Starting phenix.real_space_refine
on Tue Mar  3 18:35:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x0l_21978/03_2026/6x0l_21978.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x0l_21978/03_2026/6x0l_21978.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6x0l_21978/03_2026/6x0l_21978.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x0l_21978/03_2026/6x0l_21978.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x0l_21978/03_2026/6x0l_21978.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x0l_21978/03_2026/6x0l_21978.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 5
    Type Number    sf(0)   Gaussians
     P      40      5.49       5
     S      45      5.16       5
     C    4989      2.51       5
     N    1379      2.21       5
     O    1584      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8037
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "O"
      Number of atoms: 2488
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2488
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 13, 'TRANS': 292}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 3798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 474, 3798
          Classifications: {'peptide': 474}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 452}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 929
          Classifications: {'peptide': 114}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 110}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "I"
      Number of atoms: 204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 204
          Classifications: {'DNA': 10}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 9}
    Chain: "J"
      Number of atoms: 207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 207
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
    Chain: "i"
      Number of atoms: 207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 207
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
    Chain: "j"
      Number of atoms: 204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 204
          Classifications: {'DNA': 10}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 9}
  Time building chain proxies: 1.76, per 1000 atoms: 0.22
  Number of scatterers: 8037
  At special positions: 0
  Unit cell: (115.54, 109.18, 91.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      45     16.00
     P      40     15.00
     O    1584      8.00
     N    1379      7.00
     C    4989      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: 0.69
  Conformation dependent library (CDL) restraints added in 204.0 milliseconds
  

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1678

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 11 sheets defined
      40.4% alpha, 19.8% beta
      20 base pairs and 27 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'O' and resid 37 through 46
      removed outlier: 3.895A  pdb=" N   VAL O  41 " --> pdb=" O   LEU O  37 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 50 through 64
      removed outlier: 3.974A  pdb=" N   TYR O  54 " --> pdb=" O   PRO O  50 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 72 through 77
    Processing helix  chain 'O' and resid 82 through 88
      removed outlier: 3.500A  pdb=" N   ILE O  86 " --> pdb=" O   GLY O  82 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 160 through 176
      removed outlier: 3.785A  pdb=" N   LYS O 174 " --> pdb=" O   THR O 170 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 182 through 200
    Processing helix  chain 'O' and resid 207 through 217
    Processing helix  chain 'O' and resid 244 through 257
    Processing helix  chain 'O' and resid 260 through 268
    Processing helix  chain 'O' and resid 268 through 284
    Processing helix  chain 'O' and resid 286 through 301
      removed outlier: 4.404A  pdb=" N   GLY O 290 " --> pdb=" O   ASP O 286 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLY O 294 " --> pdb=" O   GLY O 290 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 302 through 304
      No H-bonds generated for 'chain 'O' and resid 302 through 304'
    Processing helix  chain 'O' and resid 305 through 320
      Proline residue:  O 314  - end of helix
    Processing helix  chain 'O' and resid 322 through 335
    Processing helix  chain 'P' and resid 155 through 172
    Processing helix  chain 'P' and resid 222 through 233
    Processing helix  chain 'P' and resid 234 through 248
      removed outlier: 3.532A  pdb=" N   LYS P 246 " --> pdb=" O   MET P 242 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 258 through 278
      removed outlier: 3.868A  pdb=" N   ALA P 278 " --> pdb=" O   ASP P 274 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 282 through 296
      removed outlier: 3.559A  pdb=" N   MET P 286 " --> pdb=" O   GLY P 282 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 310 through 334
      removed outlier: 3.583A  pdb=" N   LEU P 314 " --> pdb=" O   THR P 310 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 343 through 353
      removed outlier: 4.088A  pdb=" N   GLN P 347 " --> pdb=" O   HIS P 343 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 363 through 376
    Processing helix  chain 'P' and resid 398 through 403
      removed outlier: 3.764A  pdb=" N   ALA P 402 " --> pdb=" O   GLY P 398 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 421 through 429
      removed outlier: 3.745A  pdb=" N   ILE P 425 " --> pdb=" O   ASN P 421 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 438 through 442
      removed outlier: 3.575A  pdb=" N   GLY P 441 " --> pdb=" O   PRO P 438 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 453 through 459
      removed outlier: 3.588A  pdb=" N   SER P 457 " --> pdb=" O   MET P 453 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 460 through 462
      No H-bonds generated for 'chain 'P' and resid 460 through 462'
    Processing helix  chain 'P' and resid 511 through 515
    Processing helix  chain 'P' and resid 550 through 552
      No H-bonds generated for 'chain 'P' and resid 550 through 552'
    Processing helix  chain 'R' and resid 155 through 172
    Processing sheet with id=AA1, first strand: chain 'O' and resid 79 through 80
      removed outlier: 6.690A  pdb=" N   MET O 129 " --> pdb=" O   ILE O 118 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   ILE O 120 " --> pdb=" O   TYR O 127 " (cutoff:3.500A)
      removed outlier: 7.611A  pdb=" N   TYR O 127 " --> pdb=" O   ILE O 120 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   TYR O 142 " --> pdb=" O   PHE O 132 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'P' and resid 92 through 94
      removed outlier: 3.711A  pdb=" N   GLY P 139 " --> pdb=" O   TYR P 118 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'P' and resid 92 through 94
      removed outlier: 4.695A  pdb=" N   MET P 105 " --> pdb=" O   LEU P 191 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'P' and resid 96 through 97
    Processing sheet with id=AA5, first strand: chain 'P' and resid 354 through 358
      removed outlier: 5.159A  pdb=" N   MET P 386 " --> pdb=" O   ASN P 565 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ASN P 565 " --> pdb=" O   MET P 386 " (cutoff:3.500A)
      removed outlier: 5.570A  pdb=" N   LEU P 388 " --> pdb=" O   GLN P 563 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   GLN P 563 " --> pdb=" O   LEU P 388 " (cutoff:3.500A)
      removed outlier: 5.020A  pdb=" N   ARG P 557 " --> pdb=" O   VAL P 394 " (cutoff:3.500A)
      removed outlier: 8.231A  pdb=" N   LYS P 396 " --> pdb=" O   ARG P 555 " (cutoff:3.500A)
      removed outlier: 8.782A  pdb=" N   ARG P 555 " --> pdb=" O   LYS P 396 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   LEU P 474 " --> pdb=" O   ARG P 557 " (cutoff:3.500A)
      removed outlier: 5.186A  pdb=" N   LEU P 559 " --> pdb=" O   LEU P 472 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   LEU P 472 " --> pdb=" O   LEU P 559 " (cutoff:3.500A)
      removed outlier: 5.179A  pdb=" N   LYS P 561 " --> pdb=" O   GLY P 470 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   GLY P 470 " --> pdb=" O   LYS P 561 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   LEU P 471 " --> pdb=" O   SER P 417 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   SER P 417 " --> pdb=" O   LEU P 471 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'P' and resid 448 through 450
      removed outlier: 5.852A  pdb=" N   ASN P 483 " --> pdb=" O   LYS P 503 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'P' and resid 529 through 530
      removed outlier: 6.758A  pdb=" N   TYR P 543 " --> pdb=" O   LYS P 507 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   ALA P 509 " --> pdb=" O   TYR P 543 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'P' and resid 516 through 518
    Processing sheet with id=AA9, first strand: chain 'R' and resid 93 through 94
      removed outlier: 3.833A  pdb=" N   HIS R  93 " --> pdb=" O   GLU R 125 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE R 132 " --> pdb=" O   CYS R 152 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'R' and resid 93 through 94
      removed outlier: 3.833A  pdb=" N   HIS R  93 " --> pdb=" O   GLU R 125 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 96 through 97

    332 hydrogen bonds defined for protein.
    942 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      49 hydrogen bonds
      98 hydrogen bond angles
      0 basepair planarities
      20 basepair parallelities
      27 stacking parallelities
  Total time for adding SS restraints: 1.35

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2121
        1.33 -     1.45: 1667
        1.45 -     1.57: 4354
        1.57 -     1.69: 76
        1.69 -     1.81: 73
  Bond restraints: 8291
  Sorted by residual:
  bond pdb=" CA  PRO P 434 "
       pdb=" C   PRO P 434 "
    ideal  model  delta    sigma   weight residual
    1.514  1.536 -0.021 5.50e-03 3.31e+04 1.52e+01
  bond pdb=" C1'  DA i  82 "
       pdb=" N9   DA i  82 "
    ideal  model  delta    sigma   weight residual
    1.460  1.386  0.074 2.00e-02 2.50e+03 1.37e+01
  bond pdb=" C1'  DA j -81 "
       pdb=" N9   DA j -81 "
    ideal  model  delta    sigma   weight residual
    1.460  1.388  0.072 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" C1'  DA j -78 "
       pdb=" N9   DA j -78 "
    ideal  model  delta    sigma   weight residual
    1.460  1.397  0.063 2.00e-02 2.50e+03 9.84e+00
  bond pdb=" C   PRO P 434 "
       pdb=" O   PRO P 434 "
    ideal  model  delta    sigma   weight residual
    1.246  1.219  0.026 8.50e-03 1.38e+04 9.71e+00
  ... (remaining 8286 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 10866
        1.88 -     3.76: 430
        3.76 -     5.64: 41
        5.64 -     7.52: 13
        7.52 -     9.40: 2
  Bond angle restraints: 11352
  Sorted by residual:
  angle pdb=" N   THR O  93 "
        pdb=" CA  THR O  93 "
        pdb=" C   THR O  93 "
      ideal   model   delta    sigma   weight residual
     113.18  108.03    5.15 1.33e+00 5.65e-01 1.50e+01
  angle pdb=" N   LYS O 174 "
        pdb=" CA  LYS O 174 "
        pdb=" C   LYS O 174 "
      ideal   model   delta    sigma   weight residual
     112.90  108.19    4.71 1.31e+00 5.83e-01 1.29e+01
  angle pdb=" CA  LYS O 181 "
        pdb=" C   LYS O 181 "
        pdb=" O   LYS O 181 "
      ideal   model   delta    sigma   weight residual
     122.63  118.17    4.46 1.29e+00 6.01e-01 1.19e+01
  angle pdb=" C   MET P 556 "
        pdb=" N   ARG P 557 "
        pdb=" CA  ARG P 557 "
      ideal   model   delta    sigma   weight residual
     122.15  112.75    9.40 2.83e+00 1.25e-01 1.10e+01
  angle pdb=" CA  PRO P 434 "
        pdb=" C   PRO P 434 "
        pdb=" O   PRO P 434 "
      ideal   model   delta    sigma   weight residual
     120.90  118.60    2.30 7.20e-01 1.93e+00 1.02e+01
  ... (remaining 11347 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.73: 4630
       34.73 -    69.46: 260
       69.46 -   104.19: 10
      104.19 -   138.92: 0
      138.92 -   173.64: 1
  Dihedral angle restraints: 4901
    sinusoidal: 2294
      harmonic: 2607
  Sorted by residual:
  dihedral pdb=" CA  GLY R  90 "
           pdb=" C   GLY R  90 "
           pdb=" N   LYS R  91 "
           pdb=" CA  LYS R  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.41  -20.59     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  ASN P  99 "
           pdb=" C   ASN P  99 "
           pdb=" N   ASP P 100 "
           pdb=" CA  ASP P 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.89  -20.11     0      5.00e+00 4.00e-02 1.62e+01
  dihedral pdb=" C4'  DA J  80 "
           pdb=" C3'  DA J  80 "
           pdb=" O3'  DA J  80 "
           pdb=" P    DT J  81 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   46.36  173.64     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 4898 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 827
       0.044 -    0.089: 280
       0.089 -    0.133: 94
       0.133 -    0.177: 15
       0.177 -    0.222: 4
  Chirality restraints: 1220
  Sorted by residual:
  chirality pdb=" CA  ILE O 182 "
            pdb=" N   ILE O 182 "
            pdb=" C   ILE O 182 "
            pdb=" CB  ILE O 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  ILE O 176 "
            pdb=" N   ILE O 176 "
            pdb=" C   ILE O 176 "
            pdb=" CB  ILE O 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.89e-01
  chirality pdb=" C1'  DA i  82 "
            pdb=" O4'  DA i  82 "
            pdb=" C2'  DA i  82 "
            pdb=" N9   DA i  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.23    0.19 2.00e-01 2.50e+01 9.16e-01
  ... (remaining 1217 not shown)

  Planarity restraints: 1329
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE P 425 "   -0.012 2.00e-02 2.50e+03   2.31e-02 5.34e+00
        pdb=" C   ILE P 425 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ILE P 425 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU P 426 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA i  80 "   -0.032 2.00e-02 2.50e+03   1.39e-02 5.29e+00
        pdb=" N9   DA i  80 "    0.006 2.00e-02 2.50e+03
        pdb=" C8   DA i  80 "    0.011 2.00e-02 2.50e+03
        pdb=" N7   DA i  80 "    0.009 2.00e-02 2.50e+03
        pdb=" C5   DA i  80 "    0.009 2.00e-02 2.50e+03
        pdb=" C6   DA i  80 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6   DA i  80 "   -0.024 2.00e-02 2.50e+03
        pdb=" N1   DA i  80 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA i  80 "    0.006 2.00e-02 2.50e+03
        pdb=" N3   DA i  80 "    0.007 2.00e-02 2.50e+03
        pdb=" C4   DA i  80 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT j -82 "    0.024 2.00e-02 2.50e+03   1.22e-02 3.73e+00
        pdb=" N1   DT j -82 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DT j -82 "   -0.006 2.00e-02 2.50e+03
        pdb=" O2   DT j -82 "   -0.014 2.00e-02 2.50e+03
        pdb=" N3   DT j -82 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DT j -82 "    0.004 2.00e-02 2.50e+03
        pdb=" O4   DT j -82 "    0.019 2.00e-02 2.50e+03
        pdb=" C5   DT j -82 "   -0.007 2.00e-02 2.50e+03
        pdb=" C7   DT j -82 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DT j -82 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1326 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 125
        2.63 -     3.20: 7616
        3.20 -     3.77: 13417
        3.77 -     4.33: 17912
        4.33 -     4.90: 27606
  Nonbonded interactions: 66676
  Sorted by model distance:
  nonbonded pdb=" C2'  DA i  77 "
            pdb=" C7   DT i  78 "
     model   vdw
     2.067 3.860
  nonbonded pdb=" OE2 GLU O 114 "
            pdb=" OH  TYR O 317 "
     model   vdw
     2.101 3.040
  nonbonded pdb=" OH  TYR P 119 "
            pdb=" OP1  DT j -82 "
     model   vdw
     2.119 3.040
  nonbonded pdb=" OH  TYR O 109 "
            pdb=" O   GLY O 301 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" N   GLY P 506 "
            pdb=" OD1 ASN P 544 "
     model   vdw
     2.174 3.120
  ... (remaining 66671 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     8.840
  Find NCS groups from input model:        0.030
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
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      :  0.005   0.074   8291  Z= 0.255
  Angle     :  0.850   9.403  11352  Z= 0.487
  Chirality :  0.050   0.222   1220
  Planarity :  0.005   0.035   1329
  Dihedral  : 18.875 173.644   3223
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 21.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  5.36 %
    Favored  : 94.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.57 (0.26), residues: 884
  helix: -0.58 (0.26), residues: 317
  sheet: -0.40 (0.40), residues: 157
  loop : -1.62 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 140 
 TYR   0.023   0.002   TYR P 188 
 PHE   0.019   0.003   PHE P 113 
 TRP   0.022   0.003   TRP P 135 
 HIS   0.009   0.002   HIS O 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 8291)
  covalent geometry    : angle       0.85034 (11352)
  hydrogen bonds       : bond        0.14647 (  378)
  hydrogen bonds       : angle       7.01309 ( 1040)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 179
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: O  239 ARG cc_start: 0.7160 (ptp-170) cc_final: 0.6849 (ptp-110)
REVERT: O  305 PHE cc_start: 0.6355 (m-10) cc_final: 0.6062 (m-10)
REVERT: O  311 GLN cc_start: 0.7774 (mt0) cc_final: 0.7545 (mt0)
REVERT: O  327 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7440 (mm-30)
REVERT: P  108 GLN cc_start: 0.7620 (tt0) cc_final: 0.7271 (tm-30)
REVERT: P  241 MET cc_start: 0.7810 (tpt) cc_final: 0.7350 (tpt)
REVERT: P  290 ASN cc_start: 0.7103 (m110) cc_final: 0.5829 (m110)
REVERT: P  468 ASN cc_start: 0.6550 (p0) cc_final: 0.6345 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 180
  average time/residue: 0.1049
  time to fit residues: 24.6882
Evaluate side-chains
  110 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 267 GLN
P 290 ASN
** P 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P 553 GLN
** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.107173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.098890 restraints weight = 32404.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.100443 restraints weight = 18867.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.101506 restraints weight = 12301.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.102244 restraints weight = 8790.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.102763 restraints weight = 6742.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6749
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8291  Z= 0.152
  Angle     :  0.701   8.658  11352  Z= 0.371
  Chirality :  0.043   0.144   1220
  Planarity :  0.004   0.033   1329
  Dihedral  : 19.880 163.539   1394
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 16.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.24 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.27 (0.27), residues: 884
  helix:  0.70 (0.28), residues: 323
  sheet: -0.21 (0.38), residues: 161
  loop : -0.82 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG O 107 
 TYR   0.022   0.002   TYR P 543 
 PHE   0.029   0.002   PHE R 132 
 TRP   0.025   0.003   TRP O  57 
 HIS   0.005   0.001   HIS O 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8291)
  covalent geometry    : angle       0.70087 (11352)
  hydrogen bonds       : bond        0.04721 (  378)
  hydrogen bonds       : angle       5.76534 ( 1040)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.248 
Fit side-chains
REVERT: O  239 ARG cc_start: 0.7214 (ptp-170) cc_final: 0.6969 (ptp-110)
REVERT: O  311 GLN cc_start: 0.7659 (mt0) cc_final: 0.7430 (mt0)
REVERT: P  108 GLN cc_start: 0.7678 (tt0) cc_final: 0.7401 (tm-30)
REVERT: P  290 ASN cc_start: 0.7220 (m-40) cc_final: 0.6770 (m110)
REVERT: P  414 TRP cc_start: 0.7133 (m100) cc_final: 0.6899 (m100)
REVERT: R  105 MET cc_start: 0.8040 (tpp) cc_final: 0.7320 (ttt)
REVERT: R  117 LYS cc_start: 0.8369 (pttt) cc_final: 0.8107 (ptpt)
  outliers start: 14
  outliers final: 10
  residues processed: 138
  average time/residue: 0.0836
  time to fit residues: 16.0495
Evaluate side-chains
  115 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  169 LEU
Chi-restraints excluded: chain O residue  236 VAL
Chi-restraints excluded: chain P residue  109 THR
Chi-restraints excluded: chain P residue  141 VAL
Chi-restraints excluded: chain P residue  179 GLU
Chi-restraints excluded: chain P residue  353 HIS
Chi-restraints excluded: chain P residue  523 VAL
Chi-restraints excluded: chain P residue  541 LEU
Chi-restraints excluded: chain P residue  567 LEU
Chi-restraints excluded: chain R residue   95 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 48 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 89 optimal weight:    7.9990
   chunk 9 optimal weight:    0.2980
   chunk 53 optimal weight:    9.9990
   chunk 25 optimal weight:    0.6980
   chunk 83 optimal weight:    9.9990
   overall best weight:    2.1984

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

Flipped N/Q/H residues before XYZ refinement:
O 123 ASN
** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 303 HIS
** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 226 GLN
** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P 459 ASN
P 519 ASN
** P 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.105126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.096990 restraints weight = 32146.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.098465 restraints weight = 18868.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.099524 restraints weight = 12408.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.100259 restraints weight = 8801.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.100747 restraints weight = 6697.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6830
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8291  Z= 0.187
  Angle     :  0.698  10.250  11352  Z= 0.367
  Chirality :  0.043   0.149   1220
  Planarity :  0.004   0.038   1329
  Dihedral  : 19.689 162.757   1394
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 17.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 13.78 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.04 (0.28), residues: 884
  helix:  0.88 (0.28), residues: 321
  sheet: -0.28 (0.40), residues: 165
  loop : -0.57 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG O 107 
 TYR   0.032   0.002   TYR O 317 
 PHE   0.017   0.002   PHE R 163 
 TRP   0.024   0.003   TRP R 135 
 HIS   0.004   0.001   HIS O 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8291)
  covalent geometry    : angle       0.69794 (11352)
  hydrogen bonds       : bond        0.04568 (  378)
  hydrogen bonds       : angle       5.66622 ( 1040)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.184 
Fit side-chains
REVERT: O  239 ARG cc_start: 0.7404 (ptp-170) cc_final: 0.6918 (ptp-110)
REVERT: O  311 GLN cc_start: 0.7752 (mt0) cc_final: 0.7347 (mt0)
REVERT: O  317 TYR cc_start: 0.6945 (m-80) cc_final: 0.6636 (m-80)
REVERT: P  108 GLN cc_start: 0.7726 (tt0) cc_final: 0.7425 (tm-30)
REVERT: P  144 MET cc_start: 0.7767 (tmm) cc_final: 0.7036 (tmm)
REVERT: P  290 ASN cc_start: 0.7094 (m-40) cc_final: 0.6741 (m110)
REVERT: P  485 LEU cc_start: 0.7321 (mm) cc_final: 0.7092 (mm)
  outliers start: 27
  outliers final: 15
  residues processed: 126
  average time/residue: 0.0789
  time to fit residues: 13.7785
Evaluate side-chains
  111 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  174 LYS
Chi-restraints excluded: chain O residue  176 ILE
Chi-restraints excluded: chain O residue  248 LEU
Chi-restraints excluded: chain O residue  299 CYS
Chi-restraints excluded: chain P residue  109 THR
Chi-restraints excluded: chain P residue  146 GLN
Chi-restraints excluded: chain P residue  179 GLU
Chi-restraints excluded: chain P residue  195 TYR
Chi-restraints excluded: chain P residue  353 HIS
Chi-restraints excluded: chain P residue  523 VAL
Chi-restraints excluded: chain P residue  541 LEU
Chi-restraints excluded: chain P residue  567 LEU
Chi-restraints excluded: chain R residue   95 TYR
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  180 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 2 optimal weight:    8.9990
   chunk 81 optimal weight:    0.8980
   chunk 6 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 174 ASN
** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P 377 HIS
** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.106551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.098255 restraints weight = 32583.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.099840 restraints weight = 19099.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.100898 restraints weight = 12406.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.101639 restraints weight = 8823.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.102150 restraints weight = 6738.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6780
moved from start:          0.2864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8291  Z= 0.135
  Angle     :  0.663  11.206  11352  Z= 0.342
  Chirality :  0.042   0.173   1220
  Planarity :  0.003   0.043   1329
  Dihedral  : 19.609 161.071   1394
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 14.92 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.11 (0.28), residues: 884
  helix:  0.90 (0.29), residues: 322
  sheet:  0.02 (0.41), residues: 161
  loop : -0.50 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 140 
 TYR   0.027   0.001   TYR O 317 
 PHE   0.018   0.002   PHE O 305 
 TRP   0.025   0.002   TRP P 414 
 HIS   0.004   0.001   HIS O 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8291)
  covalent geometry    : angle       0.66262 (11352)
  hydrogen bonds       : bond        0.04029 (  378)
  hydrogen bonds       : angle       5.44477 ( 1040)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 106
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
REVERT: O  268 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6571 (m-80)
REVERT: O  311 GLN cc_start: 0.7565 (mt0) cc_final: 0.7210 (mt0)
REVERT: P  108 GLN cc_start: 0.7669 (tt0) cc_final: 0.7346 (tm-30)
REVERT: P  144 MET cc_start: 0.7811 (tmm) cc_final: 0.7348 (tmm)
REVERT: P  290 ASN cc_start: 0.7047 (m-40) cc_final: 0.6798 (m110)
REVERT: P  453 MET cc_start: 0.7636 (mmp) cc_final: 0.6924 (mtm)
REVERT: P  567 LEU cc_start: 0.4554 (OUTLIER) cc_final: 0.4236 (pp)
REVERT: R  105 MET cc_start: 0.8127 (tpp) cc_final: 0.7611 (tpt)
REVERT: R  135 TRP cc_start: 0.6839 (t-100) cc_final: 0.6288 (t-100)
REVERT: R  136 MET cc_start: 0.7496 (mpp) cc_final: 0.6232 (mtt)
  outliers start: 26
  outliers final: 15
  residues processed: 121
  average time/residue: 0.0844
  time to fit residues: 14.2945
Evaluate side-chains
  115 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   93 THR
Chi-restraints excluded: chain O residue  104 LEU
Chi-restraints excluded: chain O residue  268 PHE
Chi-restraints excluded: chain O residue  299 CYS
Chi-restraints excluded: chain O residue  320 LEU
Chi-restraints excluded: chain P residue  101 VAL
Chi-restraints excluded: chain P residue  109 THR
Chi-restraints excluded: chain P residue  146 GLN
Chi-restraints excluded: chain P residue  179 GLU
Chi-restraints excluded: chain P residue  353 HIS
Chi-restraints excluded: chain P residue  468 ASN
Chi-restraints excluded: chain P residue  523 VAL
Chi-restraints excluded: chain P residue  541 LEU
Chi-restraints excluded: chain P residue  567 LEU
Chi-restraints excluded: chain R residue   95 TYR
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  180 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 71 optimal weight:    0.1980
   chunk 47 optimal weight:    8.9990
   chunk 18 optimal weight:    9.9990
   chunk 84 optimal weight:   10.0000
   chunk 54 optimal weight:    5.9990
   chunk 82 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 69 optimal weight:    0.0570
   chunk 66 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    2.8504

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

Flipped N/Q/H residues before XYZ refinement:
** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 147 HIS
** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 261 GLN
** P 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.103710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.095440 restraints weight = 33050.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.096970 restraints weight = 19317.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.098021 restraints weight = 12584.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.098734 restraints weight = 8951.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.099257 restraints weight = 6877.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8291  Z= 0.207
  Angle     :  0.708  11.283  11352  Z= 0.371
  Chirality :  0.044   0.154   1220
  Planarity :  0.004   0.045   1329
  Dihedral  : 19.571 157.883   1394
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 18.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 18.24 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.06 (0.28), residues: 884
  helix:  0.76 (0.29), residues: 321
  sheet: -0.12 (0.41), residues: 160
  loop : -0.57 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R 140 
 TYR   0.021   0.002   TYR O 317 
 PHE   0.017   0.002   PHE O 305 
 TRP   0.028   0.003   TRP P 414 
 HIS   0.005   0.001   HIS O 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 8291)
  covalent geometry    : angle       0.70758 (11352)
  hydrogen bonds       : bond        0.04434 (  378)
  hydrogen bonds       : angle       5.53459 ( 1040)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 101
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
REVERT: O  268 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6790 (m-80)
REVERT: O  311 GLN cc_start: 0.7585 (mt0) cc_final: 0.7223 (mt0)
REVERT: P  108 GLN cc_start: 0.7834 (tt0) cc_final: 0.7390 (tm-30)
REVERT: P  144 MET cc_start: 0.7807 (tmm) cc_final: 0.7063 (tmm)
REVERT: P  453 MET cc_start: 0.7766 (mmp) cc_final: 0.7011 (mtm)
REVERT: R  135 TRP cc_start: 0.6778 (t-100) cc_final: 0.6558 (t-100)
  outliers start: 31
  outliers final: 21
  residues processed: 121
  average time/residue: 0.0728
  time to fit residues: 12.7654
Evaluate side-chains
  119 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   93 THR
Chi-restraints excluded: chain O residue  104 LEU
Chi-restraints excluded: chain O residue  176 ILE
Chi-restraints excluded: chain O residue  190 GLU
Chi-restraints excluded: chain O residue  257 GLU
Chi-restraints excluded: chain O residue  268 PHE
Chi-restraints excluded: chain O residue  299 CYS
Chi-restraints excluded: chain O residue  320 LEU
Chi-restraints excluded: chain P residue  101 VAL
Chi-restraints excluded: chain P residue  109 THR
Chi-restraints excluded: chain P residue  146 GLN
Chi-restraints excluded: chain P residue  179 GLU
Chi-restraints excluded: chain P residue  195 TYR
Chi-restraints excluded: chain P residue  353 HIS
Chi-restraints excluded: chain P residue  486 LEU
Chi-restraints excluded: chain P residue  523 VAL
Chi-restraints excluded: chain P residue  541 LEU
Chi-restraints excluded: chain P residue  556 MET
Chi-restraints excluded: chain P residue  567 LEU
Chi-restraints excluded: chain R residue   95 TYR
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  180 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 16 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   chunk 76 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 415 HIS
** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.105437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.097168 restraints weight = 32126.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.098671 restraints weight = 18948.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.099670 restraints weight = 12402.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.100428 restraints weight = 8966.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.100951 restraints weight = 6864.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6831
moved from start:          0.3473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8291  Z= 0.147
  Angle     :  0.665  12.632  11352  Z= 0.345
  Chirality :  0.042   0.190   1220
  Planarity :  0.003   0.030   1329
  Dihedral  : 19.461 156.900   1394
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 15.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 19.90 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.12 (0.29), residues: 884
  helix:  0.94 (0.29), residues: 321
  sheet: -0.02 (0.43), residues: 155
  loop : -0.49 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 140 
 TYR   0.024   0.002   TYR O 317 
 PHE   0.016   0.002   PHE R 132 
 TRP   0.039   0.002   TRP P 414 
 HIS   0.003   0.001   HIS P 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8291)
  covalent geometry    : angle       0.66480 (11352)
  hydrogen bonds       : bond        0.03915 (  378)
  hydrogen bonds       : angle       5.36941 ( 1040)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: O  268 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6733 (m-80)
REVERT: O  311 GLN cc_start: 0.7343 (mt0) cc_final: 0.6952 (mt0)
REVERT: P  108 GLN cc_start: 0.7836 (tt0) cc_final: 0.7323 (tm-30)
REVERT: P  144 MET cc_start: 0.7816 (tmm) cc_final: 0.7302 (tmm)
REVERT: P  411 MET cc_start: 0.6164 (tmm) cc_final: 0.5293 (ttt)
REVERT: P  453 MET cc_start: 0.7839 (mmp) cc_final: 0.7012 (mtm)
REVERT: R  135 TRP cc_start: 0.6783 (t-100) cc_final: 0.6064 (t-100)
REVERT: R  136 MET cc_start: 0.7669 (mpp) cc_final: 0.6186 (mtt)
  outliers start: 22
  outliers final: 15
  residues processed: 113
  average time/residue: 0.0722
  time to fit residues: 11.8337
Evaluate side-chains
  108 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   93 THR
Chi-restraints excluded: chain O residue  104 LEU
Chi-restraints excluded: chain O residue  217 VAL
Chi-restraints excluded: chain O residue  257 GLU
Chi-restraints excluded: chain O residue  268 PHE
Chi-restraints excluded: chain O residue  299 CYS
Chi-restraints excluded: chain O residue  320 LEU
Chi-restraints excluded: chain P residue  146 GLN
Chi-restraints excluded: chain P residue  179 GLU
Chi-restraints excluded: chain P residue  353 HIS
Chi-restraints excluded: chain P residue  523 VAL
Chi-restraints excluded: chain P residue  556 MET
Chi-restraints excluded: chain P residue  567 LEU
Chi-restraints excluded: chain R residue   95 TYR
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  180 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0060
   chunk 48 optimal weight:    7.9990
   chunk 42 optimal weight:    0.1980
   chunk 31 optimal weight:    0.0370
   chunk 58 optimal weight:    7.9990
   chunk 60 optimal weight:    9.9990
   chunk 85 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   chunk 12 optimal weight:    6.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.3874

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

Flipped N/Q/H residues before XYZ refinement:
** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 122 GLN
P 343 HIS
P 428 HIS
P 459 ASN
** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.107126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.098659 restraints weight = 32333.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.100285 restraints weight = 18861.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.101393 restraints weight = 12201.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.102155 restraints weight = 8628.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.102621 restraints weight = 6569.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6754
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8291  Z= 0.122
  Angle     :  0.664  15.170  11352  Z= 0.338
  Chirality :  0.041   0.186   1220
  Planarity :  0.003   0.027   1329
  Dihedral  : 19.318 157.873   1394
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 20.92 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.20 (0.29), residues: 884
  helix:  0.98 (0.29), residues: 323
  sheet:  0.09 (0.43), residues: 157
  loop : -0.46 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O 107 
 TYR   0.031   0.001   TYR O 317 
 PHE   0.015   0.002   PHE O 108 
 TRP   0.040   0.002   TRP P 414 
 HIS   0.002   0.000   HIS P 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8291)
  covalent geometry    : angle       0.66446 (11352)
  hydrogen bonds       : bond        0.03615 (  378)
  hydrogen bonds       : angle       5.18145 ( 1040)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  239 ARG cc_start: 0.6766 (ptp-110) cc_final: 0.6378 (ptp-170)
REVERT: O  268 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6659 (m-80)
REVERT: O  311 GLN cc_start: 0.7341 (mt0) cc_final: 0.6915 (mt0)
REVERT: P  108 GLN cc_start: 0.7718 (tt0) cc_final: 0.7123 (tm-30)
REVERT: P  144 MET cc_start: 0.7802 (tmm) cc_final: 0.7500 (tmm)
REVERT: P  312 LYS cc_start: 0.6640 (mptt) cc_final: 0.6307 (mptt)
REVERT: P  411 MET cc_start: 0.6046 (tmm) cc_final: 0.5352 (ttt)
REVERT: P  419 MET cc_start: 0.8108 (tpp) cc_final: 0.7231 (tpp)
REVERT: P  453 MET cc_start: 0.7719 (mmp) cc_final: 0.6776 (mtm)
REVERT: R  105 MET cc_start: 0.8177 (tpp) cc_final: 0.7759 (tpt)
REVERT: R  135 TRP cc_start: 0.6672 (t-100) cc_final: 0.6270 (t-100)
REVERT: R  136 MET cc_start: 0.7544 (mpp) cc_final: 0.6258 (mtt)
  outliers start: 19
  outliers final: 16
  residues processed: 121
  average time/residue: 0.0794
  time to fit residues: 13.7575
Evaluate side-chains
  115 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  104 LEU
Chi-restraints excluded: chain O residue  217 VAL
Chi-restraints excluded: chain O residue  257 GLU
Chi-restraints excluded: chain O residue  268 PHE
Chi-restraints excluded: chain O residue  320 LEU
Chi-restraints excluded: chain P residue  101 VAL
Chi-restraints excluded: chain P residue  109 THR
Chi-restraints excluded: chain P residue  122 GLN
Chi-restraints excluded: chain P residue  146 GLN
Chi-restraints excluded: chain P residue  179 GLU
Chi-restraints excluded: chain P residue  353 HIS
Chi-restraints excluded: chain P residue  486 LEU
Chi-restraints excluded: chain P residue  523 VAL
Chi-restraints excluded: chain P residue  556 MET
Chi-restraints excluded: chain P residue  567 LEU
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  180 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 41 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0070
   chunk 67 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 64 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 77 optimal weight:    8.9990
   chunk 84 optimal weight:    0.1980
   overall best weight:    0.7200

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

Flipped N/Q/H residues before XYZ refinement:
O 151 ASN
** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 122 GLN
** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.106961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.098487 restraints weight = 32106.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.100015 restraints weight = 18905.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.101121 restraints weight = 12535.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.101885 restraints weight = 8934.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.102364 restraints weight = 6826.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6766
moved from start:          0.3945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8291  Z= 0.126
  Angle     :  0.680  13.483  11352  Z= 0.346
  Chirality :  0.042   0.219   1220
  Planarity :  0.003   0.049   1329
  Dihedral  : 19.244 158.106   1394
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 22.19 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.22 (0.29), residues: 884
  helix:  1.07 (0.29), residues: 323
  sheet:  0.04 (0.43), residues: 157
  loop : -0.49 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG O 213 
 TYR   0.031   0.001   TYR O 317 
 PHE   0.019   0.001   PHE P 113 
 TRP   0.038   0.002   TRP P 414 
 HIS   0.003   0.001   HIS P 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8291)
  covalent geometry    : angle       0.68013 (11352)
  hydrogen bonds       : bond        0.03626 (  378)
  hydrogen bonds       : angle       5.17023 ( 1040)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  268 PHE cc_start: 0.7055 (OUTLIER) cc_final: 0.6663 (m-80)
REVERT: O  311 GLN cc_start: 0.7323 (mt0) cc_final: 0.6894 (mt0)
REVERT: P  108 GLN cc_start: 0.7779 (tt0) cc_final: 0.7183 (tm-30)
REVERT: P  144 MET cc_start: 0.7747 (tmm) cc_final: 0.7418 (tmm)
REVERT: P  411 MET cc_start: 0.6093 (tmm) cc_final: 0.5339 (ttt)
REVERT: P  419 MET cc_start: 0.8082 (tpp) cc_final: 0.7262 (tpp)
REVERT: P  453 MET cc_start: 0.7725 (mmp) cc_final: 0.6719 (mtm)
REVERT: R  135 TRP cc_start: 0.6756 (t-100) cc_final: 0.6362 (t-100)
REVERT: R  136 MET cc_start: 0.7573 (mpp) cc_final: 0.6342 (mtt)
  outliers start: 22
  outliers final: 16
  residues processed: 116
  average time/residue: 0.0791
  time to fit residues: 13.0646
Evaluate side-chains
  112 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  104 LEU
Chi-restraints excluded: chain O residue  257 GLU
Chi-restraints excluded: chain O residue  268 PHE
Chi-restraints excluded: chain O residue  320 LEU
Chi-restraints excluded: chain P residue  101 VAL
Chi-restraints excluded: chain P residue  109 THR
Chi-restraints excluded: chain P residue  122 GLN
Chi-restraints excluded: chain P residue  146 GLN
Chi-restraints excluded: chain P residue  179 GLU
Chi-restraints excluded: chain P residue  353 HIS
Chi-restraints excluded: chain P residue  486 LEU
Chi-restraints excluded: chain P residue  514 HIS
Chi-restraints excluded: chain P residue  523 VAL
Chi-restraints excluded: chain P residue  556 MET
Chi-restraints excluded: chain P residue  567 LEU
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  180 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0980
   chunk 67 optimal weight:    2.9990
   chunk 59 optimal weight:    9.9990
   chunk 89 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
O 151 ASN
** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 122 GLN
** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.105847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.097569 restraints weight = 32534.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.099101 restraints weight = 19092.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.100119 restraints weight = 12497.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.100875 restraints weight = 9009.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.101384 restraints weight = 6873.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6805
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8291  Z= 0.151
  Angle     :  0.703  12.836  11352  Z= 0.359
  Chirality :  0.042   0.194   1220
  Planarity :  0.003   0.044   1329
  Dihedral  : 19.223 157.840   1394
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 22.58 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.24 (0.29), residues: 884
  helix:  1.13 (0.29), residues: 317
  sheet: -0.01 (0.43), residues: 157
  loop : -0.47 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG O 213 
 TYR   0.021   0.002   TYR O 317 
 PHE   0.015   0.002   PHE O 108 
 TRP   0.043   0.002   TRP P 414 
 HIS   0.003   0.001   HIS R 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8291)
  covalent geometry    : angle       0.70307 (11352)
  hydrogen bonds       : bond        0.03788 (  378)
  hydrogen bonds       : angle       5.23656 ( 1040)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: O  268 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.6729 (m-80)
REVERT: O  311 GLN cc_start: 0.7342 (mt0) cc_final: 0.6982 (mt0)
REVERT: P  108 GLN cc_start: 0.7836 (tt0) cc_final: 0.7225 (tm-30)
REVERT: P  144 MET cc_start: 0.7829 (tmm) cc_final: 0.7286 (tmm)
REVERT: P  220 GLN cc_start: 0.7456 (pm20) cc_final: 0.7101 (pp30)
REVERT: P  320 LEU cc_start: 0.7423 (mt) cc_final: 0.7172 (mp)
REVERT: P  411 MET cc_start: 0.6135 (tmm) cc_final: 0.5391 (ttt)
REVERT: P  419 MET cc_start: 0.8061 (tpp) cc_final: 0.7219 (tpp)
REVERT: P  453 MET cc_start: 0.7748 (mmp) cc_final: 0.6805 (mtm)
REVERT: R  105 MET cc_start: 0.8306 (tpp) cc_final: 0.7903 (tpt)
REVERT: R  135 TRP cc_start: 0.6769 (t-100) cc_final: 0.6483 (t-100)
  outliers start: 22
  outliers final: 17
  residues processed: 114
  average time/residue: 0.0718
  time to fit residues: 11.8580
Evaluate side-chains
  108 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  104 LEU
Chi-restraints excluded: chain O residue  151 ASN
Chi-restraints excluded: chain O residue  257 GLU
Chi-restraints excluded: chain O residue  268 PHE
Chi-restraints excluded: chain O residue  275 MET
Chi-restraints excluded: chain O residue  320 LEU
Chi-restraints excluded: chain P residue  101 VAL
Chi-restraints excluded: chain P residue  109 THR
Chi-restraints excluded: chain P residue  146 GLN
Chi-restraints excluded: chain P residue  179 GLU
Chi-restraints excluded: chain P residue  353 HIS
Chi-restraints excluded: chain P residue  486 LEU
Chi-restraints excluded: chain P residue  514 HIS
Chi-restraints excluded: chain P residue  523 VAL
Chi-restraints excluded: chain P residue  556 MET
Chi-restraints excluded: chain P residue  567 LEU
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  180 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   chunk 58 optimal weight:    0.7980
   chunk 56 optimal weight:    0.5980
   chunk 84 optimal weight:    7.9990
   chunk 85 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 86 optimal weight:    7.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
O 151 ASN
** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 318 ASN
P 122 GLN
** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.106961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.098708 restraints weight = 32354.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.100250 restraints weight = 18997.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.101305 restraints weight = 12373.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.102065 restraints weight = 8821.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.102582 restraints weight = 6696.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6763
moved from start:          0.4190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8291  Z= 0.132
  Angle     :  0.723  12.689  11352  Z= 0.363
  Chirality :  0.042   0.194   1220
  Planarity :  0.003   0.033   1329
  Dihedral  : 19.185 158.114   1394
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 22.83 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.20 (0.29), residues: 884
  helix:  1.05 (0.29), residues: 317
  sheet: -0.01 (0.43), residues: 157
  loop : -0.45 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG O 213 
 TYR   0.026   0.001   TYR O 317 
 PHE   0.015   0.001   PHE O  53 
 TRP   0.048   0.002   TRP P 414 
 HIS   0.002   0.000   HIS P 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8291)
  covalent geometry    : angle       0.72340 (11352)
  hydrogen bonds       : bond        0.03680 (  378)
  hydrogen bonds       : angle       5.22969 ( 1040)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  268 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.6670 (m-80)
REVERT: O  311 GLN cc_start: 0.7330 (mt0) cc_final: 0.6928 (mt0)
REVERT: P  108 GLN cc_start: 0.7823 (tt0) cc_final: 0.7204 (tm-30)
REVERT: P  144 MET cc_start: 0.7726 (tmm) cc_final: 0.7344 (tmm)
REVERT: P  220 GLN cc_start: 0.7171 (pm20) cc_final: 0.6855 (pp30)
REVERT: P  411 MET cc_start: 0.6098 (tmm) cc_final: 0.5373 (ttt)
REVERT: P  419 MET cc_start: 0.8057 (tpp) cc_final: 0.7201 (tpp)
REVERT: P  453 MET cc_start: 0.7755 (mmp) cc_final: 0.6832 (mtm)
REVERT: R  105 MET cc_start: 0.8294 (tpp) cc_final: 0.7796 (tpt)
REVERT: R  129 GLN cc_start: 0.6003 (tm-30) cc_final: 0.5771 (tm-30)
REVERT: R  135 TRP cc_start: 0.6691 (t-100) cc_final: 0.6269 (t-100)
REVERT: R  136 MET cc_start: 0.7627 (mpp) cc_final: 0.6312 (mtt)
  outliers start: 21
  outliers final: 19
  residues processed: 113
  average time/residue: 0.0713
  time to fit residues: 11.4725
Evaluate side-chains
  114 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  104 LEU
Chi-restraints excluded: chain O residue  151 ASN
Chi-restraints excluded: chain O residue  257 GLU
Chi-restraints excluded: chain O residue  268 PHE
Chi-restraints excluded: chain O residue  275 MET
Chi-restraints excluded: chain O residue  318 ASN
Chi-restraints excluded: chain O residue  320 LEU
Chi-restraints excluded: chain P residue  101 VAL
Chi-restraints excluded: chain P residue  109 THR
Chi-restraints excluded: chain P residue  146 GLN
Chi-restraints excluded: chain P residue  179 GLU
Chi-restraints excluded: chain P residue  353 HIS
Chi-restraints excluded: chain P residue  486 LEU
Chi-restraints excluded: chain P residue  514 HIS
Chi-restraints excluded: chain P residue  523 VAL
Chi-restraints excluded: chain P residue  541 LEU
Chi-restraints excluded: chain P residue  556 MET
Chi-restraints excluded: chain P residue  567 LEU
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  180 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 84 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 70 optimal weight:   10.0000
   chunk 81 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** O 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 318 ASN
** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.106883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.098536 restraints weight = 32073.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.100121 restraints weight = 18764.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.101211 restraints weight = 12166.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.101972 restraints weight = 8588.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.102500 restraints weight = 6501.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6775
moved from start:          0.4204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.124   8291  Z= 0.221
  Angle     :  1.146  59.199  11352  Z= 0.694
  Chirality :  0.076   2.142   1220
  Planarity :  0.005   0.121   1329
  Dihedral  : 19.192 157.988   1394
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 17.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 22.70 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.17 (0.29), residues: 884
  helix:  1.02 (0.29), residues: 317
  sheet: -0.02 (0.43), residues: 157
  loop : -0.46 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG O 239 
 TYR   0.014   0.002   TYR P 119 
 PHE   0.016   0.001   PHE R 132 
 TRP   0.040   0.002   TRP P 414 
 HIS   0.002   0.001   HIS P 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 8291)
  covalent geometry    : angle       1.14574 (11352)
  hydrogen bonds       : bond        0.03733 (  378)
  hydrogen bonds       : angle       5.24447 ( 1040)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1369.43 seconds
wall clock time: 24 minutes 29.51 seconds (1469.51 seconds total)