Starting phenix.real_space_refine
on Wed Feb 12 08:50:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u2b_26311/02_2025/7u2b_26311.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u2b_26311/02_2025/7u2b_26311.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u2b_26311/02_2025/7u2b_26311.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u2b_26311/02_2025/7u2b_26311.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u2b_26311/02_2025/7u2b_26311.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u2b_26311/02_2025/7u2b_26311.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      53      5.49       5
     S      34      5.16       5
     C    4408      2.51       5
     N    1316      2.21       5
     O    1505      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7316
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 1111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 1111
          Classifications: {'RNA': 53}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 21, 'rna3p_pyr': 26}
          Link IDs: {'rna2p': 5, 'rna3p': 47}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'  A%rna2p_pur:plan2': 1, '  A%rna2p_pur:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "A"
      Number of atoms: 2500
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 2500
          Classifications: {'peptide': 319}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 298}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 3647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 461, 3647
          Classifications: {'peptide': 461}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 433}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG: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: 4.75, per 1000 atoms: 0.65
  Number of scatterers: 7316
  At special positions: 0
  Unit cell: (70.15, 95.45, 126.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     P      53     15.00
     O    1505      8.00
     N    1316      7.00
     C    4408      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.19
  Conformation dependent library (CDL) restraints added in 723.4 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 7 sheets defined
      42.8% alpha, 16.0% beta
      8 base pairs and 22 stacking pairs defined.
    Time for finding SS restraints: 2.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 204 through 213
    Processing helix  chain 'A' and resid 220 through 225
    Processing helix  chain 'A' and resid 233 through 253
      removed outlier: 3.507A  pdb=" N   ARG A 253 " --> pdb=" O   LYS A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 272
      removed outlier: 3.579A  pdb=" N   PHE A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 308
      removed outlier: 4.020A  pdb=" N   GLY A 303 " --> pdb=" O   THR A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 383
      removed outlier: 3.512A  pdb=" N   SER A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 434
    Processing helix  chain 'A' and resid 457 through 468
    Processing helix  chain 'A' and resid 478 through 486
      removed outlier: 4.254A  pdb=" N   SER A 483 " --> pdb=" O   PRO A 479 " (cutoff:3.500A)
      removed outlier: 5.050A  pdb=" N   TYR A 484 " --> pdb=" O   ALA A 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 51
      removed outlier: 3.659A  pdb=" N   GLU B  46 " --> pdb=" O   ASN B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 64
      removed outlier: 3.595A  pdb=" N   PHE B  63 " --> pdb=" O   ASP B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 78
      removed outlier: 3.613A  pdb=" N   ALA B  70 " --> pdb=" O   CYS B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 84
      No H-bonds generated for 'chain 'B' and resid 82 through 84'
    Processing helix  chain 'B' and resid 85 through 123
      removed outlier: 3.610A  pdb=" N   ILE B  89 " --> pdb=" O   ASP B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 132
    Processing helix  chain 'B' and resid 132 through 169
      removed outlier: 3.592A  pdb=" N   GLN B 136 " --> pdb=" O   ASP B 132 " (cutoff:3.500A)
      Proline residue:  B 154  - end of helix
      removed outlier: 4.311A  pdb=" N   LYS B 169 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 213
    Processing helix  chain 'B' and resid 220 through 225
    Processing helix  chain 'B' and resid 233 through 253
    Processing helix  chain 'B' and resid 265 through 273
      removed outlier: 3.619A  pdb=" N   PHE B 269 " --> pdb=" O   ARG B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 309
      removed outlier: 3.731A  pdb=" N   GLY B 303 " --> pdb=" O   THR B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 383
    Processing helix  chain 'B' and resid 427 through 434
      removed outlier: 3.657A  pdb=" N   ARG B 431 " --> pdb=" O   ASP B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 469
    Processing helix  chain 'B' and resid 478 through 486
      removed outlier: 4.076A  pdb=" N   SER B 483 " --> pdb=" O   PRO B 479 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   TYR B 484 " --> pdb=" O   ALA B 480 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 192
      removed outlier: 6.402A  pdb=" N   VAL A 188 " --> pdb=" O   ASP A 390 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   ASP A 390 " --> pdb=" O   VAL A 188 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ARG A 402 " --> pdb=" O   SER A 423 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   SER A 423 " --> pdb=" O   ARG A 402 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   PHE A 404 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   SER A 421 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ILE A 406 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 9.763A  pdb=" N   VAL A 419 " --> pdb=" O   CYS A 455 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   CYS A 455 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   SER A 421 " --> pdb=" O   THR A 453 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   THR A 453 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ASN A 451 " --> pdb=" O   SER A 423 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   THR A 449 " --> pdb=" O   CYS A 425 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   HIS A 448 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   VAL A 351 " --> pdb=" O   ALA A 454 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   ALA A 456 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   THR A 349 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LYS A 350 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   SER A 326 " --> pdb=" O   LYS A 350 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   SER A 325 " --> pdb=" O   MET A 258 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU B 231 " --> pdb=" O   THR A 259 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   TYR B 230 " --> pdb=" O   ARG B 216 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 216
      removed outlier: 3.702A  pdb=" N   TYR A 230 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU A 231 " --> pdb=" O   THR B 259 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   SER B 325 " --> pdb=" O   MET B 258 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   SER B 326 " --> pdb=" O   LYS B 350 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS B 350 " --> pdb=" O   SER B 326 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   THR B 349 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   ALA B 456 " --> pdb=" O   THR B 349 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   VAL B 351 " --> pdb=" O   ALA B 454 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   SER B 421 " --> pdb=" O   THR B 453 " (cutoff:3.500A)
      removed outlier: 5.621A  pdb=" N   CYS B 455 " --> pdb=" O   VAL B 419 " (cutoff:3.500A)
      removed outlier: 9.147A  pdb=" N   VAL B 419 " --> pdb=" O   CYS B 455 " (cutoff:3.500A)
      removed outlier: 5.646A  pdb=" N   GLU B 418 " --> pdb=" O   ALA B 408 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ALA B 408 " --> pdb=" O   GLU B 418 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   ASP B 390 " --> pdb=" O   VAL B 188 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   VAL B 188 " --> pdb=" O   ASP B 390 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 264
    Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 312
    Processing sheet with id=AA5, first strand: chain 'A' and resid 437 through 438
    Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 500
      removed outlier: 3.539A  pdb=" N   GLN A 499 " --> pdb=" O   THR B 312 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   HIS B 311 " --> pdb=" O   MET B 436 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   GLN B 438 " --> pdb=" O   HIS B 311 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   VAL B 313 " --> pdb=" O   GLN B 438 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 263 through 264

    291 hydrogen bonds defined for protein.
    843 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      20 hydrogen bonds
      40 hydrogen bond angles
      0 basepair planarities
      8 basepair parallelities
      22 stacking parallelities
  Total time for adding SS restraints: 2.42

  Time building geometry restraints manager: 2.45 seconds

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

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

  Histogram of bond angle deviations from ideal:
        0.00 -     4.02: 10461
        4.02 -     8.04: 55
        8.04 -    12.06: 7
       12.06 -    16.08: 0
       16.08 -    20.10: 2
  Bond angle restraints: 10525
  Sorted by residual:
  angle pdb=" O1S SSA B 601 "
        pdb=" S1  SSA B 601 "
        pdb=" O2S SSA B 601 "
      ideal   model   delta    sigma   weight residual
     121.34  101.24   20.10 3.00e+00 1.11e-01 4.49e+01
  angle pdb=" O1S SSA A 601 "
        pdb=" S1  SSA A 601 "
        pdb=" O2S SSA A 601 "
      ideal   model   delta    sigma   weight residual
     121.34  102.90   18.44 3.00e+00 1.11e-01 3.78e+01
  angle pdb=" N   THR B 426 "
        pdb=" CA  THR B 426 "
        pdb=" C   THR B 426 "
      ideal   model   delta    sigma   weight residual
     111.37  117.25   -5.88 1.64e+00 3.72e-01 1.28e+01
  angle pdb=" N1  SSA B 601 "
        pdb=" C6  SSA B 601 "
        pdb=" N6  SSA B 601 "
      ideal   model   delta    sigma   weight residual
     119.38  108.72   10.66 3.00e+00 1.11e-01 1.26e+01
  angle pdb=" N   VAL B 223 "
        pdb=" CA  VAL B 223 "
        pdb=" C   VAL B 223 "
      ideal   model   delta    sigma   weight residual
     109.34  116.64   -7.30 2.08e+00 2.31e-01 1.23e+01
  ... (remaining 10520 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.30: 4366
       30.30 -    60.61: 225
       60.61 -    90.91: 62
       90.91 -   121.22: 1
      121.22 -   151.52: 3
  Dihedral angle restraints: 4657
    sinusoidal: 2419
      harmonic: 2238
  Sorted by residual:
  dihedral pdb=" O4'   U C   9 "
           pdb=" C1'   U C   9 "
           pdb=" N1    U C   9 "
           pdb=" C2    U C   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   -8.48 -151.52     1      1.50e+01 4.44e-03 8.02e+01
  dihedral pdb=" O4'   C C   8 "
           pdb=" C1'   C C   8 "
           pdb=" N1    C C   8 "
           pdb=" C2    C C   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -10.64 -149.36     1      1.50e+01 4.44e-03 7.94e+01
  dihedral pdb=" O4'   C C  10 "
           pdb=" C1'   C C  10 "
           pdb=" N1    C C  10 "
           pdb=" C2    C C  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -16.50 -143.50     1      1.50e+01 4.44e-03 7.70e+01
  ... (remaining 4654 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 1170
       0.113 -    0.226: 32
       0.226 -    0.339: 0
       0.339 -    0.453: 0
       0.453 -    0.566: 2
  Chirality restraints: 1204
  Sorted by residual:
  chirality pdb=" CA  SSA B 601 "
            pdb=" CB  SSA B 601 "
            pdb=" C9  SSA B 601 "
            pdb=" N10 SSA B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -3.03    0.57 2.00e-01 2.50e+01 8.00e+00
  chirality pdb=" CA  SSA A 601 "
            pdb=" CB  SSA A 601 "
            pdb=" C9  SSA A 601 "
            pdb=" N10 SSA A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -3.02    0.56 2.00e-01 2.50e+01 7.75e+00
  chirality pdb=" CA  ILE A 435 "
            pdb=" N   ILE A 435 "
            pdb=" C   ILE A 435 "
            pdb=" CB  ILE A 435 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.40e-01
  ... (remaining 1201 not shown)

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

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 43
        2.53 -     3.12: 5593
        3.12 -     3.71: 11574
        3.71 -     4.31: 15512
        4.31 -     4.90: 25209
  Nonbonded interactions: 57931
  Sorted by model distance:
  nonbonded pdb=" O2    C C   8 "
            pdb=" O2'   C C  33 "
     model   vdw
     1.936 3.040
  nonbonded pdb=" O2'   A C  45 "
            pdb=" O5'   A C  46 "
     model   vdw
     2.011 3.040
  nonbonded pdb=" OG1 THR A 453 "
            pdb=" OG  SSA A 601 "
     model   vdw
     2.032 3.040
  nonbonded pdb=" OG  SER A 224 "
            pdb=" OG  SER A 228 "
     model   vdw
     2.059 3.040
  nonbonded pdb=" OH  TYR A 329 "
            pdb=" OH  TYR B 329 "
     model   vdw
     2.099 3.040
  ... (remaining 57926 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.870
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6827
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.187   7585  Z= 0.610
  Angle     :  0.962  20.098  10525  Z= 0.520
  Chirality :  0.051   0.566   1204
  Planarity :  0.004   0.043   1184
  Dihedral  : 18.560 151.523   3219
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 12.52 %
    Favored  : 87.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.29), residues: 772
  helix:  3.12 (0.28), residues: 288
  sheet:  0.78 (0.48), residues: 105
  loop :  0.40 (0.30), residues: 379

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

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

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 236
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 MET cc_start: 0.8547 (mtt) cc_final: 0.8124 (mmm)
REVERT: A  205 HIS cc_start: 0.8447 (p-80) cc_final: 0.8172 (p-80)
REVERT: A  211 LYS cc_start: 0.8708 (mtmp) cc_final: 0.8225 (tmtt)
REVERT: A  218 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7820 (mmmm)
REVERT: A  258 MET cc_start: 0.8254 (ttm) cc_final: 0.7646 (mtp)
REVERT: A  425 CYS cc_start: 0.8546 (m) cc_final: 0.8241 (t)
REVERT: A  451 ASN cc_start: 0.8559 (p0) cc_final: 0.7950 (p0)
REVERT: A  468 ASN cc_start: 0.8250 (m-40) cc_final: 0.7814 (m-40)
REVERT: A  477 VAL cc_start: 0.8386 (t) cc_final: 0.8156 (p)
REVERT: A  482 GLN cc_start: 0.8187 (mt0) cc_final: 0.7896 (pp30)
REVERT: B  153 TYR cc_start: 0.8243 (m-80) cc_final: 0.7590 (m-80)
REVERT: B  248 ASN cc_start: 0.7962 (m-40) cc_final: 0.7322 (t0)
REVERT: B  252 ARG cc_start: 0.8901 (tpp-160) cc_final: 0.8546 (ttp-110)
REVERT: B  256 THR cc_start: 0.7597 (m) cc_final: 0.6740 (p)
REVERT: B  326 SER cc_start: 0.8804 (p) cc_final: 0.8521 (t)
REVERT: B  366 GLN cc_start: 0.6857 (tt0) cc_final: 0.6395 (tm-30)
REVERT: B  437 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.6557 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 237
  average time/residue: 0.2418
  time to fit residues: 72.3966
Evaluate side-chains
  114 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 34 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:   10.0000
   chunk 47 optimal weight:    7.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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
A 375 GLN
A 448 HIS
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 244 ASN
B 438 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.135058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.107788 restraints weight = 11668.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.110409 restraints weight = 6461.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.112188 restraints weight = 4235.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7585  Z= 0.222
  Angle     :  0.642   7.726  10525  Z= 0.323
  Chirality :  0.039   0.152   1204
  Planarity :  0.005   0.090   1184
  Dihedral  : 18.684 161.380   1721
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.66 %
    Favored  : 96.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.29), residues: 772
  helix:  2.57 (0.29), residues: 301
  sheet:  1.19 (0.49), residues: 99
  loop :  0.49 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  93 
 HIS   0.008   0.001   HIS B 434 
 PHE   0.022   0.002   PHE B 247 
 TYR   0.035   0.003   TYR B  47 
 ARG   0.006   0.001   ARG B 104 

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

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 181
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8103 (tmtt)
REVERT: A  218 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8428 (mmmt)
REVERT: A  258 MET cc_start: 0.7132 (ttm) cc_final: 0.6817 (mtp)
REVERT: A  350 LYS cc_start: 0.8554 (ptmm) cc_final: 0.8214 (ptmt)
REVERT: A  405 ASP cc_start: 0.7733 (m-30) cc_final: 0.7483 (m-30)
REVERT: A  429 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7963 (mp10)
REVERT: A  482 GLN cc_start: 0.8233 (mt0) cc_final: 0.7925 (tm-30)
REVERT: B  130 GLN cc_start: 0.8453 (mt0) cc_final: 0.7789 (tm-30)
REVERT: B  153 TYR cc_start: 0.8599 (m-80) cc_final: 0.8320 (m-80)
REVERT: B  248 ASN cc_start: 0.7953 (m-40) cc_final: 0.7494 (t0)
REVERT: B  326 SER cc_start: 0.8869 (p) cc_final: 0.8590 (p)
REVERT: B  348 PHE cc_start: 0.8251 (p90) cc_final: 0.8031 (p90)
REVERT: B  353 MET cc_start: 0.7597 (mtp) cc_final: 0.7194 (mtp)
REVERT: B  366 GLN cc_start: 0.7703 (tt0) cc_final: 0.7331 (tm-30)
REVERT: B  395 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7392 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2171
  time to fit residues: 51.4468
Evaluate side-chains
  113 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 1 optimal weight:   20.0000
   chunk 55 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 20 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 75 optimal weight:    8.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 226 HIS
A 347 HIS
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.133199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.106538 restraints weight = 11667.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.109096 restraints weight = 6491.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.110788 restraints weight = 4241.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.3493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7585  Z= 0.180
  Angle     :  0.566   6.602  10525  Z= 0.285
  Chirality :  0.038   0.147   1204
  Planarity :  0.004   0.057   1184
  Dihedral  : 18.499 166.829   1721
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.44 %
    Favored  : 97.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.30), residues: 772
  helix:  2.37 (0.30), residues: 302
  sheet:  1.38 (0.50), residues: 102
  loop :  0.51 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  93 
 HIS   0.004   0.001   HIS B 190 
 PHE   0.018   0.002   PHE B 247 
 TYR   0.017   0.002   TYR B  47 
 ARG   0.005   0.001   ARG A 232 

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

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 156
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8409 (tmtt)
REVERT: A  258 MET cc_start: 0.7232 (ttm) cc_final: 0.6905 (mtp)
REVERT: A  350 LYS cc_start: 0.8729 (ptmm) cc_final: 0.8427 (ptmt)
REVERT: A  353 MET cc_start: 0.8059 (mtt) cc_final: 0.7775 (mtt)
REVERT: A  423 SER cc_start: 0.7862 (t) cc_final: 0.7079 (t)
REVERT: A  429 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7988 (mp10)
REVERT: A  451 ASN cc_start: 0.8011 (p0) cc_final: 0.7755 (p0)
REVERT: B  130 GLN cc_start: 0.8360 (mt0) cc_final: 0.7757 (tm-30)
REVERT: B  153 TYR cc_start: 0.8553 (m-80) cc_final: 0.8296 (m-80)
REVERT: B  258 MET cc_start: 0.8343 (mtp) cc_final: 0.8099 (mtp)
REVERT: B  326 SER cc_start: 0.8940 (p) cc_final: 0.8443 (t)
REVERT: B  353 MET cc_start: 0.7560 (mtp) cc_final: 0.7098 (mtt)
REVERT: B  366 GLN cc_start: 0.7615 (tt0) cc_final: 0.7338 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 157
  average time/residue: 0.2243
  time to fit residues: 45.7358
Evaluate side-chains
  106 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   chunk 2 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 347 HIS
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.127929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.100952 restraints weight = 12181.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.103337 restraints weight = 7018.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.104888 restraints weight = 4716.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.3818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7585  Z= 0.269
  Angle     :  0.607   6.892  10525  Z= 0.309
  Chirality :  0.039   0.155   1204
  Planarity :  0.004   0.034   1184
  Dihedral  : 18.547 176.397   1721
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.30), residues: 772
  helix:  2.09 (0.30), residues: 302
  sheet:  1.50 (0.52), residues: 92
  loop :  0.36 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B  93 
 HIS   0.006   0.001   HIS B 190 
 PHE   0.015   0.002   PHE B 247 
 TYR   0.024   0.002   TYR B  52 
 ARG   0.006   0.001   ARG B 203 

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

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8411 (tptp)
REVERT: A  258 MET cc_start: 0.7372 (ttm) cc_final: 0.7110 (mtp)
REVERT: A  429 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7773 (mp10)
REVERT: A  451 ASN cc_start: 0.8272 (p0) cc_final: 0.7867 (p0)
REVERT: B   52 TYR cc_start: 0.8534 (m-80) cc_final: 0.8149 (m-10)
REVERT: B  130 GLN cc_start: 0.8391 (mt0) cc_final: 0.7746 (tm-30)
REVERT: B  153 TYR cc_start: 0.8504 (m-80) cc_final: 0.8200 (m-80)
REVERT: B  258 MET cc_start: 0.8556 (mtp) cc_final: 0.8311 (mtp)
REVERT: B  326 SER cc_start: 0.9071 (p) cc_final: 0.8597 (t)
REVERT: B  366 GLN cc_start: 0.7710 (tt0) cc_final: 0.7376 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1863
  time to fit residues: 35.6385
Evaluate side-chains
  104 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.3980
   chunk 47 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 41 optimal weight:    8.9990
   chunk 23 optimal weight:    0.8980
   chunk 54 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.130528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.103388 restraints weight = 11843.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.105799 restraints weight = 6731.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.107445 restraints weight = 4496.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.4115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7585  Z= 0.174
  Angle     :  0.547   6.634  10525  Z= 0.280
  Chirality :  0.038   0.145   1204
  Planarity :  0.004   0.024   1184
  Dihedral  : 18.430 178.807   1721
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.30), residues: 772
  helix:  2.22 (0.31), residues: 301
  sheet:  1.15 (0.50), residues: 92
  loop :  0.39 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  93 
 HIS   0.004   0.001   HIS B 347 
 PHE   0.014   0.001   PHE B 247 
 TYR   0.017   0.002   TYR B  52 
 ARG   0.005   0.000   ARG B 203 

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

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.783 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8422 (tptp)
REVERT: A  258 MET cc_start: 0.7313 (ttm) cc_final: 0.7017 (mtp)
REVERT: A  353 MET cc_start: 0.7991 (mtt) cc_final: 0.7468 (mtt)
REVERT: A  429 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7999 (mp10)
REVERT: A  451 ASN cc_start: 0.8086 (p0) cc_final: 0.7826 (p0)
REVERT: B  130 GLN cc_start: 0.8228 (mt0) cc_final: 0.7677 (tm-30)
REVERT: B  153 TYR cc_start: 0.8515 (m-80) cc_final: 0.8231 (m-80)
REVERT: B  258 MET cc_start: 0.8458 (mtp) cc_final: 0.7683 (mtp)
REVERT: B  322 MET cc_start: 0.6283 (mtt) cc_final: 0.5820 (mtt)
REVERT: B  366 GLN cc_start: 0.7633 (tt0) cc_final: 0.7285 (tm-30)
REVERT: B  410 MET cc_start: 0.8929 (mpp) cc_final: 0.8703 (mpp)
REVERT: B  436 MET cc_start: 0.7602 (ttp) cc_final: 0.7104 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1933
  time to fit residues: 37.8098
Evaluate side-chains
  95 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 77 optimal weight:    0.2980
   chunk 75 optimal weight:    8.9990
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    0.2980
   chunk 60 optimal weight:    0.8980
   chunk 28 optimal weight:   10.0000
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.127147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.100563 restraints weight = 12045.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.102792 restraints weight = 7091.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.104343 restraints weight = 4843.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.4305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7585  Z= 0.241
  Angle     :  0.587   7.479  10525  Z= 0.301
  Chirality :  0.039   0.168   1204
  Planarity :  0.004   0.026   1184
  Dihedral  : 18.490 178.030   1721
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.30), residues: 772
  helix:  2.06 (0.31), residues: 301
  sheet:  1.00 (0.52), residues: 94
  loop :  0.34 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  93 
 HIS   0.004   0.001   HIS B 347 
 PHE   0.012   0.002   PHE B 404 
 TYR   0.013   0.002   TYR B 307 
 ARG   0.006   0.001   ARG B 330 

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

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8438 (tptp)
REVERT: A  258 MET cc_start: 0.7388 (ttm) cc_final: 0.7103 (mtp)
REVERT: A  353 MET cc_start: 0.8142 (mtt) cc_final: 0.7834 (mtt)
REVERT: A  389 LEU cc_start: 0.8780 (pp) cc_final: 0.8564 (pp)
REVERT: A  405 ASP cc_start: 0.7551 (m-30) cc_final: 0.7305 (m-30)
REVERT: A  451 ASN cc_start: 0.8216 (p0) cc_final: 0.7925 (p0)
REVERT: B  118 ARG cc_start: 0.8085 (tpp80) cc_final: 0.7181 (ttp80)
REVERT: B  258 MET cc_start: 0.8474 (mtp) cc_final: 0.8243 (mtp)
REVERT: B  366 GLN cc_start: 0.7747 (tt0) cc_final: 0.7442 (tm-30)
REVERT: B  391 MET cc_start: 0.7459 (tmm) cc_final: 0.6968 (tmm)
REVERT: B  410 MET cc_start: 0.8967 (mpp) cc_final: 0.8732 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1937
  time to fit residues: 36.3810
Evaluate side-chains
  102 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0270
   chunk 28 optimal weight:    5.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.7238

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 468 ASN
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.133340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.105424 restraints weight = 11758.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.107911 restraints weight = 6806.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.109516 restraints weight = 4592.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.4520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7585  Z= 0.170
  Angle     :  0.552   6.511  10525  Z= 0.284
  Chirality :  0.039   0.187   1204
  Planarity :  0.003   0.028   1184
  Dihedral  : 18.439 178.104   1721
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.30), residues: 772
  helix:  2.10 (0.31), residues: 302
  sheet:  0.95 (0.52), residues: 94
  loop :  0.35 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  93 
 HIS   0.007   0.001   HIS B 190 
 PHE   0.015   0.001   PHE A 247 
 TYR   0.020   0.002   TYR B 401 
 ARG   0.004   0.000   ARG A 227 

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

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.789 
Fit side-chains
REVERT: A  242 LEU cc_start: 0.8360 (mt) cc_final: 0.8155 (tp)
REVERT: A  258 MET cc_start: 0.7330 (ttm) cc_final: 0.7103 (mtp)
REVERT: A  353 MET cc_start: 0.8158 (mtt) cc_final: 0.7678 (mtt)
REVERT: A  429 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8067 (mp10)
REVERT: A  451 ASN cc_start: 0.8196 (p0) cc_final: 0.7838 (p0)
REVERT: B  283 ILE cc_start: 0.8240 (mm) cc_final: 0.8035 (mm)
REVERT: B  290 ARG cc_start: 0.8249 (tpm170) cc_final: 0.7956 (tpm170)
REVERT: B  347 HIS cc_start: 0.7947 (p-80) cc_final: 0.7733 (p-80)
REVERT: B  366 GLN cc_start: 0.7703 (tt0) cc_final: 0.7390 (tm-30)
REVERT: B  391 MET cc_start: 0.7578 (tmm) cc_final: 0.6952 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1918
  time to fit residues: 35.8080
Evaluate side-chains
  98 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 52 optimal weight:    0.3980
   chunk 60 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 81 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 347 HIS
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.129653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.102065 restraints weight = 11959.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.104506 restraints weight = 6844.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.106161 restraints weight = 4602.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.4638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7585  Z= 0.238
  Angle     :  0.589   6.923  10525  Z= 0.301
  Chirality :  0.039   0.149   1204
  Planarity :  0.004   0.026   1184
  Dihedral  : 18.447 175.666   1721
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.30), residues: 772
  helix:  1.95 (0.31), residues: 302
  sheet:  0.96 (0.54), residues: 94
  loop :  0.29 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  93 
 HIS   0.003   0.001   HIS A 226 
 PHE   0.014   0.002   PHE B 247 
 TYR   0.018   0.002   TYR B 401 
 ARG   0.007   0.001   ARG B 252 

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

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A  292 LYS cc_start: 0.7952 (tptp) cc_final: 0.7551 (tptm)
REVERT: A  353 MET cc_start: 0.8195 (mtt) cc_final: 0.7652 (mtt)
REVERT: A  451 ASN cc_start: 0.8287 (p0) cc_final: 0.7930 (p0)
REVERT: B  144 GLU cc_start: 0.7732 (tp30) cc_final: 0.7442 (tp30)
REVERT: B  283 ILE cc_start: 0.8377 (mm) cc_final: 0.8165 (mm)
REVERT: B  366 GLN cc_start: 0.7744 (tt0) cc_final: 0.7464 (tm-30)
REVERT: B  391 MET cc_start: 0.7706 (tmm) cc_final: 0.7216 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1988
  time to fit residues: 36.3050
Evaluate side-chains
  92 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 46 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0980
   chunk 69 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 2 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   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 201 GLN
** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.133735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.105840 restraints weight = 11878.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.108315 restraints weight = 6841.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.110041 restraints weight = 4615.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.4834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7585  Z= 0.171
  Angle     :  0.577   8.603  10525  Z= 0.292
  Chirality :  0.039   0.160   1204
  Planarity :  0.004   0.057   1184
  Dihedral  : 18.431 175.818   1721
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.30), residues: 772
  helix:  1.97 (0.31), residues: 300
  sheet:  0.80 (0.51), residues: 98
  loop :  0.27 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 409 
 HIS   0.006   0.001   HIS A 222 
 PHE   0.014   0.001   PHE B 247 
 TYR   0.025   0.002   TYR A 230 
 ARG   0.018   0.001   ARG A 227 

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

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.790 
Fit side-chains
REVERT: A  353 MET cc_start: 0.8171 (mtt) cc_final: 0.7910 (mtt)
REVERT: A  405 ASP cc_start: 0.7440 (m-30) cc_final: 0.7228 (m-30)
REVERT: A  429 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7885 (mp10)
REVERT: A  451 ASN cc_start: 0.8137 (p0) cc_final: 0.7842 (p0)
REVERT: B  153 TYR cc_start: 0.8474 (m-80) cc_final: 0.8258 (m-80)
REVERT: B  283 ILE cc_start: 0.8186 (mm) cc_final: 0.7970 (mm)
REVERT: B  322 MET cc_start: 0.7555 (mpp) cc_final: 0.6521 (mtt)
REVERT: B  366 GLN cc_start: 0.7693 (tt0) cc_final: 0.7372 (tm-30)
REVERT: B  391 MET cc_start: 0.7710 (tmm) cc_final: 0.7107 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1603
  time to fit residues: 31.2112
Evaluate side-chains
  98 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 81 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 74 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 4 optimal weight:   10.0000
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.131491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.103784 restraints weight = 11945.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.106321 restraints weight = 6833.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.107984 restraints weight = 4561.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.4951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7585  Z= 0.192
  Angle     :  0.577   6.653  10525  Z= 0.294
  Chirality :  0.039   0.158   1204
  Planarity :  0.004   0.033   1184
  Dihedral  : 18.392 173.657   1721
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.30), residues: 772
  helix:  1.99 (0.31), residues: 302
  sheet:  0.75 (0.51), residues: 98
  loop :  0.29 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  93 
 HIS   0.012   0.001   HIS A 222 
 PHE   0.022   0.002   PHE A 255 
 TYR   0.022   0.002   TYR A 230 
 ARG   0.012   0.001   ARG A 227 

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

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
REVERT: A  353 MET cc_start: 0.8097 (mtt) cc_final: 0.7841 (mtt)
REVERT: A  451 ASN cc_start: 0.8084 (p0) cc_final: 0.7763 (p0)
REVERT: B  118 ARG cc_start: 0.7989 (tpp80) cc_final: 0.7226 (ttp80)
REVERT: B  283 ILE cc_start: 0.8241 (mm) cc_final: 0.8010 (mm)
REVERT: B  322 MET cc_start: 0.7231 (mpp) cc_final: 0.6206 (mtt)
REVERT: B  366 GLN cc_start: 0.7636 (tt0) cc_final: 0.7318 (tm-30)
REVERT: B  391 MET cc_start: 0.7779 (tmm) cc_final: 0.7139 (tmm)
REVERT: B  436 MET cc_start: 0.6977 (tmm) cc_final: 0.6559 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1862
  time to fit residues: 34.6168
Evaluate side-chains
  99 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 33 optimal weight:    0.0770
   chunk 40 optimal weight:    0.0370
   chunk 52 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   chunk 38 optimal weight:    4.9990
   chunk 6 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 22 optimal weight:    6.9990
   overall best weight:    1.2018

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

Flipped N/Q/H residues before XYZ refinement:
A 201 GLN
** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.132135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.104738 restraints weight = 11825.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107101 restraints weight = 6861.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.108738 restraints weight = 4654.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.5103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7585  Z= 0.208
  Angle     :  0.594   7.722  10525  Z= 0.301
  Chirality :  0.039   0.149   1204
  Planarity :  0.004   0.036   1184
  Dihedral  : 18.402 172.428   1721
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.30), residues: 772
  helix:  2.04 (0.31), residues: 300
  sheet:  0.76 (0.51), residues: 98
  loop :  0.28 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  93 
 HIS   0.013   0.001   HIS A 222 
 PHE   0.029   0.002   PHE A 255 
 TYR   0.038   0.002   TYR A 230 
 ARG   0.010   0.001   ARG A 227 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2159.92 seconds
wall clock time: 39 minutes 29.05 seconds (2369.05 seconds total)