Starting phenix.real_space_refine
on Tue Mar  3 17:36:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u2b_26311/03_2026/7u2b_26311.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u2b_26311/03_2026/7u2b_26311.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u2b_26311/03_2026/7u2b_26311.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u2b_26311/03_2026/7u2b_26311.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u2b_26311/03_2026/7u2b_26311.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u2b_26311/03_2026/7u2b_26311.cif"
  }
  resolution = 4.1
  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=   0.003
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      53      5.49       5
     S      34      5.16       5
     C    4408      2.51       5
     N    1316      2.21       5
     O    1505      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7316
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 1111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 1111
          Classifications: {'RNA': 53}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 21, 'rna3p_pyr': 26}
          Link IDs: {'rna2p': 5, 'rna3p': 47}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'  A%rna2p_pur:plan': 1, '  A%rna2p_pur:plan2': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "A"
      Number of atoms: 2500
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 2500
          Classifications: {'peptide': 319}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 298}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 3647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 461, 3647
          Classifications: {'peptide': 461}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 433}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
    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: 1.88, per 1000 atoms: 0.26
  Number of scatterers: 7316
  At special positions: 0
  Unit cell: (70.15, 95.45, 126.5, 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      53     15.00
     O    1505      8.00
     N    1316      7.00
     C    4408      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: 0.49
  Conformation dependent library (CDL) restraints added in 251.7 milliseconds
  

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1438

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 7 sheets defined
      42.8% alpha, 16.0% beta
      8 base pairs and 22 stacking pairs defined.
    Time for finding SS restraints: 0.85
  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 253
      removed outlier: 3.507A  pdb=" N   ARG A 253 " --> pdb=" O   LYS A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 272
      removed outlier: 3.579A  pdb=" N   PHE A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 308
      removed outlier: 4.020A  pdb=" N   GLY A 303 " --> pdb=" O   THR A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 383
      removed outlier: 3.512A  pdb=" N   SER A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 434
    Processing helix  chain 'A' and resid 457 through 468
    Processing helix  chain 'A' and resid 478 through 486
      removed outlier: 4.254A  pdb=" N   SER A 483 " --> pdb=" O   PRO A 479 " (cutoff:3.500A)
      removed outlier: 5.050A  pdb=" N   TYR A 484 " --> pdb=" O   ALA A 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 51
      removed outlier: 3.659A  pdb=" N   GLU B  46 " --> pdb=" O   ASN B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 64
      removed outlier: 3.595A  pdb=" N   PHE B  63 " --> pdb=" O   ASP B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 78
      removed outlier: 3.613A  pdb=" N   ALA B  70 " --> pdb=" O   CYS B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 84
      No H-bonds generated for 'chain 'B' and resid 82 through 84'
    Processing helix  chain 'B' and resid 85 through 123
      removed outlier: 3.610A  pdb=" N   ILE B  89 " --> pdb=" O   ASP B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 132
    Processing helix  chain 'B' and resid 132 through 169
      removed outlier: 3.592A  pdb=" N   GLN B 136 " --> pdb=" O   ASP B 132 " (cutoff:3.500A)
      Proline residue:  B 154  - end of helix
      removed outlier: 4.311A  pdb=" N   LYS B 169 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 213
    Processing helix  chain 'B' and resid 220 through 225
    Processing helix  chain 'B' and resid 233 through 253
    Processing helix  chain 'B' and resid 265 through 273
      removed outlier: 3.619A  pdb=" N   PHE B 269 " --> pdb=" O   ARG B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 309
      removed outlier: 3.731A  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
      removed outlier: 3.657A  pdb=" N   ARG B 431 " --> pdb=" O   ASP B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 469
    Processing helix  chain 'B' and resid 478 through 486
      removed outlier: 4.076A  pdb=" N   SER B 483 " --> pdb=" O   PRO B 479 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   TYR B 484 " --> pdb=" O   ALA B 480 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 192
      removed outlier: 6.402A  pdb=" N   VAL A 188 " --> pdb=" O   ASP A 390 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   ASP A 390 " --> pdb=" O   VAL A 188 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ARG A 402 " --> pdb=" O   SER A 423 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   SER A 423 " --> pdb=" O   ARG A 402 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   PHE A 404 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   SER A 421 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ILE A 406 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 9.763A  pdb=" N   VAL A 419 " --> pdb=" O   CYS A 455 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   CYS A 455 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   SER A 421 " --> pdb=" O   THR A 453 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   THR A 453 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ASN A 451 " --> pdb=" O   SER A 423 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   THR A 449 " --> pdb=" O   CYS A 425 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   HIS A 448 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   VAL A 351 " --> pdb=" O   ALA A 454 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   ALA A 456 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   THR A 349 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LYS A 350 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   SER A 326 " --> pdb=" O   LYS A 350 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   SER A 325 " --> pdb=" O   MET A 258 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU B 231 " --> pdb=" O   THR A 259 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   TYR B 230 " --> pdb=" O   ARG B 216 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 216
      removed outlier: 3.702A  pdb=" N   TYR A 230 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU A 231 " --> pdb=" O   THR B 259 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   SER B 325 " --> pdb=" O   MET B 258 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   SER B 326 " --> pdb=" O   LYS B 350 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS B 350 " --> pdb=" O   SER B 326 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   THR B 349 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   ALA B 456 " --> pdb=" O   THR B 349 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   VAL B 351 " --> pdb=" O   ALA B 454 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   SER B 421 " --> pdb=" O   THR B 453 " (cutoff:3.500A)
      removed outlier: 5.621A  pdb=" N   CYS B 455 " --> pdb=" O   VAL B 419 " (cutoff:3.500A)
      removed outlier: 9.147A  pdb=" N   VAL B 419 " --> pdb=" O   CYS B 455 " (cutoff:3.500A)
      removed outlier: 5.646A  pdb=" N   GLU B 418 " --> pdb=" O   ALA B 408 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ALA B 408 " --> pdb=" O   GLU B 418 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   ASP B 390 " --> pdb=" O   VAL B 188 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   VAL B 188 " --> pdb=" O   ASP B 390 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 264
    Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 312
    Processing sheet with id=AA5, first strand: chain 'A' and resid 437 through 438
    Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 500
      removed outlier: 3.539A  pdb=" N   GLN A 499 " --> pdb=" O   THR B 312 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   HIS B 311 " --> pdb=" O   MET B 436 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   GLN B 438 " --> pdb=" O   HIS B 311 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   VAL B 313 " --> pdb=" O   GLN B 438 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 263 through 264

    291 hydrogen bonds defined for protein.
    843 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      20 hydrogen bonds
      40 hydrogen bond angles
      0 basepair planarities
      8 basepair parallelities
      22 stacking parallelities
  Total time for adding SS restraints: 1.05

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2090
        1.33 -     1.45: 1486
        1.45 -     1.57: 3841
        1.57 -     1.69: 112
        1.69 -     1.81: 56
  Bond restraints: 7585
  Sorted by residual:
  bond pdb=" C6  SSA B 601 "
       pdb=" N6  SSA B 601 "
    ideal  model  delta    sigma   weight residual
    1.333  1.520 -0.187 2.00e-02 2.50e+03 8.77e+01
  bond pdb=" C6  SSA A 601 "
       pdb=" N6  SSA A 601 "
    ideal  model  delta    sigma   weight residual
    1.333  1.519 -0.186 2.00e-02 2.50e+03 8.63e+01
  bond pdb=" O5' SSA B 601 "
       pdb=" S1  SSA B 601 "
    ideal  model  delta    sigma   weight residual
    1.581  1.731 -0.150 2.00e-02 2.50e+03 5.62e+01
  bond pdb=" O2S SSA B 601 "
       pdb=" S1  SSA B 601 "
    ideal  model  delta    sigma   weight residual
    1.435  1.584 -0.149 2.00e-02 2.50e+03 5.58e+01
  bond pdb=" O2S SSA A 601 "
       pdb=" S1  SSA A 601 "
    ideal  model  delta    sigma   weight residual
    1.435  1.581 -0.146 2.00e-02 2.50e+03 5.32e+01
  ... (remaining 7580 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.02: 10455
        4.02 -     8.04: 61
        8.04 -    12.06: 7
       12.06 -    16.08: 0
       16.08 -    20.10: 2
  Bond angle restraints: 10525
  Sorted by residual:
  angle pdb=" O1S SSA B 601 "
        pdb=" S1  SSA B 601 "
        pdb=" O2S SSA B 601 "
      ideal   model   delta    sigma   weight residual
     121.34  101.24   20.10 3.00e+00 1.11e-01 4.49e+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  102.90   18.44 3.00e+00 1.11e-01 3.78e+01
  angle pdb=" N   THR B 426 "
        pdb=" CA  THR B 426 "
        pdb=" C   THR B 426 "
      ideal   model   delta    sigma   weight residual
     111.37  117.25   -5.88 1.64e+00 3.72e-01 1.28e+01
  angle pdb=" N1  SSA B 601 "
        pdb=" C6  SSA B 601 "
        pdb=" N6  SSA B 601 "
      ideal   model   delta    sigma   weight residual
     119.38  108.72   10.66 3.00e+00 1.11e-01 1.26e+01
  angle pdb=" N   VAL B 223 "
        pdb=" CA  VAL B 223 "
        pdb=" C   VAL B 223 "
      ideal   model   delta    sigma   weight residual
     109.34  116.64   -7.30 2.08e+00 2.31e-01 1.23e+01
  ... (remaining 10520 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.30: 4362
       30.30 -    60.61: 225
       60.61 -    90.91: 66
       90.91 -   121.22: 1
      121.22 -   151.52: 3
  Dihedral angle restraints: 4657
    sinusoidal: 2419
      harmonic: 2238
  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
    -160.00   -8.48 -151.52     1      1.50e+01 4.44e-03 8.02e+01
  dihedral pdb=" O4'   C C   8 "
           pdb=" C1'   C C   8 "
           pdb=" N1    C C   8 "
           pdb=" C2    C C   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -10.64 -149.36     1      1.50e+01 4.44e-03 7.94e+01
  dihedral pdb=" O4'   C C  10 "
           pdb=" C1'   C C  10 "
           pdb=" N1    C C  10 "
           pdb=" C2    C C  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -16.50 -143.50     1      1.50e+01 4.44e-03 7.70e+01
  ... (remaining 4654 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 1164
       0.113 -    0.226: 36
       0.226 -    0.339: 2
       0.339 -    0.453: 0
       0.453 -    0.566: 2
  Chirality restraints: 1204
  Sorted by residual:
  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   -3.03    0.57 2.00e-01 2.50e+01 8.00e+00
  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    0.56 2.00e-01 2.50e+01 7.75e+00
  chirality pdb=" C3' SSA B 601 "
            pdb=" C2' SSA B 601 "
            pdb=" C4' SSA B 601 "
            pdb=" O3' SSA B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.49   -0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 1201 not shown)

  Planarity restraints: 1184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  45 "   -0.030 2.00e-02 2.50e+03   1.43e-02 5.64e+00
        pdb=" N9    A C  45 "    0.034 2.00e-02 2.50e+03
        pdb=" C8    A C  45 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    A C  45 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    A C  45 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A C  45 "   -0.005 2.00e-02 2.50e+03
        pdb=" N6    A C  45 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A C  45 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    A C  45 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A C  45 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A C  45 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 457 "   -0.029 5.00e-02 4.00e+02   4.28e-02 2.93e+00
        pdb=" N   PRO B 458 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 458 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 458 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 457 "    0.026 5.00e-02 4.00e+02   3.92e-02 2.46e+00
        pdb=" N   PRO A 458 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 458 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 458 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1181 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 43
        2.53 -     3.12: 5593
        3.12 -     3.71: 11574
        3.71 -     4.31: 15512
        4.31 -     4.90: 25209
  Nonbonded interactions: 57931
  Sorted by model distance:
  nonbonded pdb=" O2    C C   8 "
            pdb=" O2'   C C  33 "
     model   vdw
     1.936 3.040
  nonbonded pdb=" O2'   A C  45 "
            pdb=" O5'   A C  46 "
     model   vdw
     2.011 3.040
  nonbonded pdb=" OG1 THR A 453 "
            pdb=" OG  SSA A 601 "
     model   vdw
     2.032 3.040
  nonbonded pdb=" OG  SER A 224 "
            pdb=" OG  SER A 228 "
     model   vdw
     2.059 3.040
  nonbonded pdb=" OH  TYR A 329 "
            pdb=" OH  TYR B 329 "
     model   vdw
     2.099 3.040
  ... (remaining 57926 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:             0.550
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.170
  Find NCS groups from input model:        0.030
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6827
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      :  0.009   0.187   7585  Z= 0.456
  Angle     :  0.973  20.098  10525  Z= 0.522
  Chirality :  0.053   0.566   1204
  Planarity :  0.004   0.043   1184
  Dihedral  : 18.721 151.523   3219
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 12.52 %
    Favored  : 87.33 %
  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 are not related in a simple way.
  whole:  2.20 (0.29), residues: 772
  helix:  3.12 (0.28), residues: 288
  sheet:  0.78 (0.48), residues: 105
  loop :  0.40 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 432 
 TYR   0.014   0.002   TYR B 230 
 PHE   0.022   0.002   PHE B 404 
 TRP   0.015   0.003   TRP A 409 
 HIS   0.005   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00940 ( 7585)
  covalent geometry    : angle       0.97297 (10525)
  hydrogen bonds       : bond        0.15712 (  311)
  hydrogen bonds       : angle       6.87084 (  883)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 236
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 MET cc_start: 0.8547 (mtt) cc_final: 0.8124 (mmm)
REVERT: A  205 HIS cc_start: 0.8447 (p-80) cc_final: 0.8172 (p-80)
REVERT: A  211 LYS cc_start: 0.8708 (mtmp) cc_final: 0.8225 (tmtt)
REVERT: A  218 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7820 (mmmm)
REVERT: A  258 MET cc_start: 0.8254 (ttm) cc_final: 0.7646 (mtp)
REVERT: A  425 CYS cc_start: 0.8546 (m) cc_final: 0.8241 (t)
REVERT: A  451 ASN cc_start: 0.8559 (p0) cc_final: 0.7950 (p0)
REVERT: A  468 ASN cc_start: 0.8250 (m-40) cc_final: 0.7814 (m-40)
REVERT: A  477 VAL cc_start: 0.8386 (t) cc_final: 0.8156 (p)
REVERT: A  482 GLN cc_start: 0.8187 (mt0) cc_final: 0.7896 (pp30)
REVERT: B  153 TYR cc_start: 0.8243 (m-80) cc_final: 0.7590 (m-80)
REVERT: B  248 ASN cc_start: 0.7962 (m-40) cc_final: 0.7322 (t0)
REVERT: B  252 ARG cc_start: 0.8901 (tpp-160) cc_final: 0.8546 (ttp-110)
REVERT: B  256 THR cc_start: 0.7597 (m) cc_final: 0.6740 (p)
REVERT: B  326 SER cc_start: 0.8804 (p) cc_final: 0.8521 (t)
REVERT: B  366 GLN cc_start: 0.6857 (tt0) cc_final: 0.6395 (tm-30)
REVERT: B  437 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.6557 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 237
  average time/residue: 0.0990
  time to fit residues: 30.3059
Evaluate side-chains
  114 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:   20.0000
   chunk 74 optimal weight:    6.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN
A 448 HIS
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 495 HIS
B 244 ASN
B 438 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.131266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.103944 restraints weight = 12049.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.106512 restraints weight = 6775.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.108211 restraints weight = 4451.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.109280 restraints weight = 3333.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.110054 restraints weight = 2764.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7585  Z= 0.199
  Angle     :  0.673   7.010  10525  Z= 0.337
  Chirality :  0.041   0.169   1204
  Planarity :  0.005   0.074   1184
  Dihedral  : 18.565 163.231   1721
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.12 %
    Favored  : 95.73 %
  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 are not related in a simple way.
  whole:  1.82 (0.29), residues: 772
  helix:  2.28 (0.29), residues: 303
  sheet:  1.26 (0.49), residues: 97
  loop :  0.37 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 219 
 TYR   0.035   0.003   TYR B  47 
 PHE   0.024   0.002   PHE B 308 
 TRP   0.009   0.002   TRP B  93 
 HIS   0.008   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 7585)
  covalent geometry    : angle       0.67336 (10525)
  hydrogen bonds       : bond        0.05250 (  311)
  hydrogen bonds       : angle       5.31685 (  883)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 160
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8315 (tmtt)
REVERT: A  258 MET cc_start: 0.7328 (ttm) cc_final: 0.7061 (mtp)
REVERT: A  405 ASP cc_start: 0.7831 (m-30) cc_final: 0.7622 (m-30)
REVERT: A  429 GLN cc_start: 0.8487 (mm-40) cc_final: 0.7968 (mp10)
REVERT: A  482 GLN cc_start: 0.8311 (mt0) cc_final: 0.7990 (tm-30)
REVERT: B  130 GLN cc_start: 0.8371 (mt0) cc_final: 0.7741 (tm-30)
REVERT: B  153 TYR cc_start: 0.8690 (m-80) cc_final: 0.8378 (m-80)
REVERT: B  248 ASN cc_start: 0.8088 (m-40) cc_final: 0.7737 (t0)
REVERT: B  326 SER cc_start: 0.8924 (p) cc_final: 0.8397 (t)
REVERT: B  353 MET cc_start: 0.7695 (mtp) cc_final: 0.7216 (mtp)
REVERT: B  366 GLN cc_start: 0.7779 (tt0) cc_final: 0.7380 (tm-30)
REVERT: B  395 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7257 (mm-30)
REVERT: B  401 TYR cc_start: 0.8914 (t80) cc_final: 0.8683 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 161
  average time/residue: 0.0903
  time to fit residues: 19.0813
Evaluate side-chains
  108 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 81 optimal weight:    9.9990
   chunk 41 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 30 optimal weight:    9.9990
   chunk 66 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 239 GLN
A 347 HIS
A 451 ASN
A 469 GLN
B 244 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.131208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.104778 restraints weight = 11740.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107326 restraints weight = 6574.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.109019 restraints weight = 4322.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.110076 restraints weight = 3223.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.110851 restraints weight = 2667.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.3480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7585  Z= 0.126
  Angle     :  0.586   6.597  10525  Z= 0.292
  Chirality :  0.039   0.148   1204
  Planarity :  0.004   0.033   1184
  Dihedral  : 18.043 169.870   1721
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.90 %
    Favored  : 96.95 %
  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 are not related in a simple way.
  whole:  1.87 (0.30), residues: 772
  helix:  2.23 (0.30), residues: 302
  sheet:  1.22 (0.47), residues: 103
  loop :  0.51 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 227 
 TYR   0.013   0.002   TYR A 401 
 PHE   0.015   0.001   PHE A 247 
 TRP   0.005   0.001   TRP B  93 
 HIS   0.006   0.001   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7585)
  covalent geometry    : angle       0.58566 (10525)
  hydrogen bonds       : bond        0.04237 (  311)
  hydrogen bonds       : angle       4.94295 (  883)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 160
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8394 (tmtt)
REVERT: A  258 MET cc_start: 0.7328 (ttm) cc_final: 0.7026 (mtp)
REVERT: A  405 ASP cc_start: 0.7728 (m-30) cc_final: 0.7477 (m-30)
REVERT: A  429 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8042 (mp10)
REVERT: B  130 GLN cc_start: 0.8312 (mt0) cc_final: 0.7738 (tm-30)
REVERT: B  153 TYR cc_start: 0.8572 (m-80) cc_final: 0.8307 (m-80)
REVERT: B  326 SER cc_start: 0.8967 (p) cc_final: 0.8387 (t)
REVERT: B  353 MET cc_start: 0.7544 (mtp) cc_final: 0.7002 (mtt)
REVERT: B  366 GLN cc_start: 0.7690 (tt0) cc_final: 0.7295 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 160
  average time/residue: 0.0765
  time to fit residues: 16.8597
Evaluate side-chains
  110 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 14 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 34 optimal weight:    0.2980
   chunk 79 optimal weight:    5.9990
   overall best weight:    1.4586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.128964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.101510 restraints weight = 12259.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.103946 restraints weight = 6947.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.105563 restraints weight = 4619.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.106656 restraints weight = 3489.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.107233 restraints weight = 2896.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.3885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7585  Z= 0.140
  Angle     :  0.581   6.719  10525  Z= 0.293
  Chirality :  0.039   0.144   1204
  Planarity :  0.004   0.028   1184
  Dihedral  : 17.806 177.573   1721
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  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 are not related in a simple way.
  whole:  1.74 (0.30), residues: 772
  helix:  2.10 (0.30), residues: 302
  sheet:  1.20 (0.49), residues: 102
  loop :  0.44 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 227 
 TYR   0.022   0.002   TYR B  52 
 PHE   0.010   0.001   PHE A 348 
 TRP   0.005   0.001   TRP B  93 
 HIS   0.005   0.001   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7585)
  covalent geometry    : angle       0.58109 (10525)
  hydrogen bonds       : bond        0.03924 (  311)
  hydrogen bonds       : angle       4.87538 (  883)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8346 (tmtt)
REVERT: A  258 MET cc_start: 0.7394 (ttm) cc_final: 0.7113 (mtp)
REVERT: A  429 GLN cc_start: 0.8358 (mm-40) cc_final: 0.7821 (mp10)
REVERT: B  130 GLN cc_start: 0.8350 (mt0) cc_final: 0.7728 (tm-30)
REVERT: B  153 TYR cc_start: 0.8505 (m-80) cc_final: 0.8158 (m-80)
REVERT: B  258 MET cc_start: 0.8556 (mtp) cc_final: 0.8243 (mtp)
REVERT: B  326 SER cc_start: 0.8998 (p) cc_final: 0.8384 (t)
REVERT: B  366 GLN cc_start: 0.7703 (tt0) cc_final: 0.7317 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0873
  time to fit residues: 16.0998
Evaluate side-chains
  102 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   chunk 37 optimal weight:    8.9990
   chunk 39 optimal weight:   10.0000
   chunk 57 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 30 optimal weight:    8.9990
   chunk 3 optimal weight:    9.9990
   chunk 73 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 226 HIS
A 468 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.124858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.097941 restraints weight = 12573.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.100256 restraints weight = 7283.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.101840 restraints weight = 4926.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.102837 restraints weight = 3745.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.103511 restraints weight = 3130.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.4139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7585  Z= 0.219
  Angle     :  0.660   7.735  10525  Z= 0.333
  Chirality :  0.041   0.163   1204
  Planarity :  0.004   0.030   1184
  Dihedral  : 17.806 178.982   1721
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  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 are not related in a simple way.
  whole:  1.33 (0.30), residues: 772
  helix:  1.83 (0.30), residues: 301
  sheet:  0.73 (0.49), residues: 101
  loop :  0.23 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.026   0.001   ARG A 227 
 TYR   0.022   0.003   TYR B  52 
 PHE   0.016   0.002   PHE A 247 
 TRP   0.008   0.002   TRP B  93 
 HIS   0.006   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 7585)
  covalent geometry    : angle       0.65992 (10525)
  hydrogen bonds       : bond        0.04358 (  311)
  hydrogen bonds       : angle       4.93765 (  883)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8446 (tmtt)
REVERT: A  258 MET cc_start: 0.7524 (ttm) cc_final: 0.7281 (mtp)
REVERT: A  389 LEU cc_start: 0.8828 (pp) cc_final: 0.8617 (pp)
REVERT: A  405 ASP cc_start: 0.7663 (m-30) cc_final: 0.7462 (m-30)
REVERT: B  144 GLU cc_start: 0.7706 (tp30) cc_final: 0.7444 (tp30)
REVERT: B  213 ASP cc_start: 0.8629 (t0) cc_final: 0.8413 (t0)
REVERT: B  258 MET cc_start: 0.8590 (mtp) cc_final: 0.8250 (mtp)
REVERT: B  353 MET cc_start: 0.7306 (mtp) cc_final: 0.7028 (mtp)
REVERT: B  366 GLN cc_start: 0.7855 (tt0) cc_final: 0.7474 (tm-30)
REVERT: B  410 MET cc_start: 0.8956 (mpp) cc_final: 0.8695 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.0771
  time to fit residues: 14.2917
Evaluate side-chains
  104 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 13 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   chunk 26 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 226 HIS
B 190 HIS
** B 375 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 = 0.3722 r_free = 0.3722 target = 0.131612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.103871 restraints weight = 11822.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.106364 restraints weight = 6801.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.108049 restraints weight = 4559.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.109015 restraints weight = 3431.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.109817 restraints weight = 2883.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.4394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7585  Z= 0.120
  Angle     :  0.563   7.599  10525  Z= 0.286
  Chirality :  0.038   0.155   1204
  Planarity :  0.004   0.048   1184
  Dihedral  : 17.589 179.336   1721
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  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 are not related in a simple way.
  whole:  1.58 (0.30), residues: 772
  helix:  2.04 (0.31), residues: 300
  sheet:  0.78 (0.50), residues: 104
  loop :  0.39 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 227 
 TYR   0.017   0.002   TYR B 401 
 PHE   0.027   0.001   PHE A 255 
 TRP   0.005   0.001   TRP B  93 
 HIS   0.006   0.001   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 7585)
  covalent geometry    : angle       0.56347 (10525)
  hydrogen bonds       : bond        0.03715 (  311)
  hydrogen bonds       : angle       4.79775 (  883)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8440 (tmtt)
REVERT: A  258 MET cc_start: 0.7417 (ttm) cc_final: 0.7080 (mtp)
REVERT: A  292 LYS cc_start: 0.7950 (tptp) cc_final: 0.7717 (tptm)
REVERT: A  389 LEU cc_start: 0.8789 (pp) cc_final: 0.8557 (pp)
REVERT: A  405 ASP cc_start: 0.7451 (m-30) cc_final: 0.7230 (m-30)
REVERT: A  477 VAL cc_start: 0.8146 (t) cc_final: 0.7729 (p)
REVERT: B  258 MET cc_start: 0.8491 (mtp) cc_final: 0.8184 (mtp)
REVERT: B  353 MET cc_start: 0.7180 (mtp) cc_final: 0.6916 (mtp)
REVERT: B  366 GLN cc_start: 0.7761 (tt0) cc_final: 0.7357 (tm-30)
REVERT: B  391 MET cc_start: 0.7853 (tmm) cc_final: 0.7308 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0735
  time to fit residues: 14.2513
Evaluate side-chains
  104 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 64 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 30 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** B 375 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 = 0.3715 r_free = 0.3715 target = 0.131491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.103603 restraints weight = 12040.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.106096 restraints weight = 6945.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.107799 restraints weight = 4673.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.108780 restraints weight = 3559.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.109553 restraints weight = 2995.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.4571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7585  Z= 0.122
  Angle     :  0.571  10.311  10525  Z= 0.288
  Chirality :  0.039   0.147   1204
  Planarity :  0.004   0.040   1184
  Dihedral  : 17.437 176.940   1721
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  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 are not related in a simple way.
  whole:  1.59 (0.30), residues: 772
  helix:  2.05 (0.31), residues: 300
  sheet:  0.91 (0.52), residues: 94
  loop :  0.37 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 227 
 TYR   0.012   0.002   TYR B 230 
 PHE   0.039   0.002   PHE A 255 
 TRP   0.004   0.001   TRP A 409 
 HIS   0.008   0.001   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7585)
  covalent geometry    : angle       0.57134 (10525)
  hydrogen bonds       : bond        0.03629 (  311)
  hydrogen bonds       : angle       4.76903 (  883)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8444 (tmtt)
REVERT: A  258 MET cc_start: 0.7335 (ttm) cc_final: 0.6990 (mtp)
REVERT: A  477 VAL cc_start: 0.8176 (t) cc_final: 0.7760 (p)
REVERT: B  144 GLU cc_start: 0.7567 (tp30) cc_final: 0.7334 (tp30)
REVERT: B  258 MET cc_start: 0.8484 (mtp) cc_final: 0.8183 (mtp)
REVERT: B  347 HIS cc_start: 0.8021 (p-80) cc_final: 0.7801 (p-80)
REVERT: B  366 GLN cc_start: 0.7783 (tt0) cc_final: 0.7379 (tm-30)
REVERT: B  391 MET cc_start: 0.7852 (tmm) cc_final: 0.7184 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0837
  time to fit residues: 15.6202
Evaluate side-chains
  102 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 46 optimal weight:    8.9990
   chunk 4 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0870
   chunk 48 optimal weight:    1.9990
   chunk 70 optimal weight:    0.4980
   chunk 69 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A 201 GLN
A 226 HIS
** B 375 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 = 0.3736 r_free = 0.3736 target = 0.132589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.104560 restraints weight = 11999.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107159 restraints weight = 6787.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.108904 restraints weight = 4517.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.109961 restraints weight = 3411.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.110440 restraints weight = 2848.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.4761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7585  Z= 0.109
  Angle     :  0.559   6.570  10525  Z= 0.281
  Chirality :  0.038   0.172   1204
  Planarity :  0.004   0.039   1184
  Dihedral  : 17.235 176.328   1721
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.61 %
    Favored  : 99.24 %
  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 are not related in a simple way.
  whole:  1.63 (0.30), residues: 772
  helix:  2.12 (0.31), residues: 300
  sheet:  0.97 (0.52), residues: 92
  loop :  0.36 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 344 
 TYR   0.013   0.001   TYR B  52 
 PHE   0.014   0.001   PHE B 291 
 TRP   0.003   0.001   TRP B  93 
 HIS   0.007   0.001   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 7585)
  covalent geometry    : angle       0.55868 (10525)
  hydrogen bonds       : bond        0.03360 (  311)
  hydrogen bonds       : angle       4.72971 (  883)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8390 (tmtt)
REVERT: A  258 MET cc_start: 0.7359 (ttm) cc_final: 0.7006 (mtp)
REVERT: B  144 GLU cc_start: 0.7562 (tp30) cc_final: 0.7332 (tp30)
REVERT: B  258 MET cc_start: 0.8436 (mtp) cc_final: 0.8134 (mtp)
REVERT: B  347 HIS cc_start: 0.8064 (p-80) cc_final: 0.7831 (p-80)
REVERT: B  353 MET cc_start: 0.7248 (mtp) cc_final: 0.7036 (mtp)
REVERT: B  366 GLN cc_start: 0.7749 (tt0) cc_final: 0.7328 (tm-30)
REVERT: B  391 MET cc_start: 0.7842 (tmm) cc_final: 0.7270 (tmm)
REVERT: B  436 MET cc_start: 0.7317 (tmm) cc_final: 0.7103 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0796
  time to fit residues: 14.5946
Evaluate side-chains
  96 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 75 optimal weight:    8.9990
   chunk 34 optimal weight:    0.7980
   chunk 17 optimal weight:    7.9990
   chunk 81 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 226 HIS
** B 375 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 = 0.3732 r_free = 0.3732 target = 0.132344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.104469 restraints weight = 11774.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.106934 restraints weight = 6740.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.108575 restraints weight = 4537.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.109655 restraints weight = 3468.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.109997 restraints weight = 2900.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.4880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7585  Z= 0.111
  Angle     :  0.548   6.699  10525  Z= 0.279
  Chirality :  0.038   0.153   1204
  Planarity :  0.004   0.035   1184
  Dihedral  : 17.115 174.600   1721
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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 are not related in a simple way.
  whole:  1.63 (0.30), residues: 772
  helix:  2.16 (0.31), residues: 300
  sheet:  0.96 (0.52), residues: 92
  loop :  0.33 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 227 
 TYR   0.016   0.002   TYR B 343 
 PHE   0.009   0.001   PHE B 386 
 TRP   0.001   0.000   TRP A 409 
 HIS   0.005   0.001   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 7585)
  covalent geometry    : angle       0.54826 (10525)
  hydrogen bonds       : bond        0.03345 (  311)
  hydrogen bonds       : angle       4.70805 (  883)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8444 (tmtt)
REVERT: A  258 MET cc_start: 0.7278 (ttm) cc_final: 0.6957 (mtp)
REVERT: B  258 MET cc_start: 0.8473 (mtp) cc_final: 0.8149 (mtp)
REVERT: B  347 HIS cc_start: 0.7988 (p-80) cc_final: 0.7783 (p-80)
REVERT: B  353 MET cc_start: 0.7241 (mtp) cc_final: 0.7010 (mtp)
REVERT: B  366 GLN cc_start: 0.7745 (tt0) cc_final: 0.7350 (tm-30)
REVERT: B  391 MET cc_start: 0.7890 (tmm) cc_final: 0.7339 (tmm)
REVERT: B  436 MET cc_start: 0.7126 (tmm) cc_final: 0.6810 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0715
  time to fit residues: 12.7005
Evaluate side-chains
  98 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 64 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 78 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   chunk 74 optimal weight:    6.9990
   chunk 76 optimal weight:    0.7980
   chunk 71 optimal weight:    3.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 201 GLN
A 226 HIS
** B 375 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 = 0.3706 r_free = 0.3706 target = 0.130304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.102365 restraints weight = 12003.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.104792 restraints weight = 6911.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.106401 restraints weight = 4686.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.107365 restraints weight = 3595.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.108143 restraints weight = 3034.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.4962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7585  Z= 0.133
  Angle     :  0.564   6.609  10525  Z= 0.287
  Chirality :  0.038   0.147   1204
  Planarity :  0.004   0.033   1184
  Dihedral  : 17.119 172.512   1721
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.61 %
    Favored  : 99.24 %
  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 are not related in a simple way.
  whole:  1.49 (0.30), residues: 772
  helix:  2.06 (0.31), residues: 300
  sheet:  0.90 (0.54), residues: 92
  loop :  0.21 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 413 
 TYR   0.027   0.002   TYR B 343 
 PHE   0.012   0.001   PHE B 291 
 TRP   0.008   0.001   TRP B  93 
 HIS   0.004   0.001   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 7585)
  covalent geometry    : angle       0.56392 (10525)
  hydrogen bonds       : bond        0.03447 (  311)
  hydrogen bonds       : angle       4.76655 (  883)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8399 (tmtt)
REVERT: A  258 MET cc_start: 0.7437 (ttm) cc_final: 0.7046 (mtp)
REVERT: A  482 GLN cc_start: 0.7671 (tm-30) cc_final: 0.7466 (tm-30)
REVERT: B  258 MET cc_start: 0.8503 (mtp) cc_final: 0.8172 (mtp)
REVERT: B  353 MET cc_start: 0.7275 (mtp) cc_final: 0.7048 (mtp)
REVERT: B  366 GLN cc_start: 0.7811 (tt0) cc_final: 0.7408 (tm-30)
REVERT: B  391 MET cc_start: 0.8009 (tmm) cc_final: 0.7473 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0707
  time to fit residues: 12.6845
Evaluate side-chains
  103 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 54 optimal weight:    0.1980
   chunk 22 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 13 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   chunk 4 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9980
   chunk 25 optimal weight:   10.0000
   chunk 78 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 226 HIS
** B 375 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 = 0.3705 r_free = 0.3705 target = 0.130346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.102270 restraints weight = 11969.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.104722 restraints weight = 6868.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.106318 restraints weight = 4642.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.107434 restraints weight = 3543.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.108082 restraints weight = 2960.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.5036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7585  Z= 0.129
  Angle     :  0.567   6.737  10525  Z= 0.288
  Chirality :  0.039   0.145   1204
  Planarity :  0.004   0.033   1184
  Dihedral  : 17.154 171.498   1721
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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 are not related in a simple way.
  whole:  1.45 (0.30), residues: 772
  helix:  2.04 (0.31), residues: 300
  sheet:  0.82 (0.53), residues: 92
  loop :  0.19 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 227 
 TYR   0.021   0.002   TYR B 401 
 PHE   0.009   0.001   PHE B 386 
 TRP   0.007   0.001   TRP B  93 
 HIS   0.007   0.001   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7585)
  covalent geometry    : angle       0.56670 (10525)
  hydrogen bonds       : bond        0.03491 (  311)
  hydrogen bonds       : angle       4.77896 (  883)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1152.14 seconds
wall clock time: 20 minutes 34.57 seconds (1234.57 seconds total)