Starting phenix.real_space_refine
on Fri Aug 22 18:08:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pvv_17973/08_2025/8pvv_17973.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pvv_17973/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pvv_17973/08_2025/8pvv_17973.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pvv_17973/08_2025/8pvv_17973.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pvv_17973/08_2025/8pvv_17973.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pvv_17973/08_2025/8pvv_17973.map"
  }
  resolution = 2.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.43, per 1000 atoms: 0.38
  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: 0.68
  Conformation dependent library (CDL) restraints added in 400.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.84
  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: 1.27

  Time building geometry restraints manager: 0.87 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:             0.460
  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:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.670
  Find NCS groups from input model:        0.020
  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:6.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.000
-------------------------------------------------------------------------------
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 : 10.62
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.001   ARG A 334 
 TYR   0.019   0.002   TYR C 197 
 PHE   0.027   0.002   PHE C 205 
 TRP   0.008   0.001   TRP C 180 
 HIS   0.005   0.001   HIS C 187 

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

*********************** 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  : 0.235 
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: 0.5946
  time to fit residues: 51.3428
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  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A  17 ASN
A 102 ASN
C 136 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.132892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.110358 restraints weight = 24914.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 3.06
r_work: 0.3370 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3343
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3343 r_free = 0.3343    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3343 r_free = 0.3343    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3343
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   6698  Z= 0.237
  Angle     :  0.651   6.999   9308  Z= 0.351
  Chirality :  0.048   0.195   1047
  Planarity :  0.005   0.051    995
  Dihedral  : 19.313  89.246   1357
  Min Nonbonded Distance : 1.877

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  9.59 %
    Favored  : 88.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.32), residues: 658
  helix:  1.42 (0.35), residues: 218
  sheet:  0.33 (0.43), residues: 157
  loop : -0.37 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 383 
 TYR   0.017   0.002   TYR C 197 
 PHE   0.017   0.002   PHE C 205 
 TRP   0.009   0.001   TRP C 180 
 HIS   0.005   0.001   HIS C 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 ( 6698)
  covalent geometry    : angle       0.65099 ( 9308)
  hydrogen bonds       : bond        0.06006 (  300)
  hydrogen bonds       : angle       5.14193 (  866)

*********************** 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
  68 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.259 
Fit side-chains
REVERT: C   54 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7593 (ttt90)
  outliers start: 7
  outliers final: 3
  residues processed: 65
  average time/residue: 0.5730
  time to fit residues: 39.3491
Evaluate side-chains
  60 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain C residue   54 ARG
Chi-restraints excluded: chain C residue   74 ASP
Chi-restraints excluded: chain C residue  107 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 1 optimal weight:    0.7980
   chunk 66 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 40 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 59 optimal weight:    0.3980
   chunk 65 optimal weight:    3.9990
   overall best weight:    2.2386

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

Flipped N/Q/H residues before XYZ refinement:
C 137 HIS    B

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.131574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.109307 restraints weight = 17395.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 2.20
r_work: 0.3383 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3280 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3255
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3255
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079   6698  Z= 0.257
  Angle     :  0.638   6.267   9308  Z= 0.347
  Chirality :  0.048   0.197   1047
  Planarity :  0.005   0.052    995
  Dihedral  : 19.136  88.609   1357
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.55 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.32), residues: 658
  helix:  1.36 (0.34), residues: 218
  sheet:  0.24 (0.43), residues: 157
  loop : -0.43 (0.33), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 383 
 TYR   0.017   0.002   TYR A 124 
 PHE   0.017   0.002   PHE C 205 
 TRP   0.010   0.002   TRP C 180 
 HIS   0.005   0.001   HIS C 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00587 ( 6698)
  covalent geometry    : angle       0.63847 ( 9308)
  hydrogen bonds       : bond        0.06045 (  300)
  hydrogen bonds       : angle       4.95787 (  866)

*********************** 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: 9
    poor density    : 60
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  278 GLN cc_start: 0.7411 (mp10) cc_final: 0.7206 (mp-120)
REVERT: A  421 GLN cc_start: 0.8077 (mp10) cc_final: 0.7823 (mp10)
  outliers start: 9
  outliers final: 3
  residues processed: 63
  average time/residue: 0.5862
  time to fit residues: 39.0317
Evaluate side-chains
  59 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain C residue   74 ASP
Chi-restraints excluded: chain C residue  107 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 41 optimal weight:    0.1980
   chunk 13 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    1.6386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.132963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.110360 restraints weight = 16811.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 2.24
r_work: 0.3395 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3271
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3271
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   6698  Z= 0.204
  Angle     :  0.588   6.143   9308  Z= 0.323
  Chirality :  0.046   0.194   1047
  Planarity :  0.005   0.052    995
  Dihedral  : 19.052  91.375   1357
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.21 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.32), residues: 658
  helix:  1.49 (0.34), residues: 218
  sheet:  0.22 (0.43), residues: 157
  loop : -0.42 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 161 
 TYR   0.020   0.002   TYR A 124 
 PHE   0.012   0.002   PHE C 205 
 TRP   0.008   0.001   TRP C 180 
 HIS   0.004   0.001   HIS C 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 6698)
  covalent geometry    : angle       0.58774 ( 9308)
  hydrogen bonds       : bond        0.05565 (  300)
  hydrogen bonds       : angle       4.77033 (  866)

*********************** 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
  71 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7207 (ppp)
REVERT: A  278 GLN cc_start: 0.7316 (mp10) cc_final: 0.7042 (mp10)
REVERT: C  104 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7305 (pt0)
  outliers start: 11
  outliers final: 2
  residues processed: 65
  average time/residue: 0.5682
  time to fit residues: 39.1153
Evaluate side-chains
  59 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 66 optimal weight:    6.9990
   chunk 53 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   chunk 10 optimal weight:   10.0000
   overall best weight:    1.0982

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.136504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.115547 restraints weight = 20800.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 2.52
r_work: 0.3443 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3298
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3298
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1864

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= 0.163
  Angle     :  0.557   6.075   9308  Z= 0.305
  Chirality :  0.044   0.190   1047
  Planarity :  0.005   0.051    995
  Dihedral  : 18.971  92.533   1357
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.55 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.32), residues: 658
  helix:  1.66 (0.35), residues: 218
  sheet:  0.35 (0.43), residues: 157
  loop : -0.38 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 110 
 TYR   0.022   0.002   TYR A 124 
 PHE   0.011   0.001   PHE A 426 
 TRP   0.007   0.001   TRP C 180 
 HIS   0.002   0.001   HIS C 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 6698)
  covalent geometry    : angle       0.55654 ( 9308)
  hydrogen bonds       : bond        0.05214 (  300)
  hydrogen bonds       : angle       4.59067 (  866)

*********************** 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
  85 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7290 (ppp)
REVERT: A  421 GLN cc_start: 0.8153 (mp10) cc_final: 0.7893 (mp10)
  outliers start: 13
  outliers final: 7
  residues processed: 80
  average time/residue: 0.5341
  time to fit residues: 45.2898
Evaluate side-chains
  72 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  260 MET
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  332 LEU
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 41 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 6 optimal weight:    8.9990
   chunk 54 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    1.7188

-------------------------------------------------------------------------------
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 = 0.3830 r_free = 0.3830 target = 0.135289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.113481 restraints weight = 21845.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.78
r_work: 0.3391 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3366
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3366
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6698  Z= 0.210
  Angle     :  0.590   6.056   9308  Z= 0.321
  Chirality :  0.046   0.190   1047
  Planarity :  0.005   0.050    995
  Dihedral  : 18.982  90.814   1357
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.70 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.32), residues: 658
  helix:  1.55 (0.34), residues: 218
  sheet:  0.31 (0.43), residues: 162
  loop : -0.40 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 110 
 TYR   0.025   0.002   TYR A 124 
 PHE   0.012   0.002   PHE A 138 
 TRP   0.008   0.001   TRP C 180 
 HIS   0.003   0.001   HIS C 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 6698)
  covalent geometry    : angle       0.58979 ( 9308)
  hydrogen bonds       : bond        0.05532 (  300)
  hydrogen bonds       : angle       4.64988 (  866)

*********************** 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
  79 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7112 (ppp)
REVERT: A  421 GLN cc_start: 0.8347 (mp10) cc_final: 0.8084 (mp10)
  outliers start: 17
  outliers final: 11
  residues processed: 74
  average time/residue: 0.5188
  time to fit residues: 40.9110
Evaluate side-chains
  71 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
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  122 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  260 MET
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  332 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 6 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.3828 r_free = 0.3828 target = 0.134401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.112027 restraints weight = 18959.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 2.29
r_work: 0.3398 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3288 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6698  Z= 0.210
  Angle     :  0.588   6.028   9308  Z= 0.321
  Chirality :  0.046   0.204   1047
  Planarity :  0.005   0.051    995
  Dihedral  : 18.998  90.535   1357
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 15.21 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.32), residues: 658
  helix:  1.51 (0.34), residues: 218
  sheet:  0.32 (0.43), residues: 162
  loop : -0.43 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 383 
 TYR   0.027   0.002   TYR A 124 
 PHE   0.012   0.002   PHE A 138 
 TRP   0.008   0.001   TRP C 180 
 HIS   0.003   0.001   HIS C 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 6698)
  covalent geometry    : angle       0.58815 ( 9308)
  hydrogen bonds       : bond        0.05541 (  300)
  hydrogen bonds       : angle       4.65348 (  866)

*********************** 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
  84 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7305 (ppp)
REVERT: A  421 GLN cc_start: 0.8233 (mp10) cc_final: 0.7918 (mp10)
  outliers start: 20
  outliers final: 12
  residues processed: 78
  average time/residue: 0.5233
  time to fit residues: 43.2580
Evaluate side-chains
  72 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
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  122 LEU
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  328 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  365 HIS
Chi-restraints excluded: chain A residue  390 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 35 optimal weight:    0.2980
   chunk 31 optimal weight:    3.9990
   chunk 43 optimal weight:    0.1980
   chunk 47 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0980
   chunk 37 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.4782

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.140047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.117285 restraints weight = 26299.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 2.69
r_work: 0.3485 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3465
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3464 r_free = 0.3464    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3464
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6698  Z= 0.127
  Angle     :  0.538   6.309   9308  Z= 0.295
  Chirality :  0.044   0.220   1047
  Planarity :  0.004   0.049    995
  Dihedral  : 18.869  93.912   1357
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.03 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.32), residues: 658
  helix:  1.76 (0.35), residues: 217
  sheet:  0.56 (0.43), residues: 164
  loop : -0.38 (0.34), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 110 
 TYR   0.022   0.001   TYR A 124 
 PHE   0.010   0.001   PHE A 426 
 TRP   0.008   0.001   TRP C 100 
 HIS   0.003   0.001   HIS C 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6698)
  covalent geometry    : angle       0.53789 ( 9308)
  hydrogen bonds       : bond        0.04987 (  300)
  hydrogen bonds       : angle       4.39220 (  866)

*********************** 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
  89 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7016 (ppp)
REVERT: A  332 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7664 (pp)
REVERT: A  421 GLN cc_start: 0.8323 (mp10) cc_final: 0.8009 (mp10)
  outliers start: 18
  outliers final: 6
  residues processed: 81
  average time/residue: 0.5363
  time to fit residues: 45.9838
Evaluate side-chains
  72 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
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  213 ILE
Chi-restraints excluded: chain A residue  260 MET
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  390 THR
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 53 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 61 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0980
   chunk 50 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.6182

-------------------------------------------------------------------------------
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
C 159 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.139583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.117933 restraints weight = 22926.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 2.73
r_work: 0.3480 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3456
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3456 r_free = 0.3456    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3456 r_free = 0.3456    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3456
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2404

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= 0.131
  Angle     :  0.542   7.767   9308  Z= 0.296
  Chirality :  0.044   0.241   1047
  Planarity :  0.005   0.049    995
  Dihedral  : 18.683  91.654   1357
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.86 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.32), residues: 658
  helix:  1.81 (0.35), residues: 216
  sheet:  0.73 (0.43), residues: 162
  loop : -0.31 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 147 
 TYR   0.013   0.001   TYR A  13 
 PHE   0.011   0.001   PHE A 426 
 TRP   0.005   0.001   TRP C 180 
 HIS   0.002   0.001   HIS A 365 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6698)
  covalent geometry    : angle       0.54201 ( 9308)
  hydrogen bonds       : bond        0.04923 (  300)
  hydrogen bonds       : angle       4.31046 (  866)

*********************** 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: 14
    poor density    : 64
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.6997 (ppp)
REVERT: A  332 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7726 (pp)
REVERT: A  421 GLN cc_start: 0.8348 (mp10) cc_final: 0.7997 (mp10)
  outliers start: 14
  outliers final: 7
  residues processed: 71
  average time/residue: 0.5396
  time to fit residues: 40.6638
Evaluate side-chains
  69 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
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  328 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  390 THR
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 44 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 6 optimal weight:    7.9990
   chunk 8 optimal weight:    5.9990
   chunk 60 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 41 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
A  99 GLN
C 159 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.134445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.112107 restraints weight = 28289.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 3.45
r_work: 0.3339 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3311
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3311 r_free = 0.3311    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3311 r_free = 0.3311    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3311
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   6698  Z= 0.284
  Angle     :  0.655   7.425   9308  Z= 0.353
  Chirality :  0.048   0.189   1047
  Planarity :  0.005   0.050    995
  Dihedral  : 18.646  85.196   1357
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.69 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.32), residues: 658
  helix:  1.40 (0.34), residues: 217
  sheet:  0.44 (0.43), residues: 162
  loop : -0.43 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 147 
 TYR   0.027   0.003   TYR A 124 
 PHE   0.015   0.002   PHE A 138 
 TRP   0.010   0.002   TRP C 180 
 HIS   0.005   0.001   HIS C 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00648 ( 6698)
  covalent geometry    : angle       0.65461 ( 9308)
  hydrogen bonds       : bond        0.05973 (  300)
  hydrogen bonds       : angle       4.72025 (  866)

********************** 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
  73 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A  260 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7164 (ppp)
REVERT: A  332 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7864 (pp)
REVERT: A  421 GLN cc_start: 0.8154 (mp10) cc_final: 0.7850 (mp10)
  outliers start: 12
  outliers final: 7
  residues processed: 68
  average time/residue: 0.5390
  time to fit residues: 38.8852
Evaluate side-chains
  65 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
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  332 LEU
Chi-restraints excluded: chain A residue  390 THR
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 53 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0040
   chunk 6 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
A  25 ASN
A  99 GLN
C 140 ASN
C 159 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.138849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.117075 restraints weight = 28236.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 3.42
r_work: 0.3443 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3410
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3410 r_free = 0.3410    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 = 0.3410 r_free = 0.3410    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3410
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2392

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= 0.135
  Angle     :  0.560   7.269   9308  Z= 0.307
  Chirality :  0.044   0.185   1047
  Planarity :  0.005   0.049    995
  Dihedral  : 18.496  85.422   1357
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.18 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.32), residues: 658
  helix:  1.73 (0.35), residues: 216
  sheet:  0.67 (0.43), residues: 162
  loop : -0.36 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 147 
 TYR   0.025   0.002   TYR A 124 
 PHE   0.009   0.001   PHE A 426 
 TRP   0.008   0.001   TRP A 244 
 HIS   0.002   0.001   HIS C 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6698)
  covalent geometry    : angle       0.55956 ( 9308)
  hydrogen bonds       : bond        0.04986 (  300)
  hydrogen bonds       : angle       4.39372 (  866)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2284.69 seconds
wall clock time: 39 minutes 53.25 seconds (2393.25 seconds total)