Starting phenix.real_space_refine
on Wed Feb  4 00:14:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qja_53200/02_2026/9qja_53200.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qja_53200/02_2026/9qja_53200.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qja_53200/02_2026/9qja_53200.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qja_53200/02_2026/9qja_53200.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qja_53200/02_2026/9qja_53200.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qja_53200/02_2026/9qja_53200.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.021
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: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    5262      2.51       5
     N    1178      2.21       5
     O    1356      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7828
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 475, 3914
          Classifications: {'peptide': 475}
          Link IDs: {'PTRANS': 21, 'TRANS': 453}
          Chain breaks: 7
    Chain: "A"
      Number of atoms: 3914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 475, 3914
          Classifications: {'peptide': 475}
          Link IDs: {'PTRANS': 21, 'TRANS': 453}
          Chain breaks: 7
  Time building chain proxies: 1.71, per 1000 atoms: 0.22
  Number of scatterers: 7828
  At special positions: 0
  Unit cell: (102.858, 104.16, 101.556, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1356      8.00
     N    1178      7.00
     C    5262      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 258.2 milliseconds
  

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1864

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 2 sheets defined
      78.2% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'B' and resid 4 through 9
      removed outlier: 3.564A  pdb=" N   ASP B   9 " --> pdb=" O   ILE B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 32
    Processing helix  chain 'B' and resid 60 through 71
      removed outlier: 4.107A  pdb=" N   PHE B  64 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 97
    Processing helix  chain 'B' and resid 104 through 116
    Processing helix  chain 'B' and resid 117 through 148
      Proline residue:  B 136  - end of helix
    Processing helix  chain 'B' and resid 157 through 176
    Processing helix  chain 'B' and resid 177 through 189
      removed outlier: 3.600A  pdb=" N   TYR B 188 " --> pdb=" O   ARG B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 243
      removed outlier: 3.581A  pdb=" N   LYS B 215 " --> pdb=" O   ILE B 211 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   CYS B 217 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   ILE B 219 " --> pdb=" O   LYS B 215 " (cutoff:3.500A)
      Proline residue:  B 220  - end of helix
      removed outlier: 3.521A  pdb=" N   LEU B 234 " --> pdb=" O   LEU B 230 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE B 241 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 287
      Proline residue:  B 268  - end of helix
      removed outlier: 4.597A  pdb=" N   GLU B 280 " --> pdb=" O   LYS B 276 " (cutoff:3.500A)
      Proline residue:  B 281  - end of helix
    Processing helix  chain 'B' and resid 291 through 321
      removed outlier: 3.745A  pdb=" N   ILE B 305 " --> pdb=" O   LYS B 301 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE B 306 " --> pdb=" O   ASN B 302 " (cutoff:3.500A)
      Proline residue:  B 313  - end of helix
    Processing helix  chain 'B' and resid 322 through 327
      removed outlier: 4.006A  pdb=" N   HIS B 326 " --> pdb=" O   LEU B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 379
      removed outlier: 4.233A  pdb=" N   GLN B 363 " --> pdb=" O   ARG B 359 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ASN B 371 " --> pdb=" O   PHE B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 411
    Processing helix  chain 'B' and resid 413 through 428
    Processing helix  chain 'B' and resid 429 through 433
    Processing helix  chain 'B' and resid 436 through 455
    Processing helix  chain 'B' and resid 460 through 483
      removed outlier: 3.512A  pdb=" N   ILE B 464 " --> pdb=" O   LEU B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 534
      removed outlier: 3.880A  pdb=" N   SER B 513 " --> pdb=" O   GLY B 509 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   GLN B 534 " --> pdb=" O   THR B 530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 562 through 591
      removed outlier: 3.748A  pdb=" N   SER B 591 " --> pdb=" O   ILE B 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4 through 9
    Processing helix  chain 'A' and resid 25 through 32
      removed outlier: 3.841A  pdb=" N   LYS A  32 " --> pdb=" O   ASN A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 71
      removed outlier: 4.208A  pdb=" N   PHE A  64 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 97
    Processing helix  chain 'A' and resid 104 through 116
    Processing helix  chain 'A' and resid 117 through 148
      Proline residue:  A 136  - end of helix
    Processing helix  chain 'A' and resid 157 through 176
    Processing helix  chain 'A' and resid 177 through 189
      removed outlier: 3.555A  pdb=" N   TYR A 188 " --> pdb=" O   ARG A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 243
      removed outlier: 3.660A  pdb=" N   CYS A 216 " --> pdb=" O   MET A 212 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   PHE A 218 " --> pdb=" O   LYS A 214 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   ILE A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
      Proline residue:  A 220  - end of helix
      removed outlier: 3.549A  pdb=" N   LEU A 234 " --> pdb=" O   LEU A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 287
      Proline residue:  A 268  - end of helix
      removed outlier: 4.612A  pdb=" N   GLU A 280 " --> pdb=" O   LYS A 276 " (cutoff:3.500A)
      Proline residue:  A 281  - end of helix
    Processing helix  chain 'A' and resid 291 through 311
      removed outlier: 3.564A  pdb=" N   LYS A 296 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ILE A 305 " --> pdb=" O   LYS A 301 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ILE A 306 " --> pdb=" O   ASN A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 321
    Processing helix  chain 'A' and resid 321 through 327
      removed outlier: 4.138A  pdb=" N   GLY A 325 " --> pdb=" O   TYR A 321 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   HIS A 326 " --> pdb=" O   LEU A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 379
      removed outlier: 4.228A  pdb=" N   GLN A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ASN A 371 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 411
    Processing helix  chain 'A' and resid 413 through 428
    Processing helix  chain 'A' and resid 429 through 433
    Processing helix  chain 'A' and resid 436 through 454
      removed outlier: 3.597A  pdb=" N   LEU A 444 " --> pdb=" O   ASN A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 483
      removed outlier: 3.520A  pdb=" N   GLN A 474 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TYR A 483 " --> pdb=" O   LYS A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 534
      removed outlier: 3.688A  pdb=" N   SER A 513 " --> pdb=" O   GLY A 509 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLN A 534 " --> pdb=" O   THR A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 591
      removed outlier: 3.563A  pdb=" N   ILE A 566 " --> pdb=" O   SER A 562 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   SER A 591 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 41 through 42
      removed outlier: 3.511A  pdb=" N   SER B  49 " --> pdb=" O   PHE B  16 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL B  15 " --> pdb=" O   SER B  75 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER B  75 " --> pdb=" O   VAL B  15 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   ASN B  17 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
      removed outlier: 7.219A  pdb=" N   ILE B  73 " --> pdb=" O   ASN B  17 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 42
      removed outlier: 3.513A  pdb=" N   PHE A  16 " --> pdb=" O   SER A  49 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL A  15 " --> pdb=" O   SER A  75 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   SER A  75 " --> pdb=" O   VAL A  15 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ASN A  17 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   ILE A  73 " --> pdb=" O   ASN A  17 " (cutoff:3.500A)

    532 hydrogen bonds defined for protein.
    1572 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.11

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2235
        1.34 -     1.46: 1996
        1.46 -     1.58: 3775
        1.58 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 8054
  Sorted by residual:
  bond pdb=" N   ILE A 243 "
       pdb=" CA  ILE A 243 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.90e-02 2.77e+03 3.69e+00
  bond pdb=" N   ILE B 243 "
       pdb=" CA  ILE B 243 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.90e-02 2.77e+03 3.39e+00
  bond pdb=" C   ILE B 243 "
       pdb=" O   ILE B 243 "
    ideal  model  delta    sigma   weight residual
    1.231  1.252 -0.021 2.00e-02 2.50e+03 1.06e+00
  bond pdb=" C   ILE A 243 "
       pdb=" O   ILE A 243 "
    ideal  model  delta    sigma   weight residual
    1.231  1.251 -0.020 2.00e-02 2.50e+03 1.01e+00
  bond pdb=" C   ALA A  60 "
       pdb=" N   LYS A  61 "
    ideal  model  delta    sigma   weight residual
    1.341  1.324  0.016 1.65e-02 3.67e+03 9.73e-01
  ... (remaining 8049 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 10672
        1.44 -     2.89: 194
        2.89 -     4.33: 45
        4.33 -     5.78: 15
        5.78 -     7.22: 10
  Bond angle restraints: 10936
  Sorted by residual:
  angle pdb=" C   GLU A 286 "
        pdb=" N   ASN A 287 "
        pdb=" CA  ASN A 287 "
      ideal   model   delta    sigma   weight residual
     121.54  127.62   -6.08 1.91e+00 2.74e-01 1.01e+01
  angle pdb=" C   GLU B 286 "
        pdb=" N   ASN B 287 "
        pdb=" CA  ASN B 287 "
      ideal   model   delta    sigma   weight residual
     121.54  127.45   -5.91 1.91e+00 2.74e-01 9.59e+00
  angle pdb=" C   ALA A  60 "
        pdb=" N   LYS A  61 "
        pdb=" CA  LYS A  61 "
      ideal   model   delta    sigma   weight residual
     119.83  122.74   -2.91 1.11e+00 8.12e-01 6.87e+00
  angle pdb=" C   GLU A  30 "
        pdb=" N   PHE A  31 "
        pdb=" CA  PHE A  31 "
      ideal   model   delta    sigma   weight residual
     121.58  116.99    4.59 1.95e+00 2.63e-01 5.55e+00
  angle pdb=" N   VAL A 481 "
        pdb=" CA  VAL A 481 "
        pdb=" CB  VAL A 481 "
      ideal   model   delta    sigma   weight residual
     112.35  109.17    3.18 1.38e+00 5.25e-01 5.31e+00
  ... (remaining 10931 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.65: 4159
       16.65 -    33.29: 420
       33.29 -    49.94: 94
       49.94 -    66.59: 14
       66.59 -    83.24: 9
  Dihedral angle restraints: 4696
    sinusoidal: 1846
      harmonic: 2850
  Sorted by residual:
  dihedral pdb=" CA  PHE B  31 "
           pdb=" C   PHE B  31 "
           pdb=" N   LYS B  32 "
           pdb=" CA  LYS B  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.63   17.37     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CA  ASP A 476 "
           pdb=" CB  ASP A 476 "
           pdb=" CG  ASP A 476 "
           pdb=" OD1 ASP A 476 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.38   58.38     1      2.00e+01 2.50e-03 1.14e+01
  dihedral pdb=" CA  LYS A  61 "
           pdb=" C   LYS A  61 "
           pdb=" N   PRO A  62 "
           pdb=" CA  PRO A  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.39  -15.61     0      5.00e+00 4.00e-02 9.74e+00
  ... (remaining 4693 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 910
       0.041 -    0.081: 267
       0.081 -    0.122: 71
       0.122 -    0.162: 6
       0.162 -    0.203: 2
  Chirality restraints: 1256
  Sorted by residual:
  chirality pdb=" CA  ILE A 243 "
            pdb=" N   ILE A 243 "
            pdb=" C   ILE A 243 "
            pdb=" CB  ILE A 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  ILE B 243 "
            pdb=" N   ILE B 243 "
            pdb=" C   ILE B 243 "
            pdb=" CB  ILE B 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" CA  ASN A 287 "
            pdb=" N   ASN A 287 "
            pdb=" C   ASN A 287 "
            pdb=" CB  ASN A 287 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.09e-01
  ... (remaining 1253 not shown)

  Planarity restraints: 1308
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 280 "   -0.033 5.00e-02 4.00e+02   4.92e-02 3.88e+00
        pdb=" N   PRO A 281 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 281 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 281 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 280 "    0.024 5.00e-02 4.00e+02   3.66e-02 2.14e+00
        pdb=" N   PRO B 281 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B 281 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 281 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  31 "    0.010 2.00e-02 2.50e+03   1.05e-02 1.95e+00
        pdb=" CG  PHE B  31 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  31 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  31 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  31 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  31 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  31 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1305 not shown)

  Histogram of nonbonded interaction distances:
        2.54 -     3.01: 4486
        3.01 -     3.49: 9121
        3.49 -     3.96: 12546
        3.96 -     4.43: 14490
        4.43 -     4.90: 21862
  Nonbonded interactions: 62505
  Sorted by model distance:
  nonbonded pdb=" O   GLU B 286 "
            pdb=" OD1 ASN B 287 "
     model   vdw
     2.542 3.040
  nonbonded pdb=" O   GLU A 286 "
            pdb=" OD1 ASN A 287 "
     model   vdw
     2.546 3.040
  nonbonded pdb=" O   GLU A  24 "
            pdb=" OE1 GLU A  24 "
     model   vdw
     2.549 3.040
  nonbonded pdb=" O   GLU B  24 "
            pdb=" OE1 GLU B  24 "
     model   vdw
     2.599 3.040
  nonbonded pdb=" O   CYS B 465 "
            pdb=" OD1 ASN B 469 "
     model   vdw
     2.609 3.040
  ... (remaining 62500 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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=1.00 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.700
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6567
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   8054  Z= 0.131
  Angle     :  0.561   7.223  10936  Z= 0.294
  Chirality :  0.041   0.203   1256
  Planarity :  0.004   0.049   1308
  Dihedral  : 14.358  83.237   2832
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  5.28 %
    Favored  : 94.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.28), residues: 918
  helix:  1.21 (0.20), residues: 666
  sheet: -0.13 (0.77), residues: 52
  loop : -0.03 (0.47), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 359 
 TYR   0.019   0.001   TYR B 426 
 PHE   0.024   0.001   PHE B  31 
 TRP   0.011   0.001   TRP B 165 
 HIS   0.005   0.001   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8054)
  covalent geometry    : angle       0.56056 (10936)
  hydrogen bonds       : bond        0.19050 (  532)
  hydrogen bonds       : angle       6.99843 ( 1572)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 235
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    4 THR cc_start: 0.7885 (p) cc_final: 0.7313 (t)
REVERT: B    9 ASP cc_start: 0.6981 (t70) cc_final: 0.6294 (t70)
REVERT: B   11 ASN cc_start: 0.7798 (m-40) cc_final: 0.7341 (m-40)
REVERT: B   18 LYS cc_start: 0.7975 (ttpt) cc_final: 0.7463 (ttpt)
REVERT: B   27 LEU cc_start: 0.7825 (pp) cc_final: 0.7443 (pp)
REVERT: B   37 HIS cc_start: 0.7513 (p-80) cc_final: 0.7283 (p-80)
REVERT: B   66 PHE cc_start: 0.7678 (t80) cc_final: 0.7446 (t80)
REVERT: B   83 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6124 (tm-30)
REVERT: B   86 ASP cc_start: 0.7487 (m-30) cc_final: 0.7222 (m-30)
REVERT: B   90 LYS cc_start: 0.8432 (mmtm) cc_final: 0.7972 (mmtm)
REVERT: B  116 ASN cc_start: 0.8307 (m-40) cc_final: 0.7938 (t0)
REVERT: B  117 ASN cc_start: 0.8399 (t0) cc_final: 0.7993 (t0)
REVERT: B  172 PHE cc_start: 0.7188 (m-10) cc_final: 0.6971 (m-10)
REVERT: B  176 LYS cc_start: 0.7438 (tptt) cc_final: 0.6937 (tptt)
REVERT: B  178 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7728 (tm-30)
REVERT: B  196 PHE cc_start: 0.7177 (t80) cc_final: 0.6948 (t80)
REVERT: B  223 LEU cc_start: 0.7799 (mt) cc_final: 0.7487 (mt)
REVERT: B  308 LEU cc_start: 0.8191 (tt) cc_final: 0.7970 (tt)
REVERT: B  359 ARG cc_start: 0.7242 (ptm-80) cc_final: 0.6954 (ptm-80)
REVERT: B  378 MET cc_start: 0.5121 (mtt) cc_final: 0.4814 (mtt)
REVERT: B  418 LYS cc_start: 0.8082 (tptp) cc_final: 0.7687 (tptp)
REVERT: B  422 LYS cc_start: 0.8397 (tptt) cc_final: 0.7733 (tttp)
REVERT: B  447 GLN cc_start: 0.7384 (tt0) cc_final: 0.7007 (tt0)
REVERT: B  465 CYS cc_start: 0.6795 (m) cc_final: 0.6412 (m)
REVERT: B  482 LEU cc_start: 0.7803 (mm) cc_final: 0.7019 (tp)
REVERT: B  574 GLU cc_start: 0.6755 (tm-30) cc_final: 0.6352 (tm-30)
REVERT: A    9 ASP cc_start: 0.7290 (t70) cc_final: 0.6827 (t0)
REVERT: A   18 LYS cc_start: 0.7996 (ttpt) cc_final: 0.7294 (ttpt)
REVERT: A   46 LEU cc_start: 0.8415 (pp) cc_final: 0.8126 (pp)
REVERT: A   68 GLN cc_start: 0.6935 (tm-30) cc_final: 0.6402 (tm-30)
REVERT: A  117 ASN cc_start: 0.8331 (t0) cc_final: 0.8102 (t0)
REVERT: A  119 LYS cc_start: 0.8326 (mttp) cc_final: 0.7686 (mtmt)
REVERT: A  176 LYS cc_start: 0.7577 (tptt) cc_final: 0.7155 (tptt)
REVERT: A  196 PHE cc_start: 0.7114 (t80) cc_final: 0.6795 (t80)
REVERT: A  288 HIS cc_start: 0.6261 (t70) cc_final: 0.5990 (t70)
REVERT: A  296 LYS cc_start: 0.7727 (ptmm) cc_final: 0.6864 (mmtt)
REVERT: A  378 MET cc_start: 0.4975 (ttm) cc_final: 0.4594 (ttm)
REVERT: A  417 MET cc_start: 0.7770 (ttp) cc_final: 0.7535 (ttp)
REVERT: A  422 LYS cc_start: 0.8553 (tptt) cc_final: 0.7748 (tttp)
REVERT: A  442 LYS cc_start: 0.7326 (tttm) cc_final: 0.6399 (mtpt)
REVERT: A  454 PHE cc_start: 0.7264 (m-80) cc_final: 0.6985 (m-10)
REVERT: A  460 LEU cc_start: 0.7321 (mt) cc_final: 0.6948 (tp)
REVERT: A  513 SER cc_start: 0.7794 (m) cc_final: 0.7580 (p)
REVERT: A  530 THR cc_start: 0.8258 (m) cc_final: 0.8052 (p)
REVERT: A  574 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6362 (tm-30)
REVERT: A  587 ILE cc_start: 0.7653 (mt) cc_final: 0.7193 (mm)
  outliers start: 2
  outliers final: 0
  residues processed: 235
  average time/residue: 0.0749
  time to fit residues: 23.9633
Evaluate side-chains
  219 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0570
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0470
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.4196

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.161360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.138003 restraints weight = 13744.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.141957 restraints weight = 8843.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.144878 restraints weight = 6299.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.146952 restraints weight = 4829.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.148446 restraints weight = 3922.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6495
moved from start:          0.1114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   8054  Z= 0.149
  Angle     :  0.612   9.255  10936  Z= 0.313
  Chirality :  0.043   0.151   1256
  Planarity :  0.004   0.042   1308
  Dihedral  :  3.940  17.513    998
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.92 (0.28), residues: 918
  helix:  1.79 (0.20), residues: 680
  sheet: -0.43 (0.72), residues: 52
  loop : -0.01 (0.49), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 359 
 TYR   0.019   0.001   TYR B 321 
 PHE   0.027   0.002   PHE A  31 
 TRP   0.009   0.001   TRP B 165 
 HIS   0.005   0.001   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 8054)
  covalent geometry    : angle       0.61181 (10936)
  hydrogen bonds       : bond        0.05155 (  532)
  hydrogen bonds       : angle       4.82574 ( 1572)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 ASP cc_start: 0.7067 (t70) cc_final: 0.6509 (t70)
REVERT: B   18 LYS cc_start: 0.7900 (ttpt) cc_final: 0.7616 (ttpt)
REVERT: B   27 LEU cc_start: 0.7874 (pp) cc_final: 0.7410 (pp)
REVERT: B   37 HIS cc_start: 0.7462 (p-80) cc_final: 0.7187 (p-80)
REVERT: B   66 PHE cc_start: 0.7671 (t80) cc_final: 0.7466 (t80)
REVERT: B   83 GLU cc_start: 0.6662 (tm-30) cc_final: 0.6133 (tm-30)
REVERT: B   86 ASP cc_start: 0.7413 (m-30) cc_final: 0.7150 (m-30)
REVERT: B   90 LYS cc_start: 0.8402 (mmtm) cc_final: 0.7988 (mmtm)
REVERT: B  116 ASN cc_start: 0.8325 (m-40) cc_final: 0.7954 (t0)
REVERT: B  117 ASN cc_start: 0.8326 (t0) cc_final: 0.7845 (t0)
REVERT: B  172 PHE cc_start: 0.7224 (m-10) cc_final: 0.6983 (m-10)
REVERT: B  176 LYS cc_start: 0.7446 (tptt) cc_final: 0.6990 (tptt)
REVERT: B  178 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7633 (tm-30)
REVERT: B  196 PHE cc_start: 0.7200 (t80) cc_final: 0.6968 (t80)
REVERT: B  223 LEU cc_start: 0.7990 (mt) cc_final: 0.7662 (mt)
REVERT: B  304 VAL cc_start: 0.7485 (t) cc_final: 0.6838 (m)
REVERT: B  359 ARG cc_start: 0.7261 (ptm-80) cc_final: 0.6906 (ptm-80)
REVERT: B  378 MET cc_start: 0.4966 (mtt) cc_final: 0.4670 (mtt)
REVERT: B  418 LYS cc_start: 0.8030 (tptp) cc_final: 0.7645 (tptp)
REVERT: B  422 LYS cc_start: 0.8365 (tptt) cc_final: 0.7747 (tttp)
REVERT: B  447 GLN cc_start: 0.7305 (tt0) cc_final: 0.6936 (tt0)
REVERT: B  465 CYS cc_start: 0.6827 (m) cc_final: 0.6418 (m)
REVERT: B  482 LEU cc_start: 0.7486 (mm) cc_final: 0.6883 (tp)
REVERT: B  523 CYS cc_start: 0.7871 (t) cc_final: 0.7634 (t)
REVERT: B  574 GLU cc_start: 0.6770 (tm-30) cc_final: 0.6387 (tm-30)
REVERT: A   18 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7307 (ttpt)
REVERT: A   46 LEU cc_start: 0.8594 (pp) cc_final: 0.8257 (pp)
REVERT: A   53 ILE cc_start: 0.6904 (tt) cc_final: 0.6478 (pt)
REVERT: A   68 GLN cc_start: 0.7242 (tm-30) cc_final: 0.6545 (tm-30)
REVERT: A   84 LEU cc_start: 0.8087 (mp) cc_final: 0.7713 (mp)
REVERT: A  116 ASN cc_start: 0.8140 (m-40) cc_final: 0.7902 (t0)
REVERT: A  117 ASN cc_start: 0.8397 (t0) cc_final: 0.8066 (t0)
REVERT: A  119 LYS cc_start: 0.8238 (mttp) cc_final: 0.7706 (mttt)
REVERT: A  176 LYS cc_start: 0.7463 (tptt) cc_final: 0.6991 (tptt)
REVERT: A  178 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7866 (tm-30)
REVERT: A  196 PHE cc_start: 0.7170 (t80) cc_final: 0.6806 (t80)
REVERT: A  293 ASN cc_start: 0.7148 (p0) cc_final: 0.6589 (p0)
REVERT: A  296 LYS cc_start: 0.7828 (ptmm) cc_final: 0.6871 (mmtt)
REVERT: A  378 MET cc_start: 0.4908 (ttm) cc_final: 0.4393 (ttm)
REVERT: A  416 ASP cc_start: 0.7376 (m-30) cc_final: 0.6903 (m-30)
REVERT: A  422 LYS cc_start: 0.8412 (tptt) cc_final: 0.7908 (tttp)
REVERT: A  442 LYS cc_start: 0.7050 (tttm) cc_final: 0.6671 (ptmt)
REVERT: A  454 PHE cc_start: 0.7231 (m-80) cc_final: 0.7021 (m-80)
REVERT: A  482 LEU cc_start: 0.8183 (mm) cc_final: 0.7313 (tp)
REVERT: A  574 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6346 (tm-30)
REVERT: A  587 ILE cc_start: 0.7468 (mt) cc_final: 0.7132 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.0773
  time to fit residues: 25.3110
Evaluate side-chains
  224 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 58 optimal weight:    0.4980
   chunk 28 optimal weight:    0.0010
   chunk 75 optimal weight:    0.0270
   chunk 11 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 88 optimal weight:    0.2980
   chunk 15 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.3044

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

Flipped N/Q/H residues before XYZ refinement:
A 302 ASN
A 440 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.162973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.139333 restraints weight = 13727.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.143394 restraints weight = 8910.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.146118 restraints weight = 6373.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.148337 restraints weight = 4965.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.149962 restraints weight = 4034.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6475
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8054  Z= 0.131
  Angle     :  0.590   8.192  10936  Z= 0.299
  Chirality :  0.042   0.146   1256
  Planarity :  0.004   0.043   1308
  Dihedral  :  3.911  16.469    998
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.16 %
    Favored  : 95.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.09 (0.28), residues: 918
  helix:  1.95 (0.20), residues: 678
  sheet: -0.53 (0.69), residues: 52
  loop : -0.01 (0.49), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 478 
 TYR   0.033   0.001   TYR B 426 
 PHE   0.020   0.001   PHE A  31 
 TRP   0.010   0.001   TRP A 165 
 HIS   0.006   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8054)
  covalent geometry    : angle       0.58957 (10936)
  hydrogen bonds       : bond        0.04426 (  532)
  hydrogen bonds       : angle       4.50214 ( 1572)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 239
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 ASP cc_start: 0.7061 (t70) cc_final: 0.6488 (t70)
REVERT: B   18 LYS cc_start: 0.7964 (ttpt) cc_final: 0.7478 (ttpt)
REVERT: B   27 LEU cc_start: 0.7941 (pp) cc_final: 0.7238 (pp)
REVERT: B   53 ILE cc_start: 0.7120 (tt) cc_final: 0.6651 (pt)
REVERT: B   61 LYS cc_start: 0.6710 (mmmt) cc_final: 0.6509 (mmtt)
REVERT: B   83 GLU cc_start: 0.6738 (tm-30) cc_final: 0.6160 (tm-30)
REVERT: B   86 ASP cc_start: 0.7349 (m-30) cc_final: 0.7135 (m-30)
REVERT: B   90 LYS cc_start: 0.8416 (mmtm) cc_final: 0.7992 (mmtm)
REVERT: B  116 ASN cc_start: 0.8299 (m-40) cc_final: 0.7934 (t0)
REVERT: B  117 ASN cc_start: 0.8230 (t0) cc_final: 0.7761 (t0)
REVERT: B  172 PHE cc_start: 0.7296 (m-10) cc_final: 0.7061 (m-10)
REVERT: B  176 LYS cc_start: 0.7425 (tptt) cc_final: 0.6953 (tptt)
REVERT: B  178 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7622 (tm-30)
REVERT: B  196 PHE cc_start: 0.7164 (t80) cc_final: 0.6938 (t80)
REVERT: B  223 LEU cc_start: 0.8037 (mt) cc_final: 0.7714 (mt)
REVERT: B  304 VAL cc_start: 0.7448 (t) cc_final: 0.6800 (m)
REVERT: B  320 LEU cc_start: 0.7423 (mm) cc_final: 0.7213 (mp)
REVERT: B  359 ARG cc_start: 0.7191 (ptm-80) cc_final: 0.6848 (ptm-80)
REVERT: B  378 MET cc_start: 0.4981 (mtt) cc_final: 0.4740 (mtt)
REVERT: B  418 LYS cc_start: 0.8036 (tptp) cc_final: 0.7627 (tptp)
REVERT: B  422 LYS cc_start: 0.8445 (tptt) cc_final: 0.7749 (tttp)
REVERT: B  447 GLN cc_start: 0.7376 (tt0) cc_final: 0.7086 (tm-30)
REVERT: B  450 TYR cc_start: 0.6749 (m-80) cc_final: 0.6323 (m-80)
REVERT: B  465 CYS cc_start: 0.6867 (m) cc_final: 0.6408 (m)
REVERT: B  482 LEU cc_start: 0.7388 (mm) cc_final: 0.6797 (tp)
REVERT: B  523 CYS cc_start: 0.7744 (t) cc_final: 0.7490 (t)
REVERT: B  574 GLU cc_start: 0.6840 (tm-30) cc_final: 0.6410 (tm-30)
REVERT: A   18 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7233 (ttpt)
REVERT: A   46 LEU cc_start: 0.8559 (pp) cc_final: 0.8063 (pp)
REVERT: A   68 GLN cc_start: 0.7238 (tm-30) cc_final: 0.6583 (tm-30)
REVERT: A   84 LEU cc_start: 0.7957 (mp) cc_final: 0.7620 (mp)
REVERT: A   96 LYS cc_start: 0.7809 (tttt) cc_final: 0.7404 (ttmt)
REVERT: A  116 ASN cc_start: 0.8179 (m-40) cc_final: 0.7905 (t0)
REVERT: A  117 ASN cc_start: 0.8326 (t0) cc_final: 0.7948 (t0)
REVERT: A  119 LYS cc_start: 0.8130 (mttp) cc_final: 0.7720 (mttp)
REVERT: A  132 LYS cc_start: 0.7518 (ttmt) cc_final: 0.7274 (ttmt)
REVERT: A  158 TYR cc_start: 0.7548 (t80) cc_final: 0.7135 (t80)
REVERT: A  176 LYS cc_start: 0.7439 (tptt) cc_final: 0.6912 (tptt)
REVERT: A  178 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7705 (tm-30)
REVERT: A  196 PHE cc_start: 0.7137 (t80) cc_final: 0.6847 (t80)
REVERT: A  296 LYS cc_start: 0.7789 (ptmm) cc_final: 0.6811 (mmmt)
REVERT: A  311 TYR cc_start: 0.6522 (m-10) cc_final: 0.6216 (m-10)
REVERT: A  378 MET cc_start: 0.4920 (ttm) cc_final: 0.4417 (ttm)
REVERT: A  416 ASP cc_start: 0.7406 (m-30) cc_final: 0.6886 (m-30)
REVERT: A  417 MET cc_start: 0.7501 (ttp) cc_final: 0.7146 (ttp)
REVERT: A  418 LYS cc_start: 0.8115 (mmmm) cc_final: 0.7865 (mmmm)
REVERT: A  422 LYS cc_start: 0.8373 (tptt) cc_final: 0.7777 (tttp)
REVERT: A  447 GLN cc_start: 0.7369 (tt0) cc_final: 0.7101 (tt0)
REVERT: A  453 MET cc_start: 0.6121 (ptp) cc_final: 0.5788 (ptp)
REVERT: A  454 PHE cc_start: 0.7111 (m-80) cc_final: 0.6747 (m-80)
REVERT: A  465 CYS cc_start: 0.6207 (m) cc_final: 0.5983 (m)
REVERT: A  482 LEU cc_start: 0.8093 (mm) cc_final: 0.7200 (tp)
REVERT: A  487 GLU cc_start: 0.6846 (pt0) cc_final: 0.6464 (pt0)
REVERT: A  574 GLU cc_start: 0.6881 (tm-30) cc_final: 0.6348 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 239
  average time/residue: 0.0789
  time to fit residues: 25.6849
Evaluate side-chains
  221 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 220
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   chunk 31 optimal weight:    0.1980
   chunk 12 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.159724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.136377 restraints weight = 13881.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.140319 restraints weight = 8991.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.143185 restraints weight = 6432.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.145299 restraints weight = 4946.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.146612 restraints weight = 4013.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6531
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8054  Z= 0.175
  Angle     :  0.619   8.893  10936  Z= 0.315
  Chirality :  0.044   0.156   1256
  Planarity :  0.004   0.043   1308
  Dihedral  :  4.016  17.232    998
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.28), residues: 918
  helix:  1.81 (0.20), residues: 690
  sheet: -0.57 (0.67), residues: 52
  loop :  0.13 (0.51), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 359 
 TYR   0.019   0.001   TYR B 321 
 PHE   0.019   0.001   PHE B  31 
 TRP   0.007   0.001   TRP B 165 
 HIS   0.005   0.001   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 8054)
  covalent geometry    : angle       0.61934 (10936)
  hydrogen bonds       : bond        0.04631 (  532)
  hydrogen bonds       : angle       4.47332 ( 1572)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 ASP cc_start: 0.7148 (t70) cc_final: 0.6640 (t70)
REVERT: B   18 LYS cc_start: 0.7883 (ttpt) cc_final: 0.7412 (ttpt)
REVERT: B   27 LEU cc_start: 0.7977 (pp) cc_final: 0.7318 (pp)
REVERT: B   53 ILE cc_start: 0.7173 (tt) cc_final: 0.6670 (pt)
REVERT: B   83 GLU cc_start: 0.6919 (tm-30) cc_final: 0.6289 (tm-30)
REVERT: B   86 ASP cc_start: 0.7361 (m-30) cc_final: 0.7147 (m-30)
REVERT: B   90 LYS cc_start: 0.8411 (mmtm) cc_final: 0.8024 (mmtm)
REVERT: B  116 ASN cc_start: 0.8310 (m-40) cc_final: 0.7921 (t0)
REVERT: B  117 ASN cc_start: 0.8232 (t0) cc_final: 0.7764 (t0)
REVERT: B  172 PHE cc_start: 0.7390 (m-10) cc_final: 0.7134 (m-10)
REVERT: B  176 LYS cc_start: 0.7404 (tptt) cc_final: 0.6985 (tptt)
REVERT: B  178 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7653 (tm-30)
REVERT: B  196 PHE cc_start: 0.7196 (t80) cc_final: 0.6952 (t80)
REVERT: B  223 LEU cc_start: 0.8213 (mt) cc_final: 0.7883 (mt)
REVERT: B  304 VAL cc_start: 0.7441 (t) cc_final: 0.6857 (m)
REVERT: B  320 LEU cc_start: 0.7571 (mm) cc_final: 0.7349 (mp)
REVERT: B  378 MET cc_start: 0.4748 (mtt) cc_final: 0.4507 (mtt)
REVERT: B  418 LYS cc_start: 0.8014 (tptp) cc_final: 0.7592 (tptp)
REVERT: B  422 LYS cc_start: 0.8425 (tptt) cc_final: 0.7789 (tttp)
REVERT: B  447 GLN cc_start: 0.7356 (tt0) cc_final: 0.7097 (tm-30)
REVERT: B  465 CYS cc_start: 0.6852 (m) cc_final: 0.6427 (m)
REVERT: B  482 LEU cc_start: 0.7448 (mm) cc_final: 0.6855 (tp)
REVERT: B  487 GLU cc_start: 0.7098 (pt0) cc_final: 0.6687 (pt0)
REVERT: B  574 GLU cc_start: 0.6778 (tm-30) cc_final: 0.6511 (tm-30)
REVERT: A   18 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7274 (ttpt)
REVERT: A   27 LEU cc_start: 0.8232 (pp) cc_final: 0.7693 (pp)
REVERT: A   46 LEU cc_start: 0.8630 (pp) cc_final: 0.8255 (pp)
REVERT: A   68 GLN cc_start: 0.7399 (tm-30) cc_final: 0.6772 (tm-30)
REVERT: A   83 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6648 (tm-30)
REVERT: A   84 LEU cc_start: 0.7939 (mp) cc_final: 0.7454 (mt)
REVERT: A   96 LYS cc_start: 0.7763 (tttt) cc_final: 0.7335 (ttmt)
REVERT: A  116 ASN cc_start: 0.8252 (m-40) cc_final: 0.7911 (t0)
REVERT: A  117 ASN cc_start: 0.8331 (t0) cc_final: 0.8003 (t0)
REVERT: A  176 LYS cc_start: 0.7511 (tptt) cc_final: 0.6997 (tptt)
REVERT: A  178 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7760 (tm-30)
REVERT: A  196 PHE cc_start: 0.7194 (t80) cc_final: 0.6804 (t80)
REVERT: A  288 HIS cc_start: 0.5940 (t70) cc_final: 0.5457 (t70)
REVERT: A  296 LYS cc_start: 0.7550 (ptmm) cc_final: 0.6733 (mmmt)
REVERT: A  378 MET cc_start: 0.4927 (ttm) cc_final: 0.4165 (ttm)
REVERT: A  416 ASP cc_start: 0.7410 (m-30) cc_final: 0.6902 (m-30)
REVERT: A  417 MET cc_start: 0.7549 (ttp) cc_final: 0.7189 (ttp)
REVERT: A  418 LYS cc_start: 0.8177 (mmmm) cc_final: 0.7895 (mmmm)
REVERT: A  422 LYS cc_start: 0.8373 (tptt) cc_final: 0.7898 (tttp)
REVERT: A  453 MET cc_start: 0.6429 (ptp) cc_final: 0.6081 (ptp)
REVERT: A  454 PHE cc_start: 0.7154 (m-80) cc_final: 0.6780 (m-80)
REVERT: A  465 CYS cc_start: 0.6275 (m) cc_final: 0.6056 (m)
REVERT: A  482 LEU cc_start: 0.8198 (mm) cc_final: 0.7255 (tp)
REVERT: A  574 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6381 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.0723
  time to fit residues: 24.1278
Evaluate side-chains
  223 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 22 optimal weight:    0.0040
   chunk 82 optimal weight:    0.9980
   chunk 86 optimal weight:    0.6980
   chunk 32 optimal weight:    9.9990
   chunk 78 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 59 optimal weight:    0.3980
   chunk 64 optimal weight:    0.7980
   chunk 28 optimal weight:    0.1980
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.3792

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

Flipped N/Q/H residues before XYZ refinement:
** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 302 ASN
A 440 ASN
A 447 GLN
A 565 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.161343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.139061 restraints weight = 13685.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.142747 restraints weight = 9032.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.145465 restraints weight = 6547.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.147297 restraints weight = 5079.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.148759 restraints weight = 4190.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6487
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8054  Z= 0.137
  Angle     :  0.609  10.130  10936  Z= 0.304
  Chirality :  0.043   0.155   1256
  Planarity :  0.004   0.042   1308
  Dihedral  :  4.012  17.659    998
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.81 %
    Favored  : 97.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.28), residues: 918
  helix:  1.82 (0.20), residues: 690
  sheet: -0.60 (0.67), residues: 52
  loop :  0.14 (0.51), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 145 
 TYR   0.027   0.001   TYR A 426 
 PHE   0.023   0.001   PHE B  31 
 TRP   0.010   0.001   TRP B 173 
 HIS   0.006   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8054)
  covalent geometry    : angle       0.60926 (10936)
  hydrogen bonds       : bond        0.04290 (  532)
  hydrogen bonds       : angle       4.35331 ( 1572)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 241
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 ASP cc_start: 0.7049 (t70) cc_final: 0.6522 (t70)
REVERT: B   18 LYS cc_start: 0.7779 (ttpt) cc_final: 0.7311 (ttpt)
REVERT: B   27 LEU cc_start: 0.8033 (pp) cc_final: 0.7305 (pp)
REVERT: B   37 HIS cc_start: 0.7489 (p-80) cc_final: 0.7265 (p-80)
REVERT: B   53 ILE cc_start: 0.7228 (tt) cc_final: 0.6750 (pt)
REVERT: B   83 GLU cc_start: 0.6814 (tm-30) cc_final: 0.6242 (tm-30)
REVERT: B   90 LYS cc_start: 0.8339 (mmtm) cc_final: 0.7942 (mmtm)
REVERT: B  116 ASN cc_start: 0.8260 (m-40) cc_final: 0.7724 (t0)
REVERT: B  117 ASN cc_start: 0.8168 (t0) cc_final: 0.7725 (t0)
REVERT: B  172 PHE cc_start: 0.7328 (m-10) cc_final: 0.7116 (m-10)
REVERT: B  176 LYS cc_start: 0.7370 (tptt) cc_final: 0.7010 (tptt)
REVERT: B  178 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7594 (tm-30)
REVERT: B  196 PHE cc_start: 0.7167 (t80) cc_final: 0.6912 (t80)
REVERT: B  212 MET cc_start: 0.6459 (pmm) cc_final: 0.6095 (pmm)
REVERT: B  223 LEU cc_start: 0.8189 (mt) cc_final: 0.7860 (mt)
REVERT: B  304 VAL cc_start: 0.7483 (t) cc_final: 0.6855 (m)
REVERT: B  320 LEU cc_start: 0.7434 (mm) cc_final: 0.7227 (mp)
REVERT: B  378 MET cc_start: 0.4648 (mtt) cc_final: 0.4421 (mtt)
REVERT: B  418 LYS cc_start: 0.8009 (tptp) cc_final: 0.7578 (tptp)
REVERT: B  422 LYS cc_start: 0.8355 (tptt) cc_final: 0.7646 (tttp)
REVERT: B  442 LYS cc_start: 0.7103 (tttm) cc_final: 0.6900 (ttpt)
REVERT: B  447 GLN cc_start: 0.7397 (tt0) cc_final: 0.7146 (tm-30)
REVERT: B  454 PHE cc_start: 0.7097 (m-80) cc_final: 0.6835 (m-80)
REVERT: B  465 CYS cc_start: 0.6794 (m) cc_final: 0.6349 (m)
REVERT: B  482 LEU cc_start: 0.7458 (mm) cc_final: 0.6940 (tp)
REVERT: B  574 GLU cc_start: 0.6728 (tm-30) cc_final: 0.6479 (tm-30)
REVERT: A   18 LYS cc_start: 0.7923 (ttpt) cc_final: 0.7177 (ttpt)
REVERT: A   46 LEU cc_start: 0.8465 (pp) cc_final: 0.8069 (pp)
REVERT: A   68 GLN cc_start: 0.7097 (tm-30) cc_final: 0.6310 (tm-30)
REVERT: A   83 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6583 (tm-30)
REVERT: A   84 LEU cc_start: 0.7950 (mp) cc_final: 0.7435 (mt)
REVERT: A  115 THR cc_start: 0.8115 (t) cc_final: 0.7898 (m)
REVERT: A  116 ASN cc_start: 0.8188 (m-40) cc_final: 0.7792 (t0)
REVERT: A  117 ASN cc_start: 0.8361 (t0) cc_final: 0.7965 (t0)
REVERT: A  176 LYS cc_start: 0.7491 (tptt) cc_final: 0.7002 (tptt)
REVERT: A  288 HIS cc_start: 0.5855 (t70) cc_final: 0.5634 (t70)
REVERT: A  296 LYS cc_start: 0.7575 (ptmm) cc_final: 0.6772 (mmmt)
REVERT: A  378 MET cc_start: 0.4672 (ttm) cc_final: 0.3919 (ttm)
REVERT: A  417 MET cc_start: 0.7435 (ttp) cc_final: 0.7088 (ttp)
REVERT: A  418 LYS cc_start: 0.8125 (mmmm) cc_final: 0.7832 (mmmm)
REVERT: A  422 LYS cc_start: 0.8273 (tptt) cc_final: 0.7652 (tttp)
REVERT: A  454 PHE cc_start: 0.7124 (m-80) cc_final: 0.6839 (m-80)
REVERT: A  465 CYS cc_start: 0.6300 (m) cc_final: 0.6026 (m)
REVERT: A  482 LEU cc_start: 0.8090 (mm) cc_final: 0.7320 (tp)
REVERT: A  574 GLU cc_start: 0.6844 (tm-30) cc_final: 0.6300 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 241
  average time/residue: 0.0705
  time to fit residues: 23.2220
Evaluate side-chains
  222 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 221
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 76 optimal weight:    6.9990
   chunk 79 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 128 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.155196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.132185 restraints weight = 13687.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.135910 restraints weight = 9015.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.138690 restraints weight = 6508.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.140693 restraints weight = 5004.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.142211 restraints weight = 4070.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6595
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   8054  Z= 0.261
  Angle     :  0.712   9.953  10936  Z= 0.372
  Chirality :  0.047   0.159   1256
  Planarity :  0.004   0.040   1308
  Dihedral  :  4.312  20.182    998
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.28), residues: 918
  helix:  1.48 (0.20), residues: 692
  sheet: -0.46 (0.67), residues: 52
  loop :  0.05 (0.52), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 145 
 TYR   0.035   0.002   TYR B 321 
 PHE   0.036   0.002   PHE A 196 
 TRP   0.011   0.002   TRP B 173 
 HIS   0.007   0.002   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 ( 8054)
  covalent geometry    : angle       0.71237 (10936)
  hydrogen bonds       : bond        0.05322 (  532)
  hydrogen bonds       : angle       4.69345 ( 1572)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 ASP cc_start: 0.7180 (t70) cc_final: 0.6664 (t70)
REVERT: B   18 LYS cc_start: 0.7907 (ttpt) cc_final: 0.7414 (ttpt)
REVERT: B   27 LEU cc_start: 0.8220 (pp) cc_final: 0.7357 (pp)
REVERT: B   37 HIS cc_start: 0.7476 (p-80) cc_final: 0.7193 (p-80)
REVERT: B   61 LYS cc_start: 0.6873 (mmmt) cc_final: 0.6608 (mmtt)
REVERT: B   66 PHE cc_start: 0.7851 (t80) cc_final: 0.7618 (t80)
REVERT: B   83 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6711 (tm-30)
REVERT: B   90 LYS cc_start: 0.8456 (mmtm) cc_final: 0.8109 (mmtm)
REVERT: B  104 LYS cc_start: 0.6380 (tppt) cc_final: 0.6026 (tppt)
REVERT: B  117 ASN cc_start: 0.8248 (t0) cc_final: 0.7877 (t0)
REVERT: B  119 LYS cc_start: 0.8223 (mttm) cc_final: 0.7837 (mtmm)
REVERT: B  172 PHE cc_start: 0.7436 (m-10) cc_final: 0.7227 (m-10)
REVERT: B  176 LYS cc_start: 0.7410 (tptt) cc_final: 0.7117 (tptt)
REVERT: B  178 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7592 (tm-30)
REVERT: B  196 PHE cc_start: 0.7216 (t80) cc_final: 0.6924 (t80)
REVERT: B  223 LEU cc_start: 0.8242 (mt) cc_final: 0.7970 (mt)
REVERT: B  308 LEU cc_start: 0.8107 (tt) cc_final: 0.7894 (tt)
REVERT: B  418 LYS cc_start: 0.8098 (tptp) cc_final: 0.7665 (tptp)
REVERT: B  422 LYS cc_start: 0.8511 (tptt) cc_final: 0.7772 (tttp)
REVERT: B  442 LYS cc_start: 0.7269 (tttm) cc_final: 0.6929 (ttpt)
REVERT: B  447 GLN cc_start: 0.7407 (tt0) cc_final: 0.7134 (tt0)
REVERT: B  465 CYS cc_start: 0.6823 (m) cc_final: 0.6423 (m)
REVERT: B  482 LEU cc_start: 0.7404 (mm) cc_final: 0.6962 (tp)
REVERT: B  516 VAL cc_start: 0.7770 (t) cc_final: 0.7466 (p)
REVERT: B  572 PHE cc_start: 0.7492 (t80) cc_final: 0.7205 (t80)
REVERT: B  574 GLU cc_start: 0.6863 (tm-30) cc_final: 0.6505 (tm-30)
REVERT: A    9 ASP cc_start: 0.7643 (t70) cc_final: 0.7419 (t0)
REVERT: A   18 LYS cc_start: 0.7944 (ttpt) cc_final: 0.7236 (ttpt)
REVERT: A   46 LEU cc_start: 0.8558 (pp) cc_final: 0.8212 (pp)
REVERT: A   74 GLU cc_start: 0.6774 (pt0) cc_final: 0.6485 (pt0)
REVERT: A   83 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6986 (tm-30)
REVERT: A   84 LEU cc_start: 0.7967 (mp) cc_final: 0.7402 (mt)
REVERT: A  117 ASN cc_start: 0.8127 (t0) cc_final: 0.7835 (t0)
REVERT: A  176 LYS cc_start: 0.7452 (tptt) cc_final: 0.6983 (tptt)
REVERT: A  178 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7822 (tm-30)
REVERT: A  296 LYS cc_start: 0.7793 (ptmm) cc_final: 0.7081 (mmtt)
REVERT: A  378 MET cc_start: 0.4876 (ttm) cc_final: 0.4242 (ttm)
REVERT: A  417 MET cc_start: 0.7600 (ttp) cc_final: 0.7224 (ttp)
REVERT: A  418 LYS cc_start: 0.8131 (mmmm) cc_final: 0.7841 (mmmm)
REVERT: A  422 LYS cc_start: 0.8430 (tptt) cc_final: 0.7975 (tttp)
REVERT: A  454 PHE cc_start: 0.7234 (m-80) cc_final: 0.6874 (m-80)
REVERT: A  465 CYS cc_start: 0.6425 (m) cc_final: 0.6168 (m)
REVERT: A  482 LEU cc_start: 0.8250 (mm) cc_final: 0.7489 (tp)
REVERT: A  574 GLU cc_start: 0.6944 (tm-30) cc_final: 0.6387 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.0714
  time to fit residues: 23.2521
Evaluate side-chains
  224 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 19 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 91 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0770
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  68 GLN
** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 302 ASN
A 565 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.157565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.133772 restraints weight = 14248.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.137749 restraints weight = 9169.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.140653 restraints weight = 6527.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.142585 restraints weight = 4994.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.144261 restraints weight = 4103.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6541
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8054  Z= 0.158
  Angle     :  0.646  11.530  10936  Z= 0.329
  Chirality :  0.044   0.154   1256
  Planarity :  0.004   0.043   1308
  Dihedral  :  4.222  19.763    998
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.46 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.28), residues: 918
  helix:  1.63 (0.20), residues: 692
  sheet: -0.60 (0.64), residues: 52
  loop :  0.02 (0.52), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 359 
 TYR   0.021   0.001   TYR A 569 
 PHE   0.026   0.002   PHE A 582 
 TRP   0.012   0.001   TRP A 165 
 HIS   0.006   0.001   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 8054)
  covalent geometry    : angle       0.64631 (10936)
  hydrogen bonds       : bond        0.04605 (  532)
  hydrogen bonds       : angle       4.49111 ( 1572)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 235
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 ASP cc_start: 0.7156 (t70) cc_final: 0.6646 (t70)
REVERT: B   18 LYS cc_start: 0.7846 (ttpt) cc_final: 0.7373 (ttpt)
REVERT: B   27 LEU cc_start: 0.8200 (pp) cc_final: 0.7348 (pp)
REVERT: B   37 HIS cc_start: 0.7346 (p-80) cc_final: 0.7050 (p-80)
REVERT: B   66 PHE cc_start: 0.7831 (t80) cc_final: 0.7598 (t80)
REVERT: B   68 GLN cc_start: 0.8127 (pt0) cc_final: 0.7867 (pt0)
REVERT: B   83 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6631 (tm-30)
REVERT: B   90 LYS cc_start: 0.8351 (mmtm) cc_final: 0.8009 (mmtm)
REVERT: B  104 LYS cc_start: 0.6228 (tppt) cc_final: 0.5902 (tppt)
REVERT: B  117 ASN cc_start: 0.8285 (t0) cc_final: 0.7845 (t0)
REVERT: B  172 PHE cc_start: 0.7286 (m-10) cc_final: 0.7068 (m-10)
REVERT: B  173 TRP cc_start: 0.8146 (t-100) cc_final: 0.7759 (t-100)
REVERT: B  176 LYS cc_start: 0.7397 (tptt) cc_final: 0.7152 (tptt)
REVERT: B  178 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7198 (tm-30)
REVERT: B  196 PHE cc_start: 0.6811 (t80) cc_final: 0.6001 (t80)
REVERT: B  212 MET cc_start: 0.6660 (pmm) cc_final: 0.6278 (pmm)
REVERT: B  223 LEU cc_start: 0.8280 (mt) cc_final: 0.7949 (mt)
REVERT: B  304 VAL cc_start: 0.7433 (t) cc_final: 0.6808 (m)
REVERT: B  359 ARG cc_start: 0.7358 (ptm-80) cc_final: 0.6924 (ptm-80)
REVERT: B  378 MET cc_start: 0.4528 (ttm) cc_final: 0.3788 (ttm)
REVERT: B  418 LYS cc_start: 0.8040 (tptp) cc_final: 0.7553 (tptp)
REVERT: B  422 LYS cc_start: 0.8438 (tptt) cc_final: 0.7840 (tttm)
REVERT: B  442 LYS cc_start: 0.7139 (tttm) cc_final: 0.6900 (ttpt)
REVERT: B  447 GLN cc_start: 0.7369 (tt0) cc_final: 0.7014 (tt0)
REVERT: B  465 CYS cc_start: 0.6803 (m) cc_final: 0.6443 (m)
REVERT: B  482 LEU cc_start: 0.7352 (mm) cc_final: 0.6945 (tp)
REVERT: B  516 VAL cc_start: 0.7770 (t) cc_final: 0.7452 (p)
REVERT: B  523 CYS cc_start: 0.7827 (t) cc_final: 0.7613 (t)
REVERT: B  572 PHE cc_start: 0.7446 (t80) cc_final: 0.7109 (t80)
REVERT: B  574 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6594 (tm-30)
REVERT: A   18 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7224 (ttpt)
REVERT: A   27 LEU cc_start: 0.8221 (pp) cc_final: 0.7520 (pp)
REVERT: A   46 LEU cc_start: 0.8537 (pp) cc_final: 0.8207 (pp)
REVERT: A   68 GLN cc_start: 0.7094 (tp-100) cc_final: 0.6863 (tp-100)
REVERT: A   74 GLU cc_start: 0.6667 (pt0) cc_final: 0.6451 (pt0)
REVERT: A  117 ASN cc_start: 0.8125 (t0) cc_final: 0.7825 (t0)
REVERT: A  176 LYS cc_start: 0.7427 (tptt) cc_final: 0.6896 (tptt)
REVERT: A  178 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7789 (tm-30)
REVERT: A  234 LEU cc_start: 0.6700 (mt) cc_final: 0.6393 (tp)
REVERT: A  296 LYS cc_start: 0.7723 (ptmm) cc_final: 0.6852 (mmmt)
REVERT: A  311 TYR cc_start: 0.6630 (m-10) cc_final: 0.6226 (m-10)
REVERT: A  378 MET cc_start: 0.4799 (ttm) cc_final: 0.4113 (ttm)
REVERT: A  422 LYS cc_start: 0.8388 (tptt) cc_final: 0.7914 (tttp)
REVERT: A  442 LYS cc_start: 0.6876 (tttm) cc_final: 0.6674 (ptmt)
REVERT: A  454 PHE cc_start: 0.7143 (m-80) cc_final: 0.6844 (m-80)
REVERT: A  465 CYS cc_start: 0.6409 (m) cc_final: 0.6150 (m)
REVERT: A  482 LEU cc_start: 0.8179 (mm) cc_final: 0.7322 (tp)
REVERT: A  574 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6480 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 235
  average time/residue: 0.0719
  time to fit residues: 23.0284
Evaluate side-chains
  222 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 92 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 88 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 ASN
** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 302 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.156503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.134503 restraints weight = 13890.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.138034 restraints weight = 9208.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.140672 restraints weight = 6674.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.142618 restraints weight = 5151.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.143898 restraints weight = 4204.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6552
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8054  Z= 0.189
  Angle     :  0.685  10.303  10936  Z= 0.346
  Chirality :  0.045   0.157   1256
  Planarity :  0.004   0.042   1308
  Dihedral  :  4.223  21.367    998
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.35 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.66 (0.28), residues: 918
  helix:  1.61 (0.20), residues: 680
  sheet: -0.68 (0.64), residues: 52
  loop : -0.10 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 145 
 TYR   0.022   0.002   TYR B 321 
 PHE   0.038   0.002   PHE A 196 
 TRP   0.008   0.001   TRP A 165 
 HIS   0.006   0.001   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 8054)
  covalent geometry    : angle       0.68512 (10936)
  hydrogen bonds       : bond        0.04773 (  532)
  hydrogen bonds       : angle       4.53226 ( 1572)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 240
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 ASP cc_start: 0.7081 (t70) cc_final: 0.6564 (t70)
REVERT: B   18 LYS cc_start: 0.7713 (ttpt) cc_final: 0.7292 (ttpt)
REVERT: B   27 LEU cc_start: 0.8134 (pp) cc_final: 0.7660 (pp)
REVERT: B   37 HIS cc_start: 0.7344 (p-80) cc_final: 0.7043 (p-80)
REVERT: B   66 PHE cc_start: 0.7954 (t80) cc_final: 0.7721 (t80)
REVERT: B   68 GLN cc_start: 0.8089 (pt0) cc_final: 0.7771 (pt0)
REVERT: B   83 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6661 (tm-30)
REVERT: B   90 LYS cc_start: 0.8340 (mmtm) cc_final: 0.8009 (mmtm)
REVERT: B  104 LYS cc_start: 0.6000 (tppt) cc_final: 0.5726 (tppt)
REVERT: B  117 ASN cc_start: 0.8274 (t0) cc_final: 0.7824 (t0)
REVERT: B  172 PHE cc_start: 0.7241 (m-10) cc_final: 0.7037 (m-10)
REVERT: B  173 TRP cc_start: 0.8190 (t-100) cc_final: 0.7866 (t-100)
REVERT: B  176 LYS cc_start: 0.7399 (tptt) cc_final: 0.7164 (tptt)
REVERT: B  178 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7446 (tm-30)
REVERT: B  212 MET cc_start: 0.6650 (pmm) cc_final: 0.6328 (pmm)
REVERT: B  223 LEU cc_start: 0.8296 (mt) cc_final: 0.7985 (mt)
REVERT: B  304 VAL cc_start: 0.7441 (t) cc_final: 0.6830 (m)
REVERT: B  308 LEU cc_start: 0.7934 (tt) cc_final: 0.7710 (tt)
REVERT: B  359 ARG cc_start: 0.7353 (ptm-80) cc_final: 0.6931 (ptm-80)
REVERT: B  378 MET cc_start: 0.4516 (ttm) cc_final: 0.3765 (ttm)
REVERT: B  418 LYS cc_start: 0.8053 (tptp) cc_final: 0.7710 (tptp)
REVERT: B  422 LYS cc_start: 0.8448 (tptt) cc_final: 0.7801 (tttp)
REVERT: B  442 LYS cc_start: 0.7160 (tttm) cc_final: 0.6874 (ttpt)
REVERT: B  447 GLN cc_start: 0.7354 (tt0) cc_final: 0.7016 (tt0)
REVERT: B  465 CYS cc_start: 0.6816 (m) cc_final: 0.6468 (m)
REVERT: B  482 LEU cc_start: 0.7299 (mm) cc_final: 0.6818 (tp)
REVERT: B  516 VAL cc_start: 0.7554 (t) cc_final: 0.7310 (p)
REVERT: B  523 CYS cc_start: 0.7861 (t) cc_final: 0.7637 (t)
REVERT: B  572 PHE cc_start: 0.7516 (t80) cc_final: 0.7166 (t80)
REVERT: B  574 GLU cc_start: 0.6876 (tm-30) cc_final: 0.6548 (tm-30)
REVERT: A    9 ASP cc_start: 0.7586 (t70) cc_final: 0.7364 (t0)
REVERT: A   18 LYS cc_start: 0.7907 (ttpt) cc_final: 0.7237 (ttpt)
REVERT: A   27 LEU cc_start: 0.8326 (pp) cc_final: 0.7854 (pp)
REVERT: A   46 LEU cc_start: 0.8550 (pp) cc_final: 0.8071 (pp)
REVERT: A   55 ILE cc_start: 0.8625 (tt) cc_final: 0.8398 (tt)
REVERT: A   68 GLN cc_start: 0.7151 (tp-100) cc_final: 0.6762 (tp-100)
REVERT: A   74 GLU cc_start: 0.6635 (pt0) cc_final: 0.6395 (pt0)
REVERT: A   83 GLU cc_start: 0.6829 (tm-30) cc_final: 0.6576 (tm-30)
REVERT: A  105 GLN cc_start: 0.7047 (mt0) cc_final: 0.6802 (mm-40)
REVERT: A  117 ASN cc_start: 0.8107 (t0) cc_final: 0.7782 (t0)
REVERT: A  176 LYS cc_start: 0.7442 (tptt) cc_final: 0.6925 (tptt)
REVERT: A  178 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7751 (tm-30)
REVERT: A  296 LYS cc_start: 0.7771 (ptmm) cc_final: 0.6912 (mmmt)
REVERT: A  378 MET cc_start: 0.4802 (ttm) cc_final: 0.4121 (ttm)
REVERT: A  418 LYS cc_start: 0.8187 (tptm) cc_final: 0.7927 (tptm)
REVERT: A  422 LYS cc_start: 0.8266 (tptt) cc_final: 0.7574 (tttp)
REVERT: A  442 LYS cc_start: 0.6945 (tttm) cc_final: 0.6693 (ptmt)
REVERT: A  454 PHE cc_start: 0.7238 (m-80) cc_final: 0.6889 (m-80)
REVERT: A  465 CYS cc_start: 0.6422 (m) cc_final: 0.6184 (m)
REVERT: A  474 GLN cc_start: 0.7133 (mm110) cc_final: 0.6724 (tp40)
REVERT: A  482 LEU cc_start: 0.8164 (mm) cc_final: 0.7253 (tp)
REVERT: A  523 CYS cc_start: 0.7952 (t) cc_final: 0.7710 (t)
REVERT: A  574 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6369 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 240
  average time/residue: 0.0703
  time to fit residues: 23.1193
Evaluate side-chains
  229 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 39 optimal weight:    0.4980
   chunk 59 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0980
   chunk 46 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 89 optimal weight:    0.3980
   chunk 6 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0020
   chunk 30 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.3188

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

Flipped N/Q/H residues before XYZ refinement:
** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 ASN
** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 302 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.159932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.138190 restraints weight = 13691.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.141928 restraints weight = 8825.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.144779 restraints weight = 6237.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.146580 restraints weight = 4735.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.148158 restraints weight = 3860.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6487
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8054  Z= 0.135
  Angle     :  0.656  11.832  10936  Z= 0.328
  Chirality :  0.044   0.154   1256
  Planarity :  0.004   0.044   1308
  Dihedral  :  4.128  19.447    998
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.67 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.92 (0.28), residues: 918
  helix:  1.85 (0.20), residues: 680
  sheet: -0.94 (0.61), residues: 52
  loop : -0.07 (0.51), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 359 
 TYR   0.025   0.001   TYR B 426 
 PHE   0.030   0.001   PHE A  66 
 TRP   0.013   0.001   TRP A 165 
 HIS   0.007   0.001   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8054)
  covalent geometry    : angle       0.65556 (10936)
  hydrogen bonds       : bond        0.04226 (  532)
  hydrogen bonds       : angle       4.33445 ( 1572)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 238
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 ASP cc_start: 0.7068 (t70) cc_final: 0.6565 (t70)
REVERT: B   18 LYS cc_start: 0.7397 (ttpt) cc_final: 0.7023 (ttpt)
REVERT: B   27 LEU cc_start: 0.8109 (pp) cc_final: 0.7344 (pp)
REVERT: B   37 HIS cc_start: 0.7298 (p-80) cc_final: 0.6984 (p-80)
REVERT: B   52 PHE cc_start: 0.7878 (m-80) cc_final: 0.7662 (m-10)
REVERT: B   66 PHE cc_start: 0.7820 (t80) cc_final: 0.7600 (t80)
REVERT: B   68 GLN cc_start: 0.7912 (pt0) cc_final: 0.7694 (pt0)
REVERT: B   90 LYS cc_start: 0.8311 (mmtm) cc_final: 0.7968 (mmtm)
REVERT: B  104 LYS cc_start: 0.5910 (tppt) cc_final: 0.5675 (tppt)
REVERT: B  117 ASN cc_start: 0.8309 (t0) cc_final: 0.7878 (t0)
REVERT: B  173 TRP cc_start: 0.8117 (t-100) cc_final: 0.7880 (t-100)
REVERT: B  176 LYS cc_start: 0.7383 (tptt) cc_final: 0.7155 (tptt)
REVERT: B  178 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7414 (tm-30)
REVERT: B  196 PHE cc_start: 0.6876 (t80) cc_final: 0.6110 (t80)
REVERT: B  212 MET cc_start: 0.6573 (pmm) cc_final: 0.6248 (pmm)
REVERT: B  223 LEU cc_start: 0.8265 (mt) cc_final: 0.7949 (mt)
REVERT: B  304 VAL cc_start: 0.7338 (t) cc_final: 0.6696 (m)
REVERT: B  308 LEU cc_start: 0.7889 (tt) cc_final: 0.7686 (tt)
REVERT: B  359 ARG cc_start: 0.7271 (ptm-80) cc_final: 0.6840 (ptm-80)
REVERT: B  378 MET cc_start: 0.4401 (ttm) cc_final: 0.3664 (ttm)
REVERT: B  418 LYS cc_start: 0.8065 (tptp) cc_final: 0.7688 (tptp)
REVERT: B  422 LYS cc_start: 0.8395 (tptt) cc_final: 0.7721 (tttp)
REVERT: B  442 LYS cc_start: 0.7022 (tttm) cc_final: 0.6741 (ttpt)
REVERT: B  447 GLN cc_start: 0.7303 (tt0) cc_final: 0.6971 (tt0)
REVERT: B  465 CYS cc_start: 0.6766 (m) cc_final: 0.6432 (m)
REVERT: B  482 LEU cc_start: 0.7187 (mm) cc_final: 0.6871 (tp)
REVERT: B  516 VAL cc_start: 0.7570 (t) cc_final: 0.7311 (p)
REVERT: B  523 CYS cc_start: 0.7860 (t) cc_final: 0.7618 (t)
REVERT: B  572 PHE cc_start: 0.7509 (t80) cc_final: 0.7128 (t80)
REVERT: B  574 GLU cc_start: 0.6828 (tm-30) cc_final: 0.6518 (tm-30)
REVERT: A    9 ASP cc_start: 0.7467 (t70) cc_final: 0.7219 (t0)
REVERT: A   18 LYS cc_start: 0.7853 (ttpt) cc_final: 0.7200 (ttpt)
REVERT: A   46 LEU cc_start: 0.8534 (pp) cc_final: 0.8037 (pp)
REVERT: A   55 ILE cc_start: 0.8594 (tt) cc_final: 0.8376 (tt)
REVERT: A   68 GLN cc_start: 0.7265 (tp-100) cc_final: 0.6775 (tp-100)
REVERT: A   83 GLU cc_start: 0.6719 (tm-30) cc_final: 0.6463 (tm-30)
REVERT: A  105 GLN cc_start: 0.7029 (mt0) cc_final: 0.6822 (mm-40)
REVERT: A  115 THR cc_start: 0.8034 (t) cc_final: 0.7631 (m)
REVERT: A  117 ASN cc_start: 0.8032 (t0) cc_final: 0.7683 (t0)
REVERT: A  176 LYS cc_start: 0.7426 (tptt) cc_final: 0.6885 (tptt)
REVERT: A  178 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7704 (tm-30)
REVERT: A  378 MET cc_start: 0.4667 (ttm) cc_final: 0.4017 (ttm)
REVERT: A  418 LYS cc_start: 0.8217 (tptm) cc_final: 0.7949 (tptm)
REVERT: A  422 LYS cc_start: 0.8127 (tptt) cc_final: 0.7562 (tttp)
REVERT: A  465 CYS cc_start: 0.6361 (m) cc_final: 0.6091 (m)
REVERT: A  474 GLN cc_start: 0.7124 (mm110) cc_final: 0.6727 (tp40)
REVERT: A  482 LEU cc_start: 0.8168 (mm) cc_final: 0.7324 (tp)
REVERT: A  574 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6364 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 238
  average time/residue: 0.0672
  time to fit residues: 21.9324
Evaluate side-chains
  223 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 86 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 72 optimal weight:    0.0770
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 ASN
** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 447 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.158057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.134395 restraints weight = 14056.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.138378 restraints weight = 9102.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.141262 restraints weight = 6463.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.143409 restraints weight = 4974.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.144930 restraints weight = 4040.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6526
moved from start:          0.2808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8054  Z= 0.156
  Angle     :  0.699  11.812  10936  Z= 0.347
  Chirality :  0.045   0.153   1256
  Planarity :  0.004   0.043   1308
  Dihedral  :  4.099  18.249    998
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.28), residues: 918
  helix:  1.75 (0.20), residues: 680
  sheet: -0.94 (0.62), residues: 52
  loop : -0.03 (0.51), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 145 
 TYR   0.024   0.002   TYR B 569 
 PHE   0.035   0.002   PHE A 196 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.008   0.001   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 8054)
  covalent geometry    : angle       0.69942 (10936)
  hydrogen bonds       : bond        0.04388 (  532)
  hydrogen bonds       : angle       4.35282 ( 1572)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 ASP cc_start: 0.7181 (t70) cc_final: 0.6622 (t70)
REVERT: B   18 LYS cc_start: 0.7382 (ttpt) cc_final: 0.7023 (ttpt)
REVERT: B   27 LEU cc_start: 0.8021 (pp) cc_final: 0.7462 (pp)
REVERT: B   37 HIS cc_start: 0.7325 (p-80) cc_final: 0.7047 (p-80)
REVERT: B   66 PHE cc_start: 0.7936 (t80) cc_final: 0.7720 (t80)
REVERT: B   68 GLN cc_start: 0.7995 (pt0) cc_final: 0.7763 (pt0)
REVERT: B   90 LYS cc_start: 0.8351 (mmtm) cc_final: 0.7987 (mmtm)
REVERT: B  104 LYS cc_start: 0.6004 (tppt) cc_final: 0.5711 (tppt)
REVERT: B  117 ASN cc_start: 0.8307 (t0) cc_final: 0.7837 (t0)
REVERT: B  172 PHE cc_start: 0.7155 (m-10) cc_final: 0.6942 (m-10)
REVERT: B  173 TRP cc_start: 0.8151 (t-100) cc_final: 0.7900 (t-100)
REVERT: B  176 LYS cc_start: 0.7404 (tptt) cc_final: 0.7115 (tptt)
REVERT: B  178 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7423 (tm-30)
REVERT: B  196 PHE cc_start: 0.6874 (t80) cc_final: 0.6152 (t80)
REVERT: B  223 LEU cc_start: 0.8298 (mt) cc_final: 0.7974 (mt)
REVERT: B  304 VAL cc_start: 0.7284 (t) cc_final: 0.6660 (m)
REVERT: B  308 LEU cc_start: 0.7898 (tt) cc_final: 0.7670 (tt)
REVERT: B  359 ARG cc_start: 0.7405 (ptm-80) cc_final: 0.6944 (ptm-80)
REVERT: B  418 LYS cc_start: 0.8077 (tptp) cc_final: 0.7717 (tptp)
REVERT: B  422 LYS cc_start: 0.8440 (tptt) cc_final: 0.7808 (tttp)
REVERT: B  442 LYS cc_start: 0.7058 (tttm) cc_final: 0.6778 (ttpt)
REVERT: B  447 GLN cc_start: 0.7353 (tt0) cc_final: 0.7058 (tm-30)
REVERT: B  465 CYS cc_start: 0.6807 (m) cc_final: 0.6409 (m)
REVERT: B  482 LEU cc_start: 0.7217 (mm) cc_final: 0.6860 (tp)
REVERT: B  516 VAL cc_start: 0.7536 (t) cc_final: 0.7286 (p)
REVERT: B  523 CYS cc_start: 0.7930 (t) cc_final: 0.7648 (t)
REVERT: B  572 PHE cc_start: 0.7534 (t80) cc_final: 0.7157 (t80)
REVERT: B  574 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6481 (tm-30)
REVERT: A    9 ASP cc_start: 0.7640 (t70) cc_final: 0.7399 (t0)
REVERT: A   18 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7216 (ttpt)
REVERT: A   27 LEU cc_start: 0.8135 (pp) cc_final: 0.7680 (pp)
REVERT: A   46 LEU cc_start: 0.8581 (pp) cc_final: 0.8106 (pp)
REVERT: A   55 ILE cc_start: 0.8600 (tt) cc_final: 0.8370 (tt)
REVERT: A   68 GLN cc_start: 0.7237 (tp-100) cc_final: 0.6805 (tp-100)
REVERT: A   83 GLU cc_start: 0.6810 (tm-30) cc_final: 0.6557 (tm-30)
REVERT: A  105 GLN cc_start: 0.7058 (mt0) cc_final: 0.6814 (mm-40)
REVERT: A  117 ASN cc_start: 0.8067 (t0) cc_final: 0.7697 (t0)
REVERT: A  176 LYS cc_start: 0.7440 (tptt) cc_final: 0.6818 (tptt)
REVERT: A  178 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7727 (tm-30)
REVERT: A  302 ASN cc_start: 0.7294 (t0) cc_final: 0.7080 (t0)
REVERT: A  378 MET cc_start: 0.4791 (ttm) cc_final: 0.4247 (ttm)
REVERT: A  418 LYS cc_start: 0.8218 (tptm) cc_final: 0.7965 (tptm)
REVERT: A  422 LYS cc_start: 0.8330 (tptt) cc_final: 0.7852 (tttp)
REVERT: A  465 CYS cc_start: 0.6350 (m) cc_final: 0.6077 (m)
REVERT: A  474 GLN cc_start: 0.7094 (mm110) cc_final: 0.6714 (tp40)
REVERT: A  482 LEU cc_start: 0.8213 (mm) cc_final: 0.7375 (tp)
REVERT: A  574 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6378 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 241
  average time/residue: 0.0730
  time to fit residues: 24.1548
Evaluate side-chains
  228 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   chunk 70 optimal weight:    0.6980
   chunk 32 optimal weight:    8.9990
   chunk 21 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 ASN
** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 565 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.158158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.136149 restraints weight = 13711.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.139750 restraints weight = 9083.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.142381 restraints weight = 6568.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.144098 restraints weight = 5072.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.145576 restraints weight = 4198.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6541
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8054  Z= 0.184
  Angle     :  0.715  11.476  10936  Z= 0.362
  Chirality :  0.046   0.172   1256
  Planarity :  0.004   0.042   1308
  Dihedral  :  4.184  21.247    998
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.28), residues: 918
  helix:  1.61 (0.20), residues: 680
  sheet: -0.91 (0.61), residues: 52
  loop : -0.12 (0.51), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 359 
 TYR   0.018   0.002   TYR B 321 
 PHE   0.028   0.002   PHE A 140 
 TRP   0.007   0.001   TRP A 165 
 HIS   0.005   0.001   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 8054)
  covalent geometry    : angle       0.71465 (10936)
  hydrogen bonds       : bond        0.04635 (  532)
  hydrogen bonds       : angle       4.46883 ( 1572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1134.62 seconds
wall clock time: 20 minutes 24.41 seconds (1224.41 seconds total)