Starting phenix.real_space_refine
on Thu Jul  2 07:37:30 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7u2b_26311/07_2026/7u2b_26311.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u2b_26311/07_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u2b_26311/07_2026/7u2b_26311.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u2b_26311/07_2026/7u2b_26311.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7u2b_26311/07_2026/7u2b_26311.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7u2b_26311/07_2026/7u2b_26311.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u2b_26311/07_2026/7u2b_26311.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u2b_26311/07_2026/7u2b_26311.map"
  }
  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-6108/lib/python3.11/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: 9
          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: 1.63, per 1000 atoms: 0.22
  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: 0.68
  Conformation dependent library (CDL) restraints added in 447.5 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: 0.53
  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: 0.96

  Time building geometry restraints manager: 0.86 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: 4257
       30.30 -    60.61: 161
       60.61 -    90.91: 7
       90.91 -   121.22: 1
      121.22 -   151.52: 3
  Dihedral angle restraints: 4429
    sinusoidal: 2191
      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 4426 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:             0.440
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.650
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7053
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  : 14.981 151.523   2991
  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/Z
  covalent geometry    : bond        0.00940 /  0.46 ( 7585)
  covalent geometry    : angle       0.97297 /  0.52 (10525)
  hydrogen bonds       : bond        0.15712 /  9.05 (  311)
  hydrogen bonds       : angle       6.87084 /  3.98 (  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  : 0.256 
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: 0.0891
  time to fit residues: 27.1475
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  : 0.148 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 45 optimal weight:   20.0000
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3718 r_free = 0.3718 target = 0.131862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.104478 restraints weight = 12013.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.107038 restraints weight = 6734.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.108735 restraints weight = 4427.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.109884 restraints weight = 3331.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.110503 restraints weight = 2738.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7585  Z= 0.181
  Angle     :  0.664   7.236  10525  Z= 0.333
  Chirality :  0.040   0.155   1204
  Planarity :  0.005   0.070   1184
  Dihedral  : 11.532 162.895   1493
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.97 %
    Favored  : 95.88 %
  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:  1.84 (0.29), residues: 772
  helix:  2.29 (0.29), residues: 303
  sheet:  1.21 (0.49), residues: 99
  loop :  0.41 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 104 
 TYR   0.039   0.003   TYR B  47 
 PHE   0.022   0.002   PHE B 247 
 TRP   0.005   0.002   TRP B  93 
 HIS   0.007   0.001   HIS B 434 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.18 ( 7585)
  covalent geometry    : angle       0.66356 /  0.33 (10525)
  hydrogen bonds       : bond        0.05125 /  3.04 (  311)
  hydrogen bonds       : angle       5.31385 /  3.12 (  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  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8261 (tmtt)
REVERT: A  250 LEU cc_start: 0.9386 (mm) cc_final: 0.9182 (mt)
REVERT: A  258 MET cc_start: 0.7321 (ttm) cc_final: 0.7067 (mtp)
REVERT: A  429 GLN cc_start: 0.8471 (mm-40) cc_final: 0.7965 (mp10)
REVERT: A  482 GLN cc_start: 0.8306 (mt0) cc_final: 0.8001 (tm-30)
REVERT: B  130 GLN cc_start: 0.8417 (mt0) cc_final: 0.7768 (tm-30)
REVERT: B  153 TYR cc_start: 0.8688 (m-80) cc_final: 0.8369 (m-80)
REVERT: B  248 ASN cc_start: 0.8060 (m-40) cc_final: 0.7721 (t0)
REVERT: B  326 SER cc_start: 0.8913 (p) cc_final: 0.8379 (t)
REVERT: B  353 MET cc_start: 0.7662 (mtp) cc_final: 0.7245 (mtp)
REVERT: B  366 GLN cc_start: 0.7763 (tt0) cc_final: 0.7374 (tm-30)
REVERT: B  395 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7224 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 161
  average time/residue: 0.0827
  time to fit residues: 17.6025
Evaluate side-chains
  110 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 41 optimal weight:    8.9990
   chunk 37 optimal weight:    8.9990
   chunk 20 optimal weight:    0.0030
   chunk 30 optimal weight:    8.9990
   chunk 66 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    2.0994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 201 GLN
A 226 HIS
A 347 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 = 0.3671 r_free = 0.3671 target = 0.127979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.101495 restraints weight = 11962.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.103958 restraints weight = 6773.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.105592 restraints weight = 4483.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.106605 restraints weight = 3373.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.107361 restraints weight = 2808.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.3425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7585  Z= 0.180
  Angle     :  0.621   6.784  10525  Z= 0.312
  Chirality :  0.039   0.145   1204
  Planarity :  0.004   0.048   1184
  Dihedral  : 11.552 171.734   1493
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    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:  1.70 (0.29), residues: 772
  helix:  2.10 (0.30), residues: 301
  sheet:  1.16 (0.47), residues: 100
  loop :  0.39 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 104 
 TYR   0.015   0.002   TYR A 401 
 PHE   0.014   0.002   PHE B 404 
 TRP   0.007   0.001   TRP B  93 
 HIS   0.004   0.001   HIS B 347 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.18 ( 7585)
  covalent geometry    : angle       0.62093 /  0.31 (10525)
  hydrogen bonds       : bond        0.04572 /  2.72 (  311)
  hydrogen bonds       : angle       5.05348 /  2.96 (  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
  144 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8380 (tmtt)
REVERT: A  258 MET cc_start: 0.7418 (ttm) cc_final: 0.7115 (mtp)
REVERT: A  405 ASP cc_start: 0.7816 (m-30) cc_final: 0.7410 (m-30)
REVERT: A  429 GLN cc_start: 0.8484 (mm-40) cc_final: 0.7834 (mp10)
REVERT: B  130 GLN cc_start: 0.8351 (mt0) cc_final: 0.7753 (tm-30)
REVERT: B  153 TYR cc_start: 0.8601 (m-80) cc_final: 0.8323 (m-80)
REVERT: B  258 MET cc_start: 0.8337 (mtp) cc_final: 0.8070 (mtp)
REVERT: B  322 MET cc_start: 0.7602 (mtm) cc_final: 0.7286 (mtt)
REVERT: B  326 SER cc_start: 0.8970 (p) cc_final: 0.8413 (t)
REVERT: B  366 GLN cc_start: 0.7778 (tt0) cc_final: 0.7385 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.0860
  time to fit residues: 16.5294
Evaluate side-chains
  106 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 7 optimal weight:    0.2980
   chunk 27 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 217 GLN
A 239 GLN
** 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 = 0.3671 r_free = 0.3671 target = 0.128177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.101190 restraints weight = 12250.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.103583 restraints weight = 6949.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.105195 restraints weight = 4626.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.106264 restraints weight = 3486.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.106930 restraints weight = 2887.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.3822

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= 0.139
  Angle     :  0.575   6.712  10525  Z= 0.294
  Chirality :  0.038   0.147   1204
  Planarity :  0.004   0.028   1184
  Dihedral  : 11.622 178.712   1493
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  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:  1.66 (0.30), residues: 772
  helix:  2.04 (0.31), residues: 301
  sheet:  1.19 (0.52), residues: 93
  loop :  0.40 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 203 
 TYR   0.026   0.002   TYR B  52 
 PHE   0.012   0.001   PHE A 348 
 TRP   0.004   0.001   TRP B  93 
 HIS   0.010   0.001   HIS A 347 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.14 ( 7585)
  covalent geometry    : angle       0.57472 /  0.29 (10525)
  hydrogen bonds       : bond        0.04004 /  2.38 (  311)
  hydrogen bonds       : angle       4.92068 /  2.87 (  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
  144 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8348 (tmtt)
REVERT: A  258 MET cc_start: 0.7381 (ttm) cc_final: 0.7099 (mtp)
REVERT: A  389 LEU cc_start: 0.8812 (pp) cc_final: 0.8590 (pp)
REVERT: A  405 ASP cc_start: 0.7662 (m-30) cc_final: 0.7342 (m-30)
REVERT: A  429 GLN cc_start: 0.8431 (mm-40) cc_final: 0.7846 (mp10)
REVERT: B  130 GLN cc_start: 0.8291 (mt0) cc_final: 0.7699 (tm-30)
REVERT: B  153 TYR cc_start: 0.8502 (m-80) cc_final: 0.8182 (m-80)
REVERT: B  366 GLN cc_start: 0.7734 (tt0) cc_final: 0.7354 (tm-30)
REVERT: B  391 MET cc_start: 0.7454 (tmm) cc_final: 0.6815 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.0821
  time to fit residues: 15.9487
Evaluate side-chains
  107 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 37 optimal weight:    7.9990
   chunk 39 optimal weight:    8.9990
   chunk 57 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 3 optimal weight:    9.9990
   chunk 73 optimal weight:    9.9990
   chunk 24 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 347 HIS
A 438 GLN
B 190 HIS
** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.129516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.102738 restraints weight = 12137.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.105142 restraints weight = 6854.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.106784 restraints weight = 4553.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.107839 restraints weight = 3411.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.108418 restraints weight = 2823.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.4138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7585  Z= 0.115
  Angle     :  0.536   6.636  10525  Z= 0.275
  Chirality :  0.038   0.149   1204
  Planarity :  0.003   0.026   1184
  Dihedral  : 11.587 179.560   1493
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  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:  1.66 (0.30), residues: 772
  helix:  2.08 (0.31), residues: 301
  sheet:  1.04 (0.52), residues: 93
  loop :  0.41 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  77 
 TYR   0.023   0.002   TYR B  52 
 PHE   0.018   0.001   PHE A 315 
 TRP   0.003   0.001   TRP B  93 
 HIS   0.007   0.001   HIS A 347 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.11 ( 7585)
  covalent geometry    : angle       0.53609 /  0.27 (10525)
  hydrogen bonds       : bond        0.03692 /  2.20 (  311)
  hydrogen bonds       : angle       4.78551 /  2.79 (  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
  140 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8348 (tmtt)
REVERT: A  258 MET cc_start: 0.7359 (ttm) cc_final: 0.7074 (mtp)
REVERT: A  429 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8110 (mp10)
REVERT: B   52 TYR cc_start: 0.8470 (m-80) cc_final: 0.8017 (m-10)
REVERT: B  130 GLN cc_start: 0.8227 (mt0) cc_final: 0.7674 (tm-30)
REVERT: B  326 SER cc_start: 0.8962 (p) cc_final: 0.8469 (t)
REVERT: B  366 GLN cc_start: 0.7712 (tt0) cc_final: 0.7337 (tm-30)
REVERT: B  410 MET cc_start: 0.8887 (mpp) cc_final: 0.8646 (mpp)
REVERT: B  436 MET cc_start: 0.7652 (ttp) cc_final: 0.6901 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0690
  time to fit residues: 13.2882
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  : 0.153 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 13 optimal weight:    8.9990
   chunk 64 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 72 optimal weight:    5.9990
   overall best weight:    1.1786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 468 ASN
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3684 r_free = 0.3684 target = 0.128951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.102206 restraints weight = 11924.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.104550 restraints weight = 6793.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.106150 restraints weight = 4527.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.107055 restraints weight = 3408.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.107783 restraints weight = 2856.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.4347

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= 0.124
  Angle     :  0.549   6.712  10525  Z= 0.280
  Chirality :  0.038   0.146   1204
  Planarity :  0.004   0.048   1184
  Dihedral  : 11.623 177.026   1493
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  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:  1.68 (0.30), residues: 772
  helix:  2.13 (0.31), residues: 301
  sheet:  1.14 (0.53), residues: 93
  loop :  0.37 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 252 
 TYR   0.022   0.002   TYR B 153 
 PHE   0.037   0.002   PHE A 255 
 TRP   0.004   0.001   TRP B  93 
 HIS   0.008   0.001   HIS B 190 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.12 ( 7585)
  covalent geometry    : angle       0.54908 /  0.28 (10525)
  hydrogen bonds       : bond        0.03567 /  2.12 (  311)
  hydrogen bonds       : angle       4.68497 /  2.72 (  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
  130 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8867 (mtmt) cc_final: 0.8382 (tmtt)
REVERT: A  258 MET cc_start: 0.7425 (ttm) cc_final: 0.7121 (mtp)
REVERT: A  292 LYS cc_start: 0.7958 (tptp) cc_final: 0.7646 (tptm)
REVERT: A  429 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8125 (mp10)
REVERT: B  347 HIS cc_start: 0.7994 (p-80) cc_final: 0.7751 (p-80)
REVERT: B  366 GLN cc_start: 0.7766 (tt0) cc_final: 0.7375 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0897
  time to fit residues: 15.9776
Evaluate side-chains
  97 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 47 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 30 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    1.7784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 469 GLN
** 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 = 0.3700 r_free = 0.3700 target = 0.130328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.102570 restraints weight = 11977.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.105025 restraints weight = 6938.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.106636 restraints weight = 4677.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107761 restraints weight = 3571.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.108407 restraints weight = 2976.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.4516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7585  Z= 0.152
  Angle     :  0.594  12.702  10525  Z= 0.299
  Chirality :  0.039   0.171   1204
  Planarity :  0.004   0.038   1184
  Dihedral  : 11.661 175.477   1493
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  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:  1.52 (0.30), residues: 772
  helix:  2.05 (0.31), residues: 300
  sheet:  0.84 (0.52), residues: 94
  loop :  0.28 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 227 
 TYR   0.015   0.002   TYR B 153 
 PHE   0.041   0.002   PHE A 255 
 TRP   0.006   0.001   TRP B  93 
 HIS   0.006   0.001   HIS B 190 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.15 ( 7585)
  covalent geometry    : angle       0.59403 /  0.30 (10525)
  hydrogen bonds       : bond        0.03676 /  2.18 (  311)
  hydrogen bonds       : angle       4.81624 /  2.79 (  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
  132 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8402 (tmtt)
REVERT: A  258 MET cc_start: 0.7371 (ttm) cc_final: 0.7137 (mtp)
REVERT: A  389 LEU cc_start: 0.8762 (pp) cc_final: 0.8560 (pp)
REVERT: A  405 ASP cc_start: 0.7488 (m-30) cc_final: 0.7224 (m-30)
REVERT: B  118 ARG cc_start: 0.8011 (tpp80) cc_final: 0.7142 (ttp80)
REVERT: B  347 HIS cc_start: 0.7985 (p-80) cc_final: 0.7743 (p-80)
REVERT: B  366 GLN cc_start: 0.7785 (tt0) cc_final: 0.7417 (tm-30)
REVERT: B  391 MET cc_start: 0.8010 (tmm) cc_final: 0.7412 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0765
  time to fit residues: 14.1709
Evaluate side-chains
  99 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 43 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 4 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0670
   chunk 48 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.9724

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 217 GLN
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3719 r_free = 0.3719 target = 0.131547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.103772 restraints weight = 12026.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.106245 restraints weight = 6947.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.107890 restraints weight = 4692.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.108987 restraints weight = 3573.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.109602 restraints weight = 2983.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.4681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7585  Z= 0.114
  Angle     :  0.545   6.609  10525  Z= 0.277
  Chirality :  0.038   0.153   1204
  Planarity :  0.003   0.034   1184
  Dihedral  : 11.679 174.755   1493
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  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:  1.57 (0.30), residues: 772
  helix:  2.13 (0.31), residues: 301
  sheet:  0.91 (0.52), residues: 93
  loop :  0.26 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 344 
 TYR   0.014   0.002   TYR A 230 
 PHE   0.008   0.001   PHE B 386 
 TRP   0.004   0.001   TRP B  93 
 HIS   0.006   0.001   HIS B 190 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.11 ( 7585)
  covalent geometry    : angle       0.54459 /  0.28 (10525)
  hydrogen bonds       : bond        0.03445 /  2.05 (  311)
  hydrogen bonds       : angle       4.71793 /  2.70 (  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
  129 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8381 (tmtt)
REVERT: A  258 MET cc_start: 0.7414 (ttm) cc_final: 0.7018 (mtp)
REVERT: A  405 ASP cc_start: 0.7451 (m-30) cc_final: 0.7147 (m-30)
REVERT: B  290 ARG cc_start: 0.8324 (tpm170) cc_final: 0.7984 (tpm170)
REVERT: B  322 MET cc_start: 0.7155 (mtm) cc_final: 0.6914 (mtt)
REVERT: B  347 HIS cc_start: 0.7941 (p-80) cc_final: 0.7715 (p-80)
REVERT: B  366 GLN cc_start: 0.7724 (tt0) cc_final: 0.7359 (tm-30)
REVERT: B  436 MET cc_start: 0.7342 (tmm) cc_final: 0.7017 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0789
  time to fit residues: 14.3850
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  : 0.257 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 75 optimal weight:   10.0000
   chunk 34 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 77 optimal weight:    0.8980
   overall best weight:    1.6784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 469 GLN
** 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 = 0.3691 r_free = 0.3691 target = 0.129371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.101974 restraints weight = 11842.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.104362 restraints weight = 6815.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.105923 restraints weight = 4621.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.106967 restraints weight = 3528.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.107672 restraints weight = 2951.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.4759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7585  Z= 0.144
  Angle     :  0.574   7.562  10525  Z= 0.292
  Chirality :  0.039   0.163   1204
  Planarity :  0.004   0.032   1184
  Dihedral  : 11.749 172.544   1493
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  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:  1.40 (0.30), residues: 772
  helix:  2.00 (0.31), residues: 301
  sheet:  0.74 (0.52), residues: 93
  loop :  0.17 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG A 227 
 TYR   0.026   0.002   TYR A 230 
 PHE   0.015   0.002   PHE B 291 
 TRP   0.007   0.001   TRP B  93 
 HIS   0.005   0.001   HIS B 190 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.14 ( 7585)
  covalent geometry    : angle       0.57391 /  0.29 (10525)
  hydrogen bonds       : bond        0.03603 /  2.14 (  311)
  hydrogen bonds       : angle       4.78994 /  2.74 (  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
  125 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8396 (tmtt)
REVERT: A  258 MET cc_start: 0.7374 (ttm) cc_final: 0.7107 (mtp)
REVERT: A  389 LEU cc_start: 0.8725 (pp) cc_final: 0.8525 (pp)
REVERT: A  405 ASP cc_start: 0.7436 (m-30) cc_final: 0.7177 (m-30)
REVERT: B  322 MET cc_start: 0.7157 (mtm) cc_final: 0.6934 (mtt)
REVERT: B  347 HIS cc_start: 0.7947 (p-80) cc_final: 0.7737 (p-80)
REVERT: B  366 GLN cc_start: 0.7771 (tt0) cc_final: 0.7443 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0771
  time to fit residues: 13.6682
Evaluate side-chains
  100 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 71 optimal weight:    0.0470
   overall best weight:    0.7280

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3728 r_free = 0.3728 target = 0.132049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.104287 restraints weight = 11920.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.106772 restraints weight = 6858.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.108307 restraints weight = 4622.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.109489 restraints weight = 3550.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.110101 restraints weight = 2954.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.4891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7585  Z= 0.108
  Angle     :  0.557   6.874  10525  Z= 0.281
  Chirality :  0.038   0.162   1204
  Planarity :  0.004   0.032   1184
  Dihedral  : 11.760 172.143   1493
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  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:  1.47 (0.30), residues: 772
  helix:  2.09 (0.31), residues: 299
  sheet:  0.71 (0.52), residues: 93
  loop :  0.21 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 227 
 TYR   0.035   0.002   TYR A 230 
 PHE   0.011   0.001   PHE B 386 
 TRP   0.003   0.000   TRP B  93 
 HIS   0.006   0.001   HIS B 190 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.11 ( 7585)
  covalent geometry    : angle       0.55739 /  0.28 (10525)
  hydrogen bonds       : bond        0.03335 /  1.99 (  311)
  hydrogen bonds       : angle       4.70562 /  2.70 (  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
  126 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8857 (mtmt) cc_final: 0.8414 (tmtt)
REVERT: A  216 ARG cc_start: 0.8457 (tmm-80) cc_final: 0.8225 (ttt180)
REVERT: A  258 MET cc_start: 0.7334 (ttm) cc_final: 0.7009 (mtp)
REVERT: A  405 ASP cc_start: 0.7386 (m-30) cc_final: 0.7175 (m-30)
REVERT: A  482 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7530 (tm-30)
REVERT: B  347 HIS cc_start: 0.7931 (p-80) cc_final: 0.7714 (p-80)
REVERT: B  366 GLN cc_start: 0.7710 (tt0) cc_final: 0.7336 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0824
  time to fit residues: 14.3519
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  : 0.220 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 49 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0670
   chunk 78 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0470
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.5216

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 429 GLN
A 469 GLN
** 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 = 0.3738 r_free = 0.3738 target = 0.133012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.105041 restraints weight = 11845.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107536 restraints weight = 6809.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.109167 restraints weight = 4564.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.110071 restraints weight = 3489.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.110851 restraints weight = 2944.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.5008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7585  Z= 0.108
  Angle     :  0.560   8.049  10525  Z= 0.283
  Chirality :  0.038   0.145   1204
  Planarity :  0.004   0.030   1184
  Dihedral  : 11.718 170.748   1493
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.47 (0.30), residues: 772
  helix:  2.05 (0.31), residues: 300
  sheet:  0.85 (0.52), residues: 93
  loop :  0.20 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 227 
 TYR   0.032   0.002   TYR A 230 
 PHE   0.013   0.001   PHE A 247 
 TRP   0.002   0.000   TRP B  93 
 HIS   0.006   0.001   HIS B 190 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.11 ( 7585)
  covalent geometry    : angle       0.55956 /  0.28 (10525)
  hydrogen bonds       : bond        0.03259 /  1.94 (  311)
  hydrogen bonds       : angle       4.69430 /  2.69 (  883)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1177.49 seconds
wall clock time: 21 minutes 6.03 seconds (1266.03 seconds total)