Starting phenix.real_space_refine
on Wed Mar 12 15:37:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x0l_21978/03_2025/6x0l_21978.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x0l_21978/03_2025/6x0l_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_2025/6x0l_21978.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x0l_21978/03_2025/6x0l_21978.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x0l_21978/03_2025/6x0l_21978.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x0l_21978/03_2025/6x0l_21978.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.90, per 1000 atoms: 0.73
  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: 2.05
  Conformation dependent library (CDL) restraints added in 799.3 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: 2.67
  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: 2.54

  Time building geometry restraints manager: 2.41 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:             47.280
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.680
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   74.040
-------------------------------------------------------------------------------
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= 0.303
  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 : 21.30
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (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
 TRP   0.022   0.003   TRP P 135 
 HIS   0.009   0.002   HIS O 223 
 PHE   0.019   0.003   PHE P 113 
 TYR   0.023   0.002   TYR P 188 
 ARG   0.010   0.001   ARG R 140 

*********************** 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  : 0.860 
Fit side-chains
   revert: symmetry clash
REVERT: O  239 ARG cc_start: 0.7160 (ptp-170) cc_final: 0.6847 (ptp-110)
REVERT: O  305 PHE cc_start: 0.6355 (m-10) cc_final: 0.6067 (m-10)
REVERT: O  311 GLN cc_start: 0.7775 (mt0) cc_final: 0.7535 (mt0)
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: 0.7349 (tpt)
REVERT: P  290 ASN cc_start: 0.7103 (m110) cc_final: 0.5827 (m110)
REVERT: P  468 ASN cc_start: 0.6550 (p0) cc_final: 0.6346 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 180
  average time/residue: 0.2273
  time to fit residues: 53.5829
Evaluate side-chains
  111 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 69 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   chunk 47 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 83 optimal weight:    0.9980
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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**
O 303 HIS
** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 267 GLN
** P 290 ASN ** 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 519 ASN
P 553 GLN
** 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 = 0.3983 r_free = 0.3983 target = 0.106725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.098489 restraints weight = 31954.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.100044 restraints weight = 18676.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.101081 restraints weight = 12164.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6803
moved from start:          0.2027

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= 0.217
  Angle     :  0.700   9.181  11352  Z= 0.372
  Chirality :  0.043   0.149   1220
  Planarity :  0.004   0.031   1329
  Dihedral  : 19.837 162.287   1394
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 12.12 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.27), residues: 884
  helix:  0.65 (0.28), residues: 322
  sheet: -0.23 (0.39), residues: 161
  loop : -0.80 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP P 414 
 HIS   0.005   0.001   HIS O 223 
 PHE   0.026   0.002   PHE R 132 
 TYR   0.023   0.002   TYR P 543 
 ARG   0.005   0.001   ARG O 107 

*********************** 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
  138 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.911 
Fit side-chains
REVERT: O  222 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5739 (m-10)
REVERT: O  239 ARG cc_start: 0.7313 (ptp-170) cc_final: 0.6932 (ptp-110)
REVERT: O  311 GLN cc_start: 0.7639 (mt0) cc_final: 0.7363 (mt0)
REVERT: O  327 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7309 (mm-30)
REVERT: P  108 GLN cc_start: 0.7658 (tt0) cc_final: 0.7373 (tm-30)
REVERT: P  414 TRP cc_start: 0.7162 (m100) cc_final: 0.6961 (m100)
REVERT: P  485 LEU cc_start: 0.7290 (mm) cc_final: 0.7080 (mm)
  outliers start: 16
  outliers final: 9
  residues processed: 134
  average time/residue: 0.2011
  time to fit residues: 37.2083
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  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  176 ILE
Chi-restraints excluded: chain O residue  222 PHE
Chi-restraints excluded: chain O residue  236 VAL
Chi-restraints excluded: chain P residue  109 THR
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 38 optimal weight:    5.9990
   chunk 2 optimal weight:    8.9990
   chunk 88 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 76 optimal weight:   10.0000
   chunk 72 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0870
   chunk 67 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    2.5564

-------------------------------------------------------------------------------
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 147 HIS
** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 290 ASN ** 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
** 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 = 0.3947 r_free = 0.3947 target = 0.104674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.096476 restraints weight = 32730.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.098016 restraints weight = 19200.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.099073 restraints weight = 12515.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
moved from start:          0.2500

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= 0.269
  Angle     :  0.709  11.708  11352  Z= 0.373
  Chirality :  0.044   0.159   1220
  Planarity :  0.004   0.038   1329
  Dihedral  : 19.701 161.719   1394
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 17.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 14.67 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.28), residues: 884
  helix:  0.90 (0.28), residues: 321
  sheet: -0.06 (0.41), residues: 157
  loop : -0.62 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP R 135 
 HIS   0.004   0.001   HIS R 147 
 PHE   0.017   0.002   PHE R 163 
 TYR   0.031   0.002   TYR O 317 
 ARG   0.004   0.001   ARG O 107 

*********************** 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
  135 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 1.288 
Fit side-chains
REVERT: O  141 VAL cc_start: 0.7183 (OUTLIER) cc_final: 0.6960 (t)
REVERT: O  239 ARG cc_start: 0.7523 (ptp-170) cc_final: 0.7084 (ptp-110)
REVERT: O  311 GLN cc_start: 0.7665 (mt0) cc_final: 0.7362 (mt0)
REVERT: P  108 GLN cc_start: 0.7698 (tt0) cc_final: 0.7372 (tm-30)
REVERT: P  144 MET cc_start: 0.7801 (tmm) cc_final: 0.6963 (tmm)
REVERT: P  290 ASN cc_start: 0.6976 (m110) cc_final: 0.6661 (m110)
REVERT: R  105 MET cc_start: 0.8249 (tpp) cc_final: 0.7750 (tpt)
REVERT: R  140 ARG cc_start: 0.6411 (mmm160) cc_final: 0.6161 (tpt170)
  outliers start: 27
  outliers final: 14
  residues processed: 126
  average time/residue: 0.2393
  time to fit residues: 42.0978
Evaluate side-chains
  110 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   93 THR
Chi-restraints excluded: chain O residue  141 VAL
Chi-restraints excluded: chain O residue  174 LYS
Chi-restraints excluded: chain O residue  299 CYS
Chi-restraints excluded: chain O residue  320 LEU
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 88 optimal weight:    6.9990
   chunk 65 optimal weight:    7.9990
   chunk 2 optimal weight:    7.9990
   chunk 74 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 82 optimal weight:    9.9990
   chunk 80 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 174 ASN
P 226 GLN
** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 290 ASN ** 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**
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.105347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.097117 restraints weight = 32409.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.098597 restraints weight = 18988.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.099670 restraints weight = 12494.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.2922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8291  Z= 0.213
  Angle     :  0.664  11.976  11352  Z= 0.349
  Chirality :  0.042   0.178   1220
  Planarity :  0.003   0.033   1329
  Dihedral  : 19.583 159.195   1394
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 16.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 16.45 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.28), residues: 884
  helix:  0.97 (0.29), residues: 320
  sheet:  0.11 (0.42), residues: 154
  loop : -0.49 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP P 414 
 HIS   0.004   0.001   HIS O 223 
 PHE   0.021   0.002   PHE O 305 
 TYR   0.011   0.002   TYR O 317 
 ARG   0.003   0.000   ARG P 140 

*********************** 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
  133 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 0.815 
Fit side-chains
REVERT: O  268 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6648 (m-80)
REVERT: O  311 GLN cc_start: 0.7479 (mt0) cc_final: 0.7218 (mt0)
REVERT: P  105 MET cc_start: 0.7819 (tmm) cc_final: 0.7605 (tmm)
REVERT: P  108 GLN cc_start: 0.7674 (tt0) cc_final: 0.7279 (tm-30)
REVERT: P  144 MET cc_start: 0.7723 (tmm) cc_final: 0.7162 (tmm)
REVERT: P  270 LYS cc_start: 0.7826 (tppt) cc_final: 0.7383 (tptt)
REVERT: P  290 ASN cc_start: 0.6978 (m110) cc_final: 0.6734 (m110)
REVERT: P  453 MET cc_start: 0.7715 (mmp) cc_final: 0.7042 (mtm)
REVERT: R  136 MET cc_start: 0.7389 (mpp) cc_final: 0.6151 (mtt)
  outliers start: 28
  outliers final: 18
  residues processed: 123
  average time/residue: 0.1859
  time to fit residues: 32.1377
Evaluate side-chains
  116 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
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  190 GLU
Chi-restraints excluded: chain O residue  219 THR
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  486 LEU
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 87 optimal weight:    0.0470
   chunk 12 optimal weight:    8.9990
   chunk 65 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0980
   chunk 59 optimal weight:    2.9990
   chunk 70 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 77 optimal weight:   20.0000
   chunk 53 optimal weight:    8.9990
   overall best weight:    3.2284

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

Flipped N/Q/H residues before XYZ refinement:
** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 261 GLN
** P 290 ASN ** 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 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.103211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.094989 restraints weight = 32615.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.096488 restraints weight = 19192.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.097512 restraints weight = 12554.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.3257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8291  Z= 0.319
  Angle     :  0.731  11.938  11352  Z= 0.386
  Chirality :  0.044   0.169   1220
  Planarity :  0.004   0.063   1329
  Dihedral  : 19.623 157.296   1394
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 18.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 18.62 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.28), residues: 884
  helix:  0.77 (0.29), residues: 321
  sheet: -0.05 (0.42), residues: 155
  loop : -0.55 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP P 414 
 HIS   0.005   0.001   HIS O 105 
 PHE   0.024   0.003   PHE O 305 
 TYR   0.014   0.002   TYR P 558 
 ARG   0.006   0.001   ARG R 140 

*********************** 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
  130 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 100
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
REVERT: O  141 VAL cc_start: 0.7303 (OUTLIER) cc_final: 0.7101 (t)
REVERT: O  222 PHE cc_start: 0.6181 (OUTLIER) cc_final: 0.5716 (m-10)
REVERT: O  268 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6896 (m-80)
REVERT: O  275 MET cc_start: 0.7385 (mmp) cc_final: 0.7165 (mmp)
REVERT: O  296 ASP cc_start: 0.6454 (m-30) cc_final: 0.5962 (m-30)
REVERT: O  311 GLN cc_start: 0.7477 (mt0) cc_final: 0.7094 (mt0)
REVERT: P  144 MET cc_start: 0.7874 (tmm) cc_final: 0.6955 (tmm)
REVERT: P  270 LYS cc_start: 0.7914 (tppt) cc_final: 0.7595 (tptt)
  outliers start: 30
  outliers final: 21
  residues processed: 120
  average time/residue: 0.1799
  time to fit residues: 30.5017
Evaluate side-chains
  113 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
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  141 VAL
Chi-restraints excluded: chain O residue  190 GLU
Chi-restraints excluded: chain O residue  217 VAL
Chi-restraints excluded: chain O residue  222 PHE
Chi-restraints excluded: chain O residue  236 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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0060
   chunk 80 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0970
   chunk 87 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 86 optimal weight:    2.9990
   chunk 20 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.8200

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

Flipped N/Q/H residues before XYZ refinement:
** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.104503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.096237 restraints weight = 32659.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.097784 restraints weight = 19130.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.098830 restraints weight = 12463.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6898
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8291  Z= 0.217
  Angle     :  0.677  13.747  11352  Z= 0.353
  Chirality :  0.043   0.242   1220
  Planarity :  0.004   0.032   1329
  Dihedral  : 19.478 157.017   1394
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 16.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 20.15 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.29), residues: 884
  helix:  0.94 (0.29), residues: 322
  sheet: -0.05 (0.43), residues: 155
  loop : -0.51 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP P 414 
 HIS   0.004   0.001   HIS O 223 
 PHE   0.023   0.002   PHE O 305 
 TYR   0.033   0.002   TYR O 317 
 ARG   0.003   0.001   ARG R 140 

*********************** 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
  125 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
REVERT: O  222 PHE cc_start: 0.6156 (OUTLIER) cc_final: 0.5704 (m-10)
REVERT: O  268 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6802 (m-80)
REVERT: O  275 MET cc_start: 0.7939 (mmp) cc_final: 0.7616 (mmp)
REVERT: O  296 ASP cc_start: 0.6485 (m-30) cc_final: 0.6022 (m-30)
REVERT: O  311 GLN cc_start: 0.7357 (mt0) cc_final: 0.6926 (mt0)
REVERT: P  144 MET cc_start: 0.7887 (tmm) cc_final: 0.7230 (tmm)
REVERT: P  270 LYS cc_start: 0.7814 (tppt) cc_final: 0.7438 (tptt)
REVERT: P  347 GLN cc_start: 0.7277 (mp10) cc_final: 0.6718 (mp10)
REVERT: P  453 MET cc_start: 0.7830 (mmp) cc_final: 0.7025 (mtm)
REVERT: R  136 MET cc_start: 0.7615 (mpp) cc_final: 0.6350 (mtt)
REVERT: R  180 LYS cc_start: 0.7029 (pttm) cc_final: 0.6007 (pttt)
  outliers start: 28
  outliers final: 18
  residues processed: 118
  average time/residue: 0.1984
  time to fit residues: 32.4429
Evaluate side-chains
  112 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
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  123 ASN
Chi-restraints excluded: chain O residue  190 GLU
Chi-restraints excluded: chain O residue  217 VAL
Chi-restraints excluded: chain O residue  219 THR
Chi-restraints excluded: chain O residue  222 PHE
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  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   95 TYR
Chi-restraints excluded: chain R residue  101 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   chunk 48 optimal weight:    0.5980
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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
** 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 = 0.3942 r_free = 0.3942 target = 0.104607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.096351 restraints weight = 32131.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.097874 restraints weight = 18805.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.098911 restraints weight = 12270.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6900
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8291  Z= 0.211
  Angle     :  0.662  13.089  11352  Z= 0.346
  Chirality :  0.043   0.204   1220
  Planarity :  0.004   0.037   1329
  Dihedral  : 19.407 158.038   1394
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 20.41 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.29), residues: 884
  helix:  1.08 (0.29), residues: 316
  sheet: -0.10 (0.43), residues: 149
  loop : -0.51 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP P 414 
 HIS   0.004   0.001   HIS O 223 
 PHE   0.020   0.002   PHE O 305 
 TYR   0.035   0.002   TYR O 317 
 ARG   0.004   0.001   ARG R 140 

*********************** 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
  129 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 98
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
REVERT: O  141 VAL cc_start: 0.7140 (OUTLIER) cc_final: 0.6896 (t)
REVERT: O  222 PHE cc_start: 0.6207 (OUTLIER) cc_final: 0.5770 (m-10)
REVERT: O  268 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6801 (m-80)
REVERT: O  295 MET cc_start: 0.7270 (tpt) cc_final: 0.6791 (tpt)
REVERT: O  296 ASP cc_start: 0.6306 (m-30) cc_final: 0.5853 (m-30)
REVERT: O  311 GLN cc_start: 0.7294 (mt0) cc_final: 0.6862 (mt0)
REVERT: P  144 MET cc_start: 0.7782 (tmm) cc_final: 0.7103 (tmm)
REVERT: P  270 LYS cc_start: 0.7814 (tppt) cc_final: 0.7440 (tptt)
REVERT: P  411 MET cc_start: 0.6184 (tmm) cc_final: 0.5322 (ttt)
REVERT: P  453 MET cc_start: 0.7791 (mmp) cc_final: 0.6977 (mtm)
REVERT: P  559 LEU cc_start: 0.5734 (OUTLIER) cc_final: 0.4911 (tt)
REVERT: R  136 MET cc_start: 0.7593 (mpp) cc_final: 0.6317 (mtt)
REVERT: R  180 LYS cc_start: 0.6971 (pttm) cc_final: 0.5920 (pttt)
  outliers start: 31
  outliers final: 20
  residues processed: 122
  average time/residue: 0.1868
  time to fit residues: 32.6475
Evaluate side-chains
  115 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
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  123 ASN
Chi-restraints excluded: chain O residue  141 VAL
Chi-restraints excluded: chain O residue  190 GLU
Chi-restraints excluded: chain O residue  217 VAL
Chi-restraints excluded: chain O residue  219 THR
Chi-restraints excluded: chain O residue  222 PHE
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  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  477 VAL
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  559 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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 58 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 84 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 343 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.106097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.097789 restraints weight = 32394.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.099334 restraints weight = 19095.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.100384 restraints weight = 12470.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6853
moved from start:          0.3919

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= 0.173
  Angle     :  0.659  11.632  11352  Z= 0.340
  Chirality :  0.042   0.179   1220
  Planarity :  0.003   0.028   1329
  Dihedral  : 19.311 159.136   1394
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 22.07 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.29), residues: 884
  helix:  1.21 (0.30), residues: 315
  sheet:  0.04 (0.44), residues: 149
  loop : -0.45 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP P 414 
 HIS   0.004   0.001   HIS O 223 
 PHE   0.020   0.002   PHE O 305 
 TYR   0.031   0.001   TYR O 317 
 ARG   0.003   0.000   ARG O 213 

*********************** 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
  120 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.974 
Fit side-chains
REVERT: O  222 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.5642 (m-10)
REVERT: O  268 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6787 (m-80)
REVERT: O  295 MET cc_start: 0.7363 (tpt) cc_final: 0.6903 (tpt)
REVERT: O  296 ASP cc_start: 0.6373 (m-30) cc_final: 0.5950 (m-30)
REVERT: O  311 GLN cc_start: 0.7297 (mt0) cc_final: 0.6833 (mt0)
REVERT: P  144 MET cc_start: 0.7654 (tmm) cc_final: 0.7377 (tmm)
REVERT: P  270 LYS cc_start: 0.7753 (tppt) cc_final: 0.7370 (tptt)
REVERT: P  347 GLN cc_start: 0.7314 (mp10) cc_final: 0.6874 (mp10)
REVERT: P  411 MET cc_start: 0.6345 (tmm) cc_final: 0.5459 (ttt)
REVERT: P  453 MET cc_start: 0.7862 (mmp) cc_final: 0.6910 (mtm)
REVERT: R  105 MET cc_start: 0.8310 (tpp) cc_final: 0.7789 (tpt)
REVERT: R  136 MET cc_start: 0.7443 (mpp) cc_final: 0.6267 (mtt)
REVERT: R  180 LYS cc_start: 0.6900 (pttm) cc_final: 0.5966 (pttt)
  outliers start: 22
  outliers final: 15
  residues processed: 114
  average time/residue: 0.1813
  time to fit residues: 29.8596
Evaluate side-chains
  109 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
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  219 THR
Chi-restraints excluded: chain O residue  222 PHE
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  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  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  191 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 83 optimal weight:    9.9990
   chunk 32 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 9 optimal weight:    9.9990
   chunk 15 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.103764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.095574 restraints weight = 33129.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.097110 restraints weight = 19217.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.098134 restraints weight = 12427.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.4042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8291  Z= 0.275
  Angle     :  0.715  11.564  11352  Z= 0.375
  Chirality :  0.045   0.199   1220
  Planarity :  0.004   0.048   1329
  Dihedral  : 19.378 159.168   1394
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 18.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 22.96 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.29), residues: 884
  helix:  1.03 (0.29), residues: 315
  sheet: -0.20 (0.44), residues: 149
  loop : -0.39 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.003   TRP P 414 
 HIS   0.003   0.001   HIS R 147 
 PHE   0.017   0.002   PHE O 305 
 TYR   0.031   0.002   TYR O 317 
 ARG   0.008   0.001   ARG O 213 

*********************** 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: 26
    poor density    : 93
  time to evaluate  : 0.817 
Fit side-chains
REVERT: O   53 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6831 (t80)
REVERT: O  222 PHE cc_start: 0.6115 (OUTLIER) cc_final: 0.5882 (m-10)
REVERT: O  268 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6844 (m-80)
REVERT: O  295 MET cc_start: 0.7301 (tpt) cc_final: 0.6891 (tpt)
REVERT: O  311 GLN cc_start: 0.7344 (mt0) cc_final: 0.6889 (mt0)
REVERT: P  144 MET cc_start: 0.7618 (tmm) cc_final: 0.7172 (tmm)
REVERT: P  270 LYS cc_start: 0.7818 (tppt) cc_final: 0.7442 (tptt)
REVERT: P  411 MET cc_start: 0.6179 (tmm) cc_final: 0.5405 (ttt)
REVERT: P  559 LEU cc_start: 0.5789 (OUTLIER) cc_final: 0.4982 (tt)
REVERT: R  136 MET cc_start: 0.7649 (mpp) cc_final: 0.6323 (mtp)
  outliers start: 26
  outliers final: 19
  residues processed: 111
  average time/residue: 0.1788
  time to fit residues: 28.5231
Evaluate side-chains
  115 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   53 PHE
Chi-restraints excluded: chain O residue  104 LEU
Chi-restraints excluded: chain O residue  217 VAL
Chi-restraints excluded: chain O residue  219 THR
Chi-restraints excluded: chain O residue  222 PHE
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  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  443 MET
Chi-restraints excluded: chain P residue  477 VAL
Chi-restraints excluded: chain P residue  486 LEU
Chi-restraints excluded: chain P residue  519 ASN
Chi-restraints excluded: chain P residue  523 VAL
Chi-restraints excluded: chain P residue  556 MET
Chi-restraints excluded: chain P residue  559 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  191 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 84 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 82 optimal weight:    7.9990
   chunk 5 optimal weight:    0.7980
   chunk 1 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 69 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    2.3588

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.103910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.095839 restraints weight = 32620.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.097317 restraints weight = 19147.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.098375 restraints weight = 12590.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
moved from start:          0.4168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8291  Z= 0.262
  Angle     :  0.725  11.627  11352  Z= 0.380
  Chirality :  0.044   0.198   1220
  Planarity :  0.004   0.039   1329
  Dihedral  : 19.390 159.444   1394
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 18.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 23.47 %
    Favored  : 73.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.29), residues: 884
  helix:  0.96 (0.29), residues: 315
  sheet: -0.25 (0.45), residues: 148
  loop : -0.48 (0.32), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.003   TRP P 414 
 HIS   0.004   0.001   HIS P 343 
 PHE   0.018   0.002   PHE O 305 
 TYR   0.033   0.002   TYR O 317 
 ARG   0.006   0.001   ARG O 213 

********************** 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: 24
    poor density    : 95
  time to evaluate  : 0.845 
Fit side-chains
REVERT: O   53 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6839 (t80)
REVERT: O  222 PHE cc_start: 0.6298 (OUTLIER) cc_final: 0.5829 (m-10)
REVERT: O  268 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6904 (m-80)
REVERT: O  295 MET cc_start: 0.7359 (tpt) cc_final: 0.7033 (tpt)
REVERT: O  296 ASP cc_start: 0.6343 (m-30) cc_final: 0.5941 (m-30)
REVERT: O  311 GLN cc_start: 0.7272 (mt0) cc_final: 0.6814 (mt0)
REVERT: O  343 GLN cc_start: 0.6204 (mm-40) cc_final: 0.4596 (mt0)
REVERT: P  220 GLN cc_start: 0.7607 (pm20) cc_final: 0.7223 (pp30)
REVERT: P  228 LEU cc_start: 0.8381 (pp) cc_final: 0.7441 (tt)
REVERT: P  270 LYS cc_start: 0.7824 (tppt) cc_final: 0.7446 (tptt)
REVERT: P  347 GLN cc_start: 0.7295 (mp10) cc_final: 0.7007 (mp10)
REVERT: P  411 MET cc_start: 0.6322 (tmm) cc_final: 0.5390 (ttt)
REVERT: P  453 MET cc_start: 0.7793 (mmp) cc_final: 0.7039 (mtm)
REVERT: P  559 LEU cc_start: 0.5904 (OUTLIER) cc_final: 0.5055 (tt)
REVERT: R  105 MET cc_start: 0.8434 (tpp) cc_final: 0.7633 (tpt)
  outliers start: 24
  outliers final: 20
  residues processed: 113
  average time/residue: 0.1815
  time to fit residues: 29.0245
Evaluate side-chains
  116 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   53 PHE
Chi-restraints excluded: chain O residue   93 THR
Chi-restraints excluded: chain O residue  104 LEU
Chi-restraints excluded: chain O residue  219 THR
Chi-restraints excluded: chain O residue  222 PHE
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  109 THR
Chi-restraints excluded: chain P residue  141 VAL
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  443 MET
Chi-restraints excluded: chain P residue  477 VAL
Chi-restraints excluded: chain P residue  486 LEU
Chi-restraints excluded: chain P residue  519 ASN
Chi-restraints excluded: chain P residue  523 VAL
Chi-restraints excluded: chain P residue  556 MET
Chi-restraints excluded: chain P residue  559 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  191 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 90 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0470
   chunk 33 optimal weight:    8.9990
   chunk 87 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   overall best weight:    1.2080

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

Flipped N/Q/H residues before XYZ refinement:
** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 343 HIS
** 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 = 0.3954 r_free = 0.3954 target = 0.105367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.097191 restraints weight = 32580.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.098699 restraints weight = 19197.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.099755 restraints weight = 12607.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6880
moved from start:          0.4304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8291  Z= 0.200
  Angle     :  0.702  12.221  11352  Z= 0.365
  Chirality :  0.043   0.198   1220
  Planarity :  0.003   0.036   1329
  Dihedral  : 19.281 160.780   1394
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 23.09 %
    Favored  : 73.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.29), residues: 884
  helix:  1.08 (0.29), residues: 314
  sheet: -0.01 (0.46), residues: 139
  loop : -0.57 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP P 414 
 HIS   0.004   0.001   HIS P 415 
 PHE   0.017   0.002   PHE O 305 
 TYR   0.034   0.001   TYR O 317 
 ARG   0.007   0.001   ARG O 213 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3024.12 seconds
wall clock time: 55 minutes 4.45 seconds (3304.45 seconds total)