Starting phenix.real_space_refine
on Wed Aug  5 01:08:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j9g_36095/08_2026/8j9g_36095.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j9g_36095/08_2026/8j9g_36095.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j9g_36095/08_2026/8j9g_36095.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j9g_36095/08_2026/8j9g_36095.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j9g_36095/08_2026/8j9g_36095.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j9g_36095/08_2026/8j9g_36095.map"
  }
  resolution = 3.5
  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=   0.014
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      24      5.49       5
     Mg      1      5.21       5
     S      22      5.16       5
     C    5006      2.51       5
     N    1318      2.21       5
     O    1497      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7868
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 448, 3618
          Classifications: {'peptide': 448}
          Link IDs: {'PTRANS': 25, 'TRANS': 422}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 450, 3759
          Classifications: {'peptide': 450}
          Link IDs: {'PTRANS': 14, 'TRANS': 435}
    Chain: "E"
      Number of atoms: 244
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 244
          Classifications: {'DNA': 9, 'RNA': 3}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 11}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 246
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 12, 246
          Classifications: {'DNA': 12}
          Link IDs: {'rna3p': 11}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.87, per 1000 atoms: 0.24
  Number of scatterers: 7868
  At special positions: 0
  Unit cell: (91.35, 92.4, 131.25, 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      22     16.00
     P      24     15.00
     Mg      1     11.99
     O    1497      8.00
     N    1318      7.00
     C    5006      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: 0.67
  Conformation dependent library (CDL) restraints added in 438.7 milliseconds
  

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1708

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 11 sheets defined
      33.4% alpha, 13.4% beta
      6 base pairs and 11 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 17
      No H-bonds generated for 'chain 'A' and resid 15 through 17'
    Processing helix  chain 'A' and resid 22 through 30
    Processing helix  chain 'A' and resid 46 through 62
      removed outlier: 3.592A  pdb=" N   ASP A  58 " --> pdb=" O   LYS A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 82
    Processing helix  chain 'A' and resid 109 through 132
      removed outlier: 4.305A  pdb=" N   LYS A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LYS A 130 " --> pdb=" O   ILE A 126 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASN A 131 " --> pdb=" O   THR A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 216
      removed outlier: 3.883A  pdb=" N   GLU A 216 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 263
      removed outlier: 3.501A  pdb=" N   ALA A 253 " --> pdb=" O   GLU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.679A  pdb=" N   ALA A 337 " --> pdb=" O   LYS A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 372
    Processing helix  chain 'A' and resid 451 through 464
      removed outlier: 3.792A  pdb=" N   LYS A 464 " --> pdb=" O   LEU A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 493
      removed outlier: 3.953A  pdb=" N   ALA A 483 " --> pdb=" O   THR A 479 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 29
      removed outlier: 4.188A  pdb=" N   TRP B  20 " --> pdb=" O   ASP B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 51
      removed outlier: 4.517A  pdb=" N   ILE B  49 " --> pdb=" O   PHE B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 56
    Processing helix  chain 'B' and resid 71 through 89
    Processing helix  chain 'B' and resid 123 through 138
      removed outlier: 4.049A  pdb=" N   GLY B 127 " --> pdb=" O   SER B 123 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   GLN B 129 " --> pdb=" O   ALA B 125 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ASP B 130 " --> pdb=" O   LYS B 126 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU B 132 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 158
      removed outlier: 3.539A  pdb=" N   PHE B 158 " --> pdb=" O   TYR B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 238
      removed outlier: 3.922A  pdb=" N   GLU B 237 " --> pdb=" O   ASN B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 247
      removed outlier: 3.738A  pdb=" N   LEU B 247 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 243 through 247'
    Processing helix  chain 'B' and resid 257 through 272
      removed outlier: 3.630A  pdb=" N   CYS B 261 " --> pdb=" O   ARG B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 277
      removed outlier: 3.820A  pdb=" N   ARG B 276 " --> pdb=" O   ALA B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 304
      removed outlier: 3.827A  pdb=" N   ASP B 303 " --> pdb=" O   LEU B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 365
      removed outlier: 3.720A  pdb=" N   GLN B 357 " --> pdb=" O   SER B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 385
      removed outlier: 4.132A  pdb=" N   LYS B 376 " --> pdb=" O   LYS B 372 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   PHE B 380 " --> pdb=" O   LYS B 376 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU B 384 " --> pdb=" O   PHE B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 450
      removed outlier: 4.240A  pdb=" N   GLU B 441 " --> pdb=" O   GLU B 437 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3
      removed outlier: 6.912A  pdb=" N   LYS A   2 " --> pdb=" O   PHE B 411 " (cutoff:3.500A)
      removed outlier: 9.042A  pdb=" N   LYS B 413 " --> pdb=" O   LYS A   2 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLU B 169 " --> pdb=" O   GLY B 412 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   MET B 414 " --> pdb=" O   LYS B 167 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LYS B 167 " --> pdb=" O   MET B 414 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 6
      removed outlier: 7.007A  pdb=" N   GLY A 385 " --> pdb=" O   ASN A 446 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 19
      removed outlier: 3.668A  pdb=" N   GLN A  18 " --> pdb=" O   PHE A  14 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 94 through 95
      removed outlier: 3.694A  pdb=" N   PHE A 140 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE A 142 " --> pdb=" O   VAL A  44 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   LEU A 224 " --> pdb=" O   TRP A 139 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   VAL A 141 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 285
      removed outlier: 3.523A  pdb=" N   VAL A 284 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ALA A 300 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 296 through 297
      removed outlier: 3.717A  pdb=" N   GLY A 318 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 32 through 33
      removed outlier: 6.188A  pdb=" N   ILE B   5 " --> pdb=" O   TRP B  33 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 283 through 285
      removed outlier: 3.500A  pdb=" N   ALA B 292 " --> pdb=" O   TYR B 285 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 283 through 285
      removed outlier: 3.500A  pdb=" N   ALA B 292 " --> pdb=" O   TYR B 285 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LYS B 328 " --> pdb=" O   VAL B 334 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ILE B 179 " --> pdb=" O   LEU B 402 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   LEU B 402 " --> pdb=" O   ILE B 179 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 184 through 187
    Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 209
      removed outlier: 3.597A  pdb=" N   ILE B 208 " --> pdb=" O   CYS B 215 " (cutoff:3.500A)

    246 hydrogen bonds defined for protein.
    702 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      13 hydrogen bonds
      26 hydrogen bond angles
      0 basepair planarities
      6 basepair parallelities
      11 stacking parallelities
  Total time for adding SS restraints: 1.38

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2266
        1.34 -     1.45: 1396
        1.45 -     1.57: 4365
        1.57 -     1.69: 46
        1.69 -     1.81: 34
  Bond restraints: 8107
  Sorted by residual:
  bond pdb=" C3'  DC F  22 "
       pdb=" C2'  DC F  22 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.55e+00
  bond pdb=" C3'  DG F  17 "
       pdb=" C2'  DG F  17 "
    ideal  model  delta    sigma   weight residual
    1.516  1.535 -0.019 8.00e-03 1.56e+04 5.80e+00
  bond pdb=" C1'  DC F  22 "
       pdb=" N1   DC F  22 "
    ideal  model  delta    sigma   weight residual
    1.468  1.500 -0.032 1.40e-02 5.10e+03 5.18e+00
  bond pdb=" C1'   C E   7 "
       pdb=" N1    C E   7 "
    ideal  model  delta    sigma   weight residual
    1.468  1.496 -0.028 1.40e-02 5.10e+03 3.91e+00
  bond pdb=" C4'   C E   4 "
       pdb=" C3'   C E   4 "
    ideal  model  delta    sigma   weight residual
    1.529  1.510  0.019 1.00e-02 1.00e+04 3.62e+00
  ... (remaining 8102 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 10803
        1.61 -     3.22: 221
        3.22 -     4.83: 26
        4.83 -     6.44: 3
        6.44 -     8.05: 2
  Bond angle restraints: 11055
  Sorted by residual:
  angle pdb=" O4'   U E   1 "
        pdb=" C1'   U E   1 "
        pdb=" N1    U E   1 "
      ideal   model   delta    sigma   weight residual
     108.50  113.01   -4.51 7.00e-01 2.04e+00 4.16e+01
  angle pdb=" O5'   U E  10 "
        pdb=" C5'   U E  10 "
        pdb=" C4'   U E  10 "
      ideal   model   delta    sigma   weight residual
     109.40  112.99   -3.59 8.00e-01 1.56e+00 2.01e+01
  angle pdb=" N   TYR A 505 "
        pdb=" CA  TYR A 505 "
        pdb=" C   TYR A 505 "
      ideal   model   delta    sigma   weight residual
     113.15  107.99    5.16 1.19e+00 7.06e-01 1.88e+01
  angle pdb=" N3   DT F  21 "
        pdb=" C4   DT F  21 "
        pdb=" O4   DT F  21 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.72e+01
  angle pdb=" N3   DT F  13 "
        pdb=" C4   DT F  13 "
        pdb=" O4   DT F  13 "
      ideal   model   delta    sigma   weight residual
     119.90  122.34   -2.44 6.00e-01 2.78e+00 1.65e+01
  ... (remaining 11050 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.74: 4383
       27.74 -    55.48: 395
       55.48 -    83.22: 36
       83.22 -   110.96: 4
      110.96 -   138.70: 2
  Dihedral angle restraints: 4820
    sinusoidal: 2180
      harmonic: 2640
  Sorted by residual:
  dihedral pdb=" CA  ARG A 225 "
           pdb=" C   ARG A 225 "
           pdb=" N   GLU A 226 "
           pdb=" CA  GLU A 226 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.92   26.08     0      5.00e+00 4.00e-02 2.72e+01
  dihedral pdb=" CA  PRO A 499 "
           pdb=" C   PRO A 499 "
           pdb=" N   PRO A 500 "
           pdb=" CA  PRO A 500 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.28  -21.72     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" C4'  DA F  16 "
           pdb=" C3'  DA F  16 "
           pdb=" O3'  DA F  16 "
           pdb=" P    DG F  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   81.30  138.70     1      3.50e+01 8.16e-04 1.37e+01
  ... (remaining 4817 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 944
       0.049 -    0.098: 200
       0.098 -    0.147: 48
       0.147 -    0.196: 0
       0.196 -    0.245: 2
  Chirality restraints: 1194
  Sorted by residual:
  chirality pdb=" C1'   U E   1 "
            pdb=" O4'   U E   1 "
            pdb=" C2'   U E   1 "
            pdb=" N1    U E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.23    0.24 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" P     U E   1 "
            pdb=" OP1   U E   1 "
            pdb=" OP2   U E   1 "
            pdb=" O5'   U E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17    2.37   -0.20 2.00e-01 2.50e+01 9.79e-01
  chirality pdb=" CB  ILE A 219 "
            pdb=" CA  ILE A 219 "
            pdb=" CG1 ILE A 219 "
            pdb=" CG2 ILE A 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.74e-01
  ... (remaining 1191 not shown)

  Planarity restraints: 1322
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 499 "    0.058 5.00e-02 4.00e+02   8.76e-02 1.23e+01
        pdb=" N   PRO A 500 "   -0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO A 500 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 500 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 498 "    0.022 5.00e-02 4.00e+02   3.32e-02 1.76e+00
        pdb=" N   PRO A 499 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 499 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 499 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 112 "   -0.006 2.00e-02 2.50e+03   1.29e-02 1.65e+00
        pdb=" C   ILE B 112 "    0.022 2.00e-02 2.50e+03
        pdb=" O   ILE B 112 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   VAL B 113 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1319 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.58: 108
        2.58 -     3.16: 6585
        3.16 -     3.74: 13629
        3.74 -     4.32: 17402
        4.32 -     4.90: 27712
  Nonbonded interactions: 65436
  Sorted by model distance:
  nonbonded pdb=" OP1   A E   3 "
            pdb="MG    MG A 601 "
     model   vdw
     1.995 2.170
  nonbonded pdb=" OD1 ASN A 468 "
            pdb="MG    MG A 601 "
     model   vdw
     2.025 2.170
  nonbonded pdb=" ND2 ASN A 468 "
            pdb="MG    MG A 601 "
     model   vdw
     2.121 2.250
  nonbonded pdb=" O   ASN A  34 "
            pdb=" OH  TYR A 261 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" OG  SER B 385 "
            pdb=" O   ASP B 387 "
     model   vdw
     2.183 3.040
  ... (remaining 65431 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=0.68 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.270
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.940
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
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      :  0.003   0.037   8107  Z= 0.187
  Angle     :  0.545   8.050  11055  Z= 0.351
  Chirality :  0.043   0.245   1194
  Planarity :  0.004   0.088   1322
  Dihedral  : 19.064 138.697   3112
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 16.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 29.98 %
    Favored  : 69.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.28), residues: 892
  helix:  0.55 (0.34), residues: 239
  sheet: -0.98 (0.43), residues: 154
  loop : -1.78 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 407 
 TYR   0.021   0.001   TYR B 416 
 PHE   0.013   0.001   PHE A  93 
 TRP   0.006   0.001   TRP A 231 
 HIS   0.003   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.19 ( 8107)
  covalent geometry    : angle       0.54523 /  0.35 (11055)
  hydrogen bonds       : bond        0.27583 / 18.20 (  254)
  hydrogen bonds       : angle       9.20427 /  6.60 (  728)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 115
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: A  321 TYR cc_start: 0.6264 (t80) cc_final: 0.5769 (t80)
REVERT: A  435 MET cc_start: 0.8705 (mmm) cc_final: 0.8035 (mmt)
REVERT: A  474 ASP cc_start: 0.5790 (t0) cc_final: 0.5206 (t0)
REVERT: B    1 MET cc_start: 0.6309 (pmm) cc_final: 0.6010 (ptm)
REVERT: B   14 ASP cc_start: 0.8357 (p0) cc_final: 0.8135 (p0)
REVERT: B   88 LEU cc_start: 0.8882 (tp) cc_final: 0.8657 (tp)
REVERT: B   92 MET cc_start: 0.8537 (mmp) cc_final: 0.8274 (mmp)
  outliers start: 2
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1041
  time to fit residues: 16.0744
Evaluate side-chains
  92 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0050
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7398

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  51 GLN
** A  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 364 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.113624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.095498 restraints weight = 25480.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.098205 restraints weight = 13609.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.100083 restraints weight = 8958.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.101299 restraints weight = 6692.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.102060 restraints weight = 5482.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3950
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3950 r_free = 0.3950    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3950 r_free = 0.3950    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3950
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8107  Z= 0.165
  Angle     :  0.664   9.910  11055  Z= 0.356
  Chirality :  0.046   0.206   1194
  Planarity :  0.005   0.089   1322
  Dihedral  : 15.636 147.757   1243
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 16.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 31.72 %
    Favored  : 65.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.71 (0.27), residues: 892
  helix:  0.23 (0.30), residues: 259
  sheet: -0.98 (0.42), residues: 147
  loop : -2.00 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 209 
 TYR   0.034   0.002   TYR A 328 
 PHE   0.028   0.002   PHE A  93 
 TRP   0.010   0.001   TRP A 231 
 HIS   0.009   0.001   HIS A  67 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.16 ( 8107)
  covalent geometry    : angle       0.66381 /  0.36 (11055)
  hydrogen bonds       : bond        0.07293 /  4.75 (  254)
  hydrogen bonds       : angle       6.37612 /  4.67 (  728)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  302 GLN cc_start: 0.6887 (tt0) cc_final: 0.6554 (mt0)
REVERT: A  321 TYR cc_start: 0.6041 (t80) cc_final: 0.5545 (t80)
REVERT: A  435 MET cc_start: 0.8559 (mmm) cc_final: 0.7910 (mmt)
REVERT: A  507 ILE cc_start: 0.7782 (tt) cc_final: 0.7485 (tt)
REVERT: B   14 ASP cc_start: 0.8244 (p0) cc_final: 0.8003 (p0)
REVERT: B   88 LEU cc_start: 0.8935 (tp) cc_final: 0.8654 (tt)
REVERT: B   92 MET cc_start: 0.8508 (mmp) cc_final: 0.8259 (mmp)
  outliers start: 20
  outliers final: 11
  residues processed: 123
  average time/residue: 0.1034
  time to fit residues: 17.0680
Evaluate side-chains
  109 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   20 TRP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  415 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 16 optimal weight:    8.9990
   chunk 57 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 63 optimal weight:    6.9990
   chunk 79 optimal weight:    0.2980
   chunk 13 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0670
   overall best weight:    1.0520

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  56 ASN
B 147 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.113125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.094951 restraints weight = 25519.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.097620 restraints weight = 13725.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.099459 restraints weight = 9093.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.100665 restraints weight = 6819.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.101482 restraints weight = 5610.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3941 r_free = 0.3941    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3941 r_free = 0.3941    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8107  Z= 0.155
  Angle     :  0.633   9.726  11055  Z= 0.339
  Chirality :  0.046   0.196   1194
  Planarity :  0.005   0.089   1322
  Dihedral  : 15.708 147.165   1243
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 30.85 %
    Favored  : 65.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.27), residues: 892
  helix:  0.33 (0.31), residues: 260
  sheet: -0.95 (0.42), residues: 145
  loop : -2.13 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 481 
 TYR   0.017   0.001   TYR A 328 
 PHE   0.025   0.002   PHE A  93 
 TRP   0.010   0.001   TRP B 373 
 HIS   0.003   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.15 ( 8107)
  covalent geometry    : angle       0.63345 /  0.34 (11055)
  hydrogen bonds       : bond        0.05516 /  3.66 (  254)
  hydrogen bonds       : angle       5.85061 /  4.31 (  728)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  302 GLN cc_start: 0.7060 (tt0) cc_final: 0.6574 (mt0)
REVERT: A  321 TYR cc_start: 0.5940 (t80) cc_final: 0.5431 (t80)
REVERT: A  435 MET cc_start: 0.8558 (mmm) cc_final: 0.7815 (mmt)
REVERT: A  466 ASN cc_start: 0.8124 (t0) cc_final: 0.7868 (t0)
REVERT: B   14 ASP cc_start: 0.8293 (p0) cc_final: 0.8021 (p0)
REVERT: B   55 GLU cc_start: 0.5784 (tm-30) cc_final: 0.4925 (tm-30)
REVERT: B   88 LEU cc_start: 0.8912 (tp) cc_final: 0.8643 (tt)
REVERT: B   92 MET cc_start: 0.8561 (mmp) cc_final: 0.8296 (mmp)
REVERT: B  285 TYR cc_start: 0.7896 (t80) cc_final: 0.7679 (t80)
  outliers start: 27
  outliers final: 15
  residues processed: 132
  average time/residue: 0.0962
  time to fit residues: 17.1979
Evaluate side-chains
  115 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   20 TRP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  415 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 90 optimal weight:    9.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.113851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.095361 restraints weight = 25946.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.098082 restraints weight = 13955.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.099929 restraints weight = 9236.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.101054 restraints weight = 6962.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.101967 restraints weight = 5790.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3947 r_free = 0.3947    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3947 r_free = 0.3947    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (17 function evaluations)
r_final: 0.3947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8107  Z= 0.143
  Angle     :  0.645  10.058  11055  Z= 0.338
  Chirality :  0.046   0.197   1194
  Planarity :  0.005   0.089   1322
  Dihedral  : 15.720 148.117   1243
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 16.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 31.09 %
    Favored  : 65.17 %
  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 are not related in a simple way.
  whole: -1.70 (0.28), residues: 892
  helix:  0.42 (0.31), residues: 260
  sheet: -0.93 (0.43), residues: 145
  loop : -2.14 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 407 
 TYR   0.015   0.001   TYR A 328 
 PHE   0.031   0.002   PHE A  78 
 TRP   0.011   0.001   TRP A 231 
 HIS   0.004   0.001   HIS B 340 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.14 ( 8107)
  covalent geometry    : angle       0.64547 /  0.34 (11055)
  hydrogen bonds       : bond        0.04883 /  3.19 (  254)
  hydrogen bonds       : angle       5.66064 /  4.18 (  728)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 108
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.6849 (t80)
REVERT: A  302 GLN cc_start: 0.7098 (tt0) cc_final: 0.6664 (mt0)
REVERT: A  303 MET cc_start: 0.8156 (tpt) cc_final: 0.7930 (tpt)
REVERT: A  321 TYR cc_start: 0.5938 (t80) cc_final: 0.5462 (t80)
REVERT: A  406 MET cc_start: 0.7816 (pmm) cc_final: 0.7405 (pmm)
REVERT: A  435 MET cc_start: 0.8552 (mmm) cc_final: 0.7848 (mmt)
REVERT: A  466 ASN cc_start: 0.8097 (t0) cc_final: 0.7780 (t0)
REVERT: B    1 MET cc_start: 0.6586 (ptm) cc_final: 0.6127 (ptm)
REVERT: B   14 ASP cc_start: 0.8304 (p0) cc_final: 0.8035 (p0)
REVERT: B   55 GLU cc_start: 0.5945 (tm-30) cc_final: 0.4994 (tm-30)
REVERT: B   88 LEU cc_start: 0.8927 (tp) cc_final: 0.8678 (tt)
REVERT: B   92 MET cc_start: 0.8536 (mmp) cc_final: 0.8286 (mmp)
REVERT: B  285 TYR cc_start: 0.7875 (t80) cc_final: 0.7674 (t80)
  outliers start: 30
  outliers final: 18
  residues processed: 133
  average time/residue: 0.0972
  time to fit residues: 17.4958
Evaluate side-chains
  120 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   20 TRP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  415 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 70 optimal weight:    5.9990
   chunk 9 optimal weight:    8.9990
   chunk 4 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   chunk 55 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.114401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.095906 restraints weight = 25759.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.098620 restraints weight = 13909.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.100458 restraints weight = 9209.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.101726 restraints weight = 6919.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.102442 restraints weight = 5672.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3946
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3946 r_free = 0.3946    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3946 r_free = 0.3946    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8107  Z= 0.141
  Angle     :  0.638  10.111  11055  Z= 0.335
  Chirality :  0.046   0.202   1194
  Planarity :  0.005   0.089   1322
  Dihedral  : 15.718 148.980   1243
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 16.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 31.84 %
    Favored  : 64.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.71 (0.28), residues: 892
  helix:  0.39 (0.31), residues: 266
  sheet: -0.90 (0.43), residues: 145
  loop : -2.18 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 481 
 TYR   0.014   0.001   TYR B 416 
 PHE   0.021   0.002   PHE A  93 
 TRP   0.011   0.001   TRP A 231 
 HIS   0.004   0.001   HIS B 340 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.14 ( 8107)
  covalent geometry    : angle       0.63828 /  0.33 (11055)
  hydrogen bonds       : bond        0.04454 /  2.86 (  254)
  hydrogen bonds       : angle       5.45043 /  4.01 (  728)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.6934 (t80)
REVERT: A  302 GLN cc_start: 0.7219 (tt0) cc_final: 0.6812 (mt0)
REVERT: A  303 MET cc_start: 0.8089 (tpt) cc_final: 0.7799 (tpt)
REVERT: A  321 TYR cc_start: 0.5909 (t80) cc_final: 0.5434 (t80)
REVERT: A  356 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6189 (tp30)
REVERT: A  435 MET cc_start: 0.8525 (mmm) cc_final: 0.7825 (mmt)
REVERT: A  466 ASN cc_start: 0.8091 (t0) cc_final: 0.7775 (t0)
REVERT: B    1 MET cc_start: 0.6572 (ptm) cc_final: 0.6194 (ptm)
REVERT: B   14 ASP cc_start: 0.8299 (p0) cc_final: 0.8038 (p0)
REVERT: B   55 GLU cc_start: 0.5838 (tm-30) cc_final: 0.4947 (tm-30)
REVERT: B   88 LEU cc_start: 0.8942 (tp) cc_final: 0.8708 (tt)
REVERT: B   92 MET cc_start: 0.8635 (mmp) cc_final: 0.8386 (mmp)
REVERT: B  301 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6482 (pm20)
  outliers start: 27
  outliers final: 16
  residues processed: 132
  average time/residue: 0.0943
  time to fit residues: 16.7379
Evaluate side-chains
  121 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   20 TRP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  415 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 87 optimal weight:    9.9990
   chunk 82 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 16 optimal weight:    0.4980
   chunk 42 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   chunk 89 optimal weight:   10.0000
   overall best weight:    2.6988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.109760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.091458 restraints weight = 26617.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.093999 restraints weight = 14705.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.095720 restraints weight = 9879.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.096853 restraints weight = 7529.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.097523 restraints weight = 6269.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3858
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3858 r_free = 0.3858    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3858 r_free = 0.3858    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3858
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062   8107  Z= 0.263
  Angle     :  0.715   9.892  11055  Z= 0.379
  Chirality :  0.048   0.259   1194
  Planarity :  0.006   0.094   1322
  Dihedral  : 15.860 149.917   1243
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 22.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 30.47 %
    Favored  : 64.05 %
  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 are not related in a simple way.
  whole: -1.85 (0.27), residues: 892
  helix:  0.32 (0.31), residues: 260
  sheet: -1.08 (0.44), residues: 142
  loop : -2.22 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 243 
 TYR   0.016   0.002   TYR A 328 
 PHE   0.027   0.002   PHE A  93 
 TRP   0.017   0.002   TRP B 373 
 HIS   0.006   0.001   HIS B 340 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00585 /  0.26 ( 8107)
  covalent geometry    : angle       0.71461 /  0.38 (11055)
  hydrogen bonds       : bond        0.05150 /  3.29 (  254)
  hydrogen bonds       : angle       5.52431 /  4.04 (  728)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 106
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.6940 (t80)
REVERT: A  287 LYS cc_start: 0.8374 (mmmm) cc_final: 0.7997 (mmmm)
REVERT: A  302 GLN cc_start: 0.7209 (tt0) cc_final: 0.6960 (mt0)
REVERT: A  303 MET cc_start: 0.8183 (tpt) cc_final: 0.7931 (tpt)
REVERT: A  321 TYR cc_start: 0.5984 (t80) cc_final: 0.5582 (t80)
REVERT: A  466 ASN cc_start: 0.7916 (t0) cc_final: 0.7658 (t0)
REVERT: B    1 MET cc_start: 0.6603 (ptm) cc_final: 0.6206 (ptm)
REVERT: B   14 ASP cc_start: 0.8278 (p0) cc_final: 0.8020 (p0)
REVERT: B   55 GLU cc_start: 0.5872 (OUTLIER) cc_final: 0.4914 (tm-30)
REVERT: B   92 MET cc_start: 0.8601 (mmp) cc_final: 0.8356 (mmp)
REVERT: B  269 ILE cc_start: 0.6055 (OUTLIER) cc_final: 0.5722 (tt)
REVERT: B  389 ASN cc_start: 0.7526 (OUTLIER) cc_final: 0.6753 (m-40)
  outliers start: 44
  outliers final: 33
  residues processed: 140
  average time/residue: 0.0946
  time to fit residues: 18.1179
Evaluate side-chains
  140 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 103
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  279 CYS
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  457 LYS
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   20 TRP
Chi-restraints excluded: chain B residue   40 ASP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   55 GLU
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  389 ASN
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  415 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 70 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 79 optimal weight:    0.4980
   chunk 28 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  67 HIS
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.113888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.094860 restraints weight = 26439.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.097624 restraints weight = 14302.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.099519 restraints weight = 9505.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.100786 restraints weight = 7176.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.101515 restraints weight = 5913.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3930 r_free = 0.3930    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3930 r_free = 0.3930    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8107  Z= 0.135
  Angle     :  0.665   9.930  11055  Z= 0.345
  Chirality :  0.047   0.198   1194
  Planarity :  0.005   0.091   1322
  Dihedral  : 15.817 149.676   1243
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 32.21 %
    Favored  : 63.81 %
  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 are not related in a simple way.
  whole: -1.67 (0.28), residues: 892
  helix:  0.49 (0.32), residues: 266
  sheet: -0.93 (0.43), residues: 145
  loop : -2.19 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 481 
 TYR   0.015   0.001   TYR B 416 
 PHE   0.025   0.002   PHE B 343 
 TRP   0.012   0.001   TRP B 373 
 HIS   0.004   0.001   HIS A  67 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.14 ( 8107)
  covalent geometry    : angle       0.66537 /  0.34 (11055)
  hydrogen bonds       : bond        0.04055 /  2.61 (  254)
  hydrogen bonds       : angle       5.33403 /  3.92 (  728)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 108
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  287 LYS cc_start: 0.8368 (mmmm) cc_final: 0.7994 (mmmm)
REVERT: A  302 GLN cc_start: 0.7354 (tt0) cc_final: 0.7017 (mt0)
REVERT: A  303 MET cc_start: 0.8089 (tpt) cc_final: 0.7842 (tpt)
REVERT: A  321 TYR cc_start: 0.6002 (t80) cc_final: 0.5615 (t80)
REVERT: A  356 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6169 (tp30)
REVERT: A  406 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.6775 (pmm)
REVERT: A  435 MET cc_start: 0.8549 (mmm) cc_final: 0.7926 (mmt)
REVERT: A  466 ASN cc_start: 0.8051 (t0) cc_final: 0.7775 (t0)
REVERT: B    1 MET cc_start: 0.6809 (ptm) cc_final: 0.6445 (ptm)
REVERT: B   14 ASP cc_start: 0.8280 (p0) cc_final: 0.8005 (p0)
REVERT: B   55 GLU cc_start: 0.5787 (tm-30) cc_final: 0.4884 (tm-30)
REVERT: B   92 MET cc_start: 0.8689 (mmp) cc_final: 0.8433 (mmp)
  outliers start: 32
  outliers final: 24
  residues processed: 135
  average time/residue: 0.0953
  time to fit residues: 17.1645
Evaluate side-chains
  129 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  225 ARG
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  279 CYS
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   20 TRP
Chi-restraints excluded: chain B residue   40 ASP
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  291 PHE
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  415 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 54 optimal weight:    0.4980
   chunk 30 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 90 optimal weight:    9.9990
   chunk 78 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 74 optimal weight:    0.3980
   chunk 84 optimal weight:    7.9990
   chunk 25 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  51 GLN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.113152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.094575 restraints weight = 25832.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.097271 restraints weight = 13979.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.099162 restraints weight = 9260.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.100359 restraints weight = 6949.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.101074 restraints weight = 5734.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3935
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3935 r_free = 0.3935    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3935 r_free = 0.3935    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3935
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8107  Z= 0.138
  Angle     :  0.648  10.474  11055  Z= 0.335
  Chirality :  0.047   0.312   1194
  Planarity :  0.005   0.092   1322
  Dihedral  : 15.791 150.653   1243
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 31.97 %
    Favored  : 63.68 %
  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 are not related in a simple way.
  whole: -1.65 (0.28), residues: 892
  helix:  0.54 (0.32), residues: 269
  sheet: -0.91 (0.43), residues: 145
  loop : -2.21 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 243 
 TYR   0.031   0.001   TYR B 416 
 PHE   0.021   0.002   PHE A  93 
 TRP   0.016   0.001   TRP B 373 
 HIS   0.003   0.001   HIS B 340 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.14 ( 8107)
  covalent geometry    : angle       0.64770 /  0.34 (11055)
  hydrogen bonds       : bond        0.04009 /  2.58 (  254)
  hydrogen bonds       : angle       5.26404 /  3.88 (  728)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 106
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8254 (pp30)
REVERT: A  302 GLN cc_start: 0.7454 (tt0) cc_final: 0.7130 (mt0)
REVERT: A  303 MET cc_start: 0.8090 (tpt) cc_final: 0.7769 (tpt)
REVERT: A  321 TYR cc_start: 0.6024 (t80) cc_final: 0.5657 (t80)
REVERT: A  406 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.6719 (pmm)
REVERT: A  435 MET cc_start: 0.8502 (mmm) cc_final: 0.7892 (mmt)
REVERT: A  466 ASN cc_start: 0.8050 (t0) cc_final: 0.7764 (t0)
REVERT: B    1 MET cc_start: 0.6855 (ptm) cc_final: 0.6480 (ptm)
REVERT: B   14 ASP cc_start: 0.8280 (p0) cc_final: 0.8012 (p0)
REVERT: B   55 GLU cc_start: 0.5803 (OUTLIER) cc_final: 0.4876 (tm-30)
REVERT: B   92 MET cc_start: 0.8691 (mmp) cc_final: 0.8434 (mmp)
  outliers start: 35
  outliers final: 27
  residues processed: 135
  average time/residue: 0.1048
  time to fit residues: 18.8764
Evaluate side-chains
  134 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   51 GLN
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  225 ARG
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  279 CYS
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   20 TRP
Chi-restraints excluded: chain B residue   40 ASP
Chi-restraints excluded: chain B residue   55 GLU
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  291 PHE
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  415 SER
Chi-restraints excluded: chain B residue  416 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 64 optimal weight:    8.9990
   chunk 69 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  51 GLN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.112458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.093122 restraints weight = 26558.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.095862 restraints weight = 14521.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.097731 restraints weight = 9678.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.099012 restraints weight = 7340.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.099746 restraints weight = 6048.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3903
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3903 r_free = 0.3903    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3903 r_free = 0.3903    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3903
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8107  Z= 0.179
  Angle     :  0.679  10.621  11055  Z= 0.350
  Chirality :  0.048   0.435   1194
  Planarity :  0.006   0.099   1322
  Dihedral  : 15.824 150.918   1243
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 17.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 31.97 %
    Favored  : 63.68 %
  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 are not related in a simple way.
  whole: -1.68 (0.28), residues: 892
  helix:  0.44 (0.32), residues: 269
  sheet: -0.90 (0.43), residues: 145
  loop : -2.19 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 243 
 TYR   0.031   0.002   TYR B 416 
 PHE   0.023   0.002   PHE A  93 
 TRP   0.032   0.002   TRP B 373 
 HIS   0.004   0.001   HIS B 340 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.18 ( 8107)
  covalent geometry    : angle       0.67915 /  0.35 (11055)
  hydrogen bonds       : bond        0.04122 /  2.66 (  254)
  hydrogen bonds       : angle       5.28703 /  3.88 (  728)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 102
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  287 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8140 (mmmt)
REVERT: A  302 GLN cc_start: 0.7486 (tt0) cc_final: 0.7110 (mt0)
REVERT: A  303 MET cc_start: 0.8109 (tpt) cc_final: 0.7757 (tpt)
REVERT: A  321 TYR cc_start: 0.6067 (t80) cc_final: 0.5664 (t80)
REVERT: A  406 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.6833 (pmm)
REVERT: A  435 MET cc_start: 0.8469 (mmm) cc_final: 0.7909 (mmt)
REVERT: A  466 ASN cc_start: 0.8076 (t0) cc_final: 0.7807 (t0)
REVERT: B    1 MET cc_start: 0.6750 (ptm) cc_final: 0.6378 (ptm)
REVERT: B   14 ASP cc_start: 0.8319 (p0) cc_final: 0.8056 (p0)
REVERT: B   55 GLU cc_start: 0.5831 (tm-30) cc_final: 0.4894 (tm-30)
REVERT: B   92 MET cc_start: 0.8722 (mmp) cc_final: 0.8463 (mmp)
REVERT: B  389 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.6718 (m-40)
  outliers start: 35
  outliers final: 29
  residues processed: 132
  average time/residue: 0.0982
  time to fit residues: 17.4326
Evaluate side-chains
  131 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 100
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  225 ARG
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  279 CYS
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   20 TRP
Chi-restraints excluded: chain B residue   40 ASP
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  291 PHE
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  389 ASN
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  415 SER
Chi-restraints excluded: chain B residue  416 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 48 optimal weight:    0.0040
   chunk 5 optimal weight:    0.7980
   chunk 55 optimal weight:    6.9990
   chunk 85 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 43 optimal weight:    0.2980
   overall best weight:    0.5592

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  51 GLN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.115089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.096590 restraints weight = 25509.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.099319 restraints weight = 13893.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.101166 restraints weight = 9229.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.102390 restraints weight = 6950.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.103137 restraints weight = 5728.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3959
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3959 r_free = 0.3959    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3959 r_free = 0.3959    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8107  Z= 0.131
  Angle     :  0.690  11.886  11055  Z= 0.353
  Chirality :  0.047   0.203   1194
  Planarity :  0.005   0.090   1322
  Dihedral  : 15.793 151.041   1243
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 15.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 32.71 %
    Favored  : 63.93 %
  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 are not related in a simple way.
  whole: -1.60 (0.28), residues: 892
  helix:  0.52 (0.32), residues: 269
  sheet: -0.83 (0.43), residues: 145
  loop : -2.16 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 243 
 TYR   0.030   0.001   TYR B 416 
 PHE   0.020   0.002   PHE A  93 
 TRP   0.025   0.002   TRP B 373 
 HIS   0.004   0.001   HIS A  67 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 8107)
  covalent geometry    : angle       0.68992 /  0.35 (11055)
  hydrogen bonds       : bond        0.03755 /  2.42 (  254)
  hydrogen bonds       : angle       5.23499 /  3.84 (  728)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  287 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8158 (mmmt)
REVERT: A  302 GLN cc_start: 0.7386 (tt0) cc_final: 0.7076 (mt0)
REVERT: A  303 MET cc_start: 0.8000 (tpt) cc_final: 0.7601 (tpt)
REVERT: A  321 TYR cc_start: 0.5980 (t80) cc_final: 0.5571 (t80)
REVERT: A  406 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.6695 (pmm)
REVERT: A  407 ARG cc_start: 0.8495 (ptm-80) cc_final: 0.8073 (ptm-80)
REVERT: A  435 MET cc_start: 0.8415 (mmm) cc_final: 0.7848 (mmt)
REVERT: A  466 ASN cc_start: 0.8088 (t0) cc_final: 0.7829 (t0)
REVERT: B    1 MET cc_start: 0.6782 (ptm) cc_final: 0.6429 (ptm)
REVERT: B   14 ASP cc_start: 0.8272 (p0) cc_final: 0.8011 (p0)
REVERT: B   55 GLU cc_start: 0.5792 (OUTLIER) cc_final: 0.4872 (tm-30)
REVERT: B   92 MET cc_start: 0.8659 (mmp) cc_final: 0.8408 (mmp)
REVERT: B  336 MET cc_start: 0.7898 (mtp) cc_final: 0.7672 (mtt)
  outliers start: 27
  outliers final: 23
  residues processed: 128
  average time/residue: 0.0985
  time to fit residues: 16.8488
Evaluate side-chains
  126 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  225 ARG
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  279 CYS
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   20 TRP
Chi-restraints excluded: chain B residue   40 ASP
Chi-restraints excluded: chain B residue   55 GLU
Chi-restraints excluded: chain B residue  291 PHE
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  415 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 32 optimal weight:    7.9990
   chunk 89 optimal weight:    9.9990
   chunk 26 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.110013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.091530 restraints weight = 26305.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.094109 restraints weight = 14427.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.095830 restraints weight = 9687.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.097015 restraints weight = 7387.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.097581 restraints weight = 6129.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3866 r_free = 0.3866    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3866 r_free = 0.3866    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071   8107  Z= 0.258
  Angle     :  0.764  11.962  11055  Z= 0.399
  Chirality :  0.049   0.250   1194
  Planarity :  0.006   0.097   1322
  Dihedral  : 15.975 151.866   1243
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 20.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 32.84 %
    Favored  : 63.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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 are not related in a simple way.
  whole: -1.77 (0.28), residues: 892
  helix:  0.24 (0.32), residues: 264
  sheet: -0.89 (0.43), residues: 146
  loop : -2.16 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 243 
 TYR   0.028   0.002   TYR B 416 
 PHE   0.028   0.002   PHE A  93 
 TRP   0.069   0.003   TRP B 373 
 HIS   0.007   0.002   HIS A  67 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00579 /  0.26 ( 8107)
  covalent geometry    : angle       0.76351 /  0.40 (11055)
  hydrogen bonds       : bond        0.04769 /  3.05 (  254)
  hydrogen bonds       : angle       5.46478 /  3.98 (  728)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1873.50 seconds
wall clock time: 33 minutes 3.24 seconds (1983.24 seconds total)