Starting phenix.real_space_refine
on Tue Mar  3 16:45:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u2a_26310/03_2026/7u2a_26310.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u2a_26310/03_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u2a_26310/03_2026/7u2a_26310.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u2a_26310/03_2026/7u2a_26310.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u2a_26310/03_2026/7u2a_26310.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u2a_26310/03_2026/7u2a_26310.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=   0.010
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-5986/lib/python3.9/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: 12
          Planarities with less than four sites: {'  A%rna2p_pur:plan': 1, '  A%rna2p_pur:plan2': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "A"
      Number of atoms: 2500
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 2500
          Classifications: {'peptide': 319}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 298}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 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: 1.80, per 1000 atoms: 0.26
  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: 0.82
  Conformation dependent library (CDL) restraints added in 200.1 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: 0.66
  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: 1.00

  Time building geometry restraints manager: 1.03 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: 4074
       30.35 -    60.71: 207
       60.71 -    91.06: 52
       91.06 -   121.41: 1
      121.41 -   151.76: 2
  Dihedral angle restraints: 4336
    sinusoidal: 2153
      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 4333 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:             0.290
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.390
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6007
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  : 18.248 151.765   2932
  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
  covalent geometry    : bond        0.01004 ( 7084)
  covalent geometry    : angle       1.05603 ( 9773)
  hydrogen bonds       : bond        0.15500 (  307)
  hydrogen bonds       : angle       7.04915 (  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  : 0.161 
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: 0.0941
  time to fit residues: 31.6405
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  : 0.198 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
A 375 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.191462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.165283 restraints weight = 9181.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.169485 restraints weight = 5288.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.172314 restraints weight = 3476.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.174081 restraints weight = 2556.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.175567 restraints weight = 2067.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.4289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6503
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.084   7084  Z= 0.156
  Angle     :  0.691   8.383   9773  Z= 0.345
  Chirality :  0.042   0.207   1109
  Planarity :  0.006   0.083   1139
  Dihedral  : 17.234 151.418   1470
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  3.44 %
    Favored  : 96.25 %
  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:  1.85 (0.30), residues: 751
  helix:  2.47 (0.30), residues: 286
  sheet:  1.44 (0.56), residues: 86
  loop :  0.27 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 143 
 TYR   0.029   0.003   TYR B  47 
 PHE   0.020   0.002   PHE B 163 
 TRP   0.024   0.003   TRP A 409 
 HIS   0.008   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7084)
  covalent geometry    : angle       0.69083 ( 9773)
  hydrogen bonds       : bond        0.05142 (  307)
  hydrogen bonds       : angle       5.58202 (  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
  187 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 185
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.7615 (mtmt) cc_final: 0.7377 (tptt)
REVERT: A  218 LYS cc_start: 0.4779 (mtmt) cc_final: 0.4332 (pttt)
REVERT: A  332 GLU cc_start: 0.6681 (pm20) cc_final: 0.6287 (pm20)
REVERT: B   78 LYS cc_start: 0.7716 (tptt) cc_final: 0.6990 (mmtp)
REVERT: B  185 GLN cc_start: 0.7665 (mm-40) cc_final: 0.7328 (mp10)
REVERT: B  201 GLN cc_start: 0.7036 (pp30) cc_final: 0.6699 (pp30)
REVERT: B  208 ILE cc_start: 0.8099 (mm) cc_final: 0.7881 (mm)
REVERT: B  250 LEU cc_start: 0.8522 (mm) cc_final: 0.7964 (mm)
REVERT: B  353 MET cc_start: 0.5953 (mtm) cc_final: 0.5324 (mtm)
REVERT: B  438 GLN cc_start: 0.7355 (pt0) cc_final: 0.6885 (pp30)
  outliers start: 2
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0825
  time to fit residues: 20.5481
Evaluate side-chains
  131 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 4 optimal weight:    0.2980
   chunk 5 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 226 HIS
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 495 HIS
B 438 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.183775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.156416 restraints weight = 9314.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.160302 restraints weight = 5587.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.162710 restraints weight = 3816.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.164733 restraints weight = 2927.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.165629 restraints weight = 2384.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.4166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6814
moved from start:          0.4517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7084  Z= 0.199
  Angle     :  0.695   8.808   9773  Z= 0.352
  Chirality :  0.044   0.186   1109
  Planarity :  0.005   0.055   1139
  Dihedral  : 16.776 152.130   1470
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.13 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  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:  1.35 (0.30), residues: 751
  helix:  2.08 (0.30), residues: 285
  sheet:  0.56 (0.48), residues: 97
  loop :  0.12 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 330 
 TYR   0.019   0.003   TYR B  45 
 PHE   0.022   0.002   PHE A 446 
 TRP   0.005   0.001   TRP B 409 
 HIS   0.010   0.002   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 7084)
  covalent geometry    : angle       0.69462 ( 9773)
  hydrogen bonds       : bond        0.04790 (  307)
  hydrogen bonds       : angle       5.35099 (  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  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  385 HIS cc_start: 0.6561 (t70) cc_final: 0.6083 (t70)
REVERT: A  428 PHE cc_start: 0.7976 (t80) cc_final: 0.7656 (t80)
REVERT: B   78 LYS cc_start: 0.7992 (tptt) cc_final: 0.7284 (mmtp)
REVERT: B  208 ILE cc_start: 0.8231 (mm) cc_final: 0.7963 (mm)
REVERT: B  274 MET cc_start: 0.7079 (mtt) cc_final: 0.6661 (mtm)
REVERT: B  290 ARG cc_start: 0.8559 (tpt90) cc_final: 0.8065 (mmm-85)
REVERT: B  353 MET cc_start: 0.5937 (mtm) cc_final: 0.5699 (mtm)
REVERT: B  361 LEU cc_start: 0.7956 (tp) cc_final: 0.7570 (tt)
REVERT: B  428 PHE cc_start: 0.6949 (t80) cc_final: 0.6373 (t80)
REVERT: B  432 ARG cc_start: 0.7084 (mmt180) cc_final: 0.6770 (ttm170)
REVERT: B  464 LEU cc_start: 0.6847 (mt) cc_final: 0.6606 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0900
  time to fit residues: 19.7399
Evaluate side-chains
  125 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 6 optimal weight:    0.0670
   chunk 67 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9980
   chunk 23 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 42 optimal weight:   20.0000
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.4122

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4374 r_free = 0.4374 target = 0.184435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.156163 restraints weight = 9454.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.160160 restraints weight = 5690.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.162880 restraints weight = 3915.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.164800 restraints weight = 2985.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.166095 restraints weight = 2464.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.5051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7084  Z= 0.152
  Angle     :  0.628   6.786   9773  Z= 0.316
  Chirality :  0.041   0.192   1109
  Planarity :  0.005   0.081   1139
  Dihedral  : 16.564 152.058   1470
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  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:  1.17 (0.30), residues: 751
  helix:  2.15 (0.30), residues: 285
  sheet:  0.10 (0.46), residues: 109
  loop : -0.08 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 216 
 TYR   0.021   0.002   TYR B 500 
 PHE   0.018   0.002   PHE B  63 
 TRP   0.005   0.001   TRP B 409 
 HIS   0.007   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 7084)
  covalent geometry    : angle       0.62765 ( 9773)
  hydrogen bonds       : bond        0.04097 (  307)
  hydrogen bonds       : angle       5.08566 (  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
  159 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  274 MET cc_start: 0.3945 (mtp) cc_final: 0.3613 (mtt)
REVERT: A  340 ARG cc_start: 0.7673 (mtm110) cc_final: 0.7299 (mtm-85)
REVERT: A  385 HIS cc_start: 0.6417 (t70) cc_final: 0.5979 (t70)
REVERT: A  410 MET cc_start: 0.4917 (mtt) cc_final: 0.3525 (mtp)
REVERT: A  499 GLN cc_start: 0.6409 (mt0) cc_final: 0.6148 (mt0)
REVERT: B   78 LYS cc_start: 0.8185 (tptt) cc_final: 0.7445 (mmtp)
REVERT: B  210 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7349 (mm-30)
REVERT: B  274 MET cc_start: 0.7293 (mtt) cc_final: 0.7022 (mtm)
REVERT: B  290 ARG cc_start: 0.8663 (tpt90) cc_final: 0.8254 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.0869
  time to fit residues: 18.1686
Evaluate side-chains
  122 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 58 optimal weight:    0.6980
   chunk 1 optimal weight:    9.9990
   chunk 9 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 61 optimal weight:    8.9990
   chunk 70 optimal weight:    9.9990
   chunk 32 optimal weight:    0.4980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 363 GLN
A 366 GLN
B 385 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.183317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.155888 restraints weight = 9148.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.159652 restraints weight = 5505.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.162266 restraints weight = 3788.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.164002 restraints weight = 2880.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.165262 restraints weight = 2376.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.4171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6826
moved from start:          0.5463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7084  Z= 0.127
  Angle     :  0.593   7.549   9773  Z= 0.299
  Chirality :  0.040   0.190   1109
  Planarity :  0.004   0.045   1139
  Dihedral  : 16.236 151.490   1470
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  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:  1.11 (0.30), residues: 751
  helix:  2.21 (0.30), residues: 285
  sheet:  0.08 (0.47), residues: 109
  loop : -0.24 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 187 
 TYR   0.016   0.002   TYR B  45 
 PHE   0.024   0.002   PHE B 371 
 TRP   0.005   0.001   TRP B  93 
 HIS   0.006   0.001   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7084)
  covalent geometry    : angle       0.59316 ( 9773)
  hydrogen bonds       : bond        0.03700 (  307)
  hydrogen bonds       : angle       4.90385 (  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
  149 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.5384 (mtmt) cc_final: 0.4337 (pttp)
REVERT: A  258 MET cc_start: 0.6789 (mmm) cc_final: 0.6570 (mmm)
REVERT: A  274 MET cc_start: 0.3982 (mtp) cc_final: 0.3686 (mtt)
REVERT: A  340 ARG cc_start: 0.7608 (mtm110) cc_final: 0.7302 (ptp90)
REVERT: A  385 HIS cc_start: 0.6342 (t70) cc_final: 0.6041 (t70)
REVERT: A  499 GLN cc_start: 0.6621 (mt0) cc_final: 0.6270 (mt0)
REVERT: B   78 LYS cc_start: 0.8175 (tptt) cc_final: 0.7515 (mmtp)
REVERT: B  210 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7194 (mm-30)
REVERT: B  274 MET cc_start: 0.7186 (mtt) cc_final: 0.6868 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.0877
  time to fit residues: 17.2162
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  : 0.230 
-------------------------------------------------------------------------------
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:    0.0270
   chunk 12 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   chunk 15 optimal weight:    6.9990
   chunk 32 optimal weight:    0.0050
   chunk 42 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   chunk 68 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 75 optimal weight:    6.9990
   overall best weight:    1.3654

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 363 GLN
B 438 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.181402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.153994 restraints weight = 9327.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.157623 restraints weight = 5677.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.159991 restraints weight = 3923.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.161874 restraints weight = 3015.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.162723 restraints weight = 2479.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
moved from start:          0.5826

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= 0.138
  Angle     :  0.595   6.530   9773  Z= 0.302
  Chirality :  0.040   0.174   1109
  Planarity :  0.005   0.047   1139
  Dihedral  : 16.046 151.798   1470
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  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:  1.00 (0.30), residues: 751
  helix:  2.15 (0.30), residues: 285
  sheet:  0.07 (0.48), residues: 107
  loop : -0.34 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 432 
 TYR   0.026   0.002   TYR B 500 
 PHE   0.012   0.002   PHE B 428 
 TRP   0.005   0.001   TRP B  93 
 HIS   0.007   0.001   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7084)
  covalent geometry    : angle       0.59453 ( 9773)
  hydrogen bonds       : bond        0.03674 (  307)
  hydrogen bonds       : angle       4.77156 (  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: symmetry clash
REVERT: A  218 LYS cc_start: 0.5420 (mtmt) cc_final: 0.4636 (pttp)
REVERT: A  340 ARG cc_start: 0.7603 (mtm110) cc_final: 0.7308 (ptp90)
REVERT: A  385 HIS cc_start: 0.6262 (t70) cc_final: 0.5917 (t70)
REVERT: A  410 MET cc_start: 0.5334 (mtt) cc_final: 0.5126 (mtt)
REVERT: A  428 PHE cc_start: 0.8056 (t80) cc_final: 0.7696 (t80)
REVERT: B   78 LYS cc_start: 0.8419 (tptt) cc_final: 0.7697 (mmtp)
REVERT: B   99 LEU cc_start: 0.6804 (mp) cc_final: 0.6588 (mt)
REVERT: B  210 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7148 (mm-30)
REVERT: B  270 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7578 (mm-30)
REVERT: B  274 MET cc_start: 0.7131 (mtt) cc_final: 0.6841 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0845
  time to fit residues: 16.4613
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  : 0.260 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 18 optimal weight:    0.0470
   chunk 13 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0060
   chunk 6 optimal weight:    0.8980
   chunk 55 optimal weight:    0.0870
   chunk 15 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0070
   chunk 59 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0170
   overall best weight:    0.0328

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

Flipped N/Q/H residues before XYZ refinement:
A 226 HIS
** A 429 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 = 0.4402 r_free = 0.4402 target = 0.187219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.159920 restraints weight = 9187.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.163991 restraints weight = 5438.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.166757 restraints weight = 3667.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.168621 restraints weight = 2750.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.169977 restraints weight = 2237.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.4209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6778
moved from start:          0.6105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7084  Z= 0.113
  Angle     :  0.593   8.314   9773  Z= 0.297
  Chirality :  0.039   0.180   1109
  Planarity :  0.004   0.045   1139
  Dihedral  : 15.848 149.549   1470
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  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:  1.09 (0.30), residues: 751
  helix:  2.23 (0.31), residues: 287
  sheet:  0.01 (0.49), residues: 102
  loop : -0.26 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 187 
 TYR   0.018   0.002   TYR A 401 
 PHE   0.019   0.002   PHE B 291 
 TRP   0.006   0.001   TRP B 409 
 HIS   0.008   0.001   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 7084)
  covalent geometry    : angle       0.59251 ( 9773)
  hydrogen bonds       : bond        0.03284 (  307)
  hydrogen bonds       : angle       4.60993 (  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
  155 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.5381 (mtmt) cc_final: 0.4625 (pttm)
REVERT: A  274 MET cc_start: 0.3519 (mtp) cc_final: 0.3278 (mtt)
REVERT: A  340 ARG cc_start: 0.7497 (mtm110) cc_final: 0.7294 (mtm110)
REVERT: A  385 HIS cc_start: 0.6183 (t70) cc_final: 0.5893 (t70)
REVERT: A  428 PHE cc_start: 0.7995 (t80) cc_final: 0.7690 (t80)
REVERT: A  484 TYR cc_start: 0.6339 (m-80) cc_final: 0.6031 (m-80)
REVERT: A  499 GLN cc_start: 0.6120 (mt0) cc_final: 0.5886 (mt0)
REVERT: A  501 ILE cc_start: 0.6688 (pt) cc_final: 0.6176 (mt)
REVERT: B   78 LYS cc_start: 0.8462 (tptt) cc_final: 0.7763 (mmtp)
REVERT: B  210 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7077 (mm-30)
REVERT: B  270 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7529 (mm-30)
REVERT: B  274 MET cc_start: 0.7135 (mtt) cc_final: 0.6774 (mtm)
REVERT: B  361 LEU cc_start: 0.8185 (tp) cc_final: 0.7803 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.0816
  time to fit residues: 16.9534
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  : 0.221 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 4 optimal weight:    0.0040
   chunk 67 optimal weight:    0.3980
   chunk 69 optimal weight:    6.9990
   chunk 41 optimal weight:    8.9990
   chunk 31 optimal weight:    0.0370
   chunk 68 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 17 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.3870

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 HIS
** B 470 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 = 0.4382 r_free = 0.4382 target = 0.184939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.157604 restraints weight = 9203.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.161441 restraints weight = 5480.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.163948 restraints weight = 3724.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.165863 restraints weight = 2827.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.167220 restraints weight = 2302.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.4194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6802
moved from start:          0.6298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   7084  Z= 0.113
  Angle     :  0.608  10.209   9773  Z= 0.299
  Chirality :  0.040   0.165   1109
  Planarity :  0.004   0.047   1139
  Dihedral  : 15.745 148.896   1470
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  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:  0.99 (0.30), residues: 751
  helix:  2.18 (0.31), residues: 287
  sheet: -0.20 (0.48), residues: 102
  loop : -0.29 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 187 
 TYR   0.015   0.001   TYR B  45 
 PHE   0.021   0.001   PHE B 428 
 TRP   0.006   0.001   TRP B  93 
 HIS   0.009   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7084)
  covalent geometry    : angle       0.60848 ( 9773)
  hydrogen bonds       : bond        0.03251 (  307)
  hydrogen bonds       : angle       4.61005 (  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
  141 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.5304 (mtmt) cc_final: 0.4615 (pttm)
REVERT: A  293 ASP cc_start: 0.8532 (t0) cc_final: 0.8272 (t70)
REVERT: A  385 HIS cc_start: 0.6230 (t70) cc_final: 0.5877 (t70)
REVERT: A  392 PRO cc_start: 0.7209 (Cg_endo) cc_final: 0.7000 (Cg_exo)
REVERT: A  428 PHE cc_start: 0.7955 (t80) cc_final: 0.7634 (t80)
REVERT: A  484 TYR cc_start: 0.6324 (m-80) cc_final: 0.5801 (m-80)
REVERT: A  499 GLN cc_start: 0.6089 (mt0) cc_final: 0.5831 (mt0)
REVERT: A  501 ILE cc_start: 0.6707 (pt) cc_final: 0.6189 (mt)
REVERT: B  205 HIS cc_start: 0.7469 (p-80) cc_final: 0.7227 (p-80)
REVERT: B  210 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7057 (mm-30)
REVERT: B  274 MET cc_start: 0.7014 (mtt) cc_final: 0.6755 (mtm)
REVERT: B  290 ARG cc_start: 0.8334 (tpt90) cc_final: 0.7960 (tpp-160)
REVERT: B  361 LEU cc_start: 0.8195 (tp) cc_final: 0.7800 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.0649
  time to fit residues: 12.9008
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  : 0.223 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 52 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    9.9990
   chunk 42 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 363 GLN
A 429 GLN
** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 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 = 0.4296 r_free = 0.4296 target = 0.177450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.148887 restraints weight = 9477.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.152659 restraints weight = 5765.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.155258 restraints weight = 3988.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.156900 restraints weight = 3060.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.158270 restraints weight = 2554.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.4086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.6619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   7084  Z= 0.170
  Angle     :  0.657   6.458   9773  Z= 0.333
  Chirality :  0.042   0.261   1109
  Planarity :  0.005   0.048   1139
  Dihedral  : 15.633 149.420   1470
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  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:  0.79 (0.30), residues: 751
  helix:  2.01 (0.31), residues: 291
  sheet: -0.27 (0.48), residues: 102
  loop : -0.46 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 187 
 TYR   0.024   0.002   TYR B  47 
 PHE   0.025   0.002   PHE B 428 
 TRP   0.004   0.001   TRP B 409 
 HIS   0.007   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 7084)
  covalent geometry    : angle       0.65745 ( 9773)
  hydrogen bonds       : bond        0.03772 (  307)
  hydrogen bonds       : angle       4.89043 (  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
  136 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 LYS cc_start: 0.5362 (mtmt) cc_final: 0.4721 (pttm)
REVERT: A  367 LEU cc_start: 0.8851 (tp) cc_final: 0.8596 (tp)
REVERT: A  385 HIS cc_start: 0.6260 (t70) cc_final: 0.5954 (t70)
REVERT: A  392 PRO cc_start: 0.7559 (Cg_endo) cc_final: 0.7266 (Cg_exo)
REVERT: A  428 PHE cc_start: 0.8142 (t80) cc_final: 0.7766 (t80)
REVERT: A  501 ILE cc_start: 0.6789 (pt) cc_final: 0.6527 (mt)
REVERT: B  210 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7263 (mm-30)
REVERT: B  258 MET cc_start: 0.7714 (ttm) cc_final: 0.7426 (ttm)
REVERT: B  270 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7520 (mm-30)
REVERT: B  274 MET cc_start: 0.7088 (mtt) cc_final: 0.6698 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0664
  time to fit residues: 12.7390
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  : 0.176 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   chunk 22 optimal weight:    0.0670
   chunk 27 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
A 222 HIS
A 226 HIS
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
** B 470 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 = 0.4338 r_free = 0.4338 target = 0.181552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.153254 restraints weight = 9298.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.156997 restraints weight = 5653.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.159541 restraints weight = 3921.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.161276 restraints weight = 3017.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.161984 restraints weight = 2506.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.6899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7084  Z= 0.124
  Angle     :  0.628   7.837   9773  Z= 0.318
  Chirality :  0.040   0.266   1109
  Planarity :  0.005   0.050   1139
  Dihedral  : 15.493 147.806   1470
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  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:  0.75 (0.31), residues: 751
  helix:  1.92 (0.31), residues: 291
  sheet: -0.39 (0.49), residues: 102
  loop : -0.37 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 187 
 TYR   0.012   0.002   TYR B  45 
 PHE   0.027   0.002   PHE B 354 
 TRP   0.005   0.001   TRP B  93 
 HIS   0.009   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7084)
  covalent geometry    : angle       0.62825 ( 9773)
  hydrogen bonds       : bond        0.03381 (  307)
  hydrogen bonds       : angle       4.68896 (  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
  129 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.5332 (mtmt) cc_final: 0.4724 (pttm)
REVERT: A  293 ASP cc_start: 0.8521 (t0) cc_final: 0.8268 (t70)
REVERT: A  385 HIS cc_start: 0.6182 (t70) cc_final: 0.5972 (t70)
REVERT: A  392 PRO cc_start: 0.7467 (Cg_endo) cc_final: 0.7189 (Cg_exo)
REVERT: A  428 PHE cc_start: 0.7971 (t80) cc_final: 0.7633 (t80)
REVERT: A  501 ILE cc_start: 0.6763 (pt) cc_final: 0.6526 (mt)
REVERT: B   78 LYS cc_start: 0.8488 (tptt) cc_final: 0.7892 (mmtp)
REVERT: B  205 HIS cc_start: 0.7678 (p-80) cc_final: 0.7412 (p-80)
REVERT: B  210 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7124 (mm-30)
REVERT: B  270 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7417 (mm-30)
REVERT: B  274 MET cc_start: 0.6903 (mtt) cc_final: 0.6601 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0635
  time to fit residues: 11.5939
Evaluate side-chains
  103 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   chunk 53 optimal weight:    0.0570
   chunk 2 optimal weight:   10.0000
   overall best weight:    2.4106

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

Flipped N/Q/H residues before XYZ refinement:
A 226 HIS
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 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 = 0.4282 r_free = 0.4282 target = 0.176537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.147302 restraints weight = 9522.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.150832 restraints weight = 5933.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.153334 restraints weight = 4203.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.155027 restraints weight = 3291.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.156016 restraints weight = 2774.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.7144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7084  Z= 0.190
  Angle     :  0.698   7.235   9773  Z= 0.354
  Chirality :  0.043   0.234   1109
  Planarity :  0.005   0.048   1139
  Dihedral  : 15.558 148.317   1470
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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:  0.48 (0.30), residues: 751
  helix:  1.81 (0.31), residues: 291
  sheet: -0.68 (0.47), residues: 109
  loop : -0.58 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 187 
 TYR   0.026   0.003   TYR B  47 
 PHE   0.022   0.002   PHE B 354 
 TRP   0.008   0.002   TRP A 409 
 HIS   0.011   0.002   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 7084)
  covalent geometry    : angle       0.69779 ( 9773)
  hydrogen bonds       : bond        0.04093 (  307)
  hydrogen bonds       : angle       4.95019 (  863)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1155.40 seconds
wall clock time: 20 minutes 38.50 seconds (1238.50 seconds total)