Starting phenix.real_space_refine
on Thu Jul  2 18:30:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yr2_39533/07_2026/8yr2_39533.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yr2_39533/07_2026/8yr2_39533.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yr2_39533/07_2026/8yr2_39533.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yr2_39533/07_2026/8yr2_39533.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yr2_39533/07_2026/8yr2_39533.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yr2_39533/07_2026/8yr2_39533.map"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.062
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: 7
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     S      40      5.16       5
     Cl      2      4.86       5
     Na      4      4.78       5
     C    6776      2.51       5
     N    1414      2.21       5
     O    1648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9894
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4516
          Classifications: {'peptide': 565}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 544}
    Chain: "A"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4516
          Classifications: {'peptide': 565}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 544}
    Chain: "B"
      Number of atoms: 456
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 453
          Ad-hoc single atom residues: {' NA': 2, ' CL': 1}
          Unusual residues: {'41U': 1, 'A1LX7': 2, 'CLR': 11, 'PIO': 1}
          Classifications: {'undetermined': 15}
          Link IDs: {None: 13}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 397
          Ad-hoc single atom residues: {' NA': 2, ' CL': 1}
          Unusual residues: {'41U': 1, 'A1LX7': 2, 'CLR': 9, 'PIO': 1}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 11}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.34, per 1000 atoms: 0.24
  Number of scatterers: 9894
  At special positions: 0
  Unit cell: (89.79, 114.61, 89.06, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Cl      2     17.00
     S      40     16.00
     P      10     15.00
     Na      4     11.00
     O    1648      8.00
     N    1414      7.00
     C    6776      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 411.9 milliseconds
  

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2076

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 0 sheets defined
      77.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'B' and resid 61 through 74
      removed outlier: 3.688A  pdb=" N   PHE B  65 " --> pdb=" O   LYS B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 81
      removed outlier: 3.718A  pdb=" N   VAL B  79 " --> pdb=" O   ASP B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 89
    Processing helix  chain 'B' and resid 91 through 107
      removed outlier: 3.948A  pdb=" N   LEU B  95 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE B  96 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
      Proline residue:  B  97  - end of helix
      removed outlier: 3.674A  pdb=" N   LEU B 100 " --> pdb=" O   ILE B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 121
    Processing helix  chain 'B' and resid 131 through 133
      No H-bonds generated for 'chain 'B' and resid 131 through 133'
    Processing helix  chain 'B' and resid 134 through 165
      removed outlier: 3.659A  pdb=" N   GLY B 138 " --> pdb=" O   PHE B 134 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   TYR B 151 " --> pdb=" O   TYR B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 216
    Processing helix  chain 'B' and resid 220 through 224
    Processing helix  chain 'B' and resid 234 through 253
    Processing helix  chain 'B' and resid 257 through 282
      removed outlier: 3.873A  pdb=" N   LYS B 261 " --> pdb=" O   LYS B 257 " (cutoff:3.500A)
      Proline residue:  B 270  - end of helix
    Processing helix  chain 'B' and resid 286 through 296
      removed outlier: 3.618A  pdb=" N   GLY B 290 " --> pdb=" O   GLY B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 305
      removed outlier: 4.008A  pdb=" N   LYS B 303 " --> pdb=" O   TYR B 300 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   ALA B 305 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 320
      removed outlier: 3.544A  pdb=" N   ALA B 311 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLY B 320 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 331
      removed outlier: 4.264A  pdb=" N   ILE B 327 " --> pdb=" O   PHE B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 373
      removed outlier: 3.508A  pdb=" N   ASP B 342 " --> pdb=" O   ASN B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 380
      removed outlier: 3.836A  pdb=" N   VAL B 379 " --> pdb=" O   ASN B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 398
      Proline residue:  B 392  - end of helix
    Processing helix  chain 'B' and resid 400 through 435
      removed outlier: 3.520A  pdb=" N   TRP B 404 " --> pdb=" O   GLY B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 441
      removed outlier: 3.663A  pdb=" N   HIS B 441 " --> pdb=" O   VAL B 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 461
      removed outlier: 3.766A  pdb=" N   PHE B 445 " --> pdb=" O   HIS B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 464 through 494
      removed outlier: 4.007A  pdb=" N   VAL B 468 " --> pdb=" O   GLY B 464 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 509
      removed outlier: 3.887A  pdb=" N   PHE B 501 " --> pdb=" O   GLY B 497 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   SER B 502 " --> pdb=" O   VAL B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 514 through 523
    Processing helix  chain 'B' and resid 523 through 539
    Processing helix  chain 'B' and resid 551 through 579
      removed outlier: 4.040A  pdb=" N   ASN B 555 " --> pdb=" O   PRO B 551 " (cutoff:3.500A)
      Proline residue:  B 570  - end of helix
    Processing helix  chain 'B' and resid 583 through 593
    Processing helix  chain 'B' and resid 598 through 603
      removed outlier: 3.746A  pdb=" N   ALA B 602 " --> pdb=" O   HIS B 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 74
      removed outlier: 3.695A  pdb=" N   PHE A  65 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 81
      removed outlier: 3.718A  pdb=" N   VAL A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 89
    Processing helix  chain 'A' and resid 91 through 107
      removed outlier: 3.949A  pdb=" N   LEU A  95 " --> pdb=" O   GLY A  91 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ILE A  96 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      Proline residue:  A  97  - end of helix
      removed outlier: 3.675A  pdb=" N   LEU A 100 " --> pdb=" O   ILE A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 121
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 134 through 165
      removed outlier: 3.660A  pdb=" N   GLY A 138 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   TYR A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 216
    Processing helix  chain 'A' and resid 220 through 224
    Processing helix  chain 'A' and resid 234 through 253
    Processing helix  chain 'A' and resid 257 through 282
      removed outlier: 3.868A  pdb=" N   LYS A 261 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
      Proline residue:  A 270  - end of helix
    Processing helix  chain 'A' and resid 286 through 296
      removed outlier: 3.605A  pdb=" N   GLY A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 305
      removed outlier: 3.985A  pdb=" N   LYS A 303 " --> pdb=" O   TYR A 300 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   ALA A 305 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 320
      removed outlier: 3.504A  pdb=" N   ALA A 311 " --> pdb=" O   VAL A 307 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLY A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 331
      removed outlier: 4.265A  pdb=" N   ILE A 327 " --> pdb=" O   PHE A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 373
      removed outlier: 3.509A  pdb=" N   ASP A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 380
      removed outlier: 3.835A  pdb=" N   VAL A 379 " --> pdb=" O   ASN A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 398
      Proline residue:  A 392  - end of helix
    Processing helix  chain 'A' and resid 400 through 435
      removed outlier: 3.520A  pdb=" N   TRP A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 441
      removed outlier: 3.659A  pdb=" N   HIS A 441 " --> pdb=" O   VAL A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 461
      removed outlier: 3.781A  pdb=" N   PHE A 445 " --> pdb=" O   HIS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 494
      removed outlier: 4.008A  pdb=" N   VAL A 468 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 509
      removed outlier: 3.889A  pdb=" N   PHE A 501 " --> pdb=" O   GLY A 497 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER A 502 " --> pdb=" O   VAL A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 523
    Processing helix  chain 'A' and resid 523 through 539
    Processing helix  chain 'A' and resid 551 through 579
      removed outlier: 4.038A  pdb=" N   ASN A 555 " --> pdb=" O   PRO A 551 " (cutoff:3.500A)
      Proline residue:  A 570  - end of helix
    Processing helix  chain 'A' and resid 583 through 593
    Processing helix  chain 'A' and resid 598 through 603
      removed outlier: 3.747A  pdb=" N   ALA A 602 " --> pdb=" O   HIS A 598 " (cutoff:3.500A)

    584 hydrogen bonds defined for protein.
    1734 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.43

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1350
        1.30 -     1.43: 2923
        1.43 -     1.55: 5887
        1.55 -     1.68: 16
        1.68 -     1.81: 62
  Bond restraints: 10238
  Sorted by residual:
  bond pdb=" O   41U A 701 "
       pdb=" C7  41U A 701 "
    ideal  model  delta    sigma   weight residual
    1.468  1.396  0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" O   41U B 701 "
       pdb=" C7  41U B 701 "
    ideal  model  delta    sigma   weight residual
    1.468  1.397  0.071 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" C1B PIO A 702 "
       pdb=" O3C PIO A 702 "
    ideal  model  delta    sigma   weight residual
    1.331  1.398 -0.067 2.00e-02 2.50e+03 1.11e+01
  bond pdb=" C1A PIO A 702 "
       pdb=" O2C PIO A 702 "
    ideal  model  delta    sigma   weight residual
    1.332  1.398 -0.066 2.00e-02 2.50e+03 1.08e+01
  bond pdb=" C1B PIO B 702 "
       pdb=" O3C PIO B 702 "
    ideal  model  delta    sigma   weight residual
    1.331  1.396 -0.065 2.00e-02 2.50e+03 1.06e+01
  ... (remaining 10233 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.73: 13971
        5.73 -    11.46: 89
       11.46 -    17.20: 8
       17.20 -    22.93: 2
       22.93 -    28.66: 2
  Bond angle restraints: 14072
  Sorted by residual:
  angle pdb=" C19 CLR B 717 "
        pdb=" C10 CLR B 717 "
        pdb=" C9  CLR B 717 "
      ideal   model   delta    sigma   weight residual
     111.86   83.20   28.66 3.00e+00 1.11e-01 9.13e+01
  angle pdb=" C1  CLR B 717 "
        pdb=" C10 CLR B 717 "
        pdb=" C19 CLR B 717 "
      ideal   model   delta    sigma   weight residual
     109.60   82.51   27.09 3.00e+00 1.11e-01 8.15e+01
  angle pdb=" C19 CLR B 717 "
        pdb=" C10 CLR B 717 "
        pdb=" C5  CLR B 717 "
      ideal   model   delta    sigma   weight residual
     108.37   86.33   22.04 3.00e+00 1.11e-01 5.40e+01
  angle pdb=" O23 A1LX7 A 711 "
        pdb=" P24 A1LX7 A 711 "
        pdb=" O26 A1LX7 A 711 "
      ideal   model   delta    sigma   weight residual
      97.27  115.32  -18.05 3.00e+00 1.11e-01 3.62e+01
  angle pdb=" O23 A1LX7 B 713 "
        pdb=" P24 A1LX7 B 713 "
        pdb=" O26 A1LX7 B 713 "
      ideal   model   delta    sigma   weight residual
      97.27  113.42  -16.15 3.00e+00 1.11e-01 2.90e+01
  ... (remaining 14067 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.08: 6490
       35.08 -    70.16: 280
       70.16 -   105.24: 19
      105.24 -   140.32: 10
      140.32 -   175.40: 9
  Dihedral angle restraints: 6808
    sinusoidal: 3544
      harmonic: 3264
  Sorted by residual:
  dihedral pdb=" C19 CLR B 717 "
           pdb=" C1  CLR B 717 "
           pdb=" C10 CLR B 717 "
           pdb=" C2  CLR B 717 "
      ideal   model   delta sinusoidal    sigma   weight residual
      68.88 -115.72 -175.40     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C11 CLR B 717 "
           pdb=" C10 CLR B 717 "
           pdb=" C9  CLR B 717 "
           pdb=" C19 CLR B 717 "
      ideal   model   delta sinusoidal    sigma   weight residual
      51.90 -109.43  161.33     1      3.00e+01 1.11e-03 2.08e+01
  dihedral pdb=" N   41U B 701 "
           pdb=" C14 41U B 701 "
           pdb=" C15 41U B 701 "
           pdb=" C7  41U B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     298.27  139.98  158.29     1      3.00e+01 1.11e-03 2.06e+01
  ... (remaining 6805 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.379: 1621
       0.379 -    0.759: 0
       0.759 -    1.138: 0
       1.138 -    1.518: 0
       1.518 -    1.897: 1
  Chirality restraints: 1622
  Sorted by residual:
  chirality pdb=" C10 CLR B 717 "
            pdb=" C1  CLR B 717 "
            pdb=" C5  CLR B 717 "
            pdb=" C9  CLR B 717 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -0.95   -1.90 2.00e-01 2.50e+01 9.00e+01
  chirality pdb=" C10 CLR B 708 "
            pdb=" C1  CLR B 708 "
            pdb=" C5  CLR B 708 "
            pdb=" C9  CLR B 708 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.54   -0.31 2.00e-01 2.50e+01 2.37e+00
  chirality pdb=" C20 CLR B 707 "
            pdb=" C17 CLR B 707 "
            pdb=" C21 CLR B 707 "
            pdb=" C22 CLR B 707 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.29    0.31 2.00e-01 2.50e+01 2.33e+00
  ... (remaining 1619 not shown)

  Planarity restraints: 1568
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 104 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" C   ILE B 104 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   ILE B 104 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ALA B 105 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 104 "   -0.011 2.00e-02 2.50e+03   2.13e-02 4.55e+00
        pdb=" C   ILE A 104 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ILE A 104 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ALA A 105 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 103 "   -0.010 2.00e-02 2.50e+03   2.03e-02 4.11e+00
        pdb=" C   ILE B 103 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ILE B 103 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ILE B 104 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1565 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.34: 29
        2.34 -     2.98: 5375
        2.98 -     3.62: 15412
        3.62 -     4.26: 24286
        4.26 -     4.90: 39959
  Nonbonded interactions: 85061
  Sorted by model distance:
  nonbonded pdb=" O   MET A 566 "
            pdb=" C27 CLR A 713 "
     model   vdw
     1.706 3.460
  nonbonded pdb=" O   ALA A  73 "
            pdb="NA    NA A 703 "
     model   vdw
     1.707 3.210
  nonbonded pdb=" O   ILE B 227 "
            pdb=" O1  CLR B 709 "
     model   vdw
     1.785 3.040
  nonbonded pdb=" OD1 ASP A 418 "
            pdb="NA    NA A 704 "
     model   vdw
     1.789 3.210
  nonbonded pdb=" O   MET B 566 "
            pdb=" C27 CLR B 718 "
     model   vdw
     1.900 3.460
  ... (remaining 85056 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 53 through 710 or resid 715 through 716))
  selection = (chain 'B' and (resid 53 through 710 or resid 715 through 716))
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.520
  Find NCS groups from input model:        0.190
  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:6.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6277
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      :  0.008   0.446  10242  Z= 0.595
  Angle     :  1.178  28.659  14072  Z= 0.465
  Chirality :  0.076   1.897   1622
  Planarity :  0.004   0.041   1568
  Dihedral  : 17.922 175.403   4732
  Min Nonbonded Distance : 1.706

Molprobity Statistics.
  All-atom Clashscore : 21.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  :  8.93 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.23), residues: 1126
  helix: -0.48 (0.17), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.60 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 512 
 TYR   0.013   0.001   TYR B 151 
 PHE   0.012   0.001   PHE B 362 
 TRP   0.006   0.001   TRP A 553 
 HIS   0.001   0.000   HIS B 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00605 /  0.31 (10238)
  covalent geometry    : angle       1.17765 /  0.46 (14072)
  hydrogen bonds       : bond        0.13886 /  9.26 (  584)
  hydrogen bonds       : angle       6.37306 /  4.48 ( 1734)
  Misc. bond           : bond        0.25651 / 12.72 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 281
  time to evaluate  : 0.351 
Fit side-chains
REVERT: B  126 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.7720 (p)
REVERT: B  153 ASN cc_start: 0.7171 (m110) cc_final: 0.6784 (m110)
REVERT: B  215 GLU cc_start: 0.7191 (pt0) cc_final: 0.6912 (mt-10)
REVERT: B  242 MET cc_start: 0.6503 (mtp) cc_final: 0.5750 (ptt)
REVERT: B  420 SER cc_start: 0.7516 (t) cc_final: 0.7256 (m)
REVERT: B  519 LEU cc_start: 0.8635 (mt) cc_final: 0.8383 (mm)
REVERT: B  609 PHE cc_start: 0.7464 (m-10) cc_final: 0.6104 (m-80)
REVERT: A  126 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.7640 (p)
REVERT: A  153 ASN cc_start: 0.7179 (m110) cc_final: 0.6806 (m110)
REVERT: A  215 GLU cc_start: 0.7193 (pt0) cc_final: 0.6930 (mt-10)
REVERT: A  242 MET cc_start: 0.6492 (mtp) cc_final: 0.5743 (ptt)
REVERT: A  391 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.7369 (m-80)
REVERT: A  420 SER cc_start: 0.7546 (t) cc_final: 0.7301 (m)
REVERT: A  609 PHE cc_start: 0.7471 (m-10) cc_final: 0.6122 (m-80)
  outliers start: 51
  outliers final: 10
  residues processed: 313
  average time/residue: 0.3374
  time to fit residues: 117.0658
Evaluate side-chains
  178 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 165
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  615 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.5784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.190070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.157224 restraints weight = 12222.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 2.38
r_work: 0.3788 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10242  Z= 0.195
  Angle     :  0.895  28.570  14072  Z= 0.383
  Chirality :  0.068   1.972   1622
  Planarity :  0.005   0.040   1568
  Dihedral  : 16.937 178.421   2836
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 16.60 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.24), residues: 1126
  helix:  0.60 (0.18), residues: 774
  sheet:  None (None), residues: 0
  loop : -1.19 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 216 
 TYR   0.019   0.002   TYR A 572 
 PHE   0.018   0.002   PHE A 110 
 TRP   0.017   0.002   TRP A 585 
 HIS   0.005   0.001   HIS A 613 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00434 /  0.19 (10238)
  covalent geometry    : angle       0.89491 /  0.38 (14072)
  hydrogen bonds       : bond        0.06050 /  3.93 (  584)
  hydrogen bonds       : angle       5.18946 /  3.64 ( 1734)
  Misc. bond           : bond        0.00114 /  0.06 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 178
  time to evaluate  : 0.292 
Fit side-chains
REVERT: B  122 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6492 (pt0)
REVERT: B  126 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8189 (p)
REVERT: B  215 GLU cc_start: 0.7646 (pt0) cc_final: 0.7423 (mt-10)
REVERT: B  280 HIS cc_start: 0.7200 (t-90) cc_final: 0.6588 (t70)
REVERT: B  337 ASN cc_start: 0.8175 (t0) cc_final: 0.7721 (t0)
REVERT: B  375 ASN cc_start: 0.7803 (m-40) cc_final: 0.7602 (m-40)
REVERT: B  439 LYS cc_start: 0.6594 (tttt) cc_final: 0.6391 (ttpt)
REVERT: A  122 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6409 (pt0)
REVERT: A  126 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8213 (p)
REVERT: A  280 HIS cc_start: 0.7157 (t-90) cc_final: 0.6541 (t70)
REVERT: A  337 ASN cc_start: 0.8117 (t0) cc_final: 0.7655 (t0)
REVERT: A  425 GLU cc_start: 0.8246 (tm-30) cc_final: 0.8028 (tm-30)
REVERT: A  436 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7216 (mm110)
REVERT: A  439 LYS cc_start: 0.6598 (tttt) cc_final: 0.6262 (ttpt)
REVERT: A  587 ARG cc_start: 0.5912 (OUTLIER) cc_final: 0.5243 (mpt-90)
  outliers start: 56
  outliers final: 24
  residues processed: 212
  average time/residue: 0.3164
  time to fit residues: 75.6775
Evaluate side-chains
  177 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  212 GLU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  502 SER
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  615 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 17 optimal weight:    0.5980
   chunk 74 optimal weight:    8.9990
   chunk 66 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 56 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    1.2384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.186113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.152142 restraints weight = 12151.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3857 rms_B_bonded: 2.39
r_work: 0.3735 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076  10242  Z= 0.168
  Angle     :  0.851  27.546  14072  Z= 0.362
  Chirality :  0.067   1.970   1622
  Planarity :  0.004   0.036   1568
  Dihedral  : 15.951 177.408   2828
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 18.49 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.25), residues: 1126
  helix:  1.07 (0.18), residues: 774
  sheet:  None (None), residues: 0
  loop : -1.02 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 301 
 TYR   0.014   0.002   TYR A  98 
 PHE   0.017   0.002   PHE B 362 
 TRP   0.020   0.001   TRP A 585 
 HIS   0.003   0.000   HIS A 613 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00383 /  0.17 (10238)
  covalent geometry    : angle       0.85127 /  0.36 (14072)
  hydrogen bonds       : bond        0.05882 /  3.76 (  584)
  hydrogen bonds       : angle       5.07747 /  3.56 ( 1734)
  Misc. bond           : bond        0.00346 /  0.16 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 151
  time to evaluate  : 0.378 
Fit side-chains
REVERT: B   81 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7951 (mmm160)
REVERT: B  122 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6640 (pt0)
REVERT: B  126 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8116 (p)
REVERT: B  207 PHE cc_start: 0.8267 (m-80) cc_final: 0.8051 (m-10)
REVERT: B  215 GLU cc_start: 0.7615 (pt0) cc_final: 0.7391 (mt-10)
REVERT: B  280 HIS cc_start: 0.7214 (t-90) cc_final: 0.6611 (t70)
REVERT: B  337 ASN cc_start: 0.8110 (t0) cc_final: 0.7677 (t0)
REVERT: B  382 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7247 (pt0)
REVERT: B  425 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7736 (tm-30)
REVERT: A   81 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7938 (mmm160)
REVERT: A  102 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7167 (tp)
REVERT: A  126 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8272 (p)
REVERT: A  207 PHE cc_start: 0.8211 (m-80) cc_final: 0.7990 (m-10)
REVERT: A  215 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7566 (mt-10)
REVERT: A  234 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7343 (mt0)
REVERT: A  280 HIS cc_start: 0.7191 (t-90) cc_final: 0.6589 (t70)
REVERT: A  337 ASN cc_start: 0.8083 (t0) cc_final: 0.7643 (t0)
REVERT: A  382 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7231 (pt0)
REVERT: A  425 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7742 (tm-30)
REVERT: A  587 ARG cc_start: 0.5814 (OUTLIER) cc_final: 0.5132 (mpt-90)
  outliers start: 45
  outliers final: 22
  residues processed: 181
  average time/residue: 0.3754
  time to fit residues: 75.8173
Evaluate side-chains
  170 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 139
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 ARG
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  176 CYS
Chi-restraints excluded: chain B residue  212 GLU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain A residue   81 ARG
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  234 GLN
Chi-restraints excluded: chain A residue  242 MET
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  615 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   chunk 102 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 76 optimal weight:    7.9990
   chunk 111 optimal weight:    8.9990
   chunk 88 optimal weight:    7.9990
   chunk 29 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    1.4984

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.181065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.146544 restraints weight = 12315.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 2.41
r_work: 0.3640 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.4055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082  10242  Z= 0.181
  Angle     :  0.859  27.724  14072  Z= 0.366
  Chirality :  0.067   1.973   1622
  Planarity :  0.004   0.040   1568
  Dihedral  : 15.620 178.591   2828
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 17.86 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.25), residues: 1126
  helix:  1.24 (0.19), residues: 770
  sheet:  None (None), residues: 0
  loop : -0.90 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  81 
 TYR   0.021   0.002   TYR A 249 
 PHE   0.018   0.002   PHE A 475 
 TRP   0.022   0.002   TRP A 585 
 HIS   0.007   0.001   HIS B 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00419 /  0.18 (10238)
  covalent geometry    : angle       0.85898 /  0.37 (14072)
  hydrogen bonds       : bond        0.06232 /  3.97 (  584)
  hydrogen bonds       : angle       5.14177 /  3.61 ( 1734)
  Misc. bond           : bond        0.00519 /  0.25 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 142
  time to evaluate  : 0.386 
Fit side-chains
REVERT: B   81 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8340 (mmm160)
REVERT: B  102 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7900 (tp)
REVERT: B  126 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8472 (p)
REVERT: B  180 TRP cc_start: 0.4926 (OUTLIER) cc_final: 0.4506 (t60)
REVERT: B  189 LYS cc_start: 0.6380 (mttt) cc_final: 0.5844 (mmtp)
REVERT: B  191 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6666 (pp)
REVERT: B  280 HIS cc_start: 0.7496 (t-90) cc_final: 0.6865 (t70)
REVERT: B  337 ASN cc_start: 0.8226 (t0) cc_final: 0.7868 (t0)
REVERT: B  425 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7998 (tm-30)
REVERT: B  587 ARG cc_start: 0.6242 (OUTLIER) cc_final: 0.5764 (mtt-85)
REVERT: A   81 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8335 (mmm160)
REVERT: A  102 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7869 (tp)
REVERT: A  126 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8616 (p)
REVERT: A  180 TRP cc_start: 0.4898 (OUTLIER) cc_final: 0.4451 (t60)
REVERT: A  189 LYS cc_start: 0.6316 (mttt) cc_final: 0.5810 (mmtp)
REVERT: A  215 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7806 (mt-10)
REVERT: A  234 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7730 (mt0)
REVERT: A  280 HIS cc_start: 0.7475 (t-90) cc_final: 0.6834 (t70)
REVERT: A  337 ASN cc_start: 0.8233 (t0) cc_final: 0.7815 (t0)
REVERT: A  425 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8058 (tm-30)
REVERT: A  584 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7382 (tp)
REVERT: A  587 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5397 (mpt-90)
REVERT: A  612 GLN cc_start: 0.7611 (mp-120) cc_final: 0.7178 (tm-30)
  outliers start: 57
  outliers final: 28
  residues processed: 184
  average time/residue: 0.3394
  time to fit residues: 69.8314
Evaluate side-chains
  174 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 133
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 ARG
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  176 CYS
Chi-restraints excluded: chain B residue  180 TRP
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  236 GLN
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  587 ARG
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain A residue   81 ARG
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  180 TRP
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  234 GLN
Chi-restraints excluded: chain A residue  242 MET
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  615 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 98 optimal weight:    0.6980
   chunk 28 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 99 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 102 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0270
   overall best weight:    0.6038

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.184289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.150163 restraints weight = 12222.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3814 rms_B_bonded: 2.39
r_work: 0.3694 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.4129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10242  Z= 0.139
  Angle     :  0.808  28.178  14072  Z= 0.341
  Chirality :  0.064   1.924   1622
  Planarity :  0.004   0.041   1568
  Dihedral  : 15.392 178.579   2824
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 18.80 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.25), residues: 1126
  helix:  1.33 (0.19), residues: 772
  sheet:  None (None), residues: 0
  loop : -0.73 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  81 
 TYR   0.017   0.001   TYR B 249 
 PHE   0.018   0.001   PHE B 362 
 TRP   0.025   0.001   TRP B 585 
 HIS   0.003   0.000   HIS A 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.14 (10238)
  covalent geometry    : angle       0.80800 /  0.34 (14072)
  hydrogen bonds       : bond        0.05618 /  3.57 (  584)
  hydrogen bonds       : angle       5.04078 /  3.55 ( 1734)
  Misc. bond           : bond        0.00469 /  0.23 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 141
  time to evaluate  : 0.324 
Fit side-chains
REVERT: B   81 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7931 (mmm160)
REVERT: B  102 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7455 (tp)
REVERT: B  168 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7475 (p)
REVERT: B  180 TRP cc_start: 0.4740 (OUTLIER) cc_final: 0.4236 (t60)
REVERT: B  189 LYS cc_start: 0.6247 (mttt) cc_final: 0.5686 (mmtp)
REVERT: B  191 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6571 (pp)
REVERT: B  207 PHE cc_start: 0.8271 (m-80) cc_final: 0.8061 (m-80)
REVERT: B  215 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7587 (mt-10)
REVERT: B  280 HIS cc_start: 0.7229 (t-90) cc_final: 0.6556 (t70)
REVERT: B  337 ASN cc_start: 0.8195 (t0) cc_final: 0.7867 (t0)
REVERT: B  425 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7688 (tm-30)
REVERT: B  587 ARG cc_start: 0.5890 (OUTLIER) cc_final: 0.5485 (mtt-85)
REVERT: B  612 GLN cc_start: 0.7567 (mp-120) cc_final: 0.7065 (tm-30)
REVERT: A   81 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7901 (mmm160)
REVERT: A  102 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7421 (tp)
REVERT: A  126 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8243 (p)
REVERT: A  180 TRP cc_start: 0.4743 (OUTLIER) cc_final: 0.4210 (t60)
REVERT: A  189 LYS cc_start: 0.6236 (mttt) cc_final: 0.5663 (mmtp)
REVERT: A  215 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7734 (mt-10)
REVERT: A  280 HIS cc_start: 0.7171 (t-90) cc_final: 0.6545 (t70)
REVERT: A  337 ASN cc_start: 0.8168 (t0) cc_final: 0.7838 (t0)
REVERT: A  425 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7727 (tm-30)
REVERT: A  587 ARG cc_start: 0.5766 (OUTLIER) cc_final: 0.5122 (mpt-90)
REVERT: A  610 GLN cc_start: 0.7896 (mp10) cc_final: 0.7369 (pm20)
REVERT: A  612 GLN cc_start: 0.7609 (mp-120) cc_final: 0.7097 (tm-30)
  outliers start: 51
  outliers final: 21
  residues processed: 178
  average time/residue: 0.3439
  time to fit residues: 68.4585
Evaluate side-chains
  171 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 139
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 ARG
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  180 TRP
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  236 GLN
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  498 VAL
Chi-restraints excluded: chain B residue  587 ARG
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain A residue   81 ARG
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  180 TRP
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  615 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 67 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 88 optimal weight:   10.0000
   chunk 111 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   chunk 75 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.7580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.184288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.150051 restraints weight = 12289.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3835 rms_B_bonded: 2.39
r_work: 0.3719 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.4271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10242  Z= 0.140
  Angle     :  0.816  30.395  14072  Z= 0.341
  Chirality :  0.063   1.919   1622
  Planarity :  0.004   0.041   1568
  Dihedral  : 15.148 179.539   2824
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 20.80 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.25), residues: 1126
  helix:  1.51 (0.19), residues: 758
  sheet:  None (None), residues: 0
  loop : -0.68 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  81 
 TYR   0.017   0.001   TYR B 249 
 PHE   0.016   0.001   PHE A 362 
 TRP   0.029   0.001   TRP B 585 
 HIS   0.001   0.000   HIS A 613 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.14 (10238)
  covalent geometry    : angle       0.81587 /  0.34 (14072)
  hydrogen bonds       : bond        0.05567 /  3.52 (  584)
  hydrogen bonds       : angle       4.99784 /  3.53 ( 1734)
  Misc. bond           : bond        0.00612 /  0.31 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 138
  time to evaluate  : 0.376 
Fit side-chains
REVERT: B  102 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7510 (tp)
REVERT: B  180 TRP cc_start: 0.4750 (OUTLIER) cc_final: 0.4219 (t60)
REVERT: B  191 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6535 (pp)
REVERT: B  280 HIS cc_start: 0.7162 (t-90) cc_final: 0.6489 (t70)
REVERT: B  337 ASN cc_start: 0.8121 (t0) cc_final: 0.7714 (t0)
REVERT: B  425 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7631 (tm-30)
REVERT: B  584 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7305 (tp)
REVERT: B  587 ARG cc_start: 0.5896 (OUTLIER) cc_final: 0.5510 (mtt-85)
REVERT: B  610 GLN cc_start: 0.7905 (mp10) cc_final: 0.7381 (pm20)
REVERT: B  612 GLN cc_start: 0.7583 (mp-120) cc_final: 0.7107 (tm-30)
REVERT: A  102 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7400 (tp)
REVERT: A  126 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8166 (p)
REVERT: A  180 TRP cc_start: 0.4745 (OUTLIER) cc_final: 0.4206 (t60)
REVERT: A  234 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7414 (mt0)
REVERT: A  280 HIS cc_start: 0.7128 (t-90) cc_final: 0.6449 (t70)
REVERT: A  337 ASN cc_start: 0.8095 (t0) cc_final: 0.7662 (t0)
REVERT: A  425 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7679 (tm-30)
REVERT: A  519 LEU cc_start: 0.8463 (mt) cc_final: 0.8190 (mm)
REVERT: A  584 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7262 (tp)
REVERT: A  587 ARG cc_start: 0.5873 (OUTLIER) cc_final: 0.5267 (mpt-90)
REVERT: A  612 GLN cc_start: 0.7638 (mp-120) cc_final: 0.7138 (tm-30)
  outliers start: 46
  outliers final: 26
  residues processed: 175
  average time/residue: 0.3061
  time to fit residues: 60.3277
Evaluate side-chains
  177 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 140
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 ARG
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  176 CYS
Chi-restraints excluded: chain B residue  180 TRP
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  236 GLN
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  587 ARG
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain A residue   81 ARG
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  180 TRP
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  234 GLN
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  615 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 100 optimal weight:    4.9990
   chunk 107 optimal weight:    0.6980
   chunk 105 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0770
   chunk 17 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 55 optimal weight:    8.9990
   chunk 54 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.6938

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.184588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.150446 restraints weight = 12206.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3843 rms_B_bonded: 2.39
r_work: 0.3723 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.4344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10242  Z= 0.138
  Angle     :  0.809  29.890  14072  Z= 0.337
  Chirality :  0.063   1.906   1622
  Planarity :  0.004   0.039   1568
  Dihedral  : 14.944 179.881   2824
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 21.74 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.25), residues: 1126
  helix:  1.50 (0.19), residues: 760
  sheet:  None (None), residues: 0
  loop : -0.62 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  56 
 TYR   0.021   0.001   TYR B 367 
 PHE   0.016   0.001   PHE B 362 
 TRP   0.031   0.001   TRP B 585 
 HIS   0.002   0.000   HIS A 613 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.14 (10238)
  covalent geometry    : angle       0.80872 /  0.34 (14072)
  hydrogen bonds       : bond        0.05477 /  3.46 (  584)
  hydrogen bonds       : angle       4.97436 /  3.51 ( 1734)
  Misc. bond           : bond        0.00486 /  0.24 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 139
  time to evaluate  : 0.331 
Fit side-chains
REVERT: B   81 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7870 (mmm160)
REVERT: B  102 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7432 (tp)
REVERT: B  122 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6857 (pt0)
REVERT: B  180 TRP cc_start: 0.4723 (OUTLIER) cc_final: 0.4161 (t60)
REVERT: B  191 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6507 (pp)
REVERT: B  242 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6076 (ptt)
REVERT: B  280 HIS cc_start: 0.7084 (t-90) cc_final: 0.6435 (t70)
REVERT: B  337 ASN cc_start: 0.8161 (t0) cc_final: 0.7719 (t0)
REVERT: B  425 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7576 (tm-30)
REVERT: B  587 ARG cc_start: 0.5818 (OUTLIER) cc_final: 0.5451 (mtt-85)
REVERT: B  612 GLN cc_start: 0.7628 (mp-120) cc_final: 0.7102 (tm-30)
REVERT: A   81 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7864 (mmm160)
REVERT: A  102 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7200 (tp)
REVERT: A  180 TRP cc_start: 0.4689 (OUTLIER) cc_final: 0.4124 (t60)
REVERT: A  280 HIS cc_start: 0.6998 (t-90) cc_final: 0.6337 (t70)
REVERT: A  337 ASN cc_start: 0.8143 (t0) cc_final: 0.7693 (t0)
REVERT: A  349 ILE cc_start: 0.7816 (mt) cc_final: 0.7567 (mm)
REVERT: A  425 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7629 (tm-30)
REVERT: A  519 LEU cc_start: 0.8417 (mt) cc_final: 0.8147 (mm)
REVERT: A  587 ARG cc_start: 0.5807 (OUTLIER) cc_final: 0.5230 (mpt-90)
REVERT: A  610 GLN cc_start: 0.7906 (mp10) cc_final: 0.7409 (pm20)
REVERT: A  612 GLN cc_start: 0.7650 (mp-120) cc_final: 0.7114 (tm-30)
  outliers start: 43
  outliers final: 25
  residues processed: 170
  average time/residue: 0.3108
  time to fit residues: 59.4399
Evaluate side-chains
  169 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 134
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 ARG
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  176 CYS
Chi-restraints excluded: chain B residue  180 TRP
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  236 GLN
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  498 VAL
Chi-restraints excluded: chain B residue  587 ARG
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain A residue   81 ARG
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  180 TRP
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  615 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 20 optimal weight:   10.0000
   chunk 69 optimal weight:    0.0170
   chunk 95 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 23 optimal weight:    8.9990
   chunk 51 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.7220

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.184382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.150308 restraints weight = 12177.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 2.38
r_work: 0.3708 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.4442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  10242  Z= 0.140
  Angle     :  0.767  28.125  14072  Z= 0.326
  Chirality :  0.063   1.904   1622
  Planarity :  0.004   0.039   1568
  Dihedral  : 14.765 179.372   2824
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 21.53 %
    Favored  : 73.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.25), residues: 1126
  helix:  1.50 (0.19), residues: 760
  sheet:  None (None), residues: 0
  loop : -0.61 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  56 
 TYR   0.017   0.001   TYR B 249 
 PHE   0.016   0.001   PHE A 362 
 TRP   0.034   0.002   TRP B 585 
 HIS   0.002   0.000   HIS A 613 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.14 (10238)
  covalent geometry    : angle       0.76731 /  0.33 (14072)
  hydrogen bonds       : bond        0.05485 /  3.47 (  584)
  hydrogen bonds       : angle       4.97361 /  3.51 ( 1734)
  Misc. bond           : bond        0.00359 /  0.17 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 141
  time to evaluate  : 0.207 
Fit side-chains
REVERT: B   81 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7979 (mmm160)
REVERT: B  102 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7509 (tp)
REVERT: B  180 TRP cc_start: 0.4729 (OUTLIER) cc_final: 0.4181 (t60)
REVERT: B  191 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6641 (pp)
REVERT: B  264 TRP cc_start: 0.6646 (t-100) cc_final: 0.6281 (m100)
REVERT: B  280 HIS cc_start: 0.7172 (t-90) cc_final: 0.6434 (t70)
REVERT: B  337 ASN cc_start: 0.8169 (t0) cc_final: 0.7900 (t0)
REVERT: B  425 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7693 (tm-30)
REVERT: B  566 MET cc_start: 0.5948 (mtp) cc_final: 0.5739 (mtt)
REVERT: B  587 ARG cc_start: 0.5913 (OUTLIER) cc_final: 0.5547 (mtt-85)
REVERT: B  612 GLN cc_start: 0.7680 (mp-120) cc_final: 0.7165 (tm-30)
REVERT: A   81 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7973 (mmm160)
REVERT: A  180 TRP cc_start: 0.4757 (OUTLIER) cc_final: 0.4175 (t60)
REVERT: A  280 HIS cc_start: 0.7082 (t-90) cc_final: 0.6425 (t70)
REVERT: A  337 ASN cc_start: 0.8171 (t0) cc_final: 0.7877 (t0)
REVERT: A  349 ILE cc_start: 0.7869 (mt) cc_final: 0.7612 (mm)
REVERT: A  425 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7716 (tm-30)
REVERT: A  519 LEU cc_start: 0.8474 (mt) cc_final: 0.8203 (mm)
REVERT: A  556 TRP cc_start: 0.5034 (m100) cc_final: 0.4661 (t-100)
REVERT: A  587 ARG cc_start: 0.5918 (OUTLIER) cc_final: 0.5350 (mpt-90)
REVERT: A  610 GLN cc_start: 0.8025 (mp10) cc_final: 0.7525 (pm20)
REVERT: A  612 GLN cc_start: 0.7700 (mp-120) cc_final: 0.7200 (tm-30)
  outliers start: 49
  outliers final: 27
  residues processed: 179
  average time/residue: 0.2851
  time to fit residues: 57.7334
Evaluate side-chains
  172 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 137
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 ARG
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  176 CYS
Chi-restraints excluded: chain B residue  180 TRP
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  236 GLN
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  498 VAL
Chi-restraints excluded: chain B residue  587 ARG
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain A residue   81 ARG
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  180 TRP
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  615 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 111 optimal weight:    6.9990
   chunk 75 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 56 optimal weight:   10.0000
   chunk 96 optimal weight:    0.7980
   chunk 93 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 94 optimal weight:    0.6980
   overall best weight:    2.0986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.174155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.138617 restraints weight = 12255.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 2.37
r_work: 0.3556 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.4872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.101  10242  Z= 0.217
  Angle     :  0.855  28.013  14072  Z= 0.375
  Chirality :  0.067   1.912   1622
  Planarity :  0.005   0.066   1568
  Dihedral  : 14.997 178.966   2824
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 21.43 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.25), residues: 1126
  helix:  1.15 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop : -0.79 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  81 
 TYR   0.022   0.002   TYR B 249 
 PHE   0.024   0.002   PHE B 409 
 TRP   0.037   0.002   TRP A 585 
 HIS   0.003   0.001   HIS A 372 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00508 /  0.22 (10238)
  covalent geometry    : angle       0.85463 /  0.37 (14072)
  hydrogen bonds       : bond        0.07087 /  4.51 (  584)
  hydrogen bonds       : angle       5.28662 /  3.70 ( 1734)
  Misc. bond           : bond        0.00739 /  0.33 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 136
  time to evaluate  : 0.362 
Fit side-chains
REVERT: B  102 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8056 (tp)
REVERT: B  180 TRP cc_start: 0.4860 (OUTLIER) cc_final: 0.4323 (t60)
REVERT: B  189 LYS cc_start: 0.6518 (mttt) cc_final: 0.5878 (mmtp)
REVERT: B  236 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6756 (pm20)
REVERT: B  264 TRP cc_start: 0.7104 (t-100) cc_final: 0.6875 (m100)
REVERT: B  280 HIS cc_start: 0.7199 (t-90) cc_final: 0.6670 (t70)
REVERT: B  337 ASN cc_start: 0.8309 (t0) cc_final: 0.7957 (t0)
REVERT: B  382 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7799 (pt0)
REVERT: B  398 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7359 (tt)
REVERT: B  425 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7972 (tm-30)
REVERT: B  584 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7311 (tp)
REVERT: B  587 ARG cc_start: 0.6161 (OUTLIER) cc_final: 0.5562 (mpt-90)
REVERT: B  612 GLN cc_start: 0.7741 (mp-120) cc_final: 0.7245 (tm-30)
REVERT: A  168 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7650 (p)
REVERT: A  180 TRP cc_start: 0.4853 (OUTLIER) cc_final: 0.4288 (t60)
REVERT: A  189 LYS cc_start: 0.6418 (mttt) cc_final: 0.5775 (mmtp)
REVERT: A  264 TRP cc_start: 0.6997 (t-100) cc_final: 0.6783 (m100)
REVERT: A  280 HIS cc_start: 0.7307 (t-90) cc_final: 0.6635 (t70)
REVERT: A  337 ASN cc_start: 0.8339 (t0) cc_final: 0.7985 (t0)
REVERT: A  382 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7764 (pt0)
REVERT: A  425 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7972 (tm-30)
REVERT: A  587 ARG cc_start: 0.6122 (OUTLIER) cc_final: 0.5457 (mpt-90)
REVERT: A  610 GLN cc_start: 0.8092 (mp10) cc_final: 0.7643 (pm20)
REVERT: A  612 GLN cc_start: 0.7822 (mp-120) cc_final: 0.7336 (tm-30)
  outliers start: 46
  outliers final: 21
  residues processed: 171
  average time/residue: 0.3037
  time to fit residues: 58.1436
Evaluate side-chains
  164 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 132
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 ARG
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  176 CYS
Chi-restraints excluded: chain B residue  180 TRP
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  236 GLN
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  587 ARG
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain A residue   81 ARG
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  180 TRP
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  615 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 87 optimal weight:    7.9990
   chunk 48 optimal weight:    0.6980
   chunk 24 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 90 optimal weight:    0.7980
   chunk 101 optimal weight:    1.9990
   chunk 107 optimal weight:    0.8980
   overall best weight:    0.8380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.179854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.144893 restraints weight = 12119.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 2.41
r_work: 0.3597 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.4840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  10242  Z= 0.153
  Angle     :  0.806  28.168  14072  Z= 0.345
  Chirality :  0.065   1.906   1622
  Planarity :  0.005   0.056   1568
  Dihedral  : 14.697 178.507   2820
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 23.21 %
    Favored  : 73.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.25), residues: 1126
  helix:  1.26 (0.19), residues: 770
  sheet:  None (None), residues: 0
  loop : -0.73 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  56 
 TYR   0.018   0.002   TYR B 367 
 PHE   0.018   0.001   PHE A 362 
 TRP   0.039   0.002   TRP A 585 
 HIS   0.003   0.000   HIS B 372 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.15 (10238)
  covalent geometry    : angle       0.80608 /  0.35 (14072)
  hydrogen bonds       : bond        0.06052 /  3.84 (  584)
  hydrogen bonds       : angle       5.11955 /  3.59 ( 1734)
  Misc. bond           : bond        0.00386 /  0.18 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 0.242 
Fit side-chains
REVERT: B  102 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8082 (tp)
REVERT: B  180 TRP cc_start: 0.4817 (OUTLIER) cc_final: 0.4262 (t60)
REVERT: B  189 LYS cc_start: 0.6395 (mttt) cc_final: 0.5756 (mmtp)
REVERT: B  264 TRP cc_start: 0.6973 (t-100) cc_final: 0.6675 (m100)
REVERT: B  280 HIS cc_start: 0.7222 (t-90) cc_final: 0.6728 (t70)
REVERT: B  337 ASN cc_start: 0.8279 (t0) cc_final: 0.8064 (t0)
REVERT: B  398 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7234 (tt)
REVERT: B  425 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8074 (tm-30)
REVERT: B  519 LEU cc_start: 0.8700 (mt) cc_final: 0.8478 (mm)
REVERT: B  566 MET cc_start: 0.6585 (mtp) cc_final: 0.6183 (mtt)
REVERT: B  584 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7348 (tp)
REVERT: B  587 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.5713 (mpt-90)
REVERT: B  612 GLN cc_start: 0.7720 (mp-120) cc_final: 0.7237 (tm-30)
REVERT: A  180 TRP cc_start: 0.4805 (OUTLIER) cc_final: 0.4264 (t60)
REVERT: A  189 LYS cc_start: 0.6421 (mttt) cc_final: 0.5790 (mmtp)
REVERT: A  264 TRP cc_start: 0.6840 (t-100) cc_final: 0.6532 (m100)
REVERT: A  280 HIS cc_start: 0.7301 (t-90) cc_final: 0.6621 (t70)
REVERT: A  337 ASN cc_start: 0.8272 (t0) cc_final: 0.8041 (t0)
REVERT: A  382 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7616 (pt0)
REVERT: A  425 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8075 (tm-30)
REVERT: A  519 LEU cc_start: 0.8701 (mt) cc_final: 0.8451 (mm)
REVERT: A  556 TRP cc_start: 0.5409 (m100) cc_final: 0.5017 (t-100)
REVERT: A  584 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7377 (tp)
REVERT: A  587 ARG cc_start: 0.6181 (OUTLIER) cc_final: 0.5517 (mpt-90)
REVERT: A  612 GLN cc_start: 0.7893 (mp-120) cc_final: 0.7396 (tm-30)
  outliers start: 31
  outliers final: 16
  residues processed: 157
  average time/residue: 0.2585
  time to fit residues: 45.9916
Evaluate side-chains
  157 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  176 CYS
Chi-restraints excluded: chain B residue  180 TRP
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  587 ARG
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  180 TRP
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  615 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 31 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 82 optimal weight:    0.4980
   chunk 18 optimal weight:    0.0870
   chunk 70 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0010
   chunk 13 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.5166

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.182616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.148687 restraints weight = 12241.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 2.37
r_work: 0.3694 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.4807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  10242  Z= 0.141
  Angle     :  0.799  28.130  14072  Z= 0.336
  Chirality :  0.064   1.899   1622
  Planarity :  0.004   0.048   1568
  Dihedral  : 14.327 178.552   2820
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.55 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 23.63 %
    Favored  : 73.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.25), residues: 1126
  helix:  1.47 (0.19), residues: 756
  sheet:  None (None), residues: 0
  loop : -0.76 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  56 
 TYR   0.020   0.002   TYR B 572 
 PHE   0.016   0.001   PHE B 362 
 TRP   0.039   0.001   TRP A 585 
 HIS   0.002   0.000   HIS A 613 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.14 (10238)
  covalent geometry    : angle       0.79927 /  0.34 (14072)
  hydrogen bonds       : bond        0.05562 /  3.52 (  584)
  hydrogen bonds       : angle       5.02411 /  3.54 ( 1734)
  Misc. bond           : bond        0.00381 /  0.18 (    4)
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 2435.09 seconds
wall clock time: 42 minutes 14.08 seconds (2534.08 seconds total)