Starting phenix.real_space_refine
on Fri Aug 22 20:45:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ffy_29070/08_2025/8ffy_29070.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ffy_29070/08_2025/8ffy_29070.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ffy_29070/08_2025/8ffy_29070.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ffy_29070/08_2025/8ffy_29070.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ffy_29070/08_2025/8ffy_29070.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ffy_29070/08_2025/8ffy_29070.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      61      5.49       5
     S      34      5.16       5
     C    4455      2.51       5
     N    1333      2.21       5
     O    1559      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7442
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2493
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2493
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 297}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 3590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 452, 3590
          Classifications: {'peptide': 452}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 424}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 1301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 1301
          Classifications: {'RNA': 61}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 29, 'rna3p_pyr': 25}
          Link IDs: {'rna2p': 6, 'rna3p': 54}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'SSA%rna3p': 1}
          Classifications: {'undetermined': 1}
          Modifications used: {'rna3p': 1}
    Chain: "B"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'SSA%rna3p': 1}
          Classifications: {'undetermined': 1}
          Modifications used: {'rna3p': 1}
  Time building chain proxies: 2.03, per 1000 atoms: 0.27
  Number of scatterers: 7442
  At special positions: 0
  Unit cell: (105.8, 80.5, 113.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     P      61     15.00
     O    1559      8.00
     N    1333      7.00
     C    4455      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 348.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1422

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 9 sheets defined
      40.9% alpha, 17.3% beta
      20 base pairs and 16 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 204 through 213
    Processing helix  chain 'A' and resid 220 through 225
    Processing helix  chain 'A' and resid 233 through 245
      removed outlier: 3.510A  pdb=" N   LEU A 237 " --> pdb=" O   GLY A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 254
    Processing helix  chain 'A' and resid 266 through 273
    Processing helix  chain 'A' and resid 299 through 307
      removed outlier: 4.054A  pdb=" N   GLY A 303 " --> pdb=" O   THR A 299 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   TYR A 307 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 383
    Processing helix  chain 'A' and resid 427 through 434
    Processing helix  chain 'A' and resid 457 through 468
    Processing helix  chain 'A' and resid 481 through 486
    Processing helix  chain 'B' and resid 42 through 51
    Processing helix  chain 'B' and resid 59 through 65
      removed outlier: 4.155A  pdb=" N   PHE B  63 " --> pdb=" O   ASP B  59 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ALA B  65 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 78
      removed outlier: 3.536A  pdb=" N   ALA B  70 " --> pdb=" O   CYS B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 121
    Processing helix  chain 'B' and resid 132 through 168
      Proline residue:  B 154  - end of helix
    Processing helix  chain 'B' and resid 204 through 212
    Processing helix  chain 'B' and resid 220 through 225
    Processing helix  chain 'B' and resid 233 through 252
    Processing helix  chain 'B' and resid 265 through 273
      removed outlier: 3.800A  pdb=" N   PHE B 269 " --> pdb=" O   ARG B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 309
      removed outlier: 3.780A  pdb=" N   GLY B 303 " --> pdb=" O   THR B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 383
    Processing helix  chain 'B' and resid 427 through 434
    Processing helix  chain 'B' and resid 457 through 468
    Processing helix  chain 'B' and resid 481 through 486
    Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 192
      removed outlier: 7.069A  pdb=" N   VAL A 388 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 5.059A  pdb=" N   MET A 191 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
      removed outlier: 7.342A  pdb=" N   PHE A 386 " --> pdb=" O   MET A 191 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   ARG A 402 " --> pdb=" O   SER A 423 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   SER A 423 " --> pdb=" O   ARG A 402 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   PHE A 404 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   SER A 421 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ILE A 406 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 9.974A  pdb=" N   VAL A 419 " --> pdb=" O   CYS A 455 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   CYS A 455 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   SER A 421 " --> pdb=" O   THR A 453 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   THR A 453 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   CYS A 425 " --> pdb=" O   THR A 449 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR A 449 " --> pdb=" O   CYS A 425 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   HIS A 448 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   VAL A 351 " --> pdb=" O   ALA A 454 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   ALA A 456 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 7.342A  pdb=" N   THR A 349 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 231 through 232
      removed outlier: 3.618A  pdb=" N   LEU A 231 " --> pdb=" O   THR B 259 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   SER B 325 " --> pdb=" O   MET B 258 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   THR B 349 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   ALA B 456 " --> pdb=" O   THR B 349 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   VAL B 351 " --> pdb=" O   ALA B 454 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   THR B 357 " --> pdb=" O   HIS B 448 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   HIS B 448 " --> pdb=" O   THR B 357 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   SER B 421 " --> pdb=" O   THR B 453 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   CYS B 455 " --> pdb=" O   VAL B 419 " (cutoff:3.500A)
      removed outlier: 9.504A  pdb=" N   VAL B 419 " --> pdb=" O   CYS B 455 " (cutoff:3.500A)
      removed outlier: 5.424A  pdb=" N   PHE B 416 " --> pdb=" O   MET B 410 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   MET B 410 " --> pdb=" O   PHE B 416 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   GLU B 418 " --> pdb=" O   ALA B 408 " (cutoff:3.500A)
      removed outlier: 5.995A  pdb=" N   ALA B 408 " --> pdb=" O   GLU B 418 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR B 420 " --> pdb=" O   ILE B 406 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ARG B 402 " --> pdb=" O   ASN B 424 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   HIS B 190 " --> pdb=" O   VAL B 388 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ASP B 390 " --> pdb=" O   VAL B 188 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   VAL B 188 " --> pdb=" O   ASP B 390 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259
    Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 265
    Processing sheet with id=AA5, first strand: chain 'A' and resid 444 through 446
      removed outlier: 5.642A  pdb=" N   HIS A 311 " --> pdb=" O   MET A 436 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   GLN A 438 " --> pdb=" O   HIS A 311 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   VAL A 313 " --> pdb=" O   GLN A 438 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 475 through 476
      removed outlier: 3.565A  pdb=" N   VAL A 475 " --> pdb=" O   ILE A 490 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 263 through 264
    Processing sheet with id=AA8, first strand: chain 'B' and resid 436 through 438
    Processing sheet with id=AA9, first strand: chain 'B' and resid 475 through 476

    288 hydrogen bonds defined for protein.
    834 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      50 hydrogen bonds
      92 hydrogen bond angles
      0 basepair planarities
      20 basepair parallelities
      16 stacking parallelities
  Total time for adding SS restraints: 0.92

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2124
        1.34 -     1.45: 1565
        1.45 -     1.57: 3860
        1.57 -     1.69: 128
        1.69 -     1.81: 56
  Bond restraints: 7733
  Sorted by residual:
  bond pdb=" C6  SSA A 601 "
       pdb=" N6  SSA A 601 "
    ideal  model  delta    sigma   weight residual
    1.333  1.524 -0.191 2.00e-02 2.50e+03 9.13e+01
  bond pdb=" C6  SSA B 601 "
       pdb=" N6  SSA B 601 "
    ideal  model  delta    sigma   weight residual
    1.333  1.524 -0.191 2.00e-02 2.50e+03 9.09e+01
  bond pdb=" O5' SSA B 601 "
       pdb=" S1  SSA B 601 "
    ideal  model  delta    sigma   weight residual
    1.581  1.735 -0.154 2.00e-02 2.50e+03 5.89e+01
  bond pdb=" O5' SSA A 601 "
       pdb=" S1  SSA A 601 "
    ideal  model  delta    sigma   weight residual
    1.581  1.733 -0.152 2.00e-02 2.50e+03 5.78e+01
  bond pdb=" O2S SSA A 601 "
       pdb=" S1  SSA A 601 "
    ideal  model  delta    sigma   weight residual
    1.435  1.586 -0.151 2.00e-02 2.50e+03 5.72e+01
  ... (remaining 7728 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.04: 10717
        4.04 -     8.08: 40
        8.08 -    12.11: 11
       12.11 -    16.15: 0
       16.15 -    20.19: 2
  Bond angle restraints: 10770
  Sorted by residual:
  angle pdb=" C3'   U C  72 "
        pdb=" O3'   U C  72 "
        pdb=" P     G C  73 "
      ideal   model   delta    sigma   weight residual
     120.20  109.80   10.40 1.50e+00 4.44e-01 4.80e+01
  angle pdb=" O1S SSA B 601 "
        pdb=" S1  SSA B 601 "
        pdb=" O2S SSA B 601 "
      ideal   model   delta    sigma   weight residual
     121.34  101.15   20.19 3.00e+00 1.11e-01 4.53e+01
  angle pdb=" O1S SSA A 601 "
        pdb=" S1  SSA A 601 "
        pdb=" O2S SSA A 601 "
      ideal   model   delta    sigma   weight residual
     121.34  101.15   20.19 3.00e+00 1.11e-01 4.53e+01
  angle pdb=" C3'   U C  71 "
        pdb=" O3'   U C  71 "
        pdb=" P     U C  72 "
      ideal   model   delta    sigma   weight residual
     120.20  111.06    9.14 1.50e+00 4.44e-01 3.71e+01
  angle pdb=" C   HIS A 226 "
        pdb=" N   ARG A 227 "
        pdb=" CA  ARG A 227 "
      ideal   model   delta    sigma   weight residual
     122.93  113.99    8.94 1.51e+00 4.39e-01 3.51e+01
  ... (remaining 10765 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.51: 4491
       32.51 -    65.02: 269
       65.02 -    97.54: 39
       97.54 -   130.05: 0
      130.05 -   162.56: 1
  Dihedral angle restraints: 4800
    sinusoidal: 2589
      harmonic: 2211
  Sorted by residual:
  dihedral pdb=" O4'   U C   9 "
           pdb=" C1'   U C   9 "
           pdb=" N1    U C   9 "
           pdb=" C2    U C   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00  162.24   69.76     1      1.70e+01 3.46e-03 2.17e+01
  dihedral pdb=" C5'   U C   9 "
           pdb=" C4'   U C   9 "
           pdb=" C3'   U C   9 "
           pdb=" O3'   U C   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  116.13   30.87     1      8.00e+00 1.56e-02 2.12e+01
  dihedral pdb=" C3'   U C   9 "
           pdb=" C4'   U C   9 "
           pdb=" O4'   U C   9 "
           pdb=" C1'   U C   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -2.00   24.84  -26.84     1      8.00e+00 1.56e-02 1.62e+01
  ... (remaining 4797 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 1187
       0.110 -    0.220: 40
       0.220 -    0.329: 2
       0.329 -    0.439: 3
       0.439 -    0.549: 3
  Chirality restraints: 1235
  Sorted by residual:
  chirality pdb=" CA  SSA A 601 "
            pdb=" CB  SSA A 601 "
            pdb=" C9  SSA A 601 "
            pdb=" N10 SSA A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -3.02    0.55 2.00e-01 2.50e+01 7.53e+00
  chirality pdb=" CA  SSA B 601 "
            pdb=" CB  SSA B 601 "
            pdb=" C9  SSA B 601 "
            pdb=" N10 SSA B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -3.01    0.55 2.00e-01 2.50e+01 7.43e+00
  chirality pdb=" P     U C  71 "
            pdb=" OP1   U C  71 "
            pdb=" OP2   U C  71 "
            pdb=" O5'   U C  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.88   -0.47 2.00e-01 2.50e+01 5.54e+00
  ... (remaining 1232 not shown)

  Planarity restraints: 1178
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 226 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.71e+00
        pdb=" C   HIS A 226 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   HIS A 226 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ARG A 227 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U C  71 "   -0.012 2.00e-02 2.50e+03   1.25e-02 3.50e+00
        pdb=" N1    U C  71 "    0.018 2.00e-02 2.50e+03
        pdb=" C2    U C  71 "    0.020 2.00e-02 2.50e+03
        pdb=" O2    U C  71 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3    U C  71 "   -0.011 2.00e-02 2.50e+03
        pdb=" C4    U C  71 "   -0.006 2.00e-02 2.50e+03
        pdb=" O4    U C  71 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    U C  71 "    0.012 2.00e-02 2.50e+03
        pdb=" C6    U C  71 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 457 "   -0.024 5.00e-02 4.00e+02   3.59e-02 2.06e+00
        pdb=" N   PRO B 458 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 458 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 458 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1175 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 207
        2.68 -     3.24: 6870
        3.24 -     3.79: 12206
        3.79 -     4.35: 15896
        4.35 -     4.90: 25105
  Nonbonded interactions: 60284
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 333 "
            pdb=" OP2   G C   1 "
     model   vdw
     2.125 3.040
  nonbonded pdb=" OE2 GLU A 352 "
            pdb=" OG  SSA A 601 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OE2 GLU B 352 "
            pdb=" OG  SSA B 601 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OE2 GLU A 352 "
            pdb=" N10 SSA A 601 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O   GLU B 418 "
            pdb=" NH1 ARG B 459 "
     model   vdw
     2.246 3.120
  ... (remaining 60279 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.500
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6029
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   0.191   7733  Z= 0.394
  Angle     :  0.732  20.191  10770  Z= 0.369
  Chirality :  0.051   0.549   1235
  Planarity :  0.003   0.036   1178
  Dihedral  : 19.198 162.558   3378
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.48 %
    Favored  : 87.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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 aren not related in a simple way.
  whole: -0.66 (0.29), residues: 760
  helix:  1.87 (0.30), residues: 285
  sheet: -1.42 (0.46), residues: 105
  loop : -2.11 (0.27), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 227 
 TYR   0.006   0.000   TYR B 230 
 PHE   0.007   0.000   PHE A 348 
 TRP   0.001   0.000   TRP B 409 
 HIS   0.002   0.000   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00775 ( 7733)
  covalent geometry    : angle       0.73188 (10770)
  hydrogen bonds       : bond        0.11885 (  338)
  hydrogen bonds       : angle       6.40850 (  926)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 ARG cc_start: 0.7346 (mtt180) cc_final: 0.7135 (mtm-85)
REVERT: A  218 LYS cc_start: 0.8400 (mtmt) cc_final: 0.7629 (mmmt)
REVERT: A  244 ASN cc_start: 0.7760 (m-40) cc_final: 0.7385 (m110)
REVERT: A  366 GLN cc_start: 0.7153 (pt0) cc_final: 0.6864 (tm-30)
REVERT: A  438 GLN cc_start: 0.8244 (tt0) cc_final: 0.8043 (tt0)
REVERT: A  451 ASN cc_start: 0.7540 (p0) cc_final: 0.6953 (p0)
REVERT: A  460 LEU cc_start: 0.7512 (mm) cc_final: 0.7277 (mm)
REVERT: A  466 GLU cc_start: 0.6244 (mt-10) cc_final: 0.6031 (mt-10)
REVERT: B  143 ARG cc_start: 0.6815 (mmm-85) cc_final: 0.5986 (ttm170)
REVERT: B  203 ARG cc_start: 0.7968 (mtt90) cc_final: 0.7094 (mtm-85)
REVERT: B  313 VAL cc_start: 0.8292 (t) cc_final: 0.8066 (m)
REVERT: B  332 GLU cc_start: 0.7442 (tp30) cc_final: 0.7221 (mm-30)
REVERT: B  451 ASN cc_start: 0.8027 (p0) cc_final: 0.7425 (p0)
REVERT: B  499 GLN cc_start: 0.7939 (tp40) cc_final: 0.7269 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.1113
  time to fit residues: 29.3925
Evaluate side-chains
  113 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0870
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7762

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
A 226 HIS
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.186264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.155010 restraints weight = 8751.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.157954 restraints weight = 4816.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.159860 restraints weight = 3233.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.161035 restraints weight = 2520.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.161627 restraints weight = 2174.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7733  Z= 0.124
  Angle     :  0.538   6.679  10770  Z= 0.262
  Chirality :  0.038   0.183   1235
  Planarity :  0.004   0.039   1178
  Dihedral  : 18.278 168.926   1891
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.18 %
    Favored  : 78.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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 aren not related in a simple way.
  whole:  0.20 (0.30), residues: 760
  helix:  2.44 (0.31), residues: 284
  sheet: -0.53 (0.49), residues: 105
  loop : -1.61 (0.28), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 459 
 TYR   0.010   0.001   TYR A 343 
 PHE   0.010   0.001   PHE A 371 
 TRP   0.007   0.002   TRP B 409 
 HIS   0.007   0.001   HIS A 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7733)
  covalent geometry    : angle       0.53819 (10770)
  hydrogen bonds       : bond        0.03760 (  338)
  hydrogen bonds       : angle       4.59781 (  926)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 MET cc_start: 0.7462 (mpp) cc_final: 0.7124 (mtt)
REVERT: B  143 ARG cc_start: 0.7907 (mmm-85) cc_final: 0.7011 (ttm170)
REVERT: B  451 ASN cc_start: 0.8334 (p0) cc_final: 0.8072 (p0)
  outliers start: 21
  outliers final: 13
  residues processed: 130
  average time/residue: 0.1125
  time to fit residues: 18.5597
Evaluate side-chains
  100 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  430 SER
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  499 GLN
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain B residue  487 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 61 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 78 optimal weight:   20.0000
   chunk 68 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0980
   chunk 37 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
A 346 HIS
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 495 HIS
B 244 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.175623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.143138 restraints weight = 8712.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.145990 restraints weight = 4874.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.147829 restraints weight = 3352.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.148774 restraints weight = 2659.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.149438 restraints weight = 2338.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.3835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7733  Z= 0.158
  Angle     :  0.580   6.620  10770  Z= 0.288
  Chirality :  0.039   0.180   1235
  Planarity :  0.005   0.045   1178
  Dihedral  : 17.719 168.636   1891
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 18.03 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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 aren not related in a simple way.
  whole:  0.20 (0.30), residues: 760
  helix:  2.01 (0.31), residues: 296
  sheet: -0.30 (0.47), residues: 102
  loop : -1.40 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 252 
 TYR   0.015   0.002   TYR B 401 
 PHE   0.020   0.002   PHE A 291 
 TRP   0.006   0.001   TRP A 409 
 HIS   0.006   0.001   HIS A 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 7733)
  covalent geometry    : angle       0.58023 (10770)
  hydrogen bonds       : bond        0.04039 (  338)
  hydrogen bonds       : angle       4.46782 (  926)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.8369 (m-40) cc_final: 0.7949 (m110)
REVERT: A  322 MET cc_start: 0.7496 (mpp) cc_final: 0.7210 (mtt)
REVERT: A  338 GLU cc_start: 0.7862 (pp20) cc_final: 0.7579 (pp20)
REVERT: B  143 ARG cc_start: 0.7961 (mmm-85) cc_final: 0.6963 (ttm170)
REVERT: B  309 MET cc_start: 0.8646 (ttt) cc_final: 0.8401 (ttt)
REVERT: B  466 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7271 (mt-10)
  outliers start: 30
  outliers final: 22
  residues processed: 117
  average time/residue: 0.0985
  time to fit residues: 15.0426
Evaluate side-chains
  105 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  430 SER
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  499 GLN
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  491 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 81 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.171651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.139147 restraints weight = 8898.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.141785 restraints weight = 5070.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.143476 restraints weight = 3538.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.144419 restraints weight = 2839.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.145011 restraints weight = 2498.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.4340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7733  Z= 0.185
  Angle     :  0.586   6.810  10770  Z= 0.292
  Chirality :  0.040   0.186   1235
  Planarity :  0.004   0.047   1178
  Dihedral  : 17.603 168.664   1891
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 19.72 %
    Favored  : 75.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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 aren not related in a simple way.
  whole:  0.05 (0.29), residues: 760
  helix:  1.92 (0.30), residues: 297
  sheet: -0.21 (0.48), residues: 100
  loop : -1.57 (0.28), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 252 
 TYR   0.018   0.002   TYR B  45 
 PHE   0.024   0.002   PHE B 308 
 TRP   0.006   0.001   TRP A 409 
 HIS   0.004   0.001   HIS A 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 7733)
  covalent geometry    : angle       0.58595 (10770)
  hydrogen bonds       : bond        0.04163 (  338)
  hydrogen bonds       : angle       4.56910 (  926)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 86
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.8264 (m-40) cc_final: 0.7799 (m110)
REVERT: A  283 ILE cc_start: 0.8949 (mt) cc_final: 0.8709 (mm)
REVERT: A  307 TYR cc_start: 0.8902 (t80) cc_final: 0.8628 (t80)
REVERT: A  338 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7585 (pp20)
REVERT: B  143 ARG cc_start: 0.7955 (mmm-85) cc_final: 0.7079 (ttm170)
REVERT: B  309 MET cc_start: 0.8600 (ttt) cc_final: 0.8399 (ttt)
REVERT: B  466 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7555 (mt-10)
  outliers start: 34
  outliers final: 25
  residues processed: 112
  average time/residue: 0.0864
  time to fit residues: 12.6692
Evaluate side-chains
  101 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  430 SER
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  499 GLN
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  190 HIS
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  487 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 33 optimal weight:    0.4980
   chunk 61 optimal weight:    0.0070
   chunk 56 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0270
   chunk 23 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.8458

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 375 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.174908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.142597 restraints weight = 8794.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.145321 restraints weight = 4926.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.147058 restraints weight = 3388.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.148035 restraints weight = 2690.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.148716 restraints weight = 2359.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.4449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7733  Z= 0.111
  Angle     :  0.508   6.569  10770  Z= 0.253
  Chirality :  0.036   0.161   1235
  Planarity :  0.004   0.030   1178
  Dihedral  : 17.400 167.999   1891
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 21.42 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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 aren not related in a simple way.
  whole:  0.45 (0.30), residues: 760
  helix:  2.44 (0.31), residues: 285
  sheet: -0.01 (0.48), residues: 102
  loop : -1.41 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 252 
 TYR   0.010   0.001   TYR B  45 
 PHE   0.013   0.001   PHE A 371 
 TRP   0.005   0.001   TRP A 409 
 HIS   0.002   0.001   HIS A 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 7733)
  covalent geometry    : angle       0.50846 (10770)
  hydrogen bonds       : bond        0.03347 (  338)
  hydrogen bonds       : angle       4.35910 (  926)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.8032 (m-40) cc_final: 0.7592 (m110)
REVERT: A  307 TYR cc_start: 0.8689 (t80) cc_final: 0.8439 (t80)
REVERT: A  338 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7589 (pp20)
REVERT: B  143 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7018 (ttm170)
REVERT: B  466 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7083 (mt-10)
  outliers start: 27
  outliers final: 21
  residues processed: 102
  average time/residue: 0.0833
  time to fit residues: 11.1817
Evaluate side-chains
  98 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  373 SER
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  498 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0980
   chunk 26 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 375 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.171000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.138019 restraints weight = 8746.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.140747 restraints weight = 4955.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.142487 restraints weight = 3445.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.143511 restraints weight = 2750.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.144126 restraints weight = 2406.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.4755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7733  Z= 0.159
  Angle     :  0.556   6.811  10770  Z= 0.279
  Chirality :  0.038   0.162   1235
  Planarity :  0.004   0.035   1178
  Dihedral  : 17.387 167.816   1891
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 19.41 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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 aren not related in a simple way.
  whole:  0.34 (0.30), residues: 760
  helix:  2.29 (0.30), residues: 291
  sheet:  0.14 (0.49), residues: 100
  loop : -1.56 (0.28), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 203 
 TYR   0.014   0.001   TYR B  45 
 PHE   0.015   0.001   PHE A 371 
 TRP   0.007   0.001   TRP A 409 
 HIS   0.004   0.001   HIS A 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 7733)
  covalent geometry    : angle       0.55639 (10770)
  hydrogen bonds       : bond        0.03838 (  338)
  hydrogen bonds       : angle       4.40440 (  926)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 80
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  244 ASN cc_start: 0.8159 (m-40) cc_final: 0.7647 (m110)
REVERT: A  307 TYR cc_start: 0.8847 (t80) cc_final: 0.8521 (t80)
REVERT: A  322 MET cc_start: 0.7678 (mmt) cc_final: 0.7419 (mtt)
REVERT: A  338 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7713 (pp20)
REVERT: B  143 ARG cc_start: 0.7935 (mmm-85) cc_final: 0.7029 (ttm170)
REVERT: B  168 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7075 (mp)
REVERT: B  309 MET cc_start: 0.8574 (ttt) cc_final: 0.8155 (ttp)
REVERT: B  432 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7112 (mtt-85)
REVERT: B  436 MET cc_start: 0.8309 (mmm) cc_final: 0.8054 (mmt)
REVERT: B  466 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7506 (mt-10)
  outliers start: 39
  outliers final: 33
  residues processed: 113
  average time/residue: 0.0987
  time to fit residues: 14.6749
Evaluate side-chains
  108 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 72
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  430 SER
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  499 GLN
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  321 ARG
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  432 ARG
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  498 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 39 optimal weight:   10.0000
   chunk 26 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.173329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.140918 restraints weight = 8726.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.143574 restraints weight = 4985.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.145239 restraints weight = 3460.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.146232 restraints weight = 2773.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.146762 restraints weight = 2432.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.4785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7733  Z= 0.113
  Angle     :  0.520   7.302  10770  Z= 0.263
  Chirality :  0.036   0.159   1235
  Planarity :  0.004   0.031   1178
  Dihedral  : 17.347 167.611   1891
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 20.80 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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 aren not related in a simple way.
  whole:  0.58 (0.30), residues: 760
  helix:  2.44 (0.31), residues: 291
  sheet:  0.43 (0.51), residues: 100
  loop : -1.42 (0.28), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 203 
 TYR   0.010   0.001   TYR B  45 
 PHE   0.012   0.001   PHE A 371 
 TRP   0.006   0.001   TRP A 409 
 HIS   0.002   0.001   HIS A 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7733)
  covalent geometry    : angle       0.51978 (10770)
  hydrogen bonds       : bond        0.03299 (  338)
  hydrogen bonds       : angle       4.30368 (  926)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 80
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.7968 (m-40) cc_final: 0.7510 (m110)
REVERT: A  264 LEU cc_start: 0.8934 (mm) cc_final: 0.8574 (mp)
REVERT: A  307 TYR cc_start: 0.8771 (t80) cc_final: 0.8559 (t80)
REVERT: A  338 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7747 (pp20)
REVERT: B  143 ARG cc_start: 0.7883 (mmm-85) cc_final: 0.6993 (ttm170)
REVERT: B  203 ARG cc_start: 0.7697 (mtm-85) cc_final: 0.7331 (mtm-85)
REVERT: B  258 MET cc_start: 0.7952 (ttm) cc_final: 0.7382 (mmm)
REVERT: B  309 MET cc_start: 0.8541 (ttt) cc_final: 0.8141 (ttp)
REVERT: B  432 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7146 (mtt-85)
REVERT: B  436 MET cc_start: 0.8294 (mmm) cc_final: 0.8013 (mmt)
  outliers start: 34
  outliers final: 26
  residues processed: 104
  average time/residue: 0.0994
  time to fit residues: 13.6496
Evaluate side-chains
  101 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 73
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  430 SER
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  499 GLN
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  321 ARG
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  432 ARG
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  498 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 34 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 78 optimal weight:   20.0000
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.166697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.133712 restraints weight = 8871.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.136375 restraints weight = 5018.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.138114 restraints weight = 3470.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.138985 restraints weight = 2764.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.139677 restraints weight = 2442.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.5096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   7733  Z= 0.230
  Angle     :  0.636   7.043  10770  Z= 0.321
  Chirality :  0.041   0.164   1235
  Planarity :  0.005   0.030   1178
  Dihedral  : 17.470 167.390   1891
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 20.34 %
    Favored  : 73.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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 aren not related in a simple way.
  whole:  0.20 (0.29), residues: 760
  helix:  2.09 (0.30), residues: 292
  sheet:  0.21 (0.49), residues: 100
  loop : -1.61 (0.28), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 203 
 TYR   0.017   0.002   TYR B  45 
 PHE   0.021   0.002   PHE A 354 
 TRP   0.007   0.002   TRP A 409 
 HIS   0.006   0.001   HIS A 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00546 ( 7733)
  covalent geometry    : angle       0.63561 (10770)
  hydrogen bonds       : bond        0.04306 (  338)
  hydrogen bonds       : angle       4.67895 (  926)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 73
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.8100 (m-40) cc_final: 0.7577 (m110)
REVERT: A  307 TYR cc_start: 0.8849 (t80) cc_final: 0.8559 (t80)
REVERT: A  322 MET cc_start: 0.7709 (mmt) cc_final: 0.7387 (mtt)
REVERT: A  338 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7706 (pp20)
REVERT: B  168 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7186 (mp)
REVERT: B  203 ARG cc_start: 0.7790 (mtm-85) cc_final: 0.7438 (mtm-85)
REVERT: B  432 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7203 (mtt-85)
REVERT: B  436 MET cc_start: 0.8359 (mmm) cc_final: 0.8045 (mmt)
REVERT: B  466 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7628 (mt-10)
  outliers start: 39
  outliers final: 29
  residues processed: 104
  average time/residue: 0.0992
  time to fit residues: 13.5978
Evaluate side-chains
  101 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 69
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  430 SER
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  499 GLN
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  321 ARG
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  432 ARG
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  491 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 77 optimal weight:    9.9990
   chunk 64 optimal weight:    0.6980
   chunk 73 optimal weight:    0.0000
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.172558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.140167 restraints weight = 8631.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.142946 restraints weight = 4804.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.144710 restraints weight = 3285.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.145600 restraints weight = 2603.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.146315 restraints weight = 2298.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.5041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7733  Z= 0.112
  Angle     :  0.535   7.616  10770  Z= 0.270
  Chirality :  0.037   0.159   1235
  Planarity :  0.004   0.031   1178
  Dihedral  : 17.414 167.332   1891
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 21.57 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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 aren not related in a simple way.
  whole:  0.56 (0.30), residues: 760
  helix:  2.29 (0.30), residues: 298
  sheet:  0.44 (0.50), residues: 100
  loop : -1.39 (0.29), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 252 
 TYR   0.011   0.001   TYR A 229 
 PHE   0.010   0.001   PHE A 354 
 TRP   0.006   0.001   TRP A 409 
 HIS   0.005   0.001   HIS A 495 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7733)
  covalent geometry    : angle       0.53528 (10770)
  hydrogen bonds       : bond        0.03323 (  338)
  hydrogen bonds       : angle       4.34452 (  926)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 77
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.7865 (m-40) cc_final: 0.7423 (m110)
REVERT: A  322 MET cc_start: 0.7955 (mmt) cc_final: 0.7410 (mtt)
REVERT: A  338 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7750 (pp20)
REVERT: B  203 ARG cc_start: 0.7719 (mtm-85) cc_final: 0.7374 (mtm-85)
REVERT: B  309 MET cc_start: 0.8553 (ttt) cc_final: 0.8187 (ttp)
REVERT: B  322 MET cc_start: 0.7488 (mtt) cc_final: 0.7136 (mtm)
REVERT: B  432 ARG cc_start: 0.7608 (mtt90) cc_final: 0.7085 (mtp85)
REVERT: B  436 MET cc_start: 0.8313 (mmm) cc_final: 0.8022 (mmt)
  outliers start: 32
  outliers final: 22
  residues processed: 97
  average time/residue: 0.0761
  time to fit residues: 10.1204
Evaluate side-chains
  95 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  328 CYS
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  499 GLN
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  321 ARG
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  491 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 78 optimal weight:   20.0000
   chunk 47 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.170555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.137953 restraints weight = 8744.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.140700 restraints weight = 4900.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.142450 restraints weight = 3359.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.143342 restraints weight = 2664.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.144094 restraints weight = 2353.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.5098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7733  Z= 0.144
  Angle     :  0.557   7.663  10770  Z= 0.281
  Chirality :  0.038   0.159   1235
  Planarity :  0.004   0.029   1178
  Dihedral  : 17.419 167.139   1891
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 22.65 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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 aren not related in a simple way.
  whole:  0.56 (0.30), residues: 760
  helix:  2.42 (0.30), residues: 292
  sheet:  0.39 (0.50), residues: 100
  loop : -1.42 (0.29), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 252 
 TYR   0.020   0.001   TYR B 153 
 PHE   0.016   0.002   PHE A 354 
 TRP   0.007   0.001   TRP A 409 
 HIS   0.004   0.001   HIS A 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7733)
  covalent geometry    : angle       0.55689 (10770)
  hydrogen bonds       : bond        0.03563 (  338)
  hydrogen bonds       : angle       4.41571 (  926)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 71
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.7978 (m-40) cc_final: 0.7551 (m110)
REVERT: A  338 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7779 (pp20)
REVERT: B  203 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.7347 (mtm-85)
REVERT: B  432 ARG cc_start: 0.7639 (mtt90) cc_final: 0.7266 (mtt-85)
REVERT: B  436 MET cc_start: 0.8329 (mmm) cc_final: 0.8029 (mmt)
  outliers start: 23
  outliers final: 21
  residues processed: 88
  average time/residue: 0.0841
  time to fit residues: 10.0182
Evaluate side-chains
  90 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  328 CYS
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  499 GLN
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  321 ARG
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  491 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 81 optimal weight:   10.0000
   chunk 9 optimal weight:    0.0030
   chunk 54 optimal weight:    0.0000
   chunk 0 optimal weight:    9.9990
   chunk 18 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 48 optimal weight:    6.9990
   chunk 79 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.7798

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.172831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.140402 restraints weight = 8708.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.143170 restraints weight = 4823.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.144944 restraints weight = 3300.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.145794 restraints weight = 2610.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.146579 restraints weight = 2307.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.5098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7733  Z= 0.114
  Angle     :  0.534   7.741  10770  Z= 0.271
  Chirality :  0.037   0.158   1235
  Planarity :  0.004   0.029   1178
  Dihedral  : 17.397 167.099   1891
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 22.80 %
    Favored  : 73.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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 aren not related in a simple way.
  whole:  0.69 (0.30), residues: 760
  helix:  2.52 (0.30), residues: 292
  sheet:  0.53 (0.50), residues: 102
  loop : -1.38 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 252 
 TYR   0.011   0.001   TYR A 229 
 PHE   0.011   0.001   PHE A 354 
 TRP   0.007   0.001   TRP A 409 
 HIS   0.002   0.001   HIS B 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7733)
  covalent geometry    : angle       0.53402 (10770)
  hydrogen bonds       : bond        0.03274 (  338)
  hydrogen bonds       : angle       4.34208 (  926)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1172.09 seconds
wall clock time: 20 minutes 55.56 seconds (1255.56 seconds total)