  helix:  1.27 (0.34), residues: 217
  sheet:  0.14 (0.43), residues: 159
  loop : -0.47 (0.33), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 180 
 HIS   0.006   0.001   HIS C 187 
 PHE   0.020   0.002   PHE C 205 
 TYR   0.019   0.003   TYR C 197 
 ARG   0.004   0.001   ARG C  85 

*********************** 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
  69 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
REVERT: A  260 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7164 (ppp)
REVERT: A  421 GLN cc_start: 0.8015 (mp10) cc_final: 0.7739 (mp10)
  outliers start: 10
  outliers final: 6
  residues processed: 62
  average time/residue: 1.1096
  time to fit residues: 73.1100
Evaluate side-chains
  59 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 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:    0.5980
   chunk 8 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3847 r_free = 0.3847 target = 0.136177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.113559 restraints weight = 21503.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.47
r_work: 0.3443 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3336 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3312
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3312 r_free = 0.3312    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3312 r_free = 0.3312    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3312
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6698  Z= 0.202
  Angle     :  0.546   6.090   9308  Z= 0.302
  Chirality :  0.044   0.190   1047
  Planarity :  0.005   0.051    995
  Dihedral  : 18.997  93.602   1357
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.38 %
    Favored  : 83.64 %
  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:  0.77 (0.32), residues: 658
  helix:  1.70 (0.35), residues: 218
  sheet:  0.50 (0.43), residues: 155
  loop : -0.35 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 100 
 HIS   0.004   0.001   HIS C 187 
 PHE   0.011   0.001   PHE A 426 
 TYR   0.017   0.001   TYR A 124 
 ARG   0.004   0.000   ARG C 110 

*********************** 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
  84 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.676 
Fit side-chains
REVERT: A  147 ARG cc_start: 0.8081 (mpt180) cc_final: 0.7787 (mmt-90)
REVERT: A  260 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7252 (ppp)
REVERT: A  278 GLN cc_start: 0.7180 (mp10) cc_final: 0.6951 (mp10)
REVERT: A  421 GLN cc_start: 0.8079 (mp10) cc_final: 0.7843 (mp10)
REVERT: C  104 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7252 (pt0)
  outliers start: 10
  outliers final: 2
  residues processed: 76
  average time/residue: 1.1021
  time to fit residues: 88.8361
Evaluate side-chains
  65 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
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  107 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0970
   chunk 52 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0980
   chunk 64 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    1.6384

-------------------------------------------------------------------------------
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 = 0.133464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.110666 restraints weight = 24825.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 3.08
r_work: 0.3378 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6698  Z= 0.301
  Angle     :  0.587   6.142   9308  Z= 0.320
  Chirality :  0.046   0.191   1047
  Planarity :  0.005   0.050    995
  Dihedral  : 18.949  90.836   1357
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.54 %
    Favored  : 82.15 %
  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:  0.69 (0.32), residues: 658
  helix:  1.62 (0.34), residues: 218
  sheet:  0.44 (0.43), residues: 157
  loop : -0.40 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 180 
 HIS   0.003   0.001   HIS C 187 
 PHE   0.013   0.002   PHE C 205 
 TYR   0.021   0.002   TYR A 124 
 ARG   0.004   0.000   ARG C 110 

*********************** 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
  76 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.688 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7101 (ppp)
REVERT: A  278 GLN cc_start: 0.7189 (mp10) cc_final: 0.6965 (mp10)
REVERT: A  421 GLN cc_start: 0.8091 (mp10) cc_final: 0.7848 (mp10)
  outliers start: 12
  outliers final: 6
  residues processed: 70
  average time/residue: 1.0855
  time to fit residues: 80.6651
Evaluate side-chains
  67 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
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  332 LEU
Chi-restraints excluded: chain A residue  365 HIS
Chi-restraints excluded: chain C residue   74 ASP
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:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0770
   chunk 6 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.7940

-------------------------------------------------------------------------------
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 = 0.3870 r_free = 0.3870 target = 0.137435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.115137 restraints weight = 21565.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 2.42
r_work: 0.3458 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3351 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3323
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3323
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6698  Z= 0.203
  Angle     :  0.537   6.013   9308  Z= 0.295
  Chirality :  0.044   0.190   1047
  Planarity :  0.005   0.049    995
  Dihedral  : 18.911  92.845   1357
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 15.04 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.32), residues: 658
  helix:  1.70 (0.35), residues: 217
  sheet:  0.64 (0.44), residues: 157
  loop : -0.41 (0.34), residues: 284

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   0.023   0.002   TYR A 124 
 ARG   0.003   0.000   ARG C 110 

*********************** 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
  86 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.663 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7232 (ppp)
REVERT: A  278 GLN cc_start: 0.7361 (mp10) cc_final: 0.7121 (mp-120)
  outliers start: 16
  outliers final: 5
  residues processed: 78
  average time/residue: 1.1387
  time to fit residues: 94.3993
Evaluate side-chains
  66 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
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 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:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.9186

-------------------------------------------------------------------------------
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 = 0.3870 r_free = 0.3870 target = 0.137658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.115718 restraints weight = 27149.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 3.27
r_work: 0.3421 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3393
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3393
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6698  Z= 0.214
  Angle     :  0.545   5.979   9308  Z= 0.298
  Chirality :  0.044   0.215   1047
  Planarity :  0.004   0.048    995
  Dihedral  : 18.798  92.132   1357
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.87 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.32), residues: 658
  helix:  1.77 (0.35), residues: 218
  sheet:  0.73 (0.44), residues: 157
  loop : -0.36 (0.34), residues: 283

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   0.011   0.001   PHE A 426 
 TYR   0.013   0.002   TYR C  62 
 ARG   0.002   0.000   ARG A 383 

*********************** 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
  76 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.633 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7050 (ppp)
REVERT: A  278 GLN cc_start: 0.7196 (mp10) cc_final: 0.6967 (mp-120)
REVERT: A  421 GLN cc_start: 0.8269 (mp10) cc_final: 0.8019 (mp10)
  outliers start: 11
  outliers final: 7
  residues processed: 71
  average time/residue: 1.0653
  time to fit residues: 80.4165
Evaluate side-chains
  67 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 THR
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  201 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 41 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.2784

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.136338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.114153 restraints weight = 23669.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.92
r_work: 0.3411 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3387
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3387
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6698  Z= 0.253
  Angle     :  0.562   6.734   9308  Z= 0.307
  Chirality :  0.045   0.220   1047
  Planarity :  0.005   0.049    995
  Dihedral  : 18.718  90.225   1357
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.87 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.32), residues: 658
  helix:  1.68 (0.34), residues: 218
  sheet:  0.64 (0.43), residues: 162
  loop : -0.35 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 180 
 HIS   0.003   0.001   HIS C 187 
 PHE   0.011   0.001   PHE A 426 
 TYR   0.014   0.002   TYR A 225 
 ARG   0.005   0.001   ARG A 147 

*********************** 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
  74 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.675 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7071 (ppp)
REVERT: A  278 GLN cc_start: 0.7201 (mp10) cc_final: 0.6961 (mp-120)
REVERT: A  332 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7785 (pp)
REVERT: A  421 GLN cc_start: 0.8325 (mp10) cc_final: 0.7997 (mp10)
  outliers start: 13
  outliers final: 6
  residues processed: 69
  average time/residue: 1.1318
  time to fit residues: 82.9506
Evaluate side-chains
  68 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 THR
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  201 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 66 optimal weight:    7.9990
   chunk 55 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.135857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.114092 restraints weight = 19792.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 2.60
r_work: 0.3419 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3274
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3274 r_free = 0.3274    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 = 0.3274 r_free = 0.3274    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3274
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6698  Z= 0.282
  Angle     :  0.576   6.331   9308  Z= 0.315
  Chirality :  0.045   0.188   1047
  Planarity :  0.005   0.047    995
  Dihedral  : 18.602  88.260   1357
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.03 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.32), residues: 658
  helix:  1.61 (0.34), residues: 218
  sheet:  0.57 (0.43), residues: 162
  loop : -0.38 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 180 
 HIS   0.002   0.001   HIS C 187 
 PHE   0.011   0.002   PHE A 426 
 TYR   0.016   0.002   TYR A 225 
 ARG   0.006   0.001   ARG A 147 

*********************** 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
  75 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.683 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7260 (ppp)
REVERT: A  332 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7759 (pp)
REVERT: A  421 GLN cc_start: 0.8363 (mp10) cc_final: 0.8001 (mp10)
  outliers start: 13
  outliers final: 7
  residues processed: 70
  average time/residue: 1.1105
  time to fit residues: 82.5637
Evaluate side-chains
  67 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  213 ILE
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  201 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3877 r_free = 0.3877 target = 0.138389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.116372 restraints weight = 26727.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 3.17
r_work: 0.3440 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3414
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3414 r_free = 0.3414    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 = 0.3414 r_free = 0.3414    target_work(ls_wunit_k1) = 0.105         |
| 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: 0.8091
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6698  Z= 0.202
  Angle     :  0.552   6.652   9308  Z= 0.302
  Chirality :  0.044   0.186   1047
  Planarity :  0.005   0.048    995
  Dihedral  : 18.460  85.657   1357
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.20 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.32), residues: 658
  helix:  1.75 (0.34), residues: 218
  sheet:  0.62 (0.43), residues: 164
  loop : -0.39 (0.34), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  76 
 HIS   0.002   0.001   HIS C 187 
 PHE   0.010   0.001   PHE A 426 
 TYR   0.024   0.002   TYR A 124 
 ARG   0.006   0.000   ARG A 147 

********************** 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
  75 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.659 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7069 (ppp)
REVERT: A  332 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7650 (pp)
REVERT: A  421 GLN cc_start: 0.8361 (mp10) cc_final: 0.8128 (mp10)
  outliers start: 13
  outliers final: 8
  residues processed: 69
  average time/residue: 1.0000
  time to fit residues: 73.5290
Evaluate side-chains
  69 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  213 ILE
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  201 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 29 optimal weight:    0.4980
   chunk 8 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.3846 r_free = 0.3846 target = 0.135887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.114291 restraints weight = 18745.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 2.51
r_work: 0.3431 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3285
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3285
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6698  Z= 0.278
  Angle     :  0.579   6.428   9308  Z= 0.315
  Chirality :  0.045   0.187   1047
  Planarity :  0.005   0.049    995
  Dihedral  : 18.448  83.287   1357
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.36 %
    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:  0.72 (0.32), residues: 658
  helix:  1.63 (0.34), residues: 217
  sheet:  0.54 (0.42), residues: 164
  loop : -0.42 (0.34), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 180 
 HIS   0.003   0.001   HIS C 187 
 PHE   0.011   0.002   PHE A 138 
 TYR   0.015   0.002   TYR A 225 
 ARG   0.006   0.001   ARG A 147 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4454.67 seconds
wall clock time: 79 minutes 36.65 seconds (4776.65 seconds total)