Starting phenix.real_space_refine
on Thu Jul  2 06:22:13 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7u2a_26310/07_2026/7u2a_26310.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u2a_26310/07_2026/7u2a_26310.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/7u2a_26310/07_2026/7u2a_26310.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u2a_26310/07_2026/7u2a_26310.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u2a_26310/07_2026/7u2a_26310.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u2a_26310/07_2026/7u2a_26310.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7u2a_26310/07_2026/7u2a_26310.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7u2a_26310/07_2026/7u2a_26310.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=   0.010
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      38      5.49       5
     S      34      5.16       5
     C    4179      2.51       5
     N    1233      2.21       5
     O    1371      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 87 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: 6855
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 794
          Classifications: {'RNA': 38}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 15, 'rna3p_pyr': 20}
          Link IDs: {'rna2p': 2, 'rna3p': 35}
          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: 3503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 442, 3503
          Classifications: {'peptide': 442}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 415}
          Chain breaks: 2
          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: 1.47, per 1000 atoms: 0.21
  Number of scatterers: 6855
  At special positions: 0
  Unit cell: (70.15, 83.95, 117.3, 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      38     15.00
     O    1371      8.00
     N    1233      7.00
     C    4179      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: 0.59
  Conformation dependent library (CDL) restraints added in 394.8 milliseconds
  

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1404

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 7 sheets defined
      42.2% alpha, 16.7% beta
      10 base pairs and 19 stacking pairs defined.
    Time for finding SS restraints: 0.65
  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
    Processing helix  chain 'A' and resid 266 through 272
    Processing helix  chain 'A' and resid 299 through 308
      removed outlier: 4.156A  pdb=" N   GLY A 303 " --> pdb=" O   THR A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 383
    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: 4.296A  pdb=" N   SER A 483 " --> pdb=" O   PRO A 479 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   TYR A 484 " --> pdb=" O   ALA A 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 51
      removed outlier: 3.737A  pdb=" N   GLU B  46 " --> pdb=" O   ASN B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 65
      removed outlier: 4.354A  pdb=" N   ALA B  65 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 78
      removed outlier: 3.605A  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 118
      removed outlier: 3.724A  pdb=" N   ILE B  89 " --> pdb=" O   ASP B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 169
      Proline residue:  B 154  - end of helix
      removed outlier: 4.233A  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 254
    Processing helix  chain 'B' and resid 266 through 273
    Processing helix  chain 'B' and resid 299 through 309
      removed outlier: 3.888A  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 392 through 397
      removed outlier: 4.546A  pdb=" N   GLY B 397 " --> pdb=" O   THR B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 434
      removed outlier: 3.546A  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: 3.813A  pdb=" N   SER B 483 " --> pdb=" O   PRO B 479 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   TYR B 484 " --> pdb=" O   ALA B 480 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 192
      removed outlier: 6.262A  pdb=" N   ARG A 402 " --> pdb=" O   SER A 423 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   SER A 423 " --> pdb=" O   ARG A 402 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   PHE A 404 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   SER A 421 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ILE A 406 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLY A 417 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
      removed outlier: 10.080A  pdb=" N   VAL A 419 " --> pdb=" O   CYS A 455 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   CYS A 455 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 5.524A  pdb=" N   SER A 421 " --> pdb=" O   THR A 453 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   THR A 453 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ASN A 451 " --> pdb=" O   SER A 423 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   THR A 449 " --> pdb=" O   CYS A 425 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   HIS A 448 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   VAL A 351 " --> pdb=" O   ALA A 454 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   ALA A 456 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   THR A 349 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LYS A 350 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   SER A 326 " --> pdb=" O   LYS A 350 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   SER A 325 " --> pdb=" O   MET A 258 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU B 231 " --> pdb=" O   THR A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 216
      removed outlier: 3.735A  pdb=" N   TYR A 230 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   LEU A 231 " --> pdb=" O   THR B 259 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   SER B 325 " --> pdb=" O   MET B 258 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   SER B 326 " --> pdb=" O   LYS B 350 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LYS B 350 " --> pdb=" O   SER B 326 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   THR B 349 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   ALA B 456 " --> pdb=" O   THR B 349 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   VAL B 351 " --> pdb=" O   ALA B 454 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   SER B 421 " --> pdb=" O   THR B 453 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   CYS B 455 " --> pdb=" O   VAL B 419 " (cutoff:3.500A)
      removed outlier: 9.309A  pdb=" N   VAL B 419 " --> pdb=" O   CYS B 455 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ILE B 406 " --> pdb=" O   VAL B 419 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   SER B 421 " --> pdb=" O   PHE B 404 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   PHE B 404 " --> pdb=" O   SER B 421 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   ASP B 390 " --> pdb=" O   VAL B 188 " (cutoff:3.500A)
      removed outlier: 5.640A  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 265
    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: 5.869A  pdb=" N   HIS B 311 " --> pdb=" O   MET B 436 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   GLN B 438 " --> pdb=" O   HIS B 311 " (cutoff:3.500A)
      removed outlier: 6.164A  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 265

    282 hydrogen bonds defined for protein.
    813 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      25 hydrogen bonds
      50 hydrogen bond angles
      0 basepair planarities
      10 basepair parallelities
      19 stacking parallelities
  Total time for adding SS restraints: 1.13

  Time building geometry restraints manager: 0.73 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: 1888
        1.33 -     1.45: 1429
        1.45 -     1.57: 3629
        1.57 -     1.69: 82
        1.69 -     1.81: 56
  Bond restraints: 7084
  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  1.514 -0.181 2.00e-02 2.50e+03 8.18e+01
  bond pdb=" O5' SSA B 601 "
       pdb=" S1  SSA B 601 "
    ideal  model  delta    sigma   weight residual
    1.581  1.730 -0.149 2.00e-02 2.50e+03 5.55e+01
  bond pdb=" O2S SSA B 601 "
       pdb=" S1  SSA B 601 "
    ideal  model  delta    sigma   weight residual
    1.435  1.583 -0.148 2.00e-02 2.50e+03 5.46e+01
  bond pdb=" O2S SSA A 601 "
       pdb=" S1  SSA A 601 "
    ideal  model  delta    sigma   weight residual
    1.435  1.579 -0.144 2.00e-02 2.50e+03 5.17e+01
  ... (remaining 7079 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.79: 9667
        3.79 -     7.59: 93
        7.59 -    11.38: 11
       11.38 -    15.17: 0
       15.17 -    18.97: 2
  Bond angle restraints: 9773
  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  102.37   18.97 3.00e+00 1.11e-01 4.00e+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  102.72   18.62 3.00e+00 1.11e-01 3.85e+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  108.60   10.78 3.00e+00 1.11e-01 1.29e+01
  angle pdb=" N1  SSA A 601 "
        pdb=" C6  SSA A 601 "
        pdb=" N6  SSA A 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   PHE B 386 "
        pdb=" CA  PHE B 386 "
        pdb=" C   PHE B 386 "
      ideal   model   delta    sigma   weight residual
     109.24  114.98   -5.74 1.67e+00 3.59e-01 1.18e+01
  ... (remaining 9768 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.35: 4003
       30.35 -    60.71: 145
       60.71 -    91.06: 7
       91.06 -   121.41: 1
      121.41 -   151.76: 2
  Dihedral angle restraints: 4158
    sinusoidal: 1975
      harmonic: 2183
  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   -8.24 -151.76     1      1.50e+01 4.44e-03 8.03e+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  -10.36 -149.64     1      1.50e+01 4.44e-03 7.95e+01
  dihedral pdb=" O4'   A C  45 "
           pdb=" C1'   A C  45 "
           pdb=" N9    A C  45 "
           pdb=" C4    A C  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -173.42   67.42     1      1.70e+01 3.46e-03 2.05e+01
  ... (remaining 4155 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 1071
       0.118 -    0.235: 35
       0.235 -    0.353: 1
       0.353 -    0.470: 0
       0.470 -    0.588: 2
  Chirality restraints: 1109
  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   -3.06    0.59 2.00e-01 2.50e+01 8.64e+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   -3.03    0.57 2.00e-01 2.50e+01 8.01e+00
  chirality pdb=" C3' SSA A 601 "
            pdb=" C2' SSA A 601 "
            pdb=" C4' SSA A 601 "
            pdb=" O3' SSA A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.48   -0.25 2.00e-01 2.50e+01 1.58e+00
  ... (remaining 1106 not shown)

  Planarity restraints: 1139
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 221 "   -0.012 2.00e-02 2.50e+03   2.34e-02 5.49e+00
        pdb=" C   SER B 221 "    0.041 2.00e-02 2.50e+03
        pdb=" O   SER B 221 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   HIS B 222 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  45 "   -0.028 2.00e-02 2.50e+03   1.33e-02 4.87e+00
        pdb=" N9    A C  45 "    0.032 2.00e-02 2.50e+03
        pdb=" C8    A C  45 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    A C  45 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A C  45 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A C  45 "   -0.004 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 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    A C  45 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 347 "   -0.014 2.00e-02 2.50e+03   1.50e-02 3.37e+00
        pdb=" CG  HIS B 347 "    0.032 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 347 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 347 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 347 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 347 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1136 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.51: 49
        2.51 -     3.11: 5218
        3.11 -     3.71: 10911
        3.71 -     4.30: 14874
        4.30 -     4.90: 24178
  Nonbonded interactions: 55230
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 329 "
            pdb=" OH  TYR B 329 "
     model   vdw
     1.918 3.040
  nonbonded pdb=" OG  SSA A 601 "
            pdb=" O9  SSA A 601 "
     model   vdw
     2.005 3.040
  nonbonded pdb=" OD1 ASN B 451 "
            pdb=" OG  SSA B 601 "
     model   vdw
     2.019 3.040
  nonbonded pdb=" OG  SER A 224 "
            pdb=" OG  SER A 228 "
     model   vdw
     2.020 3.040
  nonbonded pdb=" O2'   A C  45 "
            pdb=" O5'   A C  46 "
     model   vdw
     2.039 3.040
  ... (remaining 55225 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:             0.250
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.130
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6139
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      :  0.010   0.187   7084  Z= 0.483
  Angle     :  1.056  18.967   9773  Z= 0.571
  Chirality :  0.057   0.588   1109
  Planarity :  0.004   0.045   1139
  Dihedral  : 14.762 151.765   2754
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 12.66 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  2.04 (0.29), residues: 751
  helix:  2.82 (0.29), residues: 296
  sheet:  1.13 (0.54), residues: 87
  loop :  0.23 (0.29), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 459 
 TYR   0.019   0.003   TYR B 230 
 PHE   0.019   0.002   PHE B 404 
 TRP   0.007   0.002   TRP A 409 
 HIS   0.016   0.002   HIS B 347 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01004 /  0.48 ( 7084)
  covalent geometry    : angle       1.05603 /  0.57 ( 9773)
  hydrogen bonds       : bond        0.15500 /  9.31 (  307)
  hydrogen bonds       : angle       7.04915 /  4.14 (  863)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 262
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 MET cc_start: 0.8645 (mtt) cc_final: 0.8163 (ttm)
REVERT: A  218 LYS cc_start: 0.4545 (mtmt) cc_final: 0.4302 (pttt)
REVERT: A  226 HIS cc_start: 0.7146 (t70) cc_final: 0.6778 (t-90)
REVERT: A  244 ASN cc_start: 0.8206 (m-40) cc_final: 0.7830 (t0)
REVERT: A  248 ASN cc_start: 0.7613 (m-40) cc_final: 0.7394 (t0)
REVERT: A  343 TYR cc_start: 0.6440 (t80) cc_final: 0.6217 (t80)
REVERT: A  369 GLU cc_start: 0.8398 (tp30) cc_final: 0.8165 (mm-30)
REVERT: A  370 GLU cc_start: 0.8711 (tt0) cc_final: 0.8411 (tm-30)
REVERT: A  378 ILE cc_start: 0.7865 (mt) cc_final: 0.7592 (mm)
REVERT: A  385 HIS cc_start: 0.5666 (t70) cc_final: 0.5207 (t70)
REVERT: A  464 LEU cc_start: 0.7543 (mt) cc_final: 0.7160 (mt)
REVERT: A  474 SER cc_start: 0.7368 (m) cc_final: 0.6596 (p)
REVERT: B   99 LEU cc_start: 0.6943 (mt) cc_final: 0.6581 (mt)
REVERT: B  290 ARG cc_start: 0.8667 (tpt90) cc_final: 0.8258 (mmm-85)
REVERT: B  344 ARG cc_start: 0.6462 (mmt180) cc_final: 0.6168 (mmm-85)
REVERT: B  363 GLN cc_start: 0.7819 (mp10) cc_final: 0.7457 (tt0)
REVERT: B  435 ILE cc_start: 0.6856 (mt) cc_final: 0.6194 (mt)
REVERT: B  501 ILE cc_start: 0.8156 (mm) cc_final: 0.7781 (mt)
  outliers start: 2
  outliers final: 0
  residues processed: 264
  average time/residue: 0.0840
  time to fit residues: 28.3552
Evaluate side-chains
  138 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0980
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.3980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 190 HIS
A 375 GLN
A 499 GLN
B  57 GLN
B 102 GLN
** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 429 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.191340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.165051 restraints weight = 9200.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.169224 restraints weight = 5327.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.172137 restraints weight = 3518.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.173987 restraints weight = 2575.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.175485 restraints weight = 2065.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.4288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6604
moved from start:          0.3447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   7084  Z= 0.158
  Angle     :  0.691   8.961   9773  Z= 0.346
  Chirality :  0.041   0.204   1109
  Planarity :  0.006   0.095   1139
  Dihedral  : 10.361 151.448   1292
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  3.59 %
    Favored  : 96.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.88 (0.30), residues: 751
  helix:  2.50 (0.30), residues: 286
  sheet:  1.50 (0.56), residues: 86
  loop :  0.26 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 187 
 TYR   0.032   0.003   TYR B  47 
 PHE   0.022   0.002   PHE B 163 
 TRP   0.025   0.004   TRP A 409 
 HIS   0.007   0.001   HIS B 205 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.16 ( 7084)
  covalent geometry    : angle       0.69107 /  0.35 ( 9773)
  hydrogen bonds       : bond        0.05111 /  2.95 (  307)
  hydrogen bonds       : angle       5.60354 /  3.34 (  863)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 182
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 HIS cc_start: 0.7763 (m90) cc_final: 0.7559 (m90)
REVERT: A  218 LYS cc_start: 0.4765 (mtmt) cc_final: 0.4304 (pttt)
REVERT: A  332 GLU cc_start: 0.6670 (pm20) cc_final: 0.6279 (pm20)
REVERT: B   78 LYS cc_start: 0.7760 (tptt) cc_final: 0.6993 (mmtp)
REVERT: B  185 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7318 (mp10)
REVERT: B  344 ARG cc_start: 0.6257 (mmt180) cc_final: 0.6043 (mmm-85)
REVERT: B  353 MET cc_start: 0.5949 (mtm) cc_final: 0.5151 (mtm)
REVERT: B  438 GLN cc_start: 0.7363 (pt0) cc_final: 0.6905 (pp30)
  outliers start: 2
  outliers final: 0
  residues processed: 184
  average time/residue: 0.0694
  time to fit residues: 17.1654
Evaluate side-chains
  132 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    0.0020
   chunk 55 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 4 optimal weight:    6.9990
   chunk 5 optimal weight:    0.1980
   chunk 31 optimal weight:    9.9990
   chunk 54 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 48 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.8390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 226 HIS
A 363 GLN
B 394 GLN
B 438 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.190344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.163539 restraints weight = 9149.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.167740 restraints weight = 5335.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.170596 restraints weight = 3543.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.172449 restraints weight = 2625.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.173900 restraints weight = 2124.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.4271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6687
moved from start:          0.4191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7084  Z= 0.143
  Angle     :  0.638   8.027   9773  Z= 0.320
  Chirality :  0.042   0.206   1109
  Planarity :  0.005   0.045   1139
  Dihedral  : 10.249 149.393   1292
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.62 (0.30), residues: 751
  helix:  2.32 (0.30), residues: 282
  sheet:  1.22 (0.53), residues: 86
  loop :  0.14 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 143 
 TYR   0.015   0.002   TYR B  47 
 PHE   0.014   0.002   PHE B 354 
 TRP   0.007   0.001   TRP B  93 
 HIS   0.012   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.14 ( 7084)
  covalent geometry    : angle       0.63794 /  0.32 ( 9773)
  hydrogen bonds       : bond        0.04460 /  2.57 (  307)
  hydrogen bonds       : angle       5.25980 /  3.09 (  863)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 ARG cc_start: 0.7487 (mtm110) cc_final: 0.6977 (mtm110)
REVERT: A  385 HIS cc_start: 0.6510 (t70) cc_final: 0.6065 (t70)
REVERT: A  428 PHE cc_start: 0.7812 (t80) cc_final: 0.7565 (t80)
REVERT: A  484 TYR cc_start: 0.6665 (m-80) cc_final: 0.6405 (m-80)
REVERT: B   78 LYS cc_start: 0.7765 (tptt) cc_final: 0.7111 (mmtp)
REVERT: B  274 MET cc_start: 0.6663 (mtt) cc_final: 0.6191 (mtm)
REVERT: B  285 ASN cc_start: 0.8009 (p0) cc_final: 0.7745 (p0)
REVERT: B  428 PHE cc_start: 0.6433 (t80) cc_final: 0.5992 (t80)
REVERT: B  438 GLN cc_start: 0.6992 (pt0) cc_final: 0.6644 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0749
  time to fit residues: 16.3477
Evaluate side-chains
  116 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 67 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 64 optimal weight:    1.9990
   chunk 23 optimal weight:   20.0000
   chunk 10 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   overall best weight:    2.3388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 226 HIS
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 217 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 = 0.4357 r_free = 0.4357 target = 0.182315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.153968 restraints weight = 9424.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.157892 restraints weight = 5685.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.160584 restraints weight = 3911.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.162188 restraints weight = 2993.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.163641 restraints weight = 2509.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
moved from start:          0.5063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7084  Z= 0.187
  Angle     :  0.658   6.382   9773  Z= 0.338
  Chirality :  0.042   0.175   1109
  Planarity :  0.005   0.067   1139
  Dihedral  : 10.424 151.834   1292
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.16 (0.30), residues: 751
  helix:  2.04 (0.30), residues: 282
  sheet:  0.42 (0.47), residues: 101
  loop : -0.09 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 431 
 TYR   0.020   0.002   TYR B  45 
 PHE   0.028   0.003   PHE B 428 
 TRP   0.003   0.001   TRP A 409 
 HIS   0.009   0.002   HIS B 347 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.19 ( 7084)
  covalent geometry    : angle       0.65779 /  0.34 ( 9773)
  hydrogen bonds       : bond        0.04347 /  2.49 (  307)
  hydrogen bonds       : angle       5.19634 /  3.09 (  863)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 ARG cc_start: 0.7484 (mtm110) cc_final: 0.7104 (mtm110)
REVERT: A  385 HIS cc_start: 0.6471 (t70) cc_final: 0.6066 (t70)
REVERT: A  428 PHE cc_start: 0.8073 (t80) cc_final: 0.7765 (t80)
REVERT: B   78 LYS cc_start: 0.8096 (tptt) cc_final: 0.7460 (mmtp)
REVERT: B  210 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7411 (tt0)
REVERT: B  274 MET cc_start: 0.7220 (mtt) cc_final: 0.6934 (mtm)
REVERT: B  290 ARG cc_start: 0.8638 (tpt90) cc_final: 0.8354 (mmm-85)
REVERT: B  353 MET cc_start: 0.6107 (mtm) cc_final: 0.5725 (mtm)
REVERT: B  377 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6779 (mm-30)
REVERT: B  428 PHE cc_start: 0.7950 (t80) cc_final: 0.7716 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.0796
  time to fit residues: 16.9904
Evaluate side-chains
  120 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 1 optimal weight:   10.0000
   chunk 9 optimal weight:    0.0670
   chunk 54 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 32 optimal weight:    0.0060
   overall best weight:    0.5534

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 226 HIS
** B 217 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 = 0.4400 r_free = 0.4400 target = 0.185559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.157827 restraints weight = 9181.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.161640 restraints weight = 5506.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.164126 restraints weight = 3766.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.166031 restraints weight = 2886.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.167079 restraints weight = 2378.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.5316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7084  Z= 0.122
  Angle     :  0.601   7.324   9773  Z= 0.300
  Chirality :  0.040   0.202   1109
  Planarity :  0.005   0.077   1139
  Dihedral  : 10.311 150.598   1292
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.26 (0.30), residues: 751
  helix:  2.27 (0.30), residues: 283
  sheet:  0.62 (0.51), residues: 97
  loop : -0.22 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 187 
 TYR   0.015   0.001   TYR B  45 
 PHE   0.013   0.001   PHE B 163 
 TRP   0.007   0.001   TRP B  93 
 HIS   0.006   0.001   HIS B 190 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 ( 7084)
  covalent geometry    : angle       0.60102 /  0.30 ( 9773)
  hydrogen bonds       : bond        0.03813 /  2.18 (  307)
  hydrogen bonds       : angle       4.91890 /  2.87 (  863)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 LYS cc_start: 0.5506 (mtmt) cc_final: 0.4320 (pttp)
REVERT: A  258 MET cc_start: 0.6668 (mmm) cc_final: 0.6441 (mmm)
REVERT: A  274 MET cc_start: 0.3833 (mtp) cc_final: 0.3560 (mtt)
REVERT: A  340 ARG cc_start: 0.7527 (mtm110) cc_final: 0.7110 (mtm110)
REVERT: A  376 MET cc_start: 0.7803 (mtp) cc_final: 0.7588 (mtp)
REVERT: A  385 HIS cc_start: 0.6252 (t70) cc_final: 0.5954 (t70)
REVERT: A  428 PHE cc_start: 0.8004 (t80) cc_final: 0.7667 (t80)
REVERT: A  499 GLN cc_start: 0.6574 (mt0) cc_final: 0.6305 (mt0)
REVERT: B   78 LYS cc_start: 0.8094 (tptt) cc_final: 0.7464 (mmtp)
REVERT: B  210 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7335 (tt0)
REVERT: B  290 ARG cc_start: 0.8496 (tpt90) cc_final: 0.7882 (mmm-85)
REVERT: B  301 GLU cc_start: 0.7200 (pp20) cc_final: 0.6952 (pp20)
REVERT: B  353 MET cc_start: 0.6117 (mtm) cc_final: 0.5712 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.0822
  time to fit residues: 16.5731
Evaluate side-chains
  116 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 42 optimal weight:   20.0000
   chunk 40 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0770
   chunk 47 optimal weight:    8.9990
   chunk 75 optimal weight:    0.0060
   overall best weight:    1.6158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 448 HIS
B 217 GLN
** B 311 HIS ** 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 = 0.4352 r_free = 0.4352 target = 0.181411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.152750 restraints weight = 9439.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.156464 restraints weight = 5786.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.159061 restraints weight = 4048.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.160527 restraints weight = 3115.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.161965 restraints weight = 2640.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.5730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7084  Z= 0.151
  Angle     :  0.605   6.369   9773  Z= 0.309
  Chirality :  0.040   0.164   1109
  Planarity :  0.004   0.047   1139
  Dihedral  : 10.345 151.335   1292
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.05 (0.30), residues: 751
  helix:  2.09 (0.31), residues: 283
  sheet:  0.41 (0.49), residues: 101
  loop : -0.31 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 227 
 TYR   0.016   0.002   TYR B  45 
 PHE   0.018   0.002   PHE A 371 
 TRP   0.005   0.001   TRP B  93 
 HIS   0.008   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.15 ( 7084)
  covalent geometry    : angle       0.60531 /  0.31 ( 9773)
  hydrogen bonds       : bond        0.03826 /  2.20 (  307)
  hydrogen bonds       : angle       4.93912 /  2.88 (  863)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 LYS cc_start: 0.5647 (mtmt) cc_final: 0.4673 (pttm)
REVERT: A  340 ARG cc_start: 0.7621 (mtm110) cc_final: 0.7167 (mtm110)
REVERT: A  385 HIS cc_start: 0.6183 (t70) cc_final: 0.5859 (t70)
REVERT: A  428 PHE cc_start: 0.7960 (t80) cc_final: 0.7615 (t80)
REVERT: A  501 ILE cc_start: 0.6875 (pt) cc_final: 0.6270 (mt)
REVERT: B   40 ASN cc_start: 0.5678 (t0) cc_final: 0.4680 (p0)
REVERT: B  353 MET cc_start: 0.6187 (mtm) cc_final: 0.5832 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0762
  time to fit residues: 15.0080
Evaluate side-chains
  112 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 18 optimal weight:    0.0770
   chunk 13 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 55 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0040
   chunk 38 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   chunk 28 optimal weight:    0.4980
   overall best weight:    1.1154

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 222 HIS
A 226 HIS
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 HIS ** 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 = 0.4376 r_free = 0.4376 target = 0.183759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.155614 restraints weight = 9284.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.159529 restraints weight = 5561.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.161959 restraints weight = 3823.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.164016 restraints weight = 2940.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.165055 restraints weight = 2410.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.4159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.5991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7084  Z= 0.133
  Angle     :  0.599   6.640   9773  Z= 0.304
  Chirality :  0.041   0.188   1109
  Planarity :  0.004   0.047   1139
  Dihedral  : 10.434 150.815   1292
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.02 (0.30), residues: 751
  helix:  2.11 (0.31), residues: 283
  sheet:  0.42 (0.49), residues: 101
  loop : -0.37 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  77 
 TYR   0.018   0.002   TYR B  45 
 PHE   0.021   0.002   PHE B 291 
 TRP   0.004   0.001   TRP B  93 
 HIS   0.013   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 7084)
  covalent geometry    : angle       0.59911 /  0.30 ( 9773)
  hydrogen bonds       : bond        0.03634 /  2.10 (  307)
  hydrogen bonds       : angle       4.78332 /  2.78 (  863)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A  274 MET cc_start: 0.3911 (mtp) cc_final: 0.3659 (mtt)
REVERT: A  340 ARG cc_start: 0.7702 (mtm110) cc_final: 0.7246 (mtm110)
REVERT: A  385 HIS cc_start: 0.6197 (t70) cc_final: 0.5865 (t70)
REVERT: A  428 PHE cc_start: 0.7936 (t80) cc_final: 0.7627 (t80)
REVERT: A  499 GLN cc_start: 0.6343 (mt0) cc_final: 0.6041 (mt0)
REVERT: A  501 ILE cc_start: 0.6902 (pt) cc_final: 0.6453 (mt)
REVERT: B   78 LYS cc_start: 0.8402 (tptt) cc_final: 0.7696 (mmtp)
REVERT: B  210 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7230 (tt0)
REVERT: B  353 MET cc_start: 0.6263 (mtm) cc_final: 0.5829 (mtm)
REVERT: B  354 PHE cc_start: 0.8136 (t80) cc_final: 0.7805 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0813
  time to fit residues: 15.5613
Evaluate side-chains
  111 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 4 optimal weight:    0.0670
   chunk 67 optimal weight:    0.5980
   chunk 69 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 31 optimal weight:    0.6980
   chunk 68 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.8720

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 226 HIS
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.182409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.154301 restraints weight = 9329.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.158221 restraints weight = 5631.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.160881 restraints weight = 3858.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.162702 restraints weight = 2951.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.163968 restraints weight = 2434.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.4162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6991
moved from start:          0.6218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7084  Z= 0.127
  Angle     :  0.607   6.342   9773  Z= 0.307
  Chirality :  0.041   0.186   1109
  Planarity :  0.004   0.053   1139
  Dihedral  : 10.427 150.012   1292
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.30), residues: 751
  helix:  2.13 (0.31), residues: 277
  sheet:  0.11 (0.48), residues: 101
  loop : -0.31 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 143 
 TYR   0.019   0.002   TYR B  45 
 PHE   0.011   0.001   PHE B  63 
 TRP   0.007   0.001   TRP B  93 
 HIS   0.005   0.001   HIS B 347 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 7084)
  covalent geometry    : angle       0.60706 /  0.31 ( 9773)
  hydrogen bonds       : bond        0.03486 /  2.01 (  307)
  hydrogen bonds       : angle       4.76733 /  2.72 (  863)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  274 MET cc_start: 0.3876 (mtp) cc_final: 0.3668 (mtt)
REVERT: A  340 ARG cc_start: 0.7725 (mtm110) cc_final: 0.7211 (mtm110)
REVERT: A  385 HIS cc_start: 0.6230 (t70) cc_final: 0.5880 (t70)
REVERT: A  428 PHE cc_start: 0.7899 (t80) cc_final: 0.7582 (t80)
REVERT: A  499 GLN cc_start: 0.6219 (mt0) cc_final: 0.5897 (mt0)
REVERT: A  501 ILE cc_start: 0.6876 (pt) cc_final: 0.6489 (mt)
REVERT: B   78 LYS cc_start: 0.8430 (tptt) cc_final: 0.7727 (mmtp)
REVERT: B  210 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7272 (tt0)
REVERT: B  270 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7601 (mm-30)
REVERT: B  353 MET cc_start: 0.6347 (mtm) cc_final: 0.5965 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0706
  time to fit residues: 12.8954
Evaluate side-chains
  107 residues out of total 644 (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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 52 optimal weight:    0.1980
   chunk 21 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 3 optimal weight:    0.2980
   chunk 42 optimal weight:    8.9990
   chunk 73 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 226 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.184537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.156111 restraints weight = 9404.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.160094 restraints weight = 5644.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.162863 restraints weight = 3849.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.164530 restraints weight = 2926.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.166004 restraints weight = 2422.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.4186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          0.6416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7084  Z= 0.123
  Angle     :  0.620   7.873   9773  Z= 0.309
  Chirality :  0.040   0.192   1109
  Planarity :  0.004   0.048   1139
  Dihedral  : 10.395 148.970   1292
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.30), residues: 751
  helix:  2.08 (0.31), residues: 279
  sheet: -0.31 (0.47), residues: 101
  loop : -0.34 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 143 
 TYR   0.018   0.002   TYR B  45 
 PHE   0.018   0.001   PHE A 371 
 TRP   0.006   0.001   TRP B 409 
 HIS   0.005   0.001   HIS B 347 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.12 ( 7084)
  covalent geometry    : angle       0.61982 /  0.31 ( 9773)
  hydrogen bonds       : bond        0.03477 /  2.01 (  307)
  hydrogen bonds       : angle       4.75627 /  2.72 (  863)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: A  274 MET cc_start: 0.3721 (mtp) cc_final: 0.3503 (mtt)
REVERT: A  340 ARG cc_start: 0.7708 (mtm110) cc_final: 0.7217 (mtm110)
REVERT: A  385 HIS cc_start: 0.6213 (t70) cc_final: 0.5861 (t70)
REVERT: A  428 PHE cc_start: 0.7888 (t80) cc_final: 0.7568 (t80)
REVERT: A  499 GLN cc_start: 0.5992 (mt0) cc_final: 0.5680 (mt0)
REVERT: A  501 ILE cc_start: 0.6652 (pt) cc_final: 0.6384 (mt)
REVERT: B   58 LEU cc_start: 0.7158 (mt) cc_final: 0.6948 (mt)
REVERT: B  210 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7331 (tt0)
REVERT: B  270 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7582 (mm-30)
REVERT: B  353 MET cc_start: 0.6254 (mtm) cc_final: 0.5943 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0651
  time to fit residues: 12.1539
Evaluate side-chains
  108 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 44 optimal weight:    7.9990
   chunk 73 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 41 optimal weight:   10.0000
   chunk 22 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 226 HIS
** A 239 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 = 0.4320 r_free = 0.4320 target = 0.179552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.151430 restraints weight = 9438.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.155219 restraints weight = 5795.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.157666 restraints weight = 4014.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.159515 restraints weight = 3100.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.160670 restraints weight = 2565.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.4102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.6745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7084  Z= 0.166
  Angle     :  0.673  10.045   9773  Z= 0.336
  Chirality :  0.042   0.187   1109
  Planarity :  0.005   0.046   1139
  Dihedral  : 10.554 149.345   1292
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.30), residues: 751
  helix:  2.01 (0.31), residues: 283
  sheet: -0.72 (0.48), residues: 102
  loop : -0.55 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 227 
 TYR   0.035   0.002   TYR B  47 
 PHE   0.036   0.002   PHE A 371 
 TRP   0.005   0.001   TRP A 409 
 HIS   0.015   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.17 ( 7084)
  covalent geometry    : angle       0.67326 /  0.34 ( 9773)
  hydrogen bonds       : bond        0.03844 /  2.23 (  307)
  hydrogen bonds       : angle       4.92953 /  2.80 (  863)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  274 MET cc_start: 0.3849 (mtp) cc_final: 0.3624 (mtt)
REVERT: A  340 ARG cc_start: 0.7672 (mtm110) cc_final: 0.7138 (mtm110)
REVERT: A  385 HIS cc_start: 0.6287 (t70) cc_final: 0.5999 (t70)
REVERT: A  392 PRO cc_start: 0.7531 (Cg_endo) cc_final: 0.7251 (Cg_exo)
REVERT: B  210 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7422 (tt0)
REVERT: B  270 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7585 (mm-30)
REVERT: B  353 MET cc_start: 0.6279 (mtm) cc_final: 0.5962 (mtm)
REVERT: B  406 ILE cc_start: 0.7580 (tt) cc_final: 0.7304 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0786
  time to fit residues: 13.7446
Evaluate side-chains
  102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 36 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9990
   chunk 23 optimal weight:    0.4980
   chunk 71 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 53 optimal weight:    4.9990
   chunk 2 optimal weight:   10.0000
   overall best weight:    2.4988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 495 HIS
** B 172 ASN ** 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 = 0.4271 r_free = 0.4271 target = 0.175180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.147051 restraints weight = 9490.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.150725 restraints weight = 5831.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.153283 restraints weight = 4063.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.154794 restraints weight = 3134.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.156208 restraints weight = 2640.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.4050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.7167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   7084  Z= 0.188
  Angle     :  0.692   7.153   9773  Z= 0.352
  Chirality :  0.043   0.271   1109
  Planarity :  0.005   0.041   1139
  Dihedral  : 10.795 149.411   1292
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.30), residues: 751
  helix:  1.72 (0.31), residues: 289
  sheet: -0.72 (0.50), residues: 102
  loop : -0.66 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 203 
 TYR   0.032   0.002   TYR B  47 
 PHE   0.035   0.003   PHE A 371 
 TRP   0.005   0.001   TRP B 409 
 HIS   0.009   0.001   HIS B 347 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00445 /  0.19 ( 7084)
  covalent geometry    : angle       0.69188 /  0.35 ( 9773)
  hydrogen bonds       : bond        0.04133 /  2.41 (  307)
  hydrogen bonds       : angle       5.04988 /  2.85 (  863)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1121.09 seconds
wall clock time: 20 minutes 6.66 seconds (1206.66 seconds total)