Starting phenix.real_space_refine
on Wed Mar 12 08:54:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u2b_26311/03_2025/7u2b_26311.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u2b_26311/03_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_26311/03_2025/7u2b_26311.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u2b_26311/03_2025/7u2b_26311.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u2b_26311/03_2025/7u2b_26311.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u2b_26311/03_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-5624/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: 4.78, 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: 2.38
  Conformation dependent library (CDL) restraints added in 739.4 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: 2.22
  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: 2.37

  Time building geometry restraints manager: 2.65 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:             0.320
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.170
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.000
-------------------------------------------------------------------------------
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  : 0.737 
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: 0.2307
  time to fit residues: 69.3429
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  : 0.789 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 64 optimal weight:    0.9980
   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:    0.8580

-------------------------------------------------------------------------------
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 = 0.3759 r_free = 0.3759 target = 0.134923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107645 restraints weight = 11675.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.110303 restraints weight = 6462.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.112049 restraints weight = 4208.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2927

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= 0.212
  Angle     :  0.636   6.481  10525  Z= 0.319
  Chirality :  0.039   0.166   1204
  Planarity :  0.005   0.086   1184
  Dihedral  : 18.691 161.623   1721
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.28
  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:  2.06 (0.29), residues: 772
  helix:  2.55 (0.29), residues: 301
  sheet:  1.20 (0.49), residues: 99
  loop :  0.51 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  93 
 HIS   0.006   0.001   HIS B 434 
 PHE   0.024   0.002   PHE B 247 
 TYR   0.038   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
  181 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8650 (mtmt) cc_final: 0.8112 (tmtt)
REVERT: A  258 MET cc_start: 0.7177 (ttm) cc_final: 0.6881 (mtp)
REVERT: A  264 LEU cc_start: 0.9167 (mm) cc_final: 0.8928 (mp)
REVERT: A  350 LYS cc_start: 0.8566 (ptmm) cc_final: 0.8264 (ptmt)
REVERT: A  405 ASP cc_start: 0.7728 (m-30) cc_final: 0.7481 (m-30)
REVERT: A  429 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7961 (mp10)
REVERT: A  482 GLN cc_start: 0.8241 (mt0) cc_final: 0.7940 (tm-30)
REVERT: B  130 GLN cc_start: 0.8455 (mt0) cc_final: 0.7795 (tm-30)
REVERT: B  153 TYR cc_start: 0.8597 (m-80) cc_final: 0.8282 (m-80)
REVERT: B  248 ASN cc_start: 0.7954 (m-40) cc_final: 0.7495 (t0)
REVERT: B  322 MET cc_start: 0.7336 (mtt) cc_final: 0.7107 (mtt)
REVERT: B  326 SER cc_start: 0.8875 (p) cc_final: 0.8599 (p)
REVERT: B  348 PHE cc_start: 0.8250 (p90) cc_final: 0.7949 (p90)
REVERT: B  353 MET cc_start: 0.7607 (mtp) cc_final: 0.7226 (mtp)
REVERT: B  366 GLN cc_start: 0.7701 (tt0) cc_final: 0.7330 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 181
  average time/residue: 0.2070
  time to fit residues: 49.2916
Evaluate side-chains
  109 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 1 optimal weight:   20.0000
   chunk 55 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0010
   chunk 53 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   chunk 75 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   overall best weight:    1.2990

-------------------------------------------------------------------------------
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 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3723 r_free = 0.3723 target = 0.131756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.105204 restraints weight = 11808.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.107649 restraints weight = 6730.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.109291 restraints weight = 4475.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.3488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7585  Z= 0.206
  Angle     :  0.577   6.681  10525  Z= 0.291
  Chirality :  0.038   0.142   1204
  Planarity :  0.004   0.032   1184
  Dihedral  : 18.641 167.735   1721
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  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:  1.89 (0.30), residues: 772
  helix:  2.24 (0.30), residues: 302
  sheet:  1.24 (0.49), residues: 102
  loop :  0.52 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  93 
 HIS   0.012   0.001   HIS A 226 
 PHE   0.017   0.002   PHE B 247 
 TYR   0.015   0.002   TYR B 307 
 ARG   0.005   0.000   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
  156 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8433 (tmtt)
REVERT: A  258 MET cc_start: 0.7336 (ttm) cc_final: 0.6959 (mtp)
REVERT: A  350 LYS cc_start: 0.8721 (ptmm) cc_final: 0.8388 (ptmt)
REVERT: A  405 ASP cc_start: 0.7704 (m-30) cc_final: 0.7493 (m-30)
REVERT: A  429 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7976 (mp10)
REVERT: B   52 TYR cc_start: 0.8757 (m-10) cc_final: 0.8552 (m-10)
REVERT: B  130 GLN cc_start: 0.8392 (mt0) cc_final: 0.7765 (tm-30)
REVERT: B  153 TYR cc_start: 0.8551 (m-80) cc_final: 0.8285 (m-80)
REVERT: B  258 MET cc_start: 0.8396 (mtp) cc_final: 0.8176 (mtp)
REVERT: B  326 SER cc_start: 0.9005 (p) cc_final: 0.8557 (t)
REVERT: B  353 MET cc_start: 0.7563 (mtp) cc_final: 0.7082 (mtt)
REVERT: B  366 GLN cc_start: 0.7643 (tt0) cc_final: 0.7285 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1938
  time to fit residues: 40.3699
Evaluate side-chains
  111 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 28 optimal weight:    0.7980
   chunk 2 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0970
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.130078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.102785 restraints weight = 12019.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.105211 restraints weight = 6785.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.106821 restraints weight = 4519.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.3776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7585  Z= 0.205
  Angle     :  0.570   6.742  10525  Z= 0.289
  Chirality :  0.038   0.147   1204
  Planarity :  0.004   0.030   1184
  Dihedral  : 18.621 175.456   1721
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  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:  1.84 (0.30), residues: 772
  helix:  2.20 (0.31), residues: 302
  sheet:  1.43 (0.51), residues: 92
  loop :  0.44 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  93 
 HIS   0.006   0.001   HIS B 190 
 PHE   0.016   0.001   PHE B 247 
 TYR   0.018   0.002   TYR A 329 
 ARG   0.004   0.001   ARG B 252 

*********************** 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  : 0.793 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8712 (mtmt) cc_final: 0.8381 (tptp)
REVERT: A  218 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8467 (mmmm)
REVERT: A  258 MET cc_start: 0.7297 (ttm) cc_final: 0.6998 (mtp)
REVERT: A  429 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8009 (mp10)
REVERT: B  104 ARG cc_start: 0.7493 (tmm160) cc_final: 0.7230 (tmm160)
REVERT: B  130 GLN cc_start: 0.8386 (mt0) cc_final: 0.7746 (tm-30)
REVERT: B  153 TYR cc_start: 0.8492 (m-80) cc_final: 0.8183 (m-80)
REVERT: B  258 MET cc_start: 0.8525 (mtp) cc_final: 0.8309 (mtp)
REVERT: B  326 SER cc_start: 0.9064 (p) cc_final: 0.8597 (t)
REVERT: B  366 GLN cc_start: 0.7657 (tt0) cc_final: 0.7310 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.2026
  time to fit residues: 38.3037
Evaluate side-chains
  107 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 41 optimal weight:    8.9990
   chunk 23 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    2.9990

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.124485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.097904 restraints weight = 12330.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.100194 restraints weight = 7172.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.101739 restraints weight = 4842.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.4117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   7585  Z= 0.344
  Angle     :  0.656   7.035  10525  Z= 0.337
  Chirality :  0.041   0.150   1204
  Planarity :  0.005   0.035   1184
  Dihedral  : 18.666 178.312   1721
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  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:  1.25 (0.30), residues: 772
  helix:  1.76 (0.30), residues: 301
  sheet:  0.77 (0.50), residues: 101
  loop :  0.16 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B  93 
 HIS   0.006   0.001   HIS B 190 
 PHE   0.017   0.002   PHE B 404 
 TYR   0.027   0.003   TYR B  52 
 ARG   0.007   0.001   ARG B 252 

*********************** 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
  132 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8457 (tptp)
REVERT: A  258 MET cc_start: 0.7366 (ttm) cc_final: 0.7067 (mtp)
REVERT: A  389 LEU cc_start: 0.8807 (pp) cc_final: 0.8597 (pp)
REVERT: A  405 ASP cc_start: 0.7714 (m-30) cc_final: 0.7478 (m-30)
REVERT: A  468 ASN cc_start: 0.8727 (m-40) cc_final: 0.7937 (t0)
REVERT: B  104 ARG cc_start: 0.7675 (tmm160) cc_final: 0.7347 (tmm160)
REVERT: B  144 GLU cc_start: 0.7740 (tp30) cc_final: 0.7513 (tp30)
REVERT: B  213 ASP cc_start: 0.8664 (t0) cc_final: 0.8464 (t0)
REVERT: B  366 GLN cc_start: 0.7863 (tt0) cc_final: 0.7557 (tm-30)
REVERT: B  410 MET cc_start: 0.8971 (mpp) cc_final: 0.8720 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1747
  time to fit residues: 31.5758
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  : 0.710 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 29 optimal weight:    0.3980
   chunk 34 optimal weight:    6.9990
   chunk 51 optimal weight:    7.9990
   chunk 77 optimal weight:    3.9990
   chunk 75 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   overall best weight:    2.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 469 GLN
B 190 HIS
** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.125441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.099045 restraints weight = 12159.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.101359 restraints weight = 7040.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.102926 restraints weight = 4746.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.4337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7585  Z= 0.253
  Angle     :  0.595   6.768  10525  Z= 0.307
  Chirality :  0.040   0.166   1204
  Planarity :  0.004   0.027   1184
  Dihedral  : 18.676 178.744   1721
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.33 (0.30), residues: 772
  helix:  1.79 (0.31), residues: 301
  sheet:  0.84 (0.53), residues: 93
  loop :  0.25 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  93 
 HIS   0.006   0.001   HIS B 347 
 PHE   0.013   0.002   PHE B 247 
 TYR   0.018   0.002   TYR B  52 
 ARG   0.005   0.000   ARG B 252 

*********************** 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
  133 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8445 (tptp)
REVERT: A  230 TYR cc_start: 0.8840 (m-80) cc_final: 0.8555 (m-80)
REVERT: A  389 LEU cc_start: 0.8776 (pp) cc_final: 0.8542 (pp)
REVERT: A  405 ASP cc_start: 0.7653 (m-30) cc_final: 0.7423 (m-30)
REVERT: A  468 ASN cc_start: 0.8705 (m-40) cc_final: 0.7985 (t0)
REVERT: B  104 ARG cc_start: 0.7651 (tmm160) cc_final: 0.7344 (ttp80)
REVERT: B  144 GLU cc_start: 0.7704 (tp30) cc_final: 0.7499 (tp30)
REVERT: B  283 ILE cc_start: 0.8193 (mm) cc_final: 0.7979 (mm)
REVERT: B  353 MET cc_start: 0.7378 (mtp) cc_final: 0.7090 (mtt)
REVERT: B  366 GLN cc_start: 0.7778 (tt0) cc_final: 0.7414 (tm-30)
REVERT: B  391 MET cc_start: 0.7884 (tmm) cc_final: 0.7350 (tmm)
REVERT: B  436 MET cc_start: 0.7741 (ttp) cc_final: 0.7495 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1917
  time to fit residues: 34.4473
Evaluate side-chains
  97 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 76 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.129552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.102258 restraints weight = 11939.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.104734 restraints weight = 6870.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.106375 restraints weight = 4621.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.4509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7585  Z= 0.212
  Angle     :  0.565   7.604  10525  Z= 0.293
  Chirality :  0.039   0.184   1204
  Planarity :  0.004   0.028   1184
  Dihedral  : 18.570 177.638   1721
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.33 (0.30), residues: 772
  helix:  1.85 (0.31), residues: 301
  sheet:  0.84 (0.54), residues: 92
  loop :  0.19 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  93 
 HIS   0.005   0.001   HIS B 347 
 PHE   0.013   0.001   PHE B 247 
 TYR   0.014   0.002   TYR B  52 
 ARG   0.005   0.000   ARG B 252 

*********************** 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
  135 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.762 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.8711 (mmpt) cc_final: 0.8467 (mmmm)
REVERT: A  230 TYR cc_start: 0.8885 (m-80) cc_final: 0.8536 (m-80)
REVERT: A  389 LEU cc_start: 0.8771 (pp) cc_final: 0.8511 (pp)
REVERT: A  405 ASP cc_start: 0.7568 (m-30) cc_final: 0.7351 (m-30)
REVERT: A  468 ASN cc_start: 0.8624 (m-40) cc_final: 0.7986 (t0)
REVERT: A  477 VAL cc_start: 0.8224 (t) cc_final: 0.7827 (p)
REVERT: B  104 ARG cc_start: 0.7710 (tmm160) cc_final: 0.7373 (ttp80)
REVERT: B  258 MET cc_start: 0.8285 (mtp) cc_final: 0.7779 (mtp)
REVERT: B  322 MET cc_start: 0.6534 (mtt) cc_final: 0.6269 (mtt)
REVERT: B  353 MET cc_start: 0.7579 (mtp) cc_final: 0.7368 (mtt)
REVERT: B  366 GLN cc_start: 0.7752 (tt0) cc_final: 0.7439 (tm-30)
REVERT: B  391 MET cc_start: 0.7862 (tmm) cc_final: 0.7347 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2784
  time to fit residues: 52.1212
Evaluate side-chains
  97 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
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:    0.0770
   chunk 60 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    0.4980
   chunk 7 optimal weight:    4.9990
   chunk 81 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0270
   chunk 39 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
A 468 ASN
A 469 GLN
** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.132846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.105509 restraints weight = 11777.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.107995 restraints weight = 6769.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.109676 restraints weight = 4544.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.4722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7585  Z= 0.163
  Angle     :  0.545   6.947  10525  Z= 0.279
  Chirality :  0.038   0.166   1204
  Planarity :  0.004   0.029   1184
  Dihedral  : 18.490 177.177   1721
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  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:  1.47 (0.30), residues: 772
  helix:  2.02 (0.31), residues: 298
  sheet:  0.83 (0.53), residues: 92
  loop :  0.26 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B  93 
 HIS   0.006   0.001   HIS B 190 
 PHE   0.039   0.002   PHE A 255 
 TYR   0.026   0.002   TYR B 343 
 ARG   0.006   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
  139 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.696 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.8679 (mmpt) cc_final: 0.8460 (mmmm)
REVERT: A  230 TYR cc_start: 0.8845 (m-80) cc_final: 0.8571 (m-80)
REVERT: A  353 MET cc_start: 0.7777 (tpp) cc_final: 0.7430 (tpp)
REVERT: A  405 ASP cc_start: 0.7507 (m-30) cc_final: 0.7241 (m-30)
REVERT: B  104 ARG cc_start: 0.7713 (tmm160) cc_final: 0.7364 (ttp80)
REVERT: B  258 MET cc_start: 0.8331 (mtp) cc_final: 0.7781 (mtp)
REVERT: B  283 ILE cc_start: 0.8163 (mm) cc_final: 0.7925 (mm)
REVERT: B  322 MET cc_start: 0.6397 (mtt) cc_final: 0.5915 (mtt)
REVERT: B  353 MET cc_start: 0.7244 (mtp) cc_final: 0.6794 (mtt)
REVERT: B  366 GLN cc_start: 0.7707 (tt0) cc_final: 0.7290 (tm-30)
REVERT: B  391 MET cc_start: 0.7817 (tmm) cc_final: 0.7313 (tmm)
REVERT: B  436 MET cc_start: 0.7544 (ttp) cc_final: 0.6953 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1862
  time to fit residues: 35.3004
Evaluate side-chains
  101 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0670
   chunk 69 optimal weight:    0.6980
   chunk 42 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.8720

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.132974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.105653 restraints weight = 11891.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.108074 restraints weight = 6857.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.109772 restraints weight = 4628.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.4886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7585  Z= 0.179
  Angle     :  0.557   6.630  10525  Z= 0.285
  Chirality :  0.039   0.159   1204
  Planarity :  0.004   0.031   1184
  Dihedral  : 18.387 175.028   1721
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  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:  1.47 (0.30), residues: 772
  helix:  2.00 (0.31), residues: 299
  sheet:  0.91 (0.53), residues: 92
  loop :  0.24 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP B  93 
 HIS   0.007   0.001   HIS B 347 
 PHE   0.018   0.002   PHE A 255 
 TYR   0.013   0.001   TYR B 307 
 ARG   0.005   0.000   ARG B 143 

*********************** 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
  132 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A  191 MET cc_start: 0.7381 (mmm) cc_final: 0.7147 (mmm)
REVERT: A  230 TYR cc_start: 0.8837 (m-80) cc_final: 0.8492 (m-80)
REVERT: A  353 MET cc_start: 0.7672 (tpp) cc_final: 0.7460 (tpp)
REVERT: A  405 ASP cc_start: 0.7455 (m-30) cc_final: 0.7230 (m-30)
REVERT: B  258 MET cc_start: 0.8342 (mtp) cc_final: 0.7854 (mtp)
REVERT: B  283 ILE cc_start: 0.8181 (mm) cc_final: 0.7949 (mm)
REVERT: B  322 MET cc_start: 0.6328 (mtt) cc_final: 0.5842 (mtt)
REVERT: B  353 MET cc_start: 0.7286 (mtp) cc_final: 0.6968 (mtt)
REVERT: B  366 GLN cc_start: 0.7670 (tt0) cc_final: 0.7268 (tm-30)
REVERT: B  391 MET cc_start: 0.7801 (tmm) cc_final: 0.7285 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1841
  time to fit residues: 32.9983
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  : 0.588 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 26 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 4 optimal weight:   10.0000
   overall best weight:    1.1984

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.131463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.103984 restraints weight = 11960.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.106483 restraints weight = 6848.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.108136 restraints weight = 4573.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.4973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7585  Z= 0.195
  Angle     :  0.582  13.365  10525  Z= 0.295
  Chirality :  0.039   0.156   1204
  Planarity :  0.004   0.032   1184
  Dihedral  : 18.389 173.511   1721
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  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:  1.38 (0.30), residues: 772
  helix:  1.94 (0.31), residues: 299
  sheet:  0.84 (0.53), residues: 92
  loop :  0.18 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  93 
 HIS   0.006   0.001   HIS A 222 
 PHE   0.022   0.002   PHE A 247 
 TYR   0.013   0.001   TYR B  52 
 ARG   0.009   0.001   ARG B 104 

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

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.756 
Fit side-chains
REVERT: A  191 MET cc_start: 0.7400 (mmm) cc_final: 0.7165 (mmm)
REVERT: A  230 TYR cc_start: 0.8849 (m-80) cc_final: 0.8497 (m-80)
REVERT: A  405 ASP cc_start: 0.7467 (m-30) cc_final: 0.7261 (m-30)
REVERT: B  283 ILE cc_start: 0.8229 (mm) cc_final: 0.7953 (mm)
REVERT: B  353 MET cc_start: 0.7226 (mtp) cc_final: 0.6838 (mtm)
REVERT: B  366 GLN cc_start: 0.7686 (tt0) cc_final: 0.7342 (tm-30)
REVERT: B  391 MET cc_start: 0.7836 (tmm) cc_final: 0.7362 (tmm)
REVERT: B  410 MET cc_start: 0.8873 (mpp) cc_final: 0.7929 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1878
  time to fit residues: 33.6888
Evaluate side-chains
  93 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 33 optimal weight:    0.7980
   chunk 40 optimal weight:    0.3980
   chunk 52 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.8386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.132446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.104964 restraints weight = 11776.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.107478 restraints weight = 6762.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.109151 restraints weight = 4525.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.5104

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= 0.171
  Angle     :  0.540   6.591  10525  Z= 0.278
  Chirality :  0.038   0.157   1204
  Planarity :  0.004   0.033   1184
  Dihedral  : 18.360 171.983   1721
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.38 (0.30), residues: 772
  helix:  1.95 (0.31), residues: 299
  sheet:  0.77 (0.53), residues: 92
  loop :  0.19 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  93 
 HIS   0.006   0.001   HIS A 222 
 PHE   0.020   0.001   PHE A 247 
 TYR   0.012   0.001   TYR B 307 
 ARG   0.010   0.001   ARG B 104 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2239.47 seconds
wall clock time: 39 minutes 40.33 seconds (2380.33 seconds total)