Starting phenix.real_space_refine
on Sun May 11 10:59:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j9g_36095/05_2025/8j9g_36095.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j9g_36095/05_2025/8j9g_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j9g_36095/05_2025/8j9g_36095.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j9g_36095/05_2025/8j9g_36095.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j9g_36095/05_2025/8j9g_36095.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j9g_36095/05_2025/8j9g_36095.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.93, per 1000 atoms: 0.63
  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: 2.20
  Conformation dependent library (CDL) restraints added in 836.8 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: 2.64
  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: 2.30

  Time building geometry restraints manager: 2.51 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=" C   MET B 345 "
       pdb=" N   ASP B 346 "
    ideal  model  delta    sigma   weight residual
    1.332  1.315  0.018 1.40e-02 5.10e+03 1.61e+00
  bond pdb=" CA  TYR A 505 "
       pdb=" C   TYR A 505 "
    ideal  model  delta    sigma   weight residual
    1.523  1.502  0.022 1.80e-02 3.09e+03 1.44e+00
  bond pdb=" C3'   C E   7 "
       pdb=" O3'   C E   7 "
    ideal  model  delta    sigma   weight residual
    1.422  1.448 -0.026 3.00e-02 1.11e+03 7.36e-01
  bond pdb=" C3'  DA F  16 "
       pdb=" O3'  DA F  16 "
    ideal  model  delta    sigma   weight residual
    1.422  1.446 -0.024 3.00e-02 1.11e+03 6.47e-01
  bond pdb=" C   TYR A 505 "
       pdb=" O   TYR A 505 "
    ideal  model  delta    sigma   weight residual
    1.236  1.225  0.011 1.47e-02 4.63e+03 5.74e-01
  ... (remaining 8102 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 10845
        1.61 -     3.22: 182
        3.22 -     4.83: 23
        4.83 -     6.44: 3
        6.44 -     8.05: 2
  Bond angle restraints: 11055
  Sorted by residual:
  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=" N   PRO A 499 "
        pdb=" CA  PRO A 499 "
        pdb=" C   PRO A 499 "
      ideal   model   delta    sigma   weight residual
     110.70  114.11   -3.41 1.22e+00 6.72e-01 7.82e+00
  angle pdb=" C   VAL A  92 "
        pdb=" N   PHE A  93 "
        pdb=" CA  PHE A  93 "
      ideal   model   delta    sigma   weight residual
     122.46  125.98   -3.52 1.41e+00 5.03e-01 6.24e+00
  angle pdb=" CA  LEU A 462 "
        pdb=" CB  LEU A 462 "
        pdb=" CG  LEU A 462 "
      ideal   model   delta    sigma   weight residual
     116.30  124.35   -8.05 3.50e+00 8.16e-02 5.29e+00
  angle pdb=" CA  LYS A 447 "
        pdb=" CB  LYS A 447 "
        pdb=" CG  LYS A 447 "
      ideal   model   delta    sigma   weight residual
     114.10  118.59   -4.49 2.00e+00 2.50e-01 5.03e+00
  ... (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 -    0.046: 937
       0.046 -    0.092: 199
       0.092 -    0.138: 55
       0.138 -    0.184: 1
       0.184 -    0.229: 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      2.46    2.23    0.23 2.00e-01 2.50e+01 1.32e+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:             0.990
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.430
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
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= 0.112
  Angle     :  0.517   8.050  11055  Z= 0.274
  Chirality :  0.041   0.229   1194
  Planarity :  0.004   0.088   1322
  Dihedral  : 19.064 138.697   3112
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 16.89
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (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
 TRP   0.006   0.001   TRP A 231 
 HIS   0.003   0.001   HIS A 251 
 PHE   0.013   0.001   PHE A  93 
 TYR   0.021   0.001   TYR B 416 
 ARG   0.004   0.000   ARG A 407 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27583 (  254)
  hydrogen bonds       : angle       9.20427 (  728)
  covalent geometry    : bond        0.00250 ( 8107)
  covalent geometry    : angle       0.51690 (11055)

*********************** 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  : 0.891 
Fit side-chains
   revert: symmetry clash
REVERT: A  321 TYR cc_start: 0.6264 (t80) cc_final: 0.5770 (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: 0.5276 (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: 0.8134 (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: 0.2357
  time to fit residues: 35.7779
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  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 23 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0470
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
** A  67 HIS ** 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 364 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.115735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.097416 restraints weight = 25508.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.100134 restraints weight = 13843.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.101953 restraints weight = 9160.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3947 r_free = 0.3947    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 = 0.3947 r_free = 0.3947    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8107  Z= 0.133
  Angle     :  0.616   8.875  11055  Z= 0.327
  Chirality :  0.045   0.228   1194
  Planarity :  0.005   0.088   1322
  Dihedral  : 15.678 144.810   1243
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 30.47 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.28), residues: 892
  helix:  0.47 (0.31), residues: 260
  sheet: -0.91 (0.42), residues: 147
  loop : -2.05 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 231 
 HIS   0.004   0.001   HIS A 251 
 PHE   0.024   0.001   PHE A  93 
 TYR   0.017   0.001   TYR B 416 
 ARG   0.005   0.001   ARG B 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05097 (  254)
  hydrogen bonds       : angle       5.76851 (  728)
  covalent geometry    : bond        0.00296 ( 8107)
  covalent geometry    : angle       0.61638 (11055)

*********************** 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
  138 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  302 GLN cc_start: 0.6968 (tt0) cc_final: 0.6465 (mt0)
REVERT: A  321 TYR cc_start: 0.5937 (t80) cc_final: 0.5428 (t80)
REVERT: A  435 MET cc_start: 0.8515 (mmm) cc_final: 0.7856 (mmt)
REVERT: A  507 ILE cc_start: 0.7784 (tt) cc_final: 0.7555 (tt)
REVERT: B    1 MET cc_start: 0.6514 (pmm) cc_final: 0.6200 (ptm)
REVERT: B   14 ASP cc_start: 0.8296 (p0) cc_final: 0.8074 (p0)
REVERT: B   88 LEU cc_start: 0.8918 (tp) cc_final: 0.8674 (tt)
REVERT: B   92 MET cc_start: 0.8523 (mmp) cc_final: 0.8245 (mmp)
REVERT: B  285 TYR cc_start: 0.7935 (t80) cc_final: 0.7629 (t80)
  outliers start: 23
  outliers final: 13
  residues processed: 135
  average time/residue: 0.2239
  time to fit residues: 40.1336
Evaluate side-chains
  121 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  298 CYS
Chi-restraints excluded: chain A residue  383 LEU
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  266 VAL
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 49 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 43 optimal weight:    8.9990
   chunk 33 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0870
   chunk 47 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 18 optimal weight:    0.5980
   chunk 45 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.2760

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

Flipped N/Q/H residues before XYZ refinement:
** A  51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.112427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.093890 restraints weight = 25875.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.096594 restraints weight = 14066.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.098401 restraints weight = 9321.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3887
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3887 r_free = 0.3887    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3887 r_free = 0.3887    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3887
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8107  Z= 0.159
  Angle     :  0.621   8.551  11055  Z= 0.324
  Chirality :  0.045   0.232   1194
  Planarity :  0.005   0.091   1322
  Dihedral  : 15.643 146.813   1243
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 15.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 30.85 %
    Favored  : 65.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.28), residues: 892
  helix:  0.66 (0.31), residues: 260
  sheet: -0.86 (0.42), residues: 146
  loop : -2.01 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 373 
 HIS   0.005   0.001   HIS B 340 
 PHE   0.023   0.002   PHE A  93 
 TYR   0.016   0.001   TYR B 416 
 ARG   0.005   0.001   ARG A 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04527 (  254)
  hydrogen bonds       : angle       5.36563 (  728)
  covalent geometry    : bond        0.00361 ( 8107)
  covalent geometry    : angle       0.62119 (11055)

*********************** 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
  143 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7522 (mm)
REVERT: A  287 LYS cc_start: 0.8350 (mmmm) cc_final: 0.8054 (mmmt)
REVERT: A  302 GLN cc_start: 0.7275 (tt0) cc_final: 0.6810 (mt0)
REVERT: A  303 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7970 (tpt)
REVERT: A  321 TYR cc_start: 0.5954 (t80) cc_final: 0.5457 (t80)
REVERT: A  435 MET cc_start: 0.8482 (mmm) cc_final: 0.7861 (mmt)
REVERT: A  466 ASN cc_start: 0.8155 (t0) cc_final: 0.7900 (t0)
REVERT: B    1 MET cc_start: 0.6744 (pmm) cc_final: 0.6532 (ptm)
REVERT: B   14 ASP cc_start: 0.8354 (p0) cc_final: 0.8099 (p0)
REVERT: B   92 MET cc_start: 0.8687 (mmp) cc_final: 0.8426 (mmp)
REVERT: B  139 ASN cc_start: 0.8812 (t0) cc_final: 0.8603 (t0)
REVERT: B  285 TYR cc_start: 0.7924 (t80) cc_final: 0.7664 (t80)
  outliers start: 30
  outliers final: 15
  residues processed: 137
  average time/residue: 0.2360
  time to fit residues: 42.4388
Evaluate side-chains
  123 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   33 LEU
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  303 MET
Chi-restraints excluded: chain A residue  383 LEU
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  300 LEU
Chi-restraints excluded: chain B residue  341 ILE
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 67 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 63 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4147 r_free = 0.4147 target = 0.113047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.094476 restraints weight = 25859.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.097118 restraints weight = 14188.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.098786 restraints weight = 9497.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3881
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3881 r_free = 0.3881    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3881 r_free = 0.3881    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3881
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8107  Z= 0.166
  Angle     :  0.637   9.303  11055  Z= 0.328
  Chirality :  0.046   0.237   1194
  Planarity :  0.005   0.091   1322
  Dihedral  : 15.770 146.828   1243
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 16.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 30.60 %
    Favored  : 64.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.28), residues: 892
  helix:  0.51 (0.32), residues: 270
  sheet: -0.97 (0.44), residues: 135
  loop : -2.09 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 373 
 HIS   0.005   0.001   HIS B 340 
 PHE   0.024   0.002   PHE A  93 
 TYR   0.015   0.001   TYR B 416 
 ARG   0.005   0.001   ARG A 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04081 (  254)
  hydrogen bonds       : angle       5.24176 (  728)
  covalent geometry    : bond        0.00381 ( 8107)
  covalent geometry    : angle       0.63737 (11055)

*********************** 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
  147 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 108
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7482 (mm)
REVERT: A   47 GLN cc_start: 0.8046 (pt0) cc_final: 0.7717 (pm20)
REVERT: A  302 GLN cc_start: 0.7324 (tt0) cc_final: 0.6878 (mt0)
REVERT: A  321 TYR cc_start: 0.6057 (t80) cc_final: 0.5612 (t80)
REVERT: A  356 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6363 (tp30)
REVERT: A  407 ARG cc_start: 0.8504 (ptm-80) cc_final: 0.8263 (ptm-80)
REVERT: A  435 MET cc_start: 0.8517 (mmm) cc_final: 0.7983 (mmt)
REVERT: A  466 ASN cc_start: 0.8180 (t0) cc_final: 0.7943 (t0)
REVERT: B   14 ASP cc_start: 0.8367 (p0) cc_final: 0.8105 (p0)
REVERT: B   92 MET cc_start: 0.8709 (mmp) cc_final: 0.8422 (mmp)
REVERT: B  285 TYR cc_start: 0.7954 (t80) cc_final: 0.7689 (t80)
  outliers start: 39
  outliers final: 24
  residues processed: 139
  average time/residue: 0.2130
  time to fit residues: 39.5416
Evaluate side-chains
  132 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   33 LEU
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  223 ILE
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  279 CYS
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  303 MET
Chi-restraints excluded: chain A residue  383 LEU
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   48 THR
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  291 PHE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  341 ILE
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 47 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0070
   chunk 56 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 67 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  56 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.114759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.096289 restraints weight = 25171.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.098989 restraints weight = 13697.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.100819 restraints weight = 9083.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3930 r_free = 0.3930    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 = 0.3930 r_free = 0.3930    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.2414

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= 0.124
  Angle     :  0.620   9.668  11055  Z= 0.315
  Chirality :  0.045   0.222   1194
  Planarity :  0.004   0.089   1322
  Dihedral  : 15.687 148.097   1243
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 31.72 %
    Favored  : 64.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.28), residues: 892
  helix:  0.68 (0.32), residues: 270
  sheet: -0.76 (0.44), residues: 145
  loop : -2.15 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 373 
 HIS   0.004   0.001   HIS B 340 
 PHE   0.022   0.002   PHE A  78 
 TYR   0.023   0.001   TYR B 416 
 ARG   0.003   0.000   ARG A 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03579 (  254)
  hydrogen bonds       : angle       5.03819 (  728)
  covalent geometry    : bond        0.00282 ( 8107)
  covalent geometry    : angle       0.62038 (11055)

*********************** 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
  147 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7651 (mm)
REVERT: A   78 PHE cc_start: 0.7546 (t80) cc_final: 0.7302 (t80)
REVERT: A  302 GLN cc_start: 0.7438 (tt0) cc_final: 0.7056 (mt0)
REVERT: A  321 TYR cc_start: 0.5943 (t80) cc_final: 0.5597 (t80)
REVERT: A  356 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6353 (tp30)
REVERT: A  406 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.6851 (pmm)
REVERT: A  435 MET cc_start: 0.8555 (mmm) cc_final: 0.7957 (mmt)
REVERT: A  466 ASN cc_start: 0.8160 (t0) cc_final: 0.7908 (t0)
REVERT: A  476 GLU cc_start: 0.8165 (pt0) cc_final: 0.7870 (pt0)
REVERT: A  505 TYR cc_start: 0.6572 (OUTLIER) cc_final: 0.6260 (m-80)
REVERT: B   14 ASP cc_start: 0.8367 (p0) cc_final: 0.8117 (p0)
REVERT: B   92 MET cc_start: 0.8715 (mmp) cc_final: 0.8422 (mmp)
REVERT: B  257 ARG cc_start: 0.8552 (mmt-90) cc_final: 0.8318 (mmp80)
REVERT: B  285 TYR cc_start: 0.7734 (t80) cc_final: 0.7475 (t80)
  outliers start: 31
  outliers final: 19
  residues processed: 142
  average time/residue: 0.2290
  time to fit residues: 43.0244
Evaluate side-chains
  124 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   33 LEU
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  214 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  225 ARG
Chi-restraints excluded: chain A residue  279 CYS
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  349 GLN
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  505 TYR
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  295 ILE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  341 ILE
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 24 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 66 optimal weight:    5.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4153 r_free = 0.4153 target = 0.113264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.094701 restraints weight = 25846.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.097345 restraints weight = 14247.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.099124 restraints weight = 9558.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3879 r_free = 0.3879    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3879 r_free = 0.3879    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8107  Z= 0.165
  Angle     :  0.649   9.615  11055  Z= 0.332
  Chirality :  0.046   0.234   1194
  Planarity :  0.005   0.090   1322
  Dihedral  : 15.780 148.067   1243
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 16.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 30.60 %
    Favored  : 64.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.28), residues: 892
  helix:  0.71 (0.32), residues: 264
  sheet: -0.83 (0.43), residues: 150
  loop : -2.09 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 373 
 HIS   0.005   0.001   HIS B 340 
 PHE   0.022   0.002   PHE A  93 
 TYR   0.022   0.001   TYR B 416 
 ARG   0.006   0.001   ARG A 481 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03806 (  254)
  hydrogen bonds       : angle       5.04442 (  728)
  covalent geometry    : bond        0.00380 ( 8107)
  covalent geometry    : angle       0.64859 (11055)

*********************** 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
  147 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 106
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7480 (mm)
REVERT: A  302 GLN cc_start: 0.7453 (tt0) cc_final: 0.7054 (mt0)
REVERT: A  321 TYR cc_start: 0.5901 (t80) cc_final: 0.5604 (t80)
REVERT: A  356 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6349 (tp30)
REVERT: A  406 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.6862 (pmm)
REVERT: A  407 ARG cc_start: 0.8463 (ptm-80) cc_final: 0.8220 (ptm-80)
REVERT: A  435 MET cc_start: 0.8464 (mmm) cc_final: 0.8035 (mmt)
REVERT: A  476 GLU cc_start: 0.8697 (pt0) cc_final: 0.8229 (pt0)
REVERT: A  482 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7721 (m-80)
REVERT: A  505 TYR cc_start: 0.6690 (OUTLIER) cc_final: 0.6298 (m-80)
REVERT: B    1 MET cc_start: 0.6526 (ptm) cc_final: 0.6235 (ptm)
REVERT: B   14 ASP cc_start: 0.8334 (p0) cc_final: 0.8068 (p0)
REVERT: B   55 GLU cc_start: 0.5814 (tm-30) cc_final: 0.4951 (tm-30)
REVERT: B   92 MET cc_start: 0.8784 (mmp) cc_final: 0.8512 (mmp)
REVERT: B  285 TYR cc_start: 0.7830 (t80) cc_final: 0.7589 (t80)
  outliers start: 41
  outliers final: 28
  residues processed: 141
  average time/residue: 0.2238
  time to fit residues: 41.9476
Evaluate side-chains
  130 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 98
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  223 ILE
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  288 ILE
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  349 GLN
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  478 VAL
Chi-restraints excluded: chain A residue  482 PHE
Chi-restraints excluded: chain A residue  505 TYR
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  291 PHE
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  341 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 78 optimal weight:    0.8980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4162 r_free = 0.4162 target = 0.114024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.095348 restraints weight = 25922.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.098073 restraints weight = 13920.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.099846 restraints weight = 9189.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3895
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3895 r_free = 0.3895    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3895 r_free = 0.3895    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3895
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8107  Z= 0.146
  Angle     :  0.660   9.900  11055  Z= 0.333
  Chirality :  0.046   0.348   1194
  Planarity :  0.004   0.088   1322
  Dihedral  : 15.826 149.053   1243
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 16.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 31.34 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.28), residues: 892
  helix:  0.75 (0.32), residues: 265
  sheet: -0.95 (0.43), residues: 155
  loop : -2.01 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 373 
 HIS   0.004   0.001   HIS B 340 
 PHE   0.023   0.002   PHE A  93 
 TYR   0.023   0.001   TYR B 416 
 ARG   0.003   0.000   ARG A 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03598 (  254)
  hydrogen bonds       : angle       4.98381 (  728)
  covalent geometry    : bond        0.00335 ( 8107)
  covalent geometry    : angle       0.65971 (11055)

*********************** 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
  142 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 105
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7534 (mm)
REVERT: A  302 GLN cc_start: 0.7381 (tt0) cc_final: 0.6869 (mt0)
REVERT: A  321 TYR cc_start: 0.5929 (t80) cc_final: 0.5656 (t80)
REVERT: A  356 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6279 (tp30)
REVERT: A  406 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.6821 (pmm)
REVERT: A  435 MET cc_start: 0.8425 (mmm) cc_final: 0.8055 (mmt)
REVERT: A  482 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7737 (m-80)
REVERT: A  505 TYR cc_start: 0.6685 (OUTLIER) cc_final: 0.6352 (m-80)
REVERT: B    1 MET cc_start: 0.6598 (ptm) cc_final: 0.6337 (ptm)
REVERT: B   14 ASP cc_start: 0.8366 (p0) cc_final: 0.8117 (p0)
REVERT: B   55 GLU cc_start: 0.5711 (tm-30) cc_final: 0.4881 (tm-30)
REVERT: B   92 MET cc_start: 0.8749 (mmp) cc_final: 0.8454 (mmp)
REVERT: B  285 TYR cc_start: 0.7820 (t80) cc_final: 0.7580 (t80)
  outliers start: 37
  outliers final: 29
  residues processed: 137
  average time/residue: 0.2252
  time to fit residues: 40.9355
Evaluate side-chains
  129 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 96
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   33 LEU
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  207 HIS
Chi-restraints excluded: chain A residue  214 LEU
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  256 ILE
Chi-restraints excluded: chain A residue  279 CYS
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  349 GLN
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  478 VAL
Chi-restraints excluded: chain A residue  482 PHE
Chi-restraints excluded: chain A residue  505 TYR
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  401 ILE
Chi-restraints excluded: chain B residue  415 SER
Chi-restraints excluded: chain B residue  416 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 78 optimal weight:    0.3980
   chunk 75 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   chunk 77 optimal weight:    0.8980
   chunk 4 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A  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 = 0.4179 r_free = 0.4179 target = 0.115039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.096499 restraints weight = 25759.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.099273 restraints weight = 13699.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.101114 restraints weight = 8955.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3918
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3918 r_free = 0.3918    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3918 r_free = 0.3918    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3918
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8107  Z= 0.130
  Angle     :  0.655  10.054  11055  Z= 0.331
  Chirality :  0.045   0.225   1194
  Planarity :  0.005   0.086   1322
  Dihedral  : 15.797 150.154   1243
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 32.34 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.28), residues: 892
  helix:  0.83 (0.33), residues: 265
  sheet: -0.94 (0.44), residues: 151
  loop : -2.00 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 373 
 HIS   0.004   0.001   HIS B 340 
 PHE   0.021   0.002   PHE A  93 
 TYR   0.023   0.001   TYR B 416 
 ARG   0.010   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03439 (  254)
  hydrogen bonds       : angle       4.93339 (  728)
  covalent geometry    : bond        0.00301 ( 8107)
  covalent geometry    : angle       0.65537 (11055)

*********************** 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
  134 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 102
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7590 (mm)
REVERT: A  302 GLN cc_start: 0.7376 (tt0) cc_final: 0.6954 (mt0)
REVERT: A  303 MET cc_start: 0.8001 (tpt) cc_final: 0.7783 (tpt)
REVERT: A  406 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.6758 (pmm)
REVERT: A  435 MET cc_start: 0.8576 (mmm) cc_final: 0.8171 (mmt)
REVERT: A  505 TYR cc_start: 0.6595 (OUTLIER) cc_final: 0.6263 (m-80)
REVERT: B    1 MET cc_start: 0.6787 (ptm) cc_final: 0.6291 (ptm)
REVERT: B   55 GLU cc_start: 0.5692 (tm-30) cc_final: 0.4773 (tm-30)
REVERT: B   92 MET cc_start: 0.8714 (mmp) cc_final: 0.8421 (mmp)
REVERT: B  285 TYR cc_start: 0.7764 (t80) cc_final: 0.7551 (t80)
  outliers start: 32
  outliers final: 23
  residues processed: 131
  average time/residue: 0.2251
  time to fit residues: 39.2780
Evaluate side-chains
  122 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   33 LEU
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  207 HIS
Chi-restraints excluded: chain A residue  214 LEU
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  256 ILE
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  349 GLN
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  505 TYR
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   40 ASP
Chi-restraints excluded: chain B residue  291 PHE
Chi-restraints excluded: chain B residue  295 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 32 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 79 optimal weight:    0.4980
   chunk 29 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  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 = 0.4193 r_free = 0.4193 target = 0.115668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.097000 restraints weight = 26571.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.099767 restraints weight = 14508.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.101603 restraints weight = 9643.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3924
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3924 r_free = 0.3924    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3924 r_free = 0.3924    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3924
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.3054

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= 0.134
  Angle     :  0.676  10.936  11055  Z= 0.340
  Chirality :  0.046   0.224   1194
  Planarity :  0.005   0.085   1322
  Dihedral  : 15.680 150.670   1243
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 15.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 33.08 %
    Favored  : 63.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.29), residues: 892
  helix:  0.84 (0.33), residues: 264
  sheet: -1.01 (0.45), residues: 143
  loop : -1.95 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 373 
 HIS   0.003   0.001   HIS B 340 
 PHE   0.022   0.002   PHE A  93 
 TYR   0.023   0.001   TYR B 416 
 ARG   0.014   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03434 (  254)
  hydrogen bonds       : angle       4.88146 (  728)
  covalent geometry    : bond        0.00311 ( 8107)
  covalent geometry    : angle       0.67638 (11055)

*********************** 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
  130 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 102
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7598 (mm)
REVERT: A  302 GLN cc_start: 0.7313 (tt0) cc_final: 0.6936 (mt0)
REVERT: A  406 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.6817 (pmm)
REVERT: A  435 MET cc_start: 0.8568 (mmm) cc_final: 0.8173 (mmt)
REVERT: A  505 TYR cc_start: 0.6548 (OUTLIER) cc_final: 0.6312 (m-80)
REVERT: B    1 MET cc_start: 0.6795 (ptm) cc_final: 0.6322 (ptm)
REVERT: B   55 GLU cc_start: 0.5672 (tm-30) cc_final: 0.4759 (tm-30)
REVERT: B   92 MET cc_start: 0.8666 (mmp) cc_final: 0.8365 (mmp)
  outliers start: 28
  outliers final: 23
  residues processed: 126
  average time/residue: 0.2231
  time to fit residues: 37.4335
Evaluate side-chains
  123 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   33 LEU
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  207 HIS
Chi-restraints excluded: chain A residue  214 LEU
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  256 ILE
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  349 GLN
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  478 VAL
Chi-restraints excluded: chain A residue  505 TYR
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   40 ASP
Chi-restraints excluded: chain B residue  291 PHE
Chi-restraints excluded: chain B residue  295 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 23 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0570
   chunk 73 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 67 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.9502

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4176 r_free = 0.4176 target = 0.114876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.096354 restraints weight = 25569.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.099109 restraints weight = 13693.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.100974 restraints weight = 8982.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3916
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3916 r_free = 0.3916    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3916 r_free = 0.3916    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3916
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.3161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8107  Z= 0.143
  Angle     :  0.681   9.747  11055  Z= 0.343
  Chirality :  0.046   0.228   1194
  Planarity :  0.004   0.086   1322
  Dihedral  : 15.415 151.158   1243
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 15.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 33.21 %
    Favored  : 63.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.29), residues: 892
  helix:  0.81 (0.33), residues: 264
  sheet: -0.94 (0.45), residues: 141
  loop : -1.95 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 373 
 HIS   0.004   0.001   HIS B 340 
 PHE   0.022   0.002   PHE A  93 
 TYR   0.023   0.001   TYR B 416 
 ARG   0.008   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03389 (  254)
  hydrogen bonds       : angle       4.88447 (  728)
  covalent geometry    : bond        0.00333 ( 8107)
  covalent geometry    : angle       0.68064 (11055)

********************** 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
  130 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 102
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7623 (mm)
REVERT: A  302 GLN cc_start: 0.7316 (tt0) cc_final: 0.7031 (mt0)
REVERT: A  303 MET cc_start: 0.7841 (tpt) cc_final: 0.7459 (mmm)
REVERT: A  406 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.6759 (pmm)
REVERT: A  435 MET cc_start: 0.8387 (mmm) cc_final: 0.7984 (mmt)
REVERT: A  505 TYR cc_start: 0.6558 (OUTLIER) cc_final: 0.6294 (m-80)
REVERT: B    1 MET cc_start: 0.6774 (ptm) cc_final: 0.6288 (ptm)
REVERT: B   55 GLU cc_start: 0.5685 (tm-30) cc_final: 0.4775 (tm-30)
  outliers start: 28
  outliers final: 24
  residues processed: 128
  average time/residue: 0.2234
  time to fit residues: 38.6523
Evaluate side-chains
  128 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   33 LEU
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  207 HIS
Chi-restraints excluded: chain A residue  214 LEU
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  256 ILE
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  349 GLN
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  478 VAL
Chi-restraints excluded: chain A residue  505 TYR
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   40 ASP
Chi-restraints excluded: chain B residue  291 PHE
Chi-restraints excluded: chain B residue  295 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 26 optimal weight:    6.9990
   chunk 18 optimal weight:    0.3980
   chunk 2 optimal weight:    0.4980
   chunk 86 optimal weight:    8.9990
   chunk 9 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4205 r_free = 0.4205 target = 0.116393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.097322 restraints weight = 26383.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.100084 restraints weight = 14538.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.101952 restraints weight = 9743.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3932
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3932 r_free = 0.3932    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3932 r_free = 0.3932    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3932
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.3315

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= 0.131
  Angle     :  0.680  10.585  11055  Z= 0.340
  Chirality :  0.046   0.222   1194
  Planarity :  0.004   0.085   1322
  Dihedral  : 15.424 151.989   1243
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 33.08 %
    Favored  : 63.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.29), residues: 892
  helix:  0.89 (0.33), residues: 264
  sheet: -0.84 (0.45), residues: 137
  loop : -1.96 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 368 
 HIS   0.004   0.001   HIS B 340 
 PHE   0.020   0.002   PHE A  93 
 TYR   0.023   0.001   TYR B 416 
 ARG   0.006   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03254 (  254)
  hydrogen bonds       : angle       4.82986 (  728)
  covalent geometry    : bond        0.00306 ( 8107)
  covalent geometry    : angle       0.67951 (11055)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3595.77 seconds
wall clock time: 63 minutes 24.71 seconds (3804.71 seconds total)